bluuebunny/crossref_metadata_2025 huggingface dataset:
Hindu-Christian Conflict in India: Globalization, Conversion, and the Coterminal Castes and Tribes
Authors: Bauman Chad M.
Published: September 2013

While Hindu-Muslim violence in India has received a great deal of scholarly attention, Hindu-Christian violence has not. This article seeks to contribute to the analysis of Hindu-Christian violence, and to elucidate the curious alliance, in that violence, of largely upper-caste, anti-minority Hindu nationalists with lower-status groups, by analyzing both with reference to the varied processes of globalization. The article begins with a short review of the history of anti-Christian rhetoric in India, and then discusses and critiques a number of inadequately unicausal explanations of communal violence before arguing, with reference to the work of Mark Taylor, that only theories linking local and even individual social behaviors to larger, global processes like globalization can adequately honor the truly “webby” nature of the social world.
Market Reaction to Corporate Press Releases
Authors: Neuhierl Andreas , Scherbina Anna , Schlusche Bernd
Published: September 2013

We classify a unique and comprehensive data set of corporate press releases into topics and study the market reaction to various types of news. While confirming prior findings regarding strong stock price responses to financial news, we also document significant reactions to news about corporate strategy, customers and partners, products and services, management changes, and legal developments. Consistent with regulators' expectations, the level of informational asymmetry in the market declines following most types of press releases. At the same time, return volatility frequently increases in the post-announcement period, which we show can be attributed to higher levels of valuation uncertainty.
Algorithmic Trading and the Market for Liquidity
Authors: Hendershott Terrence , Riordan Ryan
Published: September 2013

We examine the role of algorithmic traders (ATs) in liquidity supply and demand in the 30 Deutscher Aktien Index stocks on the Deutsche Boerse in Jan. 2008. ATs represent 52% of market order volume and 64% of nonmarketable limit order volume. ATs more actively monitor market liquidity than human traders. ATs consume liquidity when it is cheap (i.e., when the bid-ask quotes are narrow) and supply liquidity when it is expensive. When spreads are narrow ATs are less likely to submit new orders, less likely to cancel their orders, and more likely to initiate trades. ATs react more quickly to events and even more so when spreads are wide.
Fruit and vegetable intake and risk of cardiovascular disease
Authors: Woodside Jayne V. , Young Ian S. , McKinley Michelle C.
Published: September 2013

A high intake of fruit and vegetables (FV) has been shown to be associated with reduced risk of a number of chronic diseases, including CVD. This review aims to provide an overview of the evidence that increased FV intake reduces risk of CVD, focusing on studies examining total FV intake. This evidence so far available is largely based on prospective cohort studies, with meta-analyses demonstrating an association between increased FV intake and reduced risk of both CHD and stroke. Controlled intervention trials examining either clinical or cardiovascular risk factor endpoints are scarce. However, such trials have shown that an increase in FV consumption can lower blood pressure and also improve microvascular function, both of which are commensurate with a reduced risk of CVD. The effects of increased FV consumption on plasma lipid levels, risk of diabetes and body weight have yet to be firmly established. In conclusion, evidence that FV consumption reduces the risk of CVD is so far largely confined to observational epidemiology, with further intervention studies required.
British Business and the Uncertainties of Early Independence in Indonesia
Authors: Lindblad J. Thomas
Published: September 2013

British private investors were not inclined to view the leaders of newly independent Indonesia with much confidence. In 1949, when the transfer of sovereignty from the Netherlands to the Republic of Indonesia was imminent, the chairman of the United Serdang (Sumatra) Rubber Plantations disclosed the following opinion to the firm's shareholders at a gathering in London's Great Tower Street: “The Republican leaders are mainly ambitious men, whose records are well known, striving for personal aggrandizement. The measure of their interest in the welfare of the country is to be gauged by their policy of wanton destruction of life and physical assets, such as estate factories and ancillary buildings, which are essential for the restoration of the economy of the country once the political problem has been settled.” This article is about how a British enterprise dealt with the significant uncertainties prevailing in the business environment of Indonesia during the early independence period, in particular the 1950s.

The economic situation in newly independent Indonesia was a peculiar one. As a major exporter of primary products in high demand such as oil and rubber, prospects were generally bright for the Indonesian economy during and after the Korean War. Just as under colonialism, a modern, large-scale sector accounting for almost 25 per cent of GDP (gross domestic product) was still dominated by Dutch firms and British and American multinationals. Eight large Dutch trading companies handled 60 per cent of consumer goods imports. Nevertheless, the business climate had changed dramatically for foreign firms operating in Indonesia. The 1950s saw a gradual shift away from moderate policy-makers towards an increasingly vocal economic nationalism. The former were acutely aware of the country's dependence on foreign capital and know-how, whereas the latter relentlessly pushed for full decolonisation, that is not only in political but in economic terms. Nationalist sentiments gained the upper hand during the first cabinet of Ali Sastroamidjojo (July 1953–July 1955), culminating with the takeover of virtually all remaining Dutch-owned enterprises in Indonesia from December 1957 onwards, eventually followed by formal nationalisation in 1959. Although economic nationalism in the 1950s primarily targeted Dutch enterprises, British foreign firms were affected as well. At a later stage, in the context of the Indonesian military confrontation with Malaysia (1963–6), they were also seized, albeit not nationalised.
Sovereign Justice in Precolonial Maritime Asia: The Case of the Mayor's Court of Bombay, 1726–1798
Authors: Sood Gagan D. S.
Published: September 2013

From the beginning of the nineteenth century, remarkable developments in the realm of law were witnessed throughout the world. They expressed and paved the way for a new type of dispensation. For those parts of Asia and the Middle East with a substantial European presence, the legitimate rules, principles, and procedures for resolving disputes were progressively assimilated into systems of state-sanctioned legal pluralism. The process—at once gradual, charged, and punctuated—coincided with the initial consolidation of European imperial dominance and the emergence of Europe's modern global empires.

