bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural evidence for a functionally relevant second camphor binding site in P450cam: Model for substrate entry into a P450 active site
Authors: Yao Huili , McCullough Christopher R. , Costache Aurora D. , Pullela Phani Kumar , Sem Daniel S. 
Published: June 2007

AbstractP450cam has long served as a prototype for the cytochrome P450 (CYP) gene family. But, little is known about how substrate enters its active site pocket, and how access is achieved in a way that minimizes exposure of the reactive heme. We hypothesize that P450cam may first bind substrate transiently near the mobile F‐G helix that covers the active site pocket. Such a two‐step binding process is kinetically required if P450cam rarely populates an open conformation—as suggested by previous literature and the inability to obtain a crystal structure of P450cam in an open conformation. Such a mechanism would minimize exposure of the heme by allowing P450cam to stay in a closed conformation as long as possible, since only brief flexing into an open conformation would be required to allow substrate entry. To test this model, we have attempted to dock a second camphor molecule into the crystal structure of camphor‐bound P450cam. The docking identified only one potential entry site pocket, a well‐defined cavity on the F‐helix side of the F‐G flap, 16 Å from the heme iron. Location of this entry site pocket is consistent with our NMR T1 relaxation‐based measurements of distances for a camphor that binds in fast exchange (active site camphor is known to bind in slow exchange). Presence of a second camphor binding site is also confirmed with [1H‐13C] HSQC titrations of 13CH3‐threonine labeled P450cam. To confirm that camphor can bind outside of the active site pocket, 13CH3S‐pyridine was bound to the heme iron to physically block the active site, and to serve as an NMR chemical shift probe. Titration of this P450cam‐pyridine complex confirms that camphor can bind to a site outside the active site pocket, with an estimated Kd of 43 μM. The two‐site binding model that is proposed based on these data is analogous to that recently proposed for CYP3A4, and is consistent with recent crystal structures of P450cam bound to tethered‐substrates, which force a partially opened conformation. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Insight into the early stages of thermal unfolding of peanut agglutinin by molecular dynamics simulations
Authors: Hansia Priti , Dev Sagarika , Surolia Avadhesha , Vishveshwara Saraswathi 
Published: June 2007

AbstractPeanut agglutinin is a homotetrameric nonglycosylated protein. The protein has a unique open quaternary structure. Molecular dynamics simulations have been employed to follow the atomistic details of its unfolding at different temperatures. The early events of the deoligomerization of the protein have been elucidated in the present study. Simulation trajectories of the monomer as well as those of the tetramer have been compared and the tetramer is found to be substantially more stable than its monomeric counterpart. The tetramer shows retention of most of its secondary structure but considerable loss of the tertiary structure at high temperature. This observation implies the generation of a molten globule‐like intermediate in the later stages of deoligomerization. The quaternary structure of the protein has weakened to a large extent, but none of the subunits are separated. In addition, the importance of the metal‐binding to the stability of the protein structure has also been investigated. Binding of the metal ions not only enhances the local stability of the metal‐ion binding loop, but also imparts a global stability to the overall structure. The dynamics of different interfaces vary significantly as probed through interface clusters. The differences are substantially enhanced at higher temperatures. The dynamics and the stability of the interfaces have been captured mainly by cluster analysis, which has provided detailed information on the thermal deoligomerization of the protein. Proteins 2007. © 2007 Wiley‐Liss, Inc.
High incidence of ubiquitin‐like domains in human ubiquitin‐specific proteases
Authors: Zhu Xiao , Ménard Robert , Sulea Traian 
Published: June 2007

