bluuebunny/crossref_metadata_2025 huggingface dataset:
Different mechanisms for phytoalexin induction by pathogen and wound signals in
Medicago truncatula
Authors: Naoumkina Marina , Farag Mohamed A. , Sumner Lloyd W. , Tang Yuhong , Liu Chang-Jun , Dixon Richard A.
Published: October 2007

Cell suspensions of the model legume
Medicago truncatula
accumulated the isoflavonoid phytoalexin medicarpin in response to yeast elicitor or methyl jasmonate (MJ), accompanied by decreased levels of isoflavone glycosides in MJ-treated cells. DNA microarray analysis revealed rapid, massive induction of early (iso)flavonoid pathway gene transcripts in response to yeast elicitor, but not MJ, and differential induction by the two elicitors of sets of genes encoding transcription factors, ABC transporters, and β-glucosidases. In contrast, both elicitors induced genes encoding enzymes for conversion of the isoflavone formononetin to medicarpin. Four MJ-induced β-glucosidases were expressed as recombinant enzymes in yeast, and three were active with isoflavone glucosides. The most highly induced β-glucosidase was nuclear localized and preferred flavones to isoflavones. The results indicate that the genetic and biochemical mechanisms underlying accumulation of medicarpin differ depending on the nature of the stimulus and suggest a role for MJ as a signal for rapid hydrolysis of preformed, conjugated intermediates for antimicrobial biosynthesis during wound responses.
Recombinant
Plasmodium falciparum
reticulocyte homology protein 4 binds to erythrocytes and blocks invasion
Authors: Gaur Deepak , Singh Sanjay , Singh Subhash , Jiang Lubin , Diouf Ababacar , Miller Louis H.
Published: October 2007

Plasmodium falciparum
invasion of human erythrocytes involves several parasite and erythrocyte receptors that enable parasite invasion by multiple redundant pathways. A key challenge to the development of effective vaccines that block parasite infection of erythrocytes is identifying the players in these pathways and determining their function. Invasion by the parasite clone, Dd2, requires sialic acid on the erythrocyte surface; Dd2/NM is a variant selected for its ability to invade neuraminidase-treated erythrocytes that lack sialic acid. The
P. falciparum
protein, reticulocyte homology 4 (PfRH4), is uniquely up-regulated in Dd2/NM compared with Dd2, suggesting that it may be a parasite receptor involved in invasion. The aim of the present study was to determine the role of PfRH4 in invasion of erythrocytes and to determine whether it is a target of antibody-mediated blockade and thus a vaccine candidate. We show that both native PfRH4 and a recombinant 30-kDa protein to a conserved region of PfRH4 (rRH4
30
) bind strongly to neuraminidase-treated erythrocytes. rRH4
30
blocks both the erythrocyte binding of the native PfRH4 and invasion of neuraminidase-treated erythrocytes by Dd2/NM. Taken together, these results indicate that PfRH4 is a parasite receptor involved in sialic acid-independent invasion of erythrocytes. Although antibodies to rRH4
30
block binding of the native protein to erythrocytes, these antibodies failed to block invasion. These findings suggest that, although PfRH4 is required for invasion of neuraminidase-treated erythrocytes by Dd2/NM, it is inaccessible for antibody-mediated inhibition of the invasion process.
Transnational Terrorism Hot Spots: Identification and Impact Evaluation
Authors: Braithwaite Alex , LI QUAN
Published: October 2007

To combat transnational terrorism, it is important to understand its geography. The extant literature on the geography of terrorism, however, is small and focuses on the distribution and diffusion of terrorism among aggregate regions such as Europe and the Middle East. In this analysis, we study transnational terrorism hot spots at the country level. We employ local spatial statistics to identify terrorism hot spot neighborhoods and countries that are located within. We also assess empirically the impact of these hot spots on future patterns of terrorist incidents. We find that countries with significant experiences with terrorism are often located within these hot spots, but that not all countries within the hot spots have experienced large numbers of terrorist incidents. We also find in a pooled time-series analysis of 112 countries from 1975 to 1997 that when a country is located within a hot spot neighborhood, a large increase in the number of terrorist attacks is likely to occur in the next period. This effect is robust under alternative definitions of geographic proximity and across the two most popular measures of local hot spots of data—the G*i statistic and the Local Moran's I. These findings have important implications for the continuing fight against transnational terrorism.
“Draining the Swamp”: An Empirical Examination of the Production of International Terrorism, 1968—1998
Authors: Lai Brian
Published: October 2007

One central element of the current war on terrorism is “draining the swamps,” addressing conditions within a state that produce international terrorism. This paper empirically examines what factors lead a state to become a “swamp,” drawing on a theoretical approach that guides current U.S. policy. This theory looks at the ability of a state to impose costs on terrorist groups within its own borders. The lower the operating costs within a state, the greater the amount of terrorism produced within that state. Using data on the number of international terrorist events originating from a state from 1968 to 1998, an empirical model incorporating variables designed to test this theoretical argument as well as relevant control variables is employed. Strong support was found for the state strength approach, suggesting that one way to address the threat of international terrorism is to strengthen a government's ability to control its own territory.
Conical limit sets and continued fractions
Authors: Crane Edward , Short Ian
Published: October 2007