Though these changes in the realm of law date from the nineteenth century, the European presence there had long preceded them. This was perhaps most notable in maritime Asia. The Europeans in this region tended to cluster in their factories or in certain quarters of the towns and cities dotting the Indian Ocean rim. Notwithstanding differences between, say, a Mocha and an Aceh in size, location, and form of government, all these settlements had one quality in common: each was able to profit from the traffic conducted along the coast or across the high seas. As for the sovereign justice on offer, the dispensation that governed it in early modern times was far removed from its later analogue. This stemmed in large part from the rationale and basis for the European presence. In particular, Europeans could not dominate maritime Asia's provincial and imperial powers, especially those located inland, and the great majority of those arriving from western Europe intended to return as soon as possible; despite some involvement in racketeering and other forms of surplus extraction—famously in attempts to introduce and enforce a system of passports in maritime transport and travel—their interests were mainly commercial, oriented towards trade and shipping; the indigenous populations remained on the whole large and resilient; and many of the skills and techniques vested in livelihoods long associated with the region retained their primacy. As a result, the only realistic option for Europeans in maritime Asia was to reconcile themselves to the prevailing order. And this they did, with most of the region's fundamentals, not least in the realm of law, continuing to develop along what were essentially indigenous lines.
Converting nuclear energy into the energy of coherent optical radiation
Authors: Batyrbekov Erlan
Published: September 2013

This paper is devoted to the question of the conversion of nuclear energy into the energy of coherent optical radiation. The two possible ways to convert nuclear energy into laser radiation are discussed: direct and combined nuclear pumping. The concept of using laser gas active media capable of working with both direct and combined nuclear pumping is considered. The results of an investigation by Kazakh scientists on nuclear pumped lasers active media on bound–bound atomic transitions are presented.
Aquaporins in seeds
Authors: Obroucheva Natalie V.
Published: September 2013

The factual evidence for aquaporins, the constituents of water channels in cell membranes and operation of water channels is reviewed in developing, maturing and germinating seeds.
Active Cognitive Reserve Influences the Regional Atrophy to Cognition Link in Multiple Sclerosis
Authors: Booth Adam J. , Rodgers Jonathan D. , Schwartz Carolyn E. , Quaranto Brian R. , Weinstock-Guttman Bianca , Zivadinov Robert , Benedict Ralph H.B.
Published: September 2013

Recent research indicates that cognitive reserve mitigates the clinical expression of neuropsychological impairment in multiple sclerosis (MS). This literature primarily uses premorbid intelligence and lifetime experiences as indicators. However, changes in current recreational activities may also contribute to the maintenance of neural function despite brain atrophy. We examined the moderation effects of current changes in recreational activity on the relationship between brain atrophy and information processing speed in 57 relapsing-remitting MS patients. Current enrichment was assessed using the Recreation and Pastimes subscale from the Sickness Impact Profile. In patients reporting current declines in recreational activities, brain atrophy was negatively associated with cognition, but there was no such association in participants reporting stable participation. The MRI metric-by-recreational activity interaction was significant in separate hierarchical regression analyses conducted using third ventricle width, neocortical volume, T2 lesion volume, and thalamic volume as brain measures. Results suggest that recreational activities protect against brain atrophy's detrimental influence on cognition. (JINS, 2013, 19, 1–6)
Examining local-level factors shaping school nutrition policy implementation in Ontario, Canada
Authors: Vine Michelle M , Elliott Susan J
Published: September 2013

Objective

Increasing numbers of overweight and obese youth draw attention to the school as an important setting for targeted nutrition interventions, given that it is where they spend a majority of their waking time. The objective of the present study was to explore local-level factors shaping the implementation of a school nutrition policy.

Design

In-depth, semi-structured interviews were conducted in person or via the telephone (a maximum of 60 min). An interview guide was informed by the Analysis Grid for Environments Linked to Obesity (ANGELO) framework, research objectives and literature. Key themes centred on policy implementation, including facilitators and barriers (i.e. resources, capacity), user satisfaction (i.e. students) and communication strategies.

Setting

Secondary schools in Ontario, Canada.

Subjects

Twenty-two participants from local agencies supporting school nutrition programming (n8) and secondary-school principals, vice principals and teachers (n14) from nine schools across three Ontario school boards.

Results

Results are organized according to environments outlined in the ANGELO framework. The cost of healthy food for sale, revenue loss (economic), proximity of schools to off-site food outlets (physical), the restrictive nature of policy, the role of key stakeholders (political), the role of stigma and school culture (sociocultural) act as local-level barriers to policy implementation.

