bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancing dissolved oxygen control using an on-line hybrid fuzzy-neural soft-sensing model-based control system in an anaerobic/anoxic/oxic process
Authors: Huang Mingzhi , Wan Jinquan , Hu Kang , Ma Yongwen , Wang Yan
Published: September 2013

An on-line hybrid fuzzy-neural soft-sensing model-based control system was developed to optimize dissolved oxygen concentration in a bench-scale anaerobic/anoxic/oxic (A2/O) process. In order to improve the performance of the control system, a self-adapted fuzzy c-means clustering algorithm and adaptive network-based fuzzy inference system (ANFIS) models were employed. The proposed control system permits the on-line implementation of every operating strategy of the experimental system. A set of experiments involving variable hydraulic retention time (HRT), influent pH (pH), dissolved oxygen in the aerobic reactor (DO), and mixed-liquid return ratio (r) was carried out. Using the proposed system, the amount of COD in the effluent stabilized at the set-point and below. The improvement was achieved with optimum dissolved oxygen concentration because the performance of the treatment process was optimized using operating rules implemented in real time. The system allows various expert operational approaches to be deployed with the goal of minimizing organic substances in the outlet while using the minimum amount of energy.
Stigmatized Labour: An Overlooked Service Worker's Stress
Authors: Bove Liliana L. , Pervan Simon J.
Published: September 2013

Service workers like social workers are valuable to society ( LeCroy and Stinson, 2004 ), even noble and heroic ( Ashforth et al., 2007 ), yet, perversely, they are often socially stigmatized, seen as “dirty” by their communities because they deal with “tainted” people ( Ashforth and Kreiner, 1999 ). Other service workers also suffer stigmatization because their role is associated with effluent (e.g., refuse collector), they have a servile relationship with others (e.g., housekeeper), or adopt tasks that are perceived as amoral (e.g., pawnbroker) or intrusive (e.g., telemarketer). We propose that feelings of stigma lead to poor well-being and present a conceptual model which introduces the concept of “stigmatized labour” as a type of role stress. We postulate that excessive stigmatized labour (the cognitive and behavioural practices adopted by service workers to protect themselves from feelings of stigma) leads to burnout as service workers’ limited resources are exhausted to deal with the stress ( Hobfoll, 2001 ).
Different evolutionary patterns of hypoxia‐inducible factor α (HIF‐α) isoforms in the basal branches of Actinopterygii and Sarcopterygii
Authors: Chi Wei , Gan Xiaoni , Xiao Wuhan , Wang Wen , He Shunping
Published: September 2013

Hypoxia‐inducible factor (HIF) is a crucial regulator of cellular and systemic responses to low oxygen levels. Here we firstly cloned three HIF‐α isoforms from the basal branches of Osteichthyes and used computational tools to characterise the molecular change underlying the functional divergence of HIF‐α isoforms in different lineages. Only the HIF‐1α and HIF‐2α in African lungfish and amphibians were found under positive selection. HIF‐1α and ‐2α were less functionally divergent in basal ray‐finned fish than in teleosts, and showed conserved but different transcriptional activity towards specific target genes.
Efficient kinematics for jet-propelled swimming
Authors: Alben S. , Miller L. A. , Peng J.
Published: September 2013

We use computer simulations and an analytical model to study the relationship between kinematics and performance in jet-propelled jellyfish swimming. We prescribe different power-law kinematics for the bell contraction and expansion, and identify kinematics that yield high swimming speeds and/or high efficiency. In the simulations, high efficiency is found when the bell radius is a nearly linear function of time, and in a second case corresponding to ‘burst-and-coast’ kinematics. The analytical model studies the contraction phase only, and finds that the efficiency-optimizing bell radius as a function of time transitions from nearly linear (similar to the numerics) for small-to-moderate output power to exponentially decaying for large output power.
Temporal stability of eccentric Taylor–Couette–Poiseuille flow
Authors: Leclercq Colin , Pier Benoît , Scott Julian F.
Published: September 2013

The combined effects of axial flow and eccentricity on the temporal stability properties of the Taylor–Couette system are investigated using a pseudospectral method. Eccentricity is found to stabilize the Couette flow regardless of axial advection intensity. As the axial Reynolds number ${\mathit{Re}}_{z} $ is increased for any fixed eccentricity $e\leq 0. 7$, the critical mode switches from deformed toroidal Taylor vortices to helical structures with an increasing number of waves, and with helicity opposed to the inner-cylinder rotation. For a wide-gap configuration of radius ratio $\eta = 0. 5$, increasing axial advection has a stabilizing effect for low ${\mathit{Re}}_{z} $, then a weak destabilizing effect for high enough ${\mathit{Re}}_{z} $. Centrifugal effects are always destabilizing, but axial shear is responsible for the dominance of helical modes of increasing azimuthal complexity. The modes localize in the converging gap region, and the energy concentrates increasingly into axial motion for larger ${\mathit{Re}}_{z} $. Critical quantities are also computed for a small-gap case, and similar trends are observed, even though no destabilizing effect of advection is observed within the range of ${\mathit{Re}}_{z} $ considered. Comparison with the experiment of Coney & Mobbs (Proc. Inst. Mech. Engrs, vol. 184 Pt 3L, 1969–70, pp. 10–17) for $\eta = 0. 89$ shows good agreement, despite small discrepancies attributed to finite length effects.
Generalized Fourier Integral Operator Methods for Hyperbolic Equations with Singularities
Authors: Garetto Claudia , Oberguggenberger Michael
Published: September 2013