Inspired by questions of convergence in continued fraction theory, Erdős, Piranian and Thron studied the possible sets of divergence for arbitrary sequences of Möbius maps acting on the Riemann sphere,

S
2

S^2

. By identifying

S
2

S^2

with the boundary of three-dimensional hyperbolic space,

H
3

H^3

, we show that these sets of divergence are precisely the sets that arise as conical limit sets of subsets of

H
3

H^3

. Using hyperbolic geometry, we give simple geometric proofs of the theorems of Erdős, Piranian and Thron that generalise to arbitrary dimensions. New results are also obtained about the class of conical limit sets; for example, it is closed under locally quasisymmetric homeomorphisms. Applications are given to continued fractions.
On distortion of Hausdorff measures under quasiconformal mappings
Authors: Prause István
Published: October 2007

Astala (Acta Math. 173 (1994), no. 1, 37–60) gave optimal bounds for the distortion of Hausdorff dimension under planar quasiconformal maps. The corresponding estimates on the level of Hausdorff measures remain open. We show that these techniques allow for establishing absolute continuity for some weaker Hausdorff measures.
Dynamic Association of the Fragile X Mental Retardation Protein as a Messenger Ribonucleoprotein between Microtubules and Polyribosomes
Authors: Wang Houping , Dictenberg Jason B. , Ku Li , Li Wen , Bassell Gary J. , Feng Yue
Published: October 2007

The fragile X mental retardation protein (FMRP) is a selective RNA-binding protein that regulates translation and plays essential roles in synaptic function. FMRP is bound to specific mRNA ligands, actively transported into neuronal processes in a microtubule-dependent manner, and associated with polyribosomes engaged in translation elongation. However, the biochemical relationship between FMRP–microtubule association and FMRP–polyribosome association remains elusive. Here, we report that although the majority of FMRP is incorporated into elongating polyribosomes in the soluble cytoplasm, microtubule-associated FMRP is predominantly retained in translationally dormant, polyribosome-free messenger ribonucleoprotein (mRNP) complexes. Interestingly, FMRP–microtubule association is increased when mRNPs are dynamically released from polyribosomes as a result of inhibiting translation initiation. Furthermore, the I304N mutant FMRP that fails to be incorporated into polyribosomes is associated with microtubules in mRNP particles and transported into neuronal dendrites in a microtubule-dependent, 3,5-dihydroxyphenylglycine-stimulated manner with similar kinetics to that of wild-type FMRP. Hence, polyribosome-free FMRP–mRNP complexes travel on microtubules and wait for activity-dependent translational derepression at the site of function. The dual participation of FMRP in dormant mRNPs and polyribosomes suggests distinct roles of FMRP in dendritic transport and translational regulation, two distinct phases that control local protein production to accommodate synaptic plasticity.
Precursor Oxidation by Mia40 and Erv1 Promotes Vectorial Transport of Proteins into the Mitochondrial Intermembrane Space
Authors: Müller Judith M. , Milenkovic Dusanka , Guiard Bernard , Pfanner Nikolaus , Chacinska Agnieszka
Published: October 2007

The mitochondrial intermembrane space contains chaperone complexes that guide hydrophobic precursor proteins through this aqueous compartment. The chaperones consist of hetero-oligomeric complexes of small Tim proteins with conserved cysteine residues. The precursors of small Tim proteins are synthesized in the cytosol. Import of the precursors requires the essential intermembrane space proteins Mia40 and Erv1 that were proposed to form a relay for disulfide formation in the precursor proteins. However, experimental evidence for a role of Mia40 and Erv1 in the oxidation of intermembrane space precursors has been lacking. We have established a system to directly monitor the oxidation of precursors during import into mitochondria and dissected distinct steps of the import process. Reduced precursors bind to Mia40 during translocation into mitochondria. Both Mia40 and Erv1 are required for formation of oxidized monomers of the precursors that subsequently assemble into oligomeric complexes. Whereas the reduced precursors can diffuse back into the cytosol, the oxidized precursors are retained in the intermembrane space. Thus, oxidation driven by Mia40 and Erv1 determines vectorial transport of the precursors into the mitochondrial intermembrane space.
Preventing Fatalities in Building Bombings: What Can We Learn From the Oklahoma City Bombing?
Authors: Glenshaw Mary T. , Vernick Jon S. , Li Guohua , Sorock Gary S. , Brown Sheryll , Mallonee Sue
Published: October 2007

Background: Bombings are an increasing threat to the public's health. Descriptive studies of blast injuries have been published, but these injuries have not been studied using analytical epidemiological methods. This study assesses factors associated with fatality risk among individuals exposed to the 1995 Oklahoma City bombing.

Methods: Retrospective case-control analysis using multivariable logistic regression. Odds ratios (OR) of fatality are calculated among occupants of the Alfred P. Murrah Federal Building on April 19, 1995.