AbstractUbiquitin‐specific proteases (USPs) emerge as key regulators of numerous cellular processes and account for the bulk of human deubiquitinating enzymes (DUBs). Their modular structure, mostly annotated by sequence homology, is believed to determine substrate recognition and subcellular localization. Currently, a large proportion of known human USP sequences are not annotated either structurally or functionally, including regions both within and flanking their catalytic cores. To extend the current understanding of human USPs, we applied consensus fold recognition to the unannotated content of the human USP family. The most interesting discovery was the marked presence of reliably predicted ubiquitin‐like (UBL) domains in this family of enzymes. The UBL domain thus appears to be the most frequently occurring domain in the human USP family, after the characteristic catalytic domain. The presence of multiple UBL domains per USP protein, as well as of UBL domains embedded in the USP catalytic core, add to the structural complexity currently recognized for many DUBs. Possible functional roles of the newly uncovered UBL domains of human USPs, including proteasome binding, and substrate and protein target specificities, are discussed. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Phosphine resistance, respiration rate and fitness consequences in stored‐product insects
Authors: Pimentel Marco Aurélio G , Faroni Lêda Rita D'A , Tótola Marcos R , Guedes Raul Narciso C 
Published: June 2007

AbstractResistance to fumigants has been frequently reported in insect pests of stored products and is one of the obstacles in controlling these pests. The authors studied phosphine resistance and its physiological basis in adult insects of 12 populations of Tribolium castaneum (Herbst) (Tenebrionidae), ten populations of Rhyzopertha dominica (F.) (Bostrichidae) and eight populations of Oryzaephilus surinamensis L. (Silvanidae) from Brazil, and the possible existence of fitness costs associated with phosphine resistance in the absence of this fumigant. The bioassays for the detection of phosphine resistance followed the FAO standard method. The production of carbon dioxide and the instantaneous rate of population increase (ri) of each population of each species were correlated with their resistance ratios at the LC50. The resistance ratio at LC50 in T. castaneum ranged from 1.0‐ to 186.2‐fold, in R. dominica from 2.0‐ to 71.0‐fold and in O. surinamensis from 1.9‐ to 32.2‐fold. Ten populations of T. castaneum, nine populations of R. dominica and seven populations of O. surinamensis were resistant to phosphine. In all three species there was significant association (P < 0.05) between respiration rate and phosphine resistance. The populations with lower carbon dioxide production showed a higher resistance ratio, suggesting that the lower respiration rate is the physiological basis of phosphine resistance by reducing the fumigant uptake in the resistant insects. Conversely, populations with higher ri showed lower resistance ratios, which could indicate a lower rate of reproduction of the resistant populations compared with susceptible populations. Thus, management strategies based on the interruption of phosphine fumigation may result in reestablishment of susceptibility, and shows good potential for more effective management of phosphine‐resistant populations. Copyright © 2007 Society of Chemical Industry
Estimating the Jewish undercount in the 2001 Census: a comment on Graham and Waterman (2005) ‘Underenumeration of the Jewish Population in the UK 2001 Census’: Population, Space and Place 11: 89–102
Authors: Voas David 
Published: June 2007

AbstractGraham and Waterman (2005) argued that there was a substantial underenumeration of Jews in the UK 2001 Census of Population. Their observations are valuable but some of the specific pieces of evidence and the recommendations that they offer can be criticised. There is an alternative method of estimating the extent to which Jews were undercounted in the census; it produces results that largely support their claims. Copyright © 2007 John Wiley & Sons, Ltd.
Dynamic analysis of less‐than‐truckload shipments and test method to simulate this environment
Authors: Singh S. P. , Joneson E. , Singh J. , Grewal G. 
Published: June 2007

AbstractThis paper provides results from a comprehensive data measurement study that analysed the vibration dynamics produced inside the trailers used for less‐than‐truckload (LTL) shipments. The trailers used for this segment of the package transportation environment are very different in size and suspension than those used for full truckload shipments. This study measured the vertical, lateral and longitudinal vibration inside a trailer as a function of road surface. In addition, the study developed a video showing freight movement inside the trailer to determine physical displacement and shifting of the loads. A set of recommendations was developed to safely load and transport LTL shipments to reduce damage claims. Copyright © 2007 John Wiley & Sons, Ltd.
A new finite sum inequality approach to delay‐dependent H∞ control of discrete‐time systems with time‐varying delay
Authors: Zhang Xian‐Ming , Han Qing‐Long 
Published: June 2007