This paper addresses linear hyperbolic partial differential equations and pseudodifferential equations with strongly singular coefficients and data, modelled as members of algebras of generalized functions. We employ the recently developed theory of generalized Fourier integral operators to construct parametrices for the solutions and to describe propagation of singularities in this setting. As required tools, the construction of generalized solutions to eikonal and transport equations is given and results on the microlocal regularity of the kernels of generalized Fourier integral operators are obtained.
Scanning electron microscopy of the cypris larvae ofCapitulum mitella(Cirripedia: Thoracica: Scalpellomorpha)
Authors: Rao Xiaozhen , Lin Gang
Published: September 2013

Adult specimens ofCapitulum mitellawere collected in August 2011 in the intertidal zone of Dinghai, Fuzhou, Fujian, China (26°16′N 119°48′E). The morphology of the cypris larva reared under our conditions was determined using scanning electron microscopy (SEM). Special emphasis was given to the carapace, lattice organs, antennules, thoracopods and furcal rami. The whole carapace surface is sculptured by slender ridges demarcating rectangular or irregular polygonal areas with very fine pores. The cyprid possesses five pairs of lattice organs, arranged as two anterior and three posterior pairs. The second segment carries a preaxial seta 2 and a postaxial seta 2. The third segment carries a postaxial seta 3 outside the attachment disc, whereas a postaxial disc seta, an axial disc seta and two radial disc setae are located inside the attachment disc. The attachment disc is somewhat bell shaped. A series of slender cuticular flaps forms a distinct ‘velum’ around the base of the disc. The fourth segment carries four subterminal setae and five terminal setae. The cyprid bears six pairs of biramous natatory thoracopods consisting of a protopod (coxa + basis), a two-segmented exopod and a two-segmented endopod. The cyprid possesses a rudimentary abdomen and an almost completely cleaved telson with a pair of one-segmented furcal rami. The morphology and setation of the antennules ofC. mitellaresemble those ofBalanus amphitrite(=Amphibalanus amphitrite) andMegabalanus rosa, but differ in some morphological details.
Gender differences in intergenerational care in European welfare states
Authors: HABERKERN KLAUS , SCHMID TINA , SZYDLIK MARC
Published: September 2013

Elderly people with functional limitations are predominantly cared for by family members. Women – spouses and daughters – provide most of this care work. In principle, gender inequality in intergenerational care may have three causes: first, daughters and sons have different resources to provide care; second, daughters and sons respond differently to the same resources; third, welfare state programmes and cultural norms affect daughters and sons differently. In this paper, we address the empirical question whether these three assumed causes are in fact responsible for gender differences in intergenerational care. The empirical analyses, based on the Survey of Health, Ageing and Retirement in Europe (SHARE), reveal that parents in need are in fact more likely to receive care from daughters than from sons. Daughters are more responsive to the needs of their parents than sons and respond differently to the same resources. Gender inequality is highest in countries with a high level of intergenerational care, high public spending on old-age cash-benefits, a low provision of professional care services, high family obligation norms and a high level of gendered division of labour. Welfare state programmes reduce or increase gender inequality in intergenerational care by reducing or increasing the engagement of daughters in intergenerational care. In general, care-giving by sons is hardly influenced by social care policies.
The Native as Exemplum: Missionary Writings and Colonial Complexities in Eastern Indonesia, 1819–1860
Authors: Hägerdal Hans
Published: September 2013

In the year 1819, three years after the British return of the East Indies to the Netherlands, a young man of twenty arrived to Kupang, a port on the coast of West Timor. Kupang was by no means a large place but it was the centre of Dutch colonial power over this part of Indonesia, and its administration monitored the various islands that the Netherlands laid claim to: Solor, Alor, Rote, Savu, and others. This task was made the more difficult since some of these places were also claimed by Portugal, which maintained a colonial governor in Dili, in the eastern part of Timor. The last serious conflict between the two colonial powers had occurred the previous year when the little harbour Atapupu was forcibly occupied by the Dutch resident. The tempests of the Age of Napoleon had been severely felt in Timor, whose inhabitants were located at the extremities of the colonial claims of the warring parties. Britons, Dutchmen, and Portuguese had fought or intrigued for the resources of an island that was neither the richest nor the most accessible in the island world of Southeast Asia—rather the opposite.

The name of the young man was Reint Le Bruyn. Born in Zutphen, Le Bruyn had spent his early years as a child labourer in a textile factory. Coming from relatively destitute conditions, he had nevertheless picked up some education, and in 1818 he signed up for the Nederlandsch Zendeling-Genootschap (NZG), the Dutch Missionary Society. This society, the first among about fifteen to concentrate on the East Indies, had been established in 1797 by a missionary who later worked in South Africa. It was modelled on the London Missionary Society which was founded two years earlier. Societies of this kind emerged as part of the wave of rising interest in undertaking missionary activity in non-Western societies, which, interestingly, coincided with the questioning of traditional clerical hierarchy after the outbreak of the French Revolution. Biographical sketches of Le Bruyn's life have typically pointed to his Christian devotion to explain his career choice. However, it could also have been a way for poor men of ability to engage in work that provided a degree of professional recognition that they could not have hoped for at home. Missionaries received scant preparation for their task in Rotterdam; they had little knowledge of the societies that awaited them, and they only learned any substantial Malay, the main language of communication, on arrival in the Indies. Le Bruyn successfully overcame these obstacles and had an eventful career on Timor for the next ten years, to the extent that posterity hailed him as the true pioneer of the Protestant mission in these waters.
Turning Javanese: The Domination of Cuba's Sugar Industry by Java Cane Varieties
Authors: Bosma Ulbe , Curry-Machado Jonathan
Published: September 2013