Results: Of the 348 occupants exposed, 163 (46.8%) were fatally injured. Fatality risk was greatest in the collapsed region of the building (adjusted OR 176.7, 95% confidence interval [CI] 65.9–474.2). Age ≥40 was also associated with a significantly increased risk of fatality (OR 3.7, 95% CI 1.4–9.8). Among people found in the noncollapsed region of the building, employees' status compared to a visitor's or child's status was protective (OR 0.13, 95% CI 0.01–1.3)

Conclusions: Structural collapse is the most important risk factor for fatality in a building bombing. Progressive collapse may be prevented through more supportive building design. Protection of vulnerable building occupants can be improved by placement of relevant facilities in more structurally reinforced areas. Regular evacuation training of personnel and clear egress routes may also reduce fatality in a building bombing. (Disaster Med Public Health Preparedness. 2007;1:27–33)
Protecting the Public's Health Following the Virginia Tech Tragedy: Issues of Law and Policy
Authors: Hodge James G.
Published: October 2007

Assessing legal responsibility in the aftermath of the April 2007 tragedy at Virginia Polytechnic Institute and State University (Virginia Tech) is inevitable. Beyond assigning blame, law- and policymakers should examine ways to protect the public from future incidences of gun violence on campuses and other settings. Although no combination of legal responses may fully deter individuals who are intent on causing significant harm, select legal reforms have the potential to prevent future acts of gun violence. These reforms include considering more restrictive gun laws nationally, reporting individuals with known mental impairments that may endanger themselves or others to federal or state databases, and refining laws that limit institutions from acting in advance to address prospectively dangerous people. Each of these reforms has the potential to reduce acts of gun violence to improve the public's health, but also implicates individual rights and interests. (Disaster Med Public Health Preparedness. 2007;1(Suppl 1):S43–S46)
Developing a Consensus Framework for an Effective and Efficient Disaster Response Health System: A National Call to Action
Authors: Lyznicki James , Subbarao Italo , Benjamin Georges C. , James James J.
Published: October 2007

Eighteen national organizations, representing medicine, dentistry, nursing, hospital systems, public health, and emergency medical services, have worked together to create a framework for a national and regional disaster response health system that is scalable, multidisciplinary, and seamless, and based on an all-hazards approach. In July 2005 and June 2006 the American Medical Association (AMA) and the American Public Health Association (APHA) convened the AMA/APHA Linkages Leadership Summit, with funding from the Centers for Disease Control and Prevention under the Terrorism Injuries: Information Dissemination and Exchange (TIIDE) program. As cofacilitators, James J. James, MD, DrPH, MHA, director of the AMA Center for Public Health Preparedness and Disaster Response, and Georges Benjamin, MD, FACP, FACEP(E), APHA executive director, met with leaders from 16 national medical, dental, hospital, nursing, hospital systems, public health, and emergency medical services organizations in Chicago (2005) and New Orleans (2006) to deliberate the deficiencies in the medical and public health disaster response system and the lack of necessary linkages between key components of this system: the health care, emergency medical services, and public health sectors. The goal was to reach consensus on a set of overarching recommendations to improve and sustain health system preparedness and to combine each organization's advocacy expertise and experience to promote a shared policy agenda. The full summit report contains 53 consensus-based recommendations, which will serve as the framework for a coordinated national agenda for strengthening health system preparedness for terrorism and other disasters. The 9 most overarching critical recommendations from the report are highlighted here. Although the summit report presents important perspectives on the subject of preparedness for public health emergencies, we must understand that preparedness is a process and that these recommendations must be reviewed and refined continually over time. (Disaster Med Public Health Preparedness. 2007;1(Suppl 1):S51–S54)
Preventing Tragedy: Balancing Physicians' Ethical Obligations to Patients and the Public
Authors: Anderson Emily E. , Black Lee J. , Bostick Nathan A.
Published: October 2007

The recent shootings at Virginia Polytechnic Institute and State University (Virginia Tech) suggest that an increased reliance upon the medical community to support public health violence prevention efforts may be warranted. As physicians are called upon to support these efforts, they must effectively balance their obligations to promote public safety with their traditional obligations to promote the best interests of their individual patients. To meet these concurrent ethical obligations, physicians' participation in public health violence prevention should seek to improve public safety without compromising the care of patients or exposing individuals to undue harm. Physicians should, therefore, report to the appropriate authorities those patients who are at risk of committing violent acts toward the public, but should only disclose the minimal amount of information that is necessary to protect the public. Moreover, physicians should also recommend the separation of violent individuals from the community at large when necessary to improve public safety while advocating for the provision of appropriate treatment measures to improve the patients' well-being. (Disaster Med Public Health Preparedness. 2007;1(Suppl 1):S38–S42)
Regional Health System Response to the Virginia Tech Mass Casualty Incident
Authors: Kaplowitz Lisa , Reece Morris , Hershey Jody Henry , Gilbert Carol M. , Subbarao Italo
Published: October 2007

Background: On April 16, 2007 a mass shooting occurred on the campus of Virginia Polytechnic Institute and State University (Virginia Tech). Due to both distance and weather, air transport of the injured directly to a level 1 trauma center was not possible. The injured received all of their care or were initially stabilized at 3 primary hospitals that either had a level 3 trauma center designation or no trauma center designation.