Conclusions

Gaps in policy implementation include the high cost of food for sale and subsequent revenue generation, the close proximity of internal and external food environments, the need for consultation and communication between stakeholders, and strategies to reduce stigma and improve the school nutrition culture.
Bacterial diversity associated with the tunic of the model chordate Ciona intestinalis
Authors: Blasiak Leah C , Zinder Stephen H , Buckley Daniel H , Hill Russell T
Published: September 2013

The sea squirt Ciona intestinalis is a well-studied model organism in developmental biology, yet little is known about its associated bacterial community. In this study, a combination of 454 pyrosequencing of 16S ribosomal RNA genes, catalyzed reporter deposition-fluorescence in situ hybridization and bacterial culture were used to characterize the bacteria living inside and on the exterior coating, or tunic, of C. intestinalis adults. The 454 sequencing data set demonstrated that the tunic bacterial community structure is different from that of the surrounding seawater. The observed tunic bacterial consortium contained a shared community of <10 abundant bacterial phylotypes across three individuals. Culture experiments yielded four bacterial strains that were also dominant groups in the 454 sequencing data set, including novel representatives of the classes Alphaproteobacteria and Flavobacteria. The relatively simple bacterial community and availability of dominant community members in culture make C. intestinalis a promising system in which to investigate functional interactions between host-associated microbiota and the development of host innate immunity.
Peroxiredoxin-5 targeted to the mitochondrial intermembrane space attenuates hypoxia-induced reactive oxygen species signalling
Authors: Sabharwal Simran S. , Waypa Gregory B. , Marks Jeremy D. , Schumacker Paul T.
Published: September 2013

The ability to adapt to acute and chronic hypoxia is critical for cellular survival. Two established functional responses to hypoxia include the regulation of gene transcription by HIF (hypoxia-inducible factor), and the constriction of pulmonary arteries in response to alveolar hypoxia. The mechanism of O2 sensing in these responses is not established, but some studies implicate hypoxia-induced mitochondrial ROS (reactive oxygen species) signalling. To further test this hypothesis, we expressed PRDX5 (peroxiredoxin-5), a H2O2 scavenger, in the IMS (mitochondrial intermembrane space), reasoning that the scavenging of ROS in that compartment should abrogate cellular responses triggered by the release of mitochondrial oxidants to the cytosol. Using adenoviral expression of IMS-PRDX5 (IMS-targeted PRDX5) in PASMCs (pulmonary artery smooth muscle cells) we show that IMS-PRDX5 inhibits hypoxia-induced oxidant signalling in the IMS and cytosol. It also inhibits HIF-1α stabilization and HIF activity in a dose-dependent manner without disrupting cellular oxygen consumption. IMS-PRDX5 expression also attenuates the increase in cytosolic [Ca2+] in PASMCs during hypoxia. These results extend previous work by demonstrating the importance of IMS-derived ROS signalling in both the HIF and lung vascular responses to hypoxia.
Oligomerization and Ca2+/calmodulin control binding of the ER Ca2+-sensors STIM1 and STIM2 to plasma membrane lipids
Authors: Bhardwaj Rajesh , Müller Hans-Michael , Nickel Walter , Seedorf Matthias
Published: September 2013

Ca2+ (calcium) homoeostasis and signalling rely on physical contacts between Ca2+ sensors in the ER (endoplasmic reticulum) and Ca2+ channels in the PM (plasma membrane). STIM1 (stromal interaction molecule 1) and STIM2 Ca2+ sensors oligomerize upon Ca2+ depletion in the ER lumen, contact phosphoinositides at the PM via their cytosolic lysine (K)-rich domains, and activate Ca2+ channels. Differential sensitivities of STIM1 and STIM2 towards ER luminal Ca2+ have been studied but responses towards elevated cytosolic Ca2+ concentration and the mechanism of lipid binding remain unclear. We found that tetramerization of the STIM1 K-rich domain is necessary for efficient binding to PI(4,5)P2-containing PM-like liposomes consistent with an oligomerization-driven STIM1 activation. In contrast, dimerization of STIM2 K-rich domain was sufficient for lipid binding. Furthermore, the K-rich domain of STIM2, but not of STIM1, forms an amphipathic α-helix. These distinct features of the STIM2 K-rich domain cause an increased affinity for PI(4,5)P2, consistent with the lower activation threshold of STIM2 and a function as regulator of basal Ca2+ levels. Concomitant with higher affinity for PM lipids, binding of CaM (calmodulin) inhibited the interaction of the STIM2 K-rich domain with liposomes in a Ca2+ and PI(4,5)P2 concentration-dependent manner. Therefore we suggest that elevated cytosolic Ca2+ concentration down-regulates STIM2-mediated ER–PM contacts via CaM binding.
Unique role for translation initiation factor 3 in the light color regulation of photosynthetic gene expression
Authors: Gutu Andrian , Nesbit April D. , Alverson Andrew J. , Palmer Jeffrey D. , Kehoe David M.
Published: September 2013

Significance

The regulation of photosynthesis is important, yet poorly understood. Our work reveals a previously undescribed form of photosynthesis gene regulation in cyanobacteria that apparently also controls gene expression in plants, including commercially important crops. This finding may provide a unique approach to modifying the environmental responses and developmental programs of agriculturally important species. In addition, translation is a key biological process, and many of its important features and regulation remain to be described. Initiation is the rate-limiting step of translation, making it a critical point for regulation. Our finding that translation initiation factor 3 families exist with common roles in initiation and individual roles in regulating gene expression provides additional insights into the translation mechanism and its regulation.
Glucagon-like peptide 1 receptor induced suppression of food intake, and body weight is mediated by central IL-1 and IL-6
Authors: Shirazi Rozita , Palsdottir Vilborg , Collander Jim , Anesten Fredrik , Vogel Heike , Langlet Fanny , Jaschke Alexander , Schürmann Annette , Prévot Vincent , Shao Ruijin , Jansson John-Olov , Skibicka Karolina Patrycja
Published: September 2013