AbstractThis paper deals with delay‐dependent H∞ control for discrete‐time systems with time‐varying delay. A new finite sum inequality is first established to derive a delay‐dependent condition, under which the resulting closed‐loop system via a state feedback is asymptotically stable with a prescribed H∞ noise attenuation level. Then, an iterative algorithm involving convex optimization is proposed to obtain a suboptimal H∞ controller. Finally, two numerical examples are given to show the effectiveness of the proposed method. Copyright © 2007 John Wiley & Sons, Ltd.
Patterns of primary and heterotrophic productivity in an arid lowland river
Authors: Gawne Ben , Merrick Chester , Williams David G. , Rees Gavin , Oliver Rod , Bowen P. M. , Treadwell Simon , Beattie Gillian , Ellis Iain , Frankenberg Judy , Lorenz Zygmunt 
Published: June 2007

AbstractThree river conceptual models make differing predictions about the major source of primary production in lowland rivers, acknowledging the importance of primary productivity in the ecology and management of lowland rivers. Patterns of primary production in lowland rivers are still an area of considerable uncertainty. The objective of this study was to examine the major sources and transformations of organic matter in an Australian lowland river and compare them to the predictions of existing models. The broad approach adopted was to quantify the contribution from the major ecosystem components and compare these with estimates of system metabolism determined using open water measures of diel oxygen change. Three 4‐km river reaches were selected to represent the extent of variation found along the free‐flowing lowland sections of the Murray River, one of Australia's largest and most regulated rivers. Annual open water gross primary production (GPP) estimates for the Murray R. during this study ranged from 221 to 376 gC m−2 y−1 and were similar to other large rivers. Examination of the net contribution of organic matter to the channel indicates that primary productivity in the Murray R. is derived from a combination of phytoplankton, riparian vegetation and macrophytes, but that the major source varies both spatially and temporally. The present study confirms that the River Continuum Concept (RCC), the Flood Pulse Concept (FPC) and Riverine Productivity Model (RPM) all have some application to Australian lowland rivers, but that synthesis of the models will be difficult until we can incorporate the extent, causes and consequences of primary production variability. This study also highlights the importance of the microbial loop and macrophytes in the ecology of the Murray R. Copyright © 2007 John Wiley & Sons, Ltd.
Temporal trends in the frequency and longer‐term outcome of heart failure complicating myocardial infarction
Authors: Najafi Farid , Dobson Annette J. , Hobbs Michael , Jamrozik Konrad 
Published: June 2007

AbstractAims:To investigate trends in incidence and long‐term outcome of heart failure (HF) developing within 28 days of first‐ever acute myocardial infarction (AMI).Methods and results:We identified all residents of Perth, Western Australia aged 25–64 years, with no history of HF, who experienced a non‐fatal, first‐ever AMI between 1984 and 1993, and followed them for ten years. All patients (N=4006) met the criteria for ‘definite AMI’ in WHO MONItoring trends and determinants of CArdiovascular disease (MONICA) Project and 897 (22.4%) had early‐onset HF complicating the index event. After adjustment for age, current smoking, history of diabetes and hypertension, Q‐wave and anterior wall AMI, the odds of developing HF declined by 9% (odds ratio for period 1989–1993 relative to 1984–1988=0.91, 95% confidence interval (957percnt;CI): 0.78 to 1.06). Over 10 years of follow‐up, patients with early‐onset HF had a cumulative average number of re‐admissions of 28 per 100 as compared with 9 per 100 in patients without HF. After adjustment for age, history of diabetes and hypertension, the hazard of death in patients with early‐onset HF declined by 26% (HR for the period 1989–1993 relative to 1984–1988=0.74, 95%CI: 0.57 to 0.96).Conclusion:Our data suggest a decline in the incidence of, and show encouraging evidence of improvement in survival after, early‐onset HF complicating AMI.
The helminth parasites of the wild rabbitOryctolagus cuniculusand their effect on host condition in Dunas de Mira, Portugal
Authors: Eira C. , Torres J. , Miquel J. , Vingada J. 
Published: June 2007