Methods: This article is a retrospective analysis of the regional health system (prehospital, hospital, regional hospital emergency operations center, and public health local and state) response. Data records from all of the regional responding emergency medical services, hospitals, and coordinating services were reviewed and analyzed. Records for all 26 patients were reviewed and analyzed using triage designations, injury severity scores (ISS), and critical mortality.

Results: Twenty-five of the 26 patients were triaged in the field. Excluding 1 patient (asthma), the average ISS for victims presenting was 8.2. Twelve patients had an ISS of ≥9, and 5 had an ISS score of ≥15. Ten of the 26 patients (38%) required urgent intervention and surgery in the first 24 hours. The overall regional health system mortality of victims received was 3.8% (1 death [excluding 1 dead on arrival {DOA}]/ 26 victims from scene). The regional health system critical mortality rate (excluding 1 victim who was DOA) was 20% (1/5).

Discussion: The outcomes of the Virginia Tech mass casualty incident, as evidenced by the low overall regional health system mortality of victims received at 3.8% (1/26) and low critical mortality rate (excluding 1 victim who was DOA) of 20%, coupled with a need to treat a significant amount of moderately injured victims 46% (12/26 with ISS ≥9) gives credence to the successful response. The successful response occurred as a consequence of regional collaborative planning, training, and exercising, which resulted not only in increased expertise and improved communications but also in essential relationships and a sense of trust forged among all of the responders. (Disaster Med Public Health Preparedness. 2007;1(Suppl 1):S9–S13)
State of Security at US Colleges and Universities: A National Stakeholder Assessment and Recommendations
Authors: Greenberg Sheldon F.
Published: October 2007

In 2004 the US Department of Justice, Office of Community Oriented Policing Services, sponsored a National Summit on Campus Public Safety. The summit brought together various stakeholders including campus police and security officials, local police chiefs, college and university faculty and administrators, federal officials, students and parents, and community leaders to address the issues and complexities of campus safety. Delegates to the summit identified key issues in campus safety and security, which included establishing a national center on campus safety, balancing traditional open environments with the need to secure vulnerable sites, improving coordination with state and local police, reducing internal fragmentation, elevating professionalism, and increasing eligibility of campus police and security agencies to compete for federal law enforcement funds. Focus on “active shooters” on campus, resulting from the Virginia Tech incident, should not diminish attention placed on the broader, more prevalent safety and security issues facing the nation's educational campuses. Recommendations resulting from the summit called for establishing a national agenda on campus safety, formation of a national center on campus public safety, and increased opportunity for campus police and security agencies to compete for federal and state funds. (Disaster Med Public Health Preparedness. 2007;1(Suppl 1):S47–S50)
Is Overtriage Associated With Increased Mortality? Insights From a Simulation Model of Mass Casualty Trauma Care
Authors: Hupert Nathaniel , Hollingsworth Eric , Xiong Wei
Published: October 2007

Purpose: To examine the relationship between overtriage and critical mortality after a mass casualty incident (MCI) using a simulation model of trauma system response.

Methods: We created a discrete event simulation model of trauma system management of MCIs involving individual patient triage and treatment. Model variables include triage performance, treatment capability, treatment time, and time-dependent mortality of critically injured patients. We model triage as a variable selection process applied to a hypothetical population of critically and noncritically injured patients. Treatment capability is represented by staffed emergency department trauma bays with associated staffed operating rooms that are recycled after each use. We estimated critical and noncritical patient treatment times and time-dependent mortality rates from the trauma literature.

Results: In this simulation model, overtriage, the proportion of noncritical patients among all of those labeled as critical, has a positive, negative, or variable association with critical mortality depending on its etiology (ie, related to changes in triage sensitivity or to changes in the prevalence and total number of critical patients). In all of the modeled scenarios, the ratio of critical patients to treatment capability has a greater impact on critical mortality than overtriage level or time-dependent mortality assumption.

Conclusions: Increasing overtriage may have positive, negative, or mixed effects on critical mortality in this trauma system simulation model. These results, which contrast with prior analyses describing a positive linear relationship between overtriage and mortality, highlight the need for alternative metrics to describe trauma system response after MCIs. We explore using the relative number of critical patients to available and staffed treatment units, or the critical surge to capability ratio, which exhibits a consistent and nonlinear association with critical mortality in this model. (Disaster Med Public Health Preparedness. 2007;1(Suppl 1):S14–S24)
Ploidy reduction in
Saccharomyces cerevisiae
Authors: Gerstein Aleeza C , McBride Rachel M , Otto Sarah P
Published: October 2007