Significance

There is a growing interest in the gut- and hindbrain-produced hormone glucagon-like peptide 1 (GLP-1), and GLP-1–targeting drugs are in clinical trials for treatment of obesity, and already in the clinic for treatment of type 2 diabetes. Therefore, the implications of information arising from our study are clinically relevant and considerable. GLP-1 receptor stimulation decreases feeding and body weight likely via the CNS, effects of unquestioned scientific and clinical importance, considering the alarming rates of obesity. Despite this, there is scarce information about the mediators and mechanisms behind the effects of GLP-1. In this study, we found surprising evidence that two cytokines, interleukin-6 and interleukin-1, mediate antiobesity effects of GLP-1 receptor stimulation at the level of the CNS.
Teachers and school culture in the Czech Republic before and after 1989
Authors: Moree Dana
Published: September 2013

This article reports the findings of research on school culture in post‐totalitarian society in the Czech Republic. The research explored restructuralisation and reculturalisation in the Czech school education system through analysis of school culture in one school located in a midsized town in the central part of the country. In‐depth biographical interviews were carried out with teachers who taught in the school before and after 1989, the year of the fall of communism in the Czech Republic. The article offers a detailed description of how the totalitarian regime used teachers as its servants. At the same time, it offers an analysis of the changes that were provoked by the political transformation, and how teachers reacted to them. The research also reflects aspects of change in the country as a whole as it underwent dynamic development.
Lack of association between postactivation potentiation and subsequent jump performance
Authors: Pearson Stephen John , Hussain Syed Robiul
Published: September 2013

Postactivation potentiation (PAP) is a strategy that has been used to acutely enhance the performance of explosive activities. Although, isometric maximal voluntary contractions (MVCs) have previously been shown to enhance subsequent explosive performance, no information currently exists regarding (1) the optimal variables (intensity/volume) of a MVC that best elicits a PAP response, and (2) the utilisation of evoked isometric twitch contractions in combination with performance measures to directly ascertain the presence of PAP following a MVC, and its relationship to performance. Thus, the purpose of this study was to (1) investigate the influence of isometric contraction duration on the PAP response, and (2) to determine the relationship between PAP, indicated as potentiation of muscle twitch force and subsequent jump performance following different‐duration MVCs. Eight males (age: 21 ± 0.99) were assessed using performance measures [countermovement jumps] and evoked twitch contractions, before and 4 minutes after three different conditioning contractions (CCs), (1) a 3‐second MVC (MVC3), (2) a 5‐second MVC (MVC5) and (3) a 7‐second MVC (MVC7). Following all CCs, peak twitch torque of the knee extensor muscles was found to increase (MVC3, + 3.9%; MVC5, + 9.6%; MVC7, + 5.2%), although not significantly (P > 0.05). No significant increases in jump height, jump power, rate of force development or takeoff velocity were observed following any of the CCs (P > 0.05). There was also a lack of association between the changes in PAP (twitch torque) and jump height following all CCs (MVC3, r = 0.25; MVC5, r = 0.28; MVC7, r = −0.47). These data indicate that PAP as assessed via twitch contractions is not associated with performance measures subsequent to single‐set isometric CCs of varying durations.
On the symmetric enveloping algebra of planar algebra subfactors
Authors: Curran Stephen , Jones Vaughan , Shlyakhtenko Dimitri
Published: September 2013

We give a diagrammatic description of Popa’s symmetric enveloping algebras associated to planar algebra subfactors. As an application we construct a natural family of derivations on these factors and compute a certain free entropy dimension type quantity.
Secant varieties to high degree Veronese reembeddings, catalecticant matrices and smoothable Gorenstein schemes
Authors: Buczyńska Weronika , Buczyński Jarosław
Published: September 2013

We study the secant varieties of the Veronese varieties and of Veronese reembeddings of a smooth projective variety. We give some conditions, under which these secant varieties are set-theoretically cut out by determinantal equations. More precisely, they are given by minors of a catalecticant matrix. These conditions include the case when the dimension of the projective variety is at most 3 and the degree of reembedding is sufficiently high. This gives a positive answer to a set-theoretic version of a question of Eisenbud in dimension at most 3. For dimension four and higher we produce plenty of examples when the catalecticant minors are not enough to set-theoretically define the secant varieties to high degree Veronese varieties. This is done by relating the problem to smoothability of certain zero-dimensional Gorenstein schemes.
Oxysterol-binding protein (OSBP) is required for the perinuclear localization of intra-Golgi v-SNAREs
Authors: Nishimura Taki , Uchida Yasunori , Yachi Rieko , Kudlyk Tetyana , Lupashin Vladimir , Inoue Takao , Taguchi Tomohiko , Arai Hiroyuki
Published: September 2013