By the end of the nineteenth century and beginning of the twentieth, two islands had come to dominate global cane-sugar production. For most of the sixty-year period between 1870 and 1930, around half of the world's internationally traded crop came from Cuba and Java. The two islands had many topographical similarities that made them particularly well suited to the establishment of sugar plantations: both are relatively large islands with fertile soils and semi-tropical climate. They were also situated in regions that had been drawn into the European sphere of influence in the sixteenth century but that had only been lightly exploited before the nineteenth, when they were both well placed to assume leading roles in the satisfaction of the escalating demand for sugar in the industrialising societies of Europe and North America.

However, Cuba and Java existed within two very distinct sets of imperial and commercial networks: Spanish and Atlantic, and Dutch and Indian Ocean respectively. As a result of this, while there have been a plethora of studies about cane agriculture and the sugar industry in each of the islands, there has been little effort to compare their histories or explore the interconnections between them. Only recently has a start been made to study systematically the “convergence and divergence” of the sugar industry in the two hemispheres and to compare the differences and similarities to be found in the paths followed by the two islands.

Although the sugar industries of Cuba and Java took different directions, these were inextricably linked. While Cuban planters could exploit the availability of large areas of underused land to overcome the relative scarcity of labour, planters in Java took advantage of the relative abundance of labour to maximise yields from the more limited land available to them. As a consequence of this, Javanese planters influenced by the work of Cuban agronomist Álvaro Reynoso paid considerable attention to the development of scientific methods in cane cultivation. Meanwhile, Reynoso's ideas fell on deaf ears in his home island, where most planters ignored the need for a more scientific approach in the fields in favour of technological advances in the sugar factory and what they saw as their immediate commercial interests.
Stimulated Brillouin backscattering of filamented hollow Gaussian beams
Authors: Sharma R.P. , Singh Ram Kishor
Published: September 2013

This paper presents an investigation for excitation of ion acoustic wave and resulting stimulated Brillouin scattering in a collisionless plasma due to presence of a laser beam carrying null intensity at center (hollow Gaussian beam). In presence of ponderomotive nonlinearity, the pump beam get focused and affects the back stimulated Brillouin scattering process. To understand the nature of laser plasma coupling, a paraxial-ray approximation has been invoked for the propagation of the hollow Gaussian beam, ion acoustic wave, and stimulated Brillouin scattering. It is observed from the result that self-focusing and back reflectivity reduces for higher order of hollow Gaussian beam.
Weyl metrisability of two-dimensional projective structures
Authors: METTLER THOMAS
Published: September 2013

We show that on a surface locally every affine torsion-free connection is projectively equivalent to a Weyl connection. First, this is done using exterior differential system theory. Second, this is done by showing that the solutions of the relevant PDE are in one-to-one correspondence with the sections of the ‘twistor’ bundle of conformal inner products having holomorphic image. The second solution allows to use standard results in algebraic geometry to show that the Weyl connections on the two-sphere whose geodesics are the great circles are in one-to-one correspondence with the smooth quadrics without real points in the complex projective plane.
Quality of life of patients with atrial septal defect following percutaneous closure
Authors: Kahya Eren Nihan , Kırdök Ali H. , Kılıçaslan Barış , Kocabaş Uğur , Düzel Barış , Berilgen Rida , Nazli Cem , Ergene Oktay
Published: September 2013

Introduction

Quality of life has become an important outcome measure in addition to mortality and morbidity in patients with congenital heart disease. Atrial septal defect is a common congenital heart disease, and transcatheter atrial septal defect closure has become an accepted treatment modality. The aim of this study is to assess the quality of life of patients with atrial septal defect who underwent percutaneous closure.

Materials and methods

We examined the quality of life of 69 patients with atrial septal defect and 69 healthy controls matched according to age, sex, educational level, and economic, marital, and employment status. Quality of life was investigated using the Turkish version of Short Form-36.

Results

The mean age of the patients was 39.7 ± 14.2 and 26% were male. The quality of life assessment was performed at a mean follow-up time of 18.0 ± 13.8 months after the intervention. The mean scores of the domains of the Short Form-36, namely, physical functioning, role functioning, social functioning, mental health, vitality, pain, and general health, were similar in patients with atrial septal defect who underwent percutaneous closure and the control group.