Large-scale transitions in genome size from tetraploid to diploid were observed during a previous 1800-generation evolution experiment in
Saccharomyces cerevisiae
. Whether the transitions occurred via a one-step process (tetraploid to diploid) or through multiple steps (through ploidy intermediates) remained unclear. To provide insight into the mechanism involved, we investigated whether triploid-sized cells sampled from the previous experiment could also undergo ploidy loss. A batch culture experiment was conducted for approximately 200 generations, starting from four triploid-sized colonies and one contemporaneous tetraploid-sized colony. Ploidy reduction towards diploidy was observed in both triploid and tetraploid lines. Comparative genomic hybridization indicated the presence of aneuploidy in both the founder and the evolved colonies. The specific aneuploidies involved suggest that chromosome loss was not haphazard but that nearly full sets of chromosomes were lost at once, with some additional chromosome mis-segregation events. These results suggest the existence of a mitotic mechanism allowing the elimination of an entire set of chromosomes in
S. cerevisiae
, thereby reducing the ploidy level.
Towards a nanomechanical basis for temporary adhesion in barnacle cyprids (
Semibalanus balanoides
)
Authors: Phang In Yee , Aldred Nick , Clare Anthony S , Vancso G. Julius
Published: October 2007

Cypris larvae of barnacles are able to use a rapidly reversible temporary adhesion mechanism for exploring immersed surfaces. Despite decades of research interest, the means by which cyprids maintain attachment with surfaces prior to permanent settlement remain poorly understood. Here, we present novel observations on the morphology of ‘footprints’ of a putative adhesive secretion deposited by cyprids during surface exploration. Atomic force microscopy (AFM) was used to image footprints at high resolution and to acquire measurements of interaction forces. R–CH
3
- and R–NH
2
-terminated glass surfaces were used for comparison of footprint morphology, and it was noted that on R–NH
2
each footprint comprised three times the volume of material deposited for footprints on R–CH
3
. Direct scaling of adhesion forces derived from AFM measurements did not adequately predict the real attachment tenacity of cyprids, and it is suggested that a mixture of ‘wet’ and ‘dry’ adhesive mechanisms may be at work in cyprid adhesion. High-resolution images of cyprid footprints are presented that correlate well with the known morphology of the attachment structures.
Analytic formulation of Cauchy integrals for boundaries with curvilinear geometry
Authors: Steward David R , Le Grand Philippe , Janković Igor , Strack Otto D.L
Published: October 2007

A general framework for analytic evaluation of singular integral equations with a Cauchy kernel is developed for higher order line elements of curvilinear geometry. This extends existing theory which relies on numerical integration of Cauchy integrals since analytic evaluation is currently published only for straight lines, and circular and hyperbolic arcs. Analytic evaluation of Cauchy integrals along straight elements is presented to establish a context coalescing new developments within the existing body of knowledge. Curvilinear boundaries are partitioned into sectionally holomorphic elements that are conformally mapped from a local curvilinearZ-plane to a straight line in the-plane. Cauchy integrals are evaluated in these planes to achieve a simple representation of the complex potential using Chebyshev polynomials and a Taylor series expansion of the conformal mapping. Bell polynomials and the Faà di Bruno formula provide this Taylor series for mappings expressed as inverse mappings and/or compositions. Examples illustrate application of the general framework to boundary-value problems with boundaries of natural coordinates, Bezier curves and B-splines. Strings formed by the union of adjacent curvilinear elements form a large class of geometries along which Dirichlet and/or Neumann conditions may be applied. This provides a framework applicable to a wide range of fields of study including groundwater flow, electricity and magnetism, acoustic radiation, elasticity, fluid flow, air flow and heat flow.
Decadal variations of intense typhoon occurrence in the western North Pacific
Authors: Chan Johnny C.L
Published: October 2007

The causes of one of the two major oscillation periods, 16–32 years, identified through a wavelet analysis, of the time series of the frequency of intense typhoon (categories 4 and 5 in the Saffir–Simpson scale) occurrence for the period 1960–2005 in the western North Pacific (WNP) is studied in this paper. By dividing this period into sub-periods during which the frequency of intense typhoon occurrence was above or below normal on this time scale, various thermodynamic and dynamic factors in each sub-period are examined.

During the above-normal periods, the sea surface temperature in the southeastern part of the WNP (5–20° N, 150–180° E) is found to be slightly higher. Within this area, the moist static energy (MSE) is also higher and the vertical gradient of saturated MSE in the lower troposphere is more negative. At the same time, the low-level streamfunction anomalies tend to have a negative maximum and the vertical wind shear between 200 and 850 hPa is also relatively small. Thus, both the thermodynamic and dynamic conditions within this area are more conducive to the development of tropical cyclones (TCs). As these cyclones move northwestward, the favourable dynamic conditions continue to be present so that they can intensify further. The steering flow is such that many of these typhoons will stay over water for an extended period of time through low-latitude recurvature. As a result, they can intensify to become category 4 or 5 typhoons. The conditions during the below-normal periods are generally opposite.