Oxysterol-binding protein (OSBP) and OSBP-related proteins (ORPs) have been implicated in the distribution of sterols among intracellular organelles. OSBP regulates the Golgi cholesterol level, but how it relates to Golgi function is elusive. Here we report that OSBP is essential for the localization of intra-Golgi soluble vesicle N-ethylmaleimide-sensitive fusion attachment protein receptors (v-SNAREs). Depletion of OSBP by small interfering RNA causes mislocalization of intra-Golgi v-SNAREs GS28 and GS15 throughout the cytoplasm without affecting the perinuclear localization of Golgi target-SNARE syntaxin5 and reduces the abundance of a Golgi enzyme, mannosidase II (Man II). GS28 mislocalization and Man II reduction are also induced by cellular cholesterol depletion. Three domains of OSBP—an endoplasmic reticulum–targeting domain, a Golgi-targeting domain, and a sterol-binding domain—are all required for Golgi localization of GS28. Finally, GS28 mislocalization and Man II reduction in OSBP-depleted cells are largely restored by depletion of ArfGAP1, a regulator of the budding of coat protein complex (COP)-I vesicles. From these results, we postulate that Golgi cholesterol level, which is controlled by OSBP, is essential for Golgi localization of intra-Golgi v-SNAREs by ensuring proper COP-I vesicle transport.
Lung [18F]fluorodeoxyglucose Uptake and Ventilation–Perfusion Mismatch in the Early Stage of Experimental Acute Smoke Inhalation
Authors: Musch Guido , Winkler Tilo , Harris R. Scott , Vidal Melo Marcos F. , Wellman Tyler J. , de Prost Nicolas , Kradin Richard L. , Venegas Jose G.
Published: September 2013

Background:

Acute lung injury occurs in a third of patients with smoke inhalation injury. Its clinical manifestations usually do not appear until 48–72 h after inhalation. Identifying inflammatory changes that occur in pulmonary parenchyma earlier than that could provide insight into the pathogenesis of smoke-induced acute lung injury. Furthermore, noninvasive measurement of such changes might lead to earlier diagnosis and treatment. Because glucose is the main source of energy for pulmonary inflammatory cells, the authors hypothesized that its pulmonary metabolism is increased shortly after smoke inhalation, when classic manifestations of acute lung injury are not yet expected.

Methods:

In five sheep, the authors induced unilateral injury with 48 breaths of cotton smoke while the contralateral lung served as control. The authors used positron emission tomography with: (1) [18F]fluorodeoxyglucose to measure metabolic activity of pulmonary inflammatory cells; and (2) [13N]nitrogen in saline to measure shunt and ventilation–perfusion distributions separately in the smoke-exposed and control lungs.

Results:

The pulmonary [18F]fluorodeoxyglucose uptake rate was increased at 4 h after smoke inhalation (mean ± SD: 0.0031 ± 0.0013 vs. 0.0026 ± 0.0010 min−1; P < 0.05) mainly as a result of increased glucose phosphorylation. At this stage, there was no worsening in lung aeration or shunt. However, there was a shift of perfusion toward units with lower ventilation-to-perfusion ratio (mean ratio ± SD: 0.82 ± 0.10 vs. 1.12 ± 0.02; P < 0.05) and increased heterogeneity of the ventilation–perfusion distribution (mean ± SD: 0.21 ± 0.07 vs. 0.13 ± 0.01; P < 0 .05).

Conclusion:

Using noninvasive imaging, the authors demonstrated that increased pulmonary [18F]fluorodeoxyglucose uptake and ventilation–perfusion mismatch occur early after smoke inhalation.
Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov.
Authors: Lawson Paul A. , Wawrik Boris , Allen Toby D. , Johnson Crystal N. , Marks Christopher R. , Tanner Ralph S. , Harriman Brian H. , Strąpoć Dariusz , Callaghan Amy V.
Published: September 2013

A taxonomic study employing a polyphasic approach was performed on a novel anaerobic bacterium isolated from natural gas production-water. The bacterium stained Gram-negative and consisted of non-motile, non-spore-forming, rod-shaped cells. Products of glucose or starch fermentation were ethanol, CO2, formate, acetate and H2. The predominant fatty acids were C16 : 0ALDE and summed feature 3 comprising C16 : 1ω7cand/or C16 : 1ω6c. The DNA G+C content was 45.5 mol%. 16S rRNA gene sequence analysis demonstrated that the nearest phylogenetic neighbours of the novel strain wereAcetivibrio multivoransDSM 6139T(98.5 %) andProteiniclasticum ruminisJCM 14817T(95.4 %). The DNA–DNA hybridization value between the novel organism andAcetivibrio multivoransPeC1 DSM 6139Twas determined to be only 30.2 %, demonstrating the separateness of the two species. Based on phylogenetic, phenotypic and chemotaxonomic evidence that clearly distinguished strain 232.1TfromProteiniclasticum ruminisand other close relatives, it is proposed that the novel isolate be classified as representing a novel species of a new genus within the familyClostridiaceae,Youngiibacter fragilisgen. nov., sp. nov. The type strain of the type species is 232.1T( = ATCC BAA-2257T = DSM 24749T). In addition,Acetivibrio multivoransis proposed to be reclassified asYoungiibacter multivoranscomb. nov.
Methyloversatilis thermotolerans sp. nov., a novel thermotolerant facultative methylotroph isolated from a hot spring
Authors: Doronina Nina V. , Kaparullina Elena N. , Trotsenko Yuri A.
Published: September 2013