Conclusion

Adult patients who underwent percutaneous atrial septal defect closure perceive their quality of life to be as good as their healthy counterparts.
Quantum Conductance in Silicon Oxide Resistive Memory Devices
Authors: Mehonic A. , Vrajitoarea A. , Cueff S. , Hudziak S. , Howe H. , Labbé C. , Rizk R. , Pepper M. , Kenyon A. J.
Published: September 2013

Resistive switching offers a promising route to universal electronic memory, potentially replacing current technologies that are approaching their fundamental limits. In many cases switching originates from the reversible formation and dissolution of nanometre-scale conductive filaments, which constrain the motion of electrons, leading to the quantisation of device conductance into multiples of the fundamental unit of conductance, G0. Such quantum effects appear when the constriction diameter approaches the Fermi wavelength of the electron in the medium – typically several nanometres. Here we find that the conductance of silicon-rich silica (SiOx) resistive switches is quantised in half-integer multiples of G0. In contrast to other resistive switching systems this quantisation is intrinsic to SiOx and is not due to drift of metallic ions. Half-integer quantisation is explained in terms of the filament structure and formation mechanism, which allows us to distinguish between systems that exhibit integer and half-integer quantisation.
Surface control of blastospore attachment and ligand-mediated hyphae adhesion ofCandida albicans
Authors: Varghese Nisha , Yang Sijie , Sejwal Preeti , Luk Yan-Yeung
Published: September 2013

Controlling the adhesion ofCandida albicanson surfaces by the selected ligand deconvolutes effects from multiple adhesins and nonspecific interactions.
Perceptuo-motor, cognitive, and description-based decision-making seem equally good
Authors: Jarvstad Andreas , Hahn Ulrike , Rushton Simon K. , Warren Paul A.
Published: September 2013

Significance

Human decision-making seems fundamentally domain dependent. Sensory-motor decisions (e.g., where to put your feet on a rocky ridge) seem near-optimal, whereas decisions based on numerical information (e.g., choosing between financial options) seem suboptimal. Additionally, when people rely on information gained through experience, they make choices that are often the opposite of those they make when relying on described information. However, comparing results across domains on the basis of past results is difficult, because decision-making is studied very differently in different domains. We compared decision-making performance across domains under precisely matched conditions, finding evidence against the idea that fundamental dissociations exist. In fact, peoples’ ability to make decisions seem rather good, although not perfect, in both sensory-motor and cognitive domains.
Management of fisheries on forage species: the test-bed for ecosystem approaches to fisheries
Authors: Rice Jake , Duplisea Daniel
Published: September 2013

Rice, J., and Duplisea, D. 2013. Management of fisheries on forage species: the test-bed for ecosystem approaches to fisheries. – ICES Journal of Marine Science, 71: . In the 1970s and 1980s, core ideas about management of fisheries on forage species emerged from work on the dynamics of foodweb models and multispecies assessments, leading to proposals for management that took some account of the role of forage species in marine ecosystems. Key developments in those years are summarized in the first part of this paper. From the 1980s to the 2000s, studies of the response of forage species to environmental variation brought into question the robustness of management strategies for forage species. As a result, additional management strategies were proposed to accommodate environmental drivers as well as dependent predators. The paper reviews these developments. This paper brings these separate lines together in a systematic framework for evaluating the performance of six different management strategies for forage species, relative to four different ecosystem considerations, as well as relative to the contribution of forage fisheries to economic prosperity and food security. The tabulated outcomes synthesize primary and secondary literature and meeting deliberations as the application of an ecosystem approach to management has evolved. No strategy is optional for all forage fisheries. As experience accumulates, the guidance in the tables comprising the framework will improve.
CD28 signaling in primary CD4+ T cells: identification of both tyrosine phosphorylation-dependent and phosphorylation-independent pathways
Authors: Ogawa Shuhei , Watanabe Masashi , Sakurai Yuichi , Inutake Yu , Watanabe Shiho , Tai Xuguang , Abe Ryo
Published: September 2013

In addition to TCR signaling, the activation and proliferation of naive T cells require CD28-mediated co-stimulation. Once engaged, CD28 is phosphorylated and can then activate signaling pathways by recruiting molecules to its YMNM motif and two PxxP motifs. In this study, we analyzed the relationship between tyrosine phosphorylation and the co-stimulatory function of CD28 in murine primary CD4+ T cells. Tyrosine phosphorylation is decreased in CD28 where the N-terminal PxxP motif is mutated (nPA). In cells expressing nPA, activation of Akt and functional co-stimulation were decreased. In contrast, where the C-terminal PxxP motif is mutated, tyrosine phosphorylation and activation of the ERK, Akt and NF-κB were intact, but proliferation and IL-2 production were decreased. Using the Y189 to F mutant, we also demonstrated that in naive CD4+ T cells, tyrosine at position 189 in the YMNM motif is critical for both tyrosine phosphorylation and the functional co-stimulatory effects of CD28. This mutation did not affect unfractionated T-cell populations. Overall, our data suggest that CD28 signaling uses tyrosine phosphorylation-dependent and phosphorylation-independent pathways.
Subarcsecond high-sensitivity measurements of the DG Tau jet with e-MERLIN
Authors: Ainsworth Rachael E. , Ray Tom P. , Scaife Anna M. M. , Greaves Jane S. , Beswick Rob J.
Published: September 2013