A major conclusion from the results of this study is that the frequency of intense typhoon occurrence undergoes a strong multi-decadal (16–32 years) variation due to similar variations in the planetary scale oceanographic and atmospheric conditions that govern the formation, intensification and movement of TCs. These latter variations are largely contributed by the El Niño and the Pacific Decadal Oscillation on similar time scales.
Evolution of direct and indirect reciprocity
Authors: Roberts Gilbert
Published: October 2007

Indirect reciprocity (IR) occurs when individuals help those who help others. It is important as a potential explanation for why people might develop cooperative reputations. However, previous models of IR are based on the assumption that individuals never meet again. Yet humans and other animals often interact repeatedly within groups, thereby violating the fundamental basis of these models. Whenever re-meeting can occur, discriminating reciprocators can decide whether to help those who helped others (IR) or those who helped them (direct reciprocity, DR). Here I used simulation models to investigate the conditions in which we can expect the different forms of reciprocity to predominate. I show that IR through image scoring becomes unstable with respect to DR by experience scoring as the probability of re-meeting increases. However, using the standing strategy, which takes into account the context of observed defections, IR can be stable with respect to DR even when individuals interact with few partners many times. The findings are important in showing that IR cannot explain a concern for reputation in typical societies unless reputations provide as reliable a guide to cooperative behaviour as does experience.
Modelling studies to estimate the prevalence of foot-and-mouth disease carriers after reactive vaccination
Authors: Arnold M.E , Paton D.J , Ryan E , Cox S.J , Wilesmith J.W
Published: October 2007

Foot-and-mouth disease (FMD) is a highly contagious and economically significant viral disease of cloven-hoofed animals. Vaccination can be used to help restrict the spread of the infection, but evidence must be provided to show that the infection has been eradicated in order to regain the FMD-free status. While serological tests have been developed, which can identify animals that have been infected regardless of vaccination status, it is vital to know the probable prevalence of herds with FMD carriers and the within-herd prevalence of those carriers in order to design efficient post-epidemic surveillance strategies that establish freedom from disease. Here, we present the results of a study to model the expected prevalence of carriers after application of emergency vaccination and the impact of this on the sensitivity of test systems for their detection. Results showed that the expected prevalence of carrier-containing herds after reactive vaccination is likely to be very low, approximately 0.2%, and there will only be a small number of carriers, most likely one, in the positive herds. Therefore, sensitivity for carrier detection can be optimized by adopting an individual-based testing regime in which all animals in all vaccinated herds are tested and positive animals rather than herds are culled.
First direct evidence of a vertebrate three-level trophic chain in the fossil record
Authors: Kriwet Jürgen , Witzmann Florian , Klug Stefanie , Heidtke Ulrich H.J
Published: October 2007

We describe the first known occurrence of a Permian shark specimen preserving two temnospondyl amphibians in its digestive tract as well as the remains of an acanthodian fish, which was ingested by one of the temnospondyls. This exceptional find provides for the first time direct evidence of a vertebrate three-level food chain in the fossil record with the simultaneous preservation of three trophic levels. Our analysis shows that small-sized Lower Permian xenacanthid sharks of the genus
Triodus
preyed on larval piscivorous amphibians. The recorded trophic interaction can be explained by the adaptation of certain xenacanthids to fully freshwater environments and the fact that in these same environments, large temnospondyls occupied the niche of modern crocodiles. This unique faunal association has not been documented after the Permian and Triassic. Therefore, this Palaeozoic three-level food chain provides strong and independent support for changes in aquatic trophic chain structures through time.
Social diffusion of novel foraging methods in brown capuchin monkeys (Cebus apella)
Authors: Dindo Marietta , Thierry Bernard , Whiten Andrew
Published: October 2007

It has been reported that wild capuchin monkeys exhibit several group-specific behavioural traditions. By contrast, experiments have found little evidence for the social learning assumed necessary to support such traditions. The present study used a diffusion chain paradigm to investigate whether a novel foraging task could be observationally learned by capuchins (Cebus apella) and then transmitted along a chain of individuals. We used a two-action paradigm to control for independent learning. Either of two methods (lift or slide) could be used to open the door of a foraging apparatus to retrieve food. Two chains were tested (N1=4;N2=5), each beginning with an experimenter-trained model who demonstrated to a partner its group-specific method for opening the foraging apparatus. After the demonstration, if the observer was able to open the apparatus 20 times by either method, then it became the demonstrator for a new subject, thus simulating the spread of a foraging tradition among ‘generations’ of group members. Each method was transmitted along these respective chains with high fidelity, echoing similar results presently available only for chimpanzees and children. These results provide the first clear evidence for faithful diffusion of alternative foraging methods in monkeys, consistent with claims for capuchin traditions in the wild.
The structure of the Mn4Ca2+cluster of photosystem II and its protein environment as revealed by X-ray crystallography
Authors: Barber James , Murray James W
Published: October 2007

The location, structure and protein environment of the Mn4Ca2+cluster, which catalyses the light-driven, water-splitting reaction of photosystem II, has been revealed by X-ray crystallography. However, owing to the low resolutions of the crystal structures reported to date, and the possibility of radiation damage at the catalytic centre, the precise position of each metal ion remains unknown. To some extent, these problems have been overcome by applying spectroscopic techniques like extended X-ray absorption fine structure. Taking into account the most recent results obtained with these two X-ray-based techniques, we have attempted to refine models of the structure of the Mn4Ca2+cluster and its protein environment.
QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II
Authors: Sproviero Eduardo M , Shinopoulos Katherine , Gascón José A , McEvoy James P , Brudvig Gary W , Batista Victor S
Published: October 2007