A newly isolated facultatively methylotrophic bacterium (strain 3tT) was investigated. Cells of the isolate were Gram-stain-negative, asporogenous, non-motile rods that multiplied by binary fission. The strain utilized methanol, methylamine and a variety of multicarbon compounds as carbon and energy sources. Growth occurred at pH 6.5–8.5 (optimally at 7.0–7.5) and at 10–45 °C (optimally at 30–37 °C). The major fatty acids of methanol-grown cells were C16 : 1ω7cand C16 : 0. The predominant phospholipids were phosphatidylethanolamine and phosphatidylglycerol. The major ubiquinone was Q-8. Strain 3tTpossessed pyrroloquinoline quinone (PQQ)-linked methanol dehydrogenase and assimilated C1units at the level of formaldehyde and CO2via the serine cycle. The DNA G+C content of the strain was 63.6 mol% (Tm). On the basis of 16S rRNA gene sequence similarity (98.1 %) and rather low DNA–DNA relatedness (30 %) with the type strain of the type species of the genusMethyloversatilis(Methyloversatilis universalisFAM5T), and physiological and biochemical characteristics, the isolate was classified as a representative of a new species of the genus and namedMethyloversatilis thermotolerans3tT( = VKM B-2692T = CCUG 61694T = DSM 25156T).
Taxonomic study of the genus Tepidiphilus: transfer of Petrobacter succinatimandens to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov., emended description of the genus Tepidiphilus and description of Tepidiphilus thermophilus sp. nov., isolated from a terrestrial hot spring
Authors: Poddar Abhijit , Lepcha Rinchen T. , Das Subrata K.
Published: September 2013

Comparative phenotypic, chemotaxonomic and genetic analysis revealed significant similarities among strains of the genera

Tepidiphilus

and

Petrobacter

. Analysis of 16S rRNA gene sequences and DNA–DNA relatedness of the type strains

Tepidiphilus margaritifer

N2-214T and

Petrobacter succinatimandens

4BONT showed sequence similarity of 98.9 % and less than 40 % relatedness, indicating that these strains represent different species of same genus. Both strains had phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol as major polar lipids. Their fatty acid profiles were almost identical, with the predominant fatty acids C16 : 0, C17 : 0 cyclo and C19 : 0 cyclo ω8c. In view of this, we propose to transfer the member of the genus

Petrobacter

to the genus

Tepidiphilus

as Tepidiphilus succinatimandens comb. nov. and to emend the description of the genus

Tepidiphilus

. Further, a novel bacterium, strain JHK30T, was isolated from a terrestrial hot spring located at Jharkhand, India, and was identified following a polyphasic approach. Cells were non-sporulating, aerobic, Gram-stain-negative rods and motile by a single polar flagellum. Optimum temperature for growth was 50–55 °C at pH 6.5–7.0. 16S rRNA gene sequence analysis revealed 99.71 % similarity with

P. succinatimandens

4BONT ( = DSM 15512T) and 98.71 % with

T. margaritifer

N2-214T ( = DSM 15129T). However, DNA–DNA relatedness of strain JHK30T with these two type strains was well below 70 %. The DNA G+C base composition was 66.1 mol%. Strain JHK30T represents a novel species of the genus

Tepidiphilus

for which the name Tepidiphilus thermophilus sp. nov. is proposed. The type strain is JHK30T ( = JCM 19170T = LMG 27587T= DSM 27220T).
Water Uptake along the Length of Grapevine Fine Roots: Developmental Anatomy, Tissue-Specific Aquaporin Expression, and Pathways of Water Transport
Authors: Gambetta Gregory A. , Fei Jiong , Rost Thomas L. , Knipfer Thorsten , Matthews Mark A. , Shackel Ken A. , Walker M. Andrew , McElrone Andrew J.
Published: September 2013

To better understand water uptake patterns in root systems of woody perennial crops, we detailed the developmental anatomy and hydraulic physiology along the length of grapevine (Vitis berlandieri × Vitis rupestris) fine roots from the tip to secondary growth zones. Our characterization included the localization of suberized structures and aquaporin gene expression and the determination of hydraulic conductivity (Lp  r) and aquaporin protein activity (via chemical inhibition) in different root zones under both osmotic and hydrostatic pressure gradients. Tissue-specific messenger RNA levels of the plasma membrane aquaporin isogenes (VvPIPs) were quantified using laser-capture microdissection and quantitative polymerase chain reaction. Our results highlight dramatic changes in structure and function along the length of grapevine fine roots. Although the root tip lacked suberization altogether, a suberized exodermis and endodermis developed in the maturation zone, which gave way to the secondary growth zone containing a multilayer suberized periderm. Longitudinally, VvPIP isogenes exhibited strong peaks of expression in the root tip that decreased precipitously along the root length in a pattern similar to Arabidopsis (Arabidopsis thaliana) roots. In the radial orientation, expression was always greatest in interior tissues (i.e. stele, endodermis, and/or vascular tissues) for all root zones. High Lp  r and aquaporin protein activity were associated with peak VvPIP expression levels in the root tip. This suggests that aquaporins play a limited role in controlling water uptake in secondary growth zones, which contradicts existing theoretical predictions. Despite having significantly lower Lp  r, woody roots can constitute the vast majority of the root system surface area in mature vines and thus provide for significant water uptake potential.
Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis
Authors: Furt Fabienne , Allen William J. , Widhalm Joshua R. , Madzelan Peter , Rizzo Robert C. , Basset Gilles , Wilson Mark A.
Published: September 2013