We present very high spatial resolution deep radio continuum observations at 5 GHz (6 cm) made with the extended Multi-Element Radio Linked Interferometer Network (e-MERLIN) of the young stars DG Tau A and B. Assuming it is launched very close (≃1 au) from the star, our results suggest that the DG Tau A outflow initially starts as a poorly focused wind and undergoes significant collimation farther along the jet (≃50 au). We derive jet parameters for DG Tau A and find an initial jet opening angle of 86° within 2 au of the source, a mass-loss rate of 1.5 × 10−8 M⊙ yr−1 for the ionized component of the jet, and the total ejection-to-accretion ratio to range from 0.06 to 0.3. These results are in line with predictions from magnetohydrodynamic jet-launching theories.
Intracellular dynamics of archaeal FANCM homologue Hef in response to halted DNA replication
Authors: Lestini Roxane , Laptenok Sergey P. , Kühn Joëlle , Hink Mark A. , Schanne-Klein Marie-Claire , Liebl Ursula , Myllykallio Hannu
Published: September 2013

Hef is an archaeal member of the DNA repair endonuclease XPF (XPF)/Crossover junction endonuclease MUS81 (MUS81)/Fanconi anemia, complementation group M (FANCM) protein family that in eukaryotes participates in the restart of stalled DNA replication forks. To investigate the physiological roles of Hef in maintaining genome stability in living archaeal cells, we studied the localization of Hef–green fluorescent protein fusions by fluorescence microscopy. Our studies revealed that Haloferax volcanii Hef proteins formed specific localization foci under regular growth conditions, the number of which specifically increased in response to replication arrest. Purification of the full-length Hef protein from its native host revealed that it forms a stable homodimer in solution, with a peculiar elongated configuration. Altogether our data indicate that the shape of Hef, significant physicochemical constraints and/or interactions with DNA limit the apparent cytosolic diffusion of halophilic DNA replication/repair complexes, and demonstrate that Hef proteins are dynamically recruited to archaeal eukaryotic-like chromatin to counteract DNA replication stress. We suggest that the evolutionary conserved function of Hef/FANCM proteins is to enhance replication fork stability by directly interacting with collapsed replication forks.
Aquibacter zeaxanthinifaciens gen. nov., sp. nov., a zeaxanthin-producing bacterium of the family Flavobacteriaceae isolated from surface seawater, and emended descriptions of the genera Aestuariibaculum and Gaetbulibacter
Authors: Hameed Asif , Shahina Mariyam , Lin Shih-Yao , Lai Wei-An , Hsu Yi-Han , Liu You-Cheng , Young Chiu-Chung
Published: September 2013

A Gram-stain-negative, strictly aerobic, rod-shaped, non-flagellated, non-spore-forming and gliding marine bacterium, designated strain CC-AMZ-304T, was isolated from coastal surface seawater near Taichung harbour, Taiwan. Strain CC-AMZ-304T predominantly synthesized zeaxanthin and thus formed yellow colonies on marine agar. The novel strain showed an unstable phylogenetic position, although sharing high pairwise 16S rRNA gene sequence similarities of 95.9–94.9, 95.7 and 95.1–93.9 % with

Gaetbulibacter

species (n = 4),

Aestuariibaculum suncheonense

SC17T and

Bizionia

species (n = 7), respectively. The polar lipid profile of strain CC-AMZ-304T consisted of phosphatidylethanolamine, five unidentified lipids, one unidentified phospholipid, two unidentified aminolipids and one unidentified glycolipid. The major (>5 % of the total) fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and C15 : 1ω5c. The DNA G+C content was 36.0 mol%. Menaquinone-6 (MK-6) was the sole respiratory quinone and the major polyamine was triamine sym-homospermidine. Phylogenetic distinctiveness, unique polar lipid composition, presence of significant amounts of branched hydroxyl fatty acids (iso-C17 : 0 3-OH and iso-C15 : 0 3-OH) and a low amount of anteiso-C15 : 0, and several additional distinguishing biochemical features clearly discriminated strain CC-AMZ-304T from the type species of the genera

Aestuariibaculum

and

Gaetbulibacter

. Thus, based on data from the present polyphasic study, strain CC-AMZ-304T is considered to represent a novel species of a new genus within the family

Flavobacteriaceae

, for which the name Aquibacter zeaxanthinifaciens gen. nov., sp. nov. is proposed; the type strain of Aquibacter zeaxanthinifaciens is CC-AMZ-304T ( = JCM 18557T = BCRC 80463T). Emended descriptions of the genera

Aestuariibaculum

and

Gaetbulibacter

are also proposed.
Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature
Authors: Parshina Sofiya N. , Ermakova Anna V. , Bomberg Malin , Detkova Ekaterina N.
Published: September 2013

A psychrotolerant hydrogenotrophic methanogen, strain Pt1, was isolated from a syntrophic propionate-oxidizing methanogenic consortium obtained from granulated biomass of a two-stage low-temperature (3–8 °C) anaerobic expanded granular sludge bed (EGSB) bioreactor, fed with a mixture of volatile fatty acids (VFAs) (acetate, propionate and butyrate). The strain was strictly anaerobic, and cells were curved rods, 0.4–0.5×7.5–25 µm, that sometimes formed wavy filaments from 25 to several hundred micrometres in length. Cells stained Gram-negative and were non-sporulating. They were gently motile by means of tufted flagella. The strain grew at 5–37 °C (optimum at 20–30 °C), at pH 6.0–10 (optimum 7.0–7.5) and with 0–0.3 M NaCl (optimum 0 M NaCl). Growth and methane production was found with H2/CO2and very weak growth with formate. Acetate and yeast extract stimulated growth, but were not essential. The G+C content of the DNA of strain Pt1 was 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Pt1 was a member of the genusMethanospirillumand showed 97.5 % sequence similarity toMethanospirillum hungateiJF1Tand 94 % sequence similarity toMethanospirillum lacunaeKi8-1T. DNA–DNA hybridization of strain Pt1 withMethanospirillum hungateiJF1Trevealed 39 % relatedness. On the basis of its phenotypic characteristics and phylogenetic position, strain Pt1 is a representative of a novel species of the genusMethanospirillum, for which the nameMethanospirillum stamsiisp. nov. is proposed. The type strain is Pt1T( = DSM 26304T = VKM B-2808T).
The Importance of Size and Disorder in the Cryoprotective Effects of Dehydrins
Authors: Hughes Stephanie L. , Schart Verena , Malcolmson Janet , Hogarth Kaley A. , Martynowicz David M. , Tralman-Baker Erik , Patel Shruti N. , Graether Steffen P.
Published: September 2013