AbstractThe present study focuses on the helminth parasite community of the wild rabbit in a sand dune area in Portugal over a 5-year period. The influence of host sex and year on the composition of the helminth community is assessed, along with the potential effect of the detected helminths on host body condition. The basic structure of the helminth community comprisesMosgovoyia ctenoides,Graphidium strigosum,Trichostrongylus retortaeformis,Nematodiroides zembraeandPassalurus ambiguus. Mean intensities ofG. strigosumvaried between years. GeneralG. strigosumintensities were also found to vary according to both year and host sex, but not according to the interaction of both factors. When assessing the effect of helminths on rabbit body condition (expressed by the kidney fat index), higher burdens ofM. ctenoides, a cestode that presents a relatively large body mass, were found to induce a reduction in rabbit condition.
The role of path dependence in the development of US bankruptcy law, 1880–1938
Authors: HANSEN BRADLEY A. , HANSEN MARY ESCHELBACH 
Published: June 2007

Abstract:We illustrate mechanisms that can give rise to path dependence in legislation. Specifically, we show how debtor-friendly bankruptcy law arose in the United States as a result of a path dependent process. The 1898 Bankruptcy Act was not regarded as debtor-friendly at the time of its enactment, but the enactment of the law gave rise to changes in interest groups, changes in beliefs about the purpose of bankruptcy law, and changes in the Democratic Party's position on bankruptcy that set the United States on a path to debtor-friendly bankruptcy law. An analysis of the path dependence of bankruptcy law produces an interpretation that is more consistent with the evidence than the conventional interpretation that debtor-friendliness in bankruptcy law began with political compromises to obtain the 1898 Bankruptcy Act.
Biodiversity among luminescent symbionts from squid of the genera Uroteuthis, Loliolus and Euprymna (Mollusca: Cephalopoda)
Authors: Guerrero‐Ferreira R. C. , Nishiguchi M. K. 
Published: June 2007

AbstractLuminescent bacteria in the family Vibrionaceae (Bacteria: γ‐Proteobacteria) are commonly found in complex, bilobed light organs of sepiolid and loliginid squids. Although morphology of these organs in both families of squid is similar, the species of bacteria that inhabit each host has yet to be verified. We utilized sequences of 16S ribosomal RNA, luciferase α‐subunit (luxA) and the glyceraldehyde‐3‐phosphate dehydrogenase (gapA) genes to determine phylogenetic relationships between 63 strains of Vibrio bacteria, which included representatives from different environments as well as unidentified luminescent isolates from loliginid and sepiolid squid from Thailand. A combined phylogenetic analysis was used including biochemical data such as carbon use, growth and luminescence. Results demonstrated that certain symbiotic Thai isolates found in the same geographic area were included in a clade containing bacterial species phenotypically suitable to colonize light organs. Moreover, multiple strains isolated from a single squid host were identified as more than one bacteria species in our phylogeny. This research presents evidence of species of luminescent bacteria that have not been previously described as symbiotic strains colonizing light organs of Indo‐West Pacific loliginid and sepiolid squids, and supports the hypothesis of a non‐species‐specific association between certain sepiolid and loliginid squids and marine luminescent bacteria.© The Willi Hennig Society 2007.
Varying effects of anadromous sockeye salmon on the trophic ecology of two species of resident salmonids in southwest Alaska
Authors: SCHEUERELL MARK D. , MOORE JONATHAN W. , SCHINDLER DANIEL E. , HARVEY CHRIS J. 
Published: June 2007