The synthesis of phylloquinone (vitamin K1) in photosynthetic organisms requires a thioesterase that hydrolyzes 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to release 1,4-dihydroxy-2-naphthoate (DHNA). Cyanobacteria and plants contain distantly related hotdog-fold thioesterases that catalyze this reaction, although the structural basis of these convergent enzymatic activities is unknown. To investigate this, the crystal structures of hotdog-fold DHNA-CoA thioesterases from the cyanobacteriumSynechocystis(Slr0204) and the flowering plantArabidopsis thaliana(AtDHNAT1) were determined. These enzymes form distinct homotetramers and use different active sites to catalyze hydrolysis of DHNA-CoA, similar to the 4-hydroxybenzoyl-CoA (4-HBA-CoA) thioesterases fromPseudomonasandArthrobacter. Like the 4-HBA-CoA thioesterases, the DHNA-CoA thioesterases contain either an active-site aspartate (Slr0204) or glutamate (AtDHNAT1) that are predicted to be catalytically important. Computational modeling of the substrate-bound forms of both enzymes indicates the residues that are likely to be involved in substrate binding and catalysis. Both enzymes are selective for DHNA-CoA as a substrate, but this selectivity is achieved using divergent predicted binding strategies. The Slr0204 binding pocket is predominantly hydrophobic and closely conforms to DHNA, while that of AtDHNAT1 is more polar and solvent-exposed. Considered in light of the related 4-HBA-CoA thioesterases, these structures indicate that hotdog-fold thioesterases using either an active-site aspartate or glutamate diverged into distinct clades prior to the evolution of strong substrate specificity in these enzymes.
Structural basis for the antibody neutralization ofHerpes simplex virus
Authors: Lee Cheng-Chung , Lin Li-Ling , Chan Woan-Eng , Ko Tzu-Ping , Lai Jiann-Shiun , Wang Andrew H.-J.
Published: September 2013

Glycoprotein D (gD) ofHerpes simplex virus(HSV) binds to a host cell surface receptor, which is required to trigger membrane fusion for virion entry into the host cell. gD has become a validated anti-HSV target for therapeutic antibody development. The highly inhibitory human monoclonal antibody E317 (mAb E317) was previously raised against HSV gD for viral neutralization. To understand the structural basis of antibody neutralization, crystals of the gD ectodomain bound to the E317 Fab domain were obtained. The structure of the complex reveals that E317 interacts with gD mainly through the heavy chain, which covers a large area for epitope recognition on gD, with a flexible N-terminal and C-terminal conformation. The epitope core structure maps to the external surface of gD, corresponding to the binding sites of two receptors, herpesvirus entry mediator (HVEM) and nectin-1, which mediate HSV infection. E317 directly recognizes the gD–nectin-1 interface and occludes the HVEM contact site of gD to block its binding to either receptor. The binding of E317 to gD also prohibits the formation of the N-terminal hairpin of gD for HVEM recognition. The major E317-binding site on gD overlaps with either the nectin-1-binding residues or the neutralizing antigenic sites identified thus far (Tyr38, Asp215, Arg222 and Phe223). The epitopes of gD for E317 binding are highly conserved between two types of human herpesvirus (HSV-1 and HSV-2). This study enables the virus-neutralizing epitopes to be correlated with the receptor-binding regions. The results further strengthen the previously demonstrated therapeutic and diagnostic potential of the E317 antibody.
A functional and structural study of the major metalloprotease secreted by the pathogenic fungusAspergillus fumigatus
Authors: Fernández Daniel , Russi Silvia , Vendrell Josep , Monod Michel , Pallarès Irantzu
Published: September 2013

Fungalysins are secreted fungal peptidases with the ability to degrade the extracellular matrix proteins elastin and collagen and are thought to act as virulence factors in diseases caused by fungi. Fungalysins constitute a unique family among zinc-dependent peptidases that bears low sequence similarity to known bacterial peptidases of the thermolysin family. The crystal structure of the archetype of the fungalysin family,Aspergillus fumigatusmetalloprotease (AfuMep), has been obtained for the first time. The 1.8 Å resolution structure of AfuMep corresponds to that of an autoproteolyzed proenzyme with separate polypeptide chains corresponding to the N-terminal prodomain in a binary complex with the C-terminal zinc-bound catalytic domain. The prodomain consists of a tandem of cystatin-like folds whose C-terminal end is buried into the active-site cleft of the catalytic domain. The catalytic domain harbouring the key catalytic zinc ion and its ligands, two histidines and one glutamic acid, undergoes a conspicuous rearrangement of its N-terminal end during maturation. One key positively charged amino-acid residue and the C-terminal disulfide bridge appear to contribute to its structural–functional properties. Thus, structural, biophysical and biochemical analysis were combined to provide a deeper comprehension of the underlying properties ofA. fumigatusfungalysin, serving as a framework for the as yet poorly known metallopeptidases from pathogenic fungi.
Structure of the polypeptide crotamine from the Brazilian rattlesnakeCrotalus durissus terrificus
Authors: Coronado Monika A. , Gabdulkhakov Azat , Georgieva Dessislava , Sankaran Banumathi , Murakami Mario T. , Arni Raghuvir K. , Betzel Christian
Published: September 2013

The crystal structure of the myotoxic, cell-penetrating, basic polypeptide crotamine isolated from the venom ofCrotalus durissus terrificushas been determined by single-wavelength anomalous dispersion techniques and refined at 1.7 Å resolution. The structure reveals distinct cationic and hydrophobic surface regions that are located on opposite sides of the molecule. This surface-charge distribution indicates its possible mode of interaction with negatively charged phospholipids and other molecular targets to account for its diverse pharmacological activities. Although the sequence identity between crotamine and human β-defensins is low, the three-dimensional structures of these functionally related peptides are similar. Since crotamine is a leading member of a large family of myotoxic peptides, its structure will provide a basis for the design of novel cell-penetrating molecules.
Structure of fully liganded Hb ζ2β2strapped in a tense conformation
Authors: Safo Martin K. , Ko Tzu-Ping , Abdulmalik Osheiza , He Zhenning , Wang Andrew H.-J. , Schreiter Eric R. , Russell J. Eric
Published: September 2013