Dehydrins protect plant proteins and membranes from damage during drought and cold. Vitis riparia K2 is a 48-residue protein that can protect lactate dehydrogenase from freeze-thaw damage by preventing the aggregation and denaturation of the enzyme. To further elucidate its mechanism, we used a series of V. riparia K2 concatemers (K4, K6, K8, and K10) and natural dehydrins (V. riparia YSK2, 60 kilodalton peach dehydrin [PCA60], barley dehydrin5 [Dhn5], Thellungiella salsuginea dehydrin2 [TsDHN-2], and Opuntia streptacantha dehydrin1 [OpsDHN-1]) to test the effect of the number of K-segments and dehydrin size on their ability to protect lactate dehydrogenase from freeze-thaw damage. The results show that the larger the hydrodynamic radius of the dehydrin, the more effective the cryoprotection. A similar trend is observed with polyethylene glycol, which would suggest that the protection is simply a nonspecific volume exclusion effect that can be manifested by any protein. However, structured proteins of a similar range of sizes did not show the same pattern and level of cryoprotection. Our results suggest that with respect to enzyme protection, dehydrins function primarily as molecular shields and that their intrinsic disorder is required for them to be an effective cryoprotectant. Lastly, we show that the cryoprotection by a dehydrin is not due to any antifreeze protein-like activity, as has been reported previously.
Structure of the periplasmic copper-binding protein CueP fromSalmonella entericaserovar Typhimurium
Authors: Yoon Bo-Young , Kim Yong-Hak , Kim Nahee , Yun Bo-Young , Kim Jin-Sik , Lee Joon-Hee , Cho Hyun-Soo , Lee Kangseok , Ha Nam-Chul
Published: September 2013

CueP was initially identified as a copper-resistance gene inSalmonella entericaserovar Typhimurium, which has evolved to survive in the phagosomes of macrophages. Recently, CueP was determined to be a periplasmic copper-binding protein and has been implicated in the transfer of copper ions to SodCII in the periplasm. In this study, the crystal structure of CueP has been determined, revealing a V-shaped dimeric structure. The conserved cysteine and histidine residues are clustered on the surface of one side of the C-terminal domain, suggesting that this cysteine- and histidine-rich region is related to the function of CueP. LC-MS/MS analysis established the presence of a disulfide bond between Cys96 and Cys176 under aerobic conditions. Subsequent biophysical analyses showed that the CueP protein binds copper and zinc, and the mutation of Cys104 to serine (C104S) dramatically reduced the binding affinity for copper and zinc, suggesting that the cysteine- and histidine-rich cluster is responsible for copper binding. This study provides a structural basis for the participation of CueP in the resistance of the intracellular pathogenSalmonellato copper.
A quality comparison of protein crystals grown under containerless conditions generated by diamagnetic levitation, silicone oil and agarose gel
Authors: Cao Hui-Ling , Sun Li-Hua , Li Jian , Tang Lin , Lu Hui-Meng , Guo Yun-Zhu , He Jin , Liu Yong-Ming , Xie Xu-Zhuo , Shen He-Fang , Zhang Chen-Yan , Guo Wei-Hong , Huang Lin-Jun , Shang Peng , He Jian-Hua , Yin Da-Chuan
Published: September 2013

High-quality crystals are key to obtaining accurate three-dimensional structures of proteins using X-ray diffraction techniques. However, obtaining such protein crystals is often a challenge. Several containerless crystallization techniques have been reported to have the ability to improve crystal quality, but it is unknown which is the most favourable way to grow high-quality protein crystals. In this paper, a quality comparison of protein crystals which were grown under three containerless conditions provided by diamagnetic levitation, silicone oil and agarose gel was conducted. A control experiment on a vessel wall was also simultaneously carried out. Seven different proteins were crystallized under the four conditions, and the crystal quality was assessed in terms of the resolution limit, the mosaicity and theRmerge. It was found that the crystals grown under the three containerless conditions demonstrated better morphology than those of the control. X-ray diffraction data indicated that the quality of the crystals grown under the three containerless conditions was better than that of the control. Of the three containerless crystallization techniques, the diamagnetic levitation technique exhibited the best performance in enhancing crystal quality. This paper is to our knowledge the first report of improvement of crystal quality using a diamagnetic levitation technique. Crystals obtained from agarose gel demonstrated the second best improvement in crystal quality. The study indicated that the diamagnetic levitation technique is indeed a favourable method for growing high-quality protein crystals, and its utilization is thus potentially useful in practical efforts to obtain well diffracting protein crystals.
The DNA-binding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators
Authors: Alanazi Amer M. , Neidle Ellen L. , Momany Cory
Published: September 2013