This paper reports computational studies of substrate water binding to the oxygen-evolving centre (OEC) of photosystem II (PSII), completely ligated by amino acid residues, water, hydroxide and chloride. The calculations are based on quantum mechanics/molecular mechanics hybrid models of the OEC of PSII, recently developed in conjunction with the X-ray crystal structure of PSII from the cyanobacterium
Thermosynechococcus elongatus
. The model OEC involves a cuboidal Mn
3
CaO
4
Mn metal cluster with three closely associated manganese ions linked to a single μ
4
-oxo-ligated Mn ion, often called the ‘dangling manganese’. Two water molecules bound to calcium and the dangling manganese are postulated to be substrate molecules, responsible for dioxygen formation. It is found that the energy barriers for the Mn(4)-bound water agree nicely with those of model complexes. However, the barriers for Ca-bound waters are substantially larger. Water binding is not simply correlated to the formal oxidation states of the metal centres but rather to their corresponding electrostatic potential atomic charges as modulated by charge-transfer interactions. The calculations of structural rearrangements during water exchange provide support for the experimental finding that the exchange rates with bulk
18
O-labelled water should be smaller for water molecules coordinated to calcium than for water molecules attached to the dangling manganese. The models also predict that the S
1
→S
2
transition should produce opposite effects on the two water-exchange rates.
Mechanism and energy diagram for O–O bond formation in the oxygen-evolving complex in photosystem II
Authors: Siegbahn Per E.M
Published: October 2007

The recent finding of a transition state with a significantly lower barrier than previously found, has made the mechanism for O–O bond formation in photosystem II much clearer. The full mechanism can be described in the following way. Electrons and protons are ejected from the oxygen-evolving complex (OEC) in an alternating fashion, avoiding unnecessary build-up of charge. The S
0
–S
1
and S
1
–S
2
transitions are quite exergonic, while the S
2
–S
3
transition is only weakly exergonic. The strong endergonic S
3
–S
4
transition is a key step in the mechanism in which an oxygen radical is produced, held by the dangling manganese outside the Mn
3
Ca cube. The O–O bond formation in the S
4
-state occurs by an attack of the oxygen radical on a bridging oxo ligand in the cube. The mechanism explains the presence of both a cube with bridging oxo ligands and a dangling manganese. Optimal orbital overlap puts further constraints on the structure of the OEC. An alternating spin alignment is necessary for a low barrier. The computed rate-limiting barrier of 14.7 kcal mol
−1
is in good agreement with experiments.
Why did Nature choose manganese to make oxygen?
Authors: Armstrong Fraser A
Published: October 2007

This paper discusses the suitability of manganese for its function in catalysing the formation of molecular oxygen from water. Manganese is an abundant element. In terms of its inherent properties, Mn has a particularly rich redox chemistry compared with other d-block elements, with several oxidizing states accessible. The most stable-state Mn2+behaves like a Group 2 element—it is mobile, weakly complexing, easily taken up by cells and redox-inactive in simple aqueous media. Only in the presence of suitable ligands does Mn2+become oxidized, so it provides an uncomplicated building unit for the oxygen-evolving centre (OEC). The intermediate oxidation states Mn(III) and Mn(IV) are strongly complexed by O2−and form robust mixed-valence poly-oxo clusters in which the Mn(IV)/Mn(III) ratio can be elevated, one electron at a time, accumulating oxidizing potential and capacity. The OEC is a Mn4CaOxcluster that undergoes sequential oxidations by P680+at potentials above 1 V, ultimately to a super-oxidized level that includes one Mn(V) or a Mn(IV)-oxyl radical. The latter is powerfully oxidizing and provides the crucial ‘power stroke’ necessary to generate an O–O bond. This leaves a centre still rich in Mn(IV), ensuring a rapid follow-through to O2.
A ligand field chemistry of oxygen generation by the oxygen-evolving complex and synthetic active sites
Authors: Betley Theodore A , Surendranath Yogesh , Childress Montana V , Alliger Glen E , Fu Ross , Cummins Christopher C , Nocera Daniel G
Published: October 2007

Oxygen–oxygen bond formation and O
2
generation occur from the S
4
state of the oxygen-evolving complex (OEC). Several mechanistic possibilities have been proposed for water oxidation, depending on the formal oxidation state of the Mn atoms. All fall under two general classifications: the AB mechanism in which nucleophilic oxygen (base, B) attacks electrophilic oxygen (acid, A) of the Mn
4
Ca cluster or the RC mechanism in which radical-like oxygen species couple within OEC. The critical intermediate in either mechanism involves a metal oxo, though the nature of this oxo for AB and RC mechanisms is disparate. In the case of the AB mechanism, assembly of an even-electron count, high-valent metal-oxo proximate to a hydroxide is needed whereas, in an RC mechanism, two odd-electron count, high-valent metal oxos are required. Thus the two mechanisms give rise to very different design criteria for functional models of the OEC active site. This discussion presents the electron counts and ligand geometries that support metal oxos for AB and RC O–O bond-forming reactions. The construction of architectures that bring two oxygen functionalities together under the purview of the AB and RC scenarios are described.
Bacillus pocheonensis sp. nov., a moderately halotolerant, aerobic bacterium isolated from soil of a ginseng field
Authors: Ten Leonid N. , Baek Sang-Hun , Im Wan-Taek , Larina Liudmila L. , Lee Jung-Sook , Oh Hee-Mock , Lee Sung-Taik
Published: October 2007