A variant Hb ζ2β2sthat is formed from sickle hemoglobin (Hb S; α2β2s) by exchanging adult α-globin with embryonic ζ-globin subunits shows promise as a therapeutic agent for sickle-cell disease (SCD). Hb ζ2β2sinhibits the polymerization of deoxygenated Hb Sin vitroand reverses characteristic features of SCDin vivoin mouse models of the disorder. When compared with either Hb S or with normal human adult Hb A (α2β2), Hb ζ2β2sexhibits atypical properties that include a high oxygen affinity, reduced cooperativity, a weak Bohr effect and blunted 2,3-diphosphoglycerate allostery. Here, the 1.95 Å resolution crystal structure of human Hb ζ2β2sthat was expressed in complex transgenic knockout mice and purified from their erythrocytes is presented. When fully liganded with carbon monoxide, Hb ζ2β2sdisplays a central water cavity, a ζ1–βs2 (or ζ2–βs1) interface, intersubunit salt-bridge/hydrogen-bond interactions, C-terminal βHis146 salt-bridge interactions, and a β-cleft, that are highly unusual for a relaxed hemoglobin structure and are more typical of a tense conformation. These quaternary tense-like features contrast with the tertiary relaxed-like conformations of the ζ1βs1 dimer and the CD and FG corners, as well as the overall structures of the heme cavities. This crystallographic study provides insights into the altered oxygen-transport properties of Hb ζ2β2sand, moreover, decouples tertiary- and quaternary-structural events that are critical to Hb ligand binding and allosteric function.
Structure of a bifunctional alcohol dehydrogenase involved in bioethanol generation inGeobacillus thermoglucosidasius
Authors: Extance Jonathan , Crennell Susan J. , Eley Kirstin , Cripps Roger , Hough David W. , Danson Michael J.
Published: September 2013

Bifunctional alcohol/aldehyde dehydrogenase (ADHE) enzymes are found within many fermentative microorganisms. They catalyse the conversion of an acyl-coenzyme A to an alcoholviaan aldehyde intermediate; this is coupled to the oxidation of two NADH molecules to maintain the NAD+pool during fermentative metabolism. The structure of the alcohol dehydrogenase (ADH) domain of an ADHE protein from the ethanol-producing thermophileGeobacillus thermoglucosidasiushas been determined to 2.5 Å resolution. This is the first structure to be reported for such a domain.In silicomodelling has been carried out to generate a homology model of the aldehyde dehydrogenase domain, and this was subsequently docked with the ADH-domain structure to model the structure of the complete ADHE protein. This model suggests, for the first time, a structural mechanism for the formation of the large multimeric assemblies or `spirosomes' that are observed for this ADHE protein and which have previously been reported for ADHEs from other organisms.
Three-dimensional domain swapping and supramolecular protein assembly: insights from the X-ray structure of a dimeric swapped variant of human pancreatic RNase
Authors: Pica Andrea , Merlino Antonello , Buell Alexander K. , Knowles Tuomas P. J. , Pizzo Elio , D'Alessio Giuseppe , Sica Filomena , Mazzarella Lelio
Published: September 2013

The deletion of five residues in the loop connecting the N-terminal helix to the core of monomeric human pancreatic ribonuclease leads to the formation of an enzymatically active domain-swapped dimer (desHP). The crystal structure of desHP reveals the generation of an intriguing fibril-like aggregate of desHP molecules that extends along theccrystallographic axis. Dimers are formed by three-dimensional domain swapping. Tetramers are formed by the aggregation of swapped dimers with slightly different quaternary structures. The tetramers interact in such a way as to form an infinite rod-like structure that propagates throughout the crystal. The observed supramolecular assembly captured in the crystal predicts that desHP fibrils could form in solution; this has been confirmed by atomic force microscopy. These results provide new evidence that three-dimensional domain swapping can be a mechanism for the formation of elaborate large assemblies in which the protein, apart from the swapping, retains its original fold.
Conformational changes in human prolyl-tRNA synthetase upon binding of the substrates proline and ATP and the inhibitor halofuginone
Authors: Son Jonghyeon , Lee Eun Hye , Park Minyoung , Kim Jong Hyun , Kim Junsoo , Kim Sunghoon , Jeon Young Ho , Hwang Kwang Yeon
Published: September 2013

Aminoacyl-tRNA synthetases recognize cognate amino acids and tRNAs from their noncognate counterparts and catalyze the formation of aminoacyl-tRNAs. Halofuginone (HF), a coccidiostat used in veterinary medicine, exerts its effects by acting as a high-affinity inhibitor of the enzyme glutamyl-prolyl-tRNA synthetase (EPRS). In order to elucidate the precise molecular basis of this inhibition mechanism of human EPRS, the crystal structures of the prolyl-tRNA synthetase domain of human EPRS (hPRS) at 2.4 Å resolution (hPRS-apo), ofhPRS complexed with ATP and the substrate proline at 2.3 Å resolution (hPRS-sub) and ofhPRS complexed with HF at 2.62 Å resolution (hPRS-HF) are presented. These structures show plainly that motif 1 functions as a cap inhPRS, which is loosely opened inhPRS-apo, tightly closed inhPRS-sub and incorrectly closed inhPRS-HF. In addition, the structural analyses are consistent with more effective binding ofhPRS to HF with ATP. Mutagenesis and biochemical analysis confirmed the key roles of two residues, Phe1097 and Arg1152, in the HF inhibition mechanism. These structures will lead to the development of more potent and selectivehPRS inhibitors for promoting inflammatory resolution.