LysR-type transcriptional regulators (LTTRs) play critical roles in metabolism and constitute the largest family of bacterial regulators. To understand protein–DNA interactions, atomic structures of the DNA-binding domain and linker-helix regions of a prototypical LTTR, BenM, were determined by X-ray crystallography. BenM structures with and without bound DNA reveal a set of highly conserved amino acids that interact directly with DNA bases. At the N-terminal end of the recognition helix (α3) of a winged-helix–turn–helix DNA-binding motif, several residues create hydrophobic pockets (Pro30, Pro31 and Ser33). These pockets interact with the methyl groups of two thymines in the DNA-recognition motif and its complementary strand, T-N11-A. This motif usually includes some dyad symmetry, as exemplified by a sequence that binds two subunits of a BenM tetramer (ATAC-N7-GTAT). Gln29 forms hydrogen bonds to adenine in the first position of the recognition half-site (ATAC). Another hydrophobic pocket defined by Ala28, Pro30 and Pro31 interacts with the methyl group of thymine, complementary to the base at the third position of the half-site. Arg34 interacts with the complementary base of the 3′ position. Arg53, in the wing, provides AT-tract recognition in the minor groove. For DNA recognition, LTTRs use highly conserved interactions between amino acids and nucleotide bases as well as numerous less-conserved secondary interactions.
Cross-protomer interaction with the photoactive site in oligomeric proteorhodopsin complexes
Authors: Ran Tingting , Ozorowski Gabriel , Gao Yanyan , Sineshchekov Oleg A. , Wang Weiwu , Spudich John L. , Luecke Hartmut
Published: September 2013

Proteorhodopsins (PRs), members of the microbial rhodopsin superfamily of seven-transmembrane-helix proteins that use retinal chromophores, comprise the largest subfamily of rhodopsins, yet very little structural information is available. PRs are ubiquitous throughout the biosphere and their genes have been sequenced in numerous species of bacteria. They have been shown to exhibit ion-pumping activity like their archaeal homolog bacteriorhodopsin (BR). Here, the first crystal structure of a proteorhodopsin, that of a blue-light-absorbing proteorhodopsin (BPR) isolated from the Mediterranean Sea at a depth of 12 m (Med12BPR), is reported. Six molecules ofMed12BPR form a doughnut-shapedC6hexameric ring, unlike BR, which forms a trimer. Furthermore, the structures of two mutants of a related BPR isolated from the Pacific Ocean near Hawaii at a depth of 75 m (HOT75BPR), which show aC5pentameric arrangement, are reported. In all three structures the retinal polyene chain is shifted towards helixCwhen compared with other microbial rhodopsins, and the putative proton-release group in BPR differs significantly from those of BR and xanthorhodopsin (XR). The most striking feature of proteorhodopsin is the position of the conserved active-site histidine (His75, also found in XR), which forms a hydrogen bond to the proton acceptor from the same molecule (Asp97) and also to Trp34 of a neighboring protomer. Trp34 may function by stabilizing His75 in a conformation that favors a deprotonated Asp97 in the dark state, and suggests cooperative behavior between protomers when the protein is in an oligomeric form. Mutation-induced alterations in proton transfers in the BPR photocycle inEscherichia colicells provide evidence for a similar cross-protomer interaction of BPR in living cells and a functional role of the inter-protomer Trp34–His75 interaction in ion transport. Finally, Wat402, a key molecule responsible for proton translocation between the Schiff base and the proton acceptor in BR, appears to be absent in PR, suggesting that the ion-transfer mechanism may differ between PR and BR.
Structure of the Sgt2 dimerization domain complexed with the Get5 UBL domain involved in the targeting of tail-anchored membrane proteins to the endoplasmic reticulum
Authors: Tung Jung-Yu , Li Yi-Chuan , Lin Tai-Wen , Hsiao Chwan-Deng
Published: September 2013

The insertion of tail-anchored membrane (TA) proteins into the appropriate membrane is a post-translational event that requires stabilization of the transmembrane domain and targeting to the proper destination. Sgt2, a small glutamine-rich tetratricopeptide-repeat protein, is a heat-shock protein cognate (HSC) co-chaperone that preferentially binds endoplasmic reticulum-destined TA proteins and directs them to the GET pathwayviaGet4 and Get5. The N-terminal domain of Sgt2 seems to exert dual functions. It mediates Get5 interaction and allows substrate delivery to Get3. Following the N-terminus of Get5 is a ubiquitin-like (Ubl) domain that interacts with the N-terminus of Sgt2. Here, the crystal structure of the Sgt2 dimerization domain complexed with the Get5 Ubl domain (Sgt2N–Get5Ubl) is reported. This complex reveals an intimate interaction between one Sgt2 dimer and one Get5 monomer. This research further demonstrates that hydrophobic residues from both Sgt2 and Get5 play an important role in cell survival under heat stress. This study provides detailed molecular insights into the specific binding of this GET-pathway complex.
Structures of thePorphyromonas gingivalisOxyR regulatory domain explain differences in expression of the OxyR regulon inEscherichia coliandP. gingivalis
Authors: Svintradze David V. , Peterson Darrell L. , Collazo-Santiago Evys A. , Lewis Janina P. , Wright H. Tonie
Published: September 2013