A Gram-positive, non-motile, endospore-forming bacterial strain, designated Gsoil 420T, was isolated from soil of a ginseng field in Pocheon Province, South Korea, and was characterized, using a polyphasic approach, in order to determine its taxonomic position. The novel isolate consisted of strictly aerobic, rod-shaped cells and was able to grow in medium supplemented with up to 12 % NaCl at 25 °C and pH 6.5–7.0. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 420T fell within the radiation of the cluster comprising Bacillus species and formed a coherent cluster with Bacillus niacini (16S rRNA gene sequence similarity, 98.6 %), Bacillus bataviensis (98.6 %), Bacillus soli (98.3 %), Bacillus drentensis (98.0 %), Bacillus novalis (98.0 %), Bacillus vireti (97.9 %), Bacillus foraminis (97.6 %), Bacillus fumarioli (97.4 %) and Bacillus jeotgali (97.0 %). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species with validly published names were less than 96.8 %. Strain Gsoil 420T had a genomic DNA G+C content of 44.9 mol% and the predominant respiratory quinone was MK-7. The major fatty acids were anteiso-C15 : 0 (33.9 %), iso-C15 : 0 (24.5 %) and iso-C14 : 0 (19.9 %). These chemotaxonomic results supported the affiliation of strain Gsoil 420T to the genus Bacillus. However, low DNA–DNA relatedness values and distinguishing phenotypic characteristics allowed genotypic and phenotypic differentiation of strain Gsoil 420T from recognized Bacillus species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 420T represents a novel species of the genus Bacillus, for which the name Bacillus pocheonensis sp. nov. is proposed. The type strain is Gsoil 420T (=KCTC 13943T=DSM 18135T).
Labedella gwakjiensis gen. nov., sp. nov., a novel actinomycete of the family Microbacteriaceae
Authors: Lee Soon Dong
Published: October 2007

A Gram-positive, non-motile, non-mycelium-forming, rod-shaped actinomycete, designated KSW2-17T, was isolated from dried seaweed collected from beach sand along the coast of Jeju, Republic of Korea. The organism had ornithine as the diagnostic cell-wall diamino acid, MK-10 and MK-11 as the major menaquinones, and phosphatidylglycerol and diphosphatidylglycerol as polar lipids. The fatty acid profile included predominantly iso- and anteiso-branched acids and a minor amount of tuberculostearic acid (10-methyl C18 : 0). The DNA G+C content was 68.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the seaweed isolate formed a distinct clade within the radiation of the familyMicrobacteriaceaeand had highest sequence similarity (96.1–96.3 %) to members of the generaCryobacterium,FrigoribacteriumandRathayibacter. On the basis of phenotypic and genotypic evidence, strain KSW2-17Tis considered to represent a novel species of a new genus, for which the nameLabedella gwakjiensisgen. nov., sp. nov. is proposed. The type strain is KSW2-17T(=JCM 14008T=KCTC 19176T).
Burkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plant-pathogenic fungus Rhizopus microsporus
Authors: Partida-Martinez Laila P. , Groth Ingrid , Schmitt Imke , Richter Walter , Roth Martin , Hertweck Christian
Published: October 2007

Several strains of the fungus Rhizopus microsporus harbour endosymbiotic bacteria for the production of the causal agent of rice seedling blight, rhizoxin, and the toxic cyclopeptide rhizonin. R. microsporus and isolated endobacteria were selected for freeze–fracture electron microscopy, which allowed visualization of bacterial cells within the fungal cytosol by their two parallel-running envelope membranes and by the fine structure of the lipopolysaccharide layer of the outer membrane. Two representatives of bacterial endosymbionts were chosen for phylogenetic analyses on the basis of full 16S rRNA gene sequences, which revealed that the novel fungal endosymbionts formed a monophyletic group within the genus Burkholderia. Inter-sequence similarities ranged from 98.94 to 100 %, and sequence similarities to members of the Burkholderia pseudomallei group, the closest neighbours, were 96.74–97.38 %. In addition, the bacterial strains were distinguished from their phylogenetic neighbours by their fatty acid profiles and other biochemical characteristics. The phylogenetic studies based on 16S rRNA gene sequence data, together with conclusive DNA–DNA reassociation experiments, strongly support the proposal that these strains represent two novel species within the genus Burkholderia, for which the names Burkholderia rhizoxinica sp. nov. (type strain, HKI 454T=DSM 19002T=CIP 109453T) and Burkholderia endofungorum sp. nov. (type strain, HKI 456T=DSM 19003T=CIP 109454T) are proposed.