OxyR transcriptionally regulatesEscherichia colioxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast toE. coliOxyR regulatory-domain structures, crystal structures ofPorphyromonas gingivalisOxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of theP. gingivalisOxyR regulatory-domain dimer closely resembles the oxidized (activating) form of theE. coliOxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes inP. gingivalisand is attributable to a single amino-acid insertion inP. gingivalisOxyR relative toE. coliOxyR. Modelling of full-lengthP. gingivalis,E. coliandNeisseria meningitidisOxyR–DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.
Different orientations of low-molecular-weight fragments in the binding pocket of a BRD4 bromodomain
Authors: Lolli Graziano , Battistutta Roberto
Published: September 2013

Bromodomains are involved in the regulation of chromatin architecture and transcription through the recognition of acetylated lysines in histones and other proteins. Many of them are considered to be relevant pharmacological targets for different pathologies. Three crystallographic structures of the N-terminal bromodomain of BRD4 in complex with low-molecular-weight fragments are presented. They show that similar molecules mimicking acetylated lysine bind the bromodomain with different orientations and exploit different interactions. It is also advised to avoid DMSO when searching for low-affinity fragments that interact with bromodomains since DMSO binds in the acetylated lysine-recognition pocket of BRD4.
Structural analysis and insights into the glycon specificity of the rice GH1 Os7BGlu26 β-D-mannosidase
Authors: Tankrathok Anupong , Iglesias-Fernández Javier , Luang Sukanya , Robinson Robert C. , Kimura Atsuo , Rovira Carme , Hrmova Maria , Ketudat Cairns James R.
Published: September 2013

Rice Os7BGlu26 is a GH1 family glycoside hydrolase with a threefold higherkcat/Kmvalue for 4-nitrophenyl β-D-mannoside (4NPMan) compared with 4-nitrophenyl β-D-glucoside (4NPGlc). To investigate its selectivity for β-D-mannoside and β-D-glucoside substrates, the structures of apo Os7BGlu26 at a resolution of 2.20 Å and of Os7BGlu26 with mannose at a resolution of 2.45 Å were elucidated from isomorphous crystals in space groupP212121. The (β/α)8-barrel structure is similar to other GH1 family structures, but with a narrower active-site cleft. The Os7BGlu26 structure with D-mannose corresponds to a product complex, with β-D-mannose in the1S5skew-boat conformation. Docking of the1S3,1S5,2SOand3S1pyranose-ring conformations of 4NPMan and 4NPGlc substrates into the active site of Os7BGlu26 indicated that the lowest energies were in the1S5and1S3skew-boat conformations. Comparison of these docked conformers with other rice GH1 structures revealed differences in the residues interacting with the catalytic acid/base between enzymes with and without β-D-mannosidase activity. The mutation of Tyr134 to Trp in Os7BGlu26 resulted in similarkcat/Kmvalues for 4NPMan and 4NPGlc, while mutation of Tyr134 to Phe resulted in a 37-fold higherkcat/Kmfor 4NPMan than 4NPGlc. Mutation of Cys182 to Thr decreased both the activity and the selectivity for β-D-mannoside. It was concluded that interactions with the catalytic acid/base play a significant role in glycon selection.
Thirty years of disability psychotherapy, a paradigm shift?
Authors: Frankish Pat
Published: September 2013

Purpose

– This paper charts the development and practice of disability psychotherapy for the author and for services.

Design/methodology/approach

– A personal account relating events to the development of thinking and practice.

Findings

– The author suggests that a paradigm shift has occurred over the 30 years to a position of “doing with” as opposed to “doing to”.

Originality/value

– This has not previously been put forward as a way of understanding present day services.
The core conflictual relationship theme (CCRT) method: testing with adult offenders who have intellectual and developmental disabilities
Authors: Scott Hackett Simon , Porter Jill , L. Taylor John
Published: September 2013

Purpose

– The aim of this paper is to investigate the feasibility of using the core conflictual relationship theme (CCRT) method, used to assess relationship patterns and interpersonal schemas, within a small group of men who had intellectual and developmental disabilities (IDD). The relationship anecdote paradigm interview, with minor adaptation, was used to collect material from participants necessary to generate a CCRT. CCRTs formulated in the study are described and consideration is given to the potential clinical application of CCRT method in this patient group.

Design/methodology/approach

– A small sample of four men with IDD was taken from a medium-low secure forensic service. Initial interviews, necessary to elicit narrative anecdotes for CCRT formulation, were conducted at the start of a psychotherapeutic treatment study. Trained judges completed a CCRT formulation for each participant.

Findings

– Participants in the study were able to provide personal information necessary to formulate a CCRT. Unexpected common themes were shared in participants who had committed contact sexual offences, this differed from a participant with autistic spectrum disorder who had committed a non-contact sexual offence. The CCRT method can be feasibly used in a mild IDD population. The CCRT method is clinically relevant and provides an opportunity for the exploration of clinical micro-theories related to interpersonal schemas found in offenders who have IDD.

Originality/value

– This is the first study, to our knowledge, reporting results of the CCRT method with adults who have mild intellectual disabilities.