Summary1. Anadromous salmon transport marine‐derived nutrients and carbon to freshwater and riparian ecosystems upon their return to natal spawning systems. The ecological implications of these subsidies on the trophic ecology of resident fish remain poorly understood despite broad recognition of their potential importance.2. We studied the within‐year changes in the ration size, composition and stable isotope signature of the diets of two resident salmonids (rainbow trout,Oncorhynchus mykiss; Arctic grayling,Thymallus arcticus) before and after the arrival of sockeye salmon (Oncorhynchus nerka) to their spawning grounds in the Bristol Bay region of southwest Alaska.3. Ration size and energy intake increased by 480–620% for both species after salmon arrived. However, the cause of the increases differed between species such that rainbow trout switched to consuming salmon eggs, salmon flesh and blowflies that colonized salmon carcasses, whereas grayling primarily ate more benthic invertebrates that were presumably made available because of physical disturbances by spawning salmon.4. We also observed an increase in theδ15N of rainbow trout diets post‐salmon, but not for grayling. This presumably led to the observed increase in theδ15N of rainbow trout with increasing body mass, but not for grayling.5. Using a bioenergetics model, we predicted that salmon‐derived resources contributed a large majority of the energy necessary for growth in this resident fish community. Furthermore, the bioenergetics model also showed how seasonal changes in diet affected the stable isotope ratios of both species. These results expand upon a growing body of literature that highlights the different pathways whereby anadromous salmon influence coastal ecosystems, particularly resident fish.
Role of Sand Fly Saliva in Human and Experimental Leishmaniasis: Current Insights
Authors: Andrade B. B. , De Oliveira C. I. , Brodskyn C. I. , Barral A. , Barral‐Netto M. 
Published: June 2007

AbstractLeishmaniases are wide spread diseases transmitted to their vertebrate host by infected sand fly. The saliva from these arthropods contains a vast repertoire of pharmacologically active molecules that hampers the host’s haemostatic, inflammatory and immune responses. The early interactions between Leishmania and the host’s immune response are closely linked to disease evolution or protection against the protozoan, and the ectoparasite saliva contributes directly to these interactions. Current studies have depicted these features, and these relations are being widely explored. There are concrete indications that the host response against sand fly saliva influences disease outcome in leishmaniasis. Additionally, there are demonstrations that immunization with whole sand fly saliva, or its components, leads to protection against leishmaniasis in different host species. The combination of these evidences opens up optimistic perspectives for improving vaccine development against Leishmania infection.
Multiple subcutaneous nodules leading to the diagnosis of pulmonary aspergillosis in a renal transplant recipient
Authors: Özcan Deren , Güleç Ayşe Tülin , Haberal Mehmet 
Published: June 2007

Abstract: Aspergillosis is the second most frequent opportunistic fungal infection in solid organ transplant recipients; however, cutaneous aspergillosis occurs very rarely. Herein, we report a 34‐yr‐old male renal transplant recipient with secondary cutaneous aspergillosis due to Aspergillus fumigatus in whom cutaneous lesions led to the correct diagnosis. To the best of our knowledge, this is the first case of secondary cutaneous aspergillosis reported in the setting of a solid organ transplantation.
KETANSERIN‐INDUCED BAROREFLEX ENHANCEMENT IN SPONTANEOUSLY HYPERTENSIVE RATS DEPENDS ON CENTRAL 5‐HT2A RECEPTORS
Authors: Shen Fu‐Ming , Wang Jin , Ni Can‐Rong , Yu Jian‐Guang , Wang Wei‐Zhong , Su Ding‐Feng 
Published: June 2007

SUMMARY

Ketanserin may influence baroreflex function by blocking 5‐HT2A receptors and/or α1‐adrenoceptors through central and/or peripheral mechanisms.
In the present study, we tested the hypothesis that the baroreflex sensitivity (BRS)‐enhancing effects of ketanserin are mediated by central 5‐HT2A receptors in spontaneously hypertensive rats (SHR).
Using a conjugate of a monoclonal antibody to the serotonin reuptake transporter (SERT) and the toxin saporin (anti‐SERT‐SAP), which specifically eliminates the neurons that express SERT, the effects of ketanserin (0.3 and 3.0 mg/kg, i.g.) on BRS, blood pressure (BP), heart period (HP) and blood pressure variability (BPV) were compared between conscious intact SHR and SHR pretreated with anti‐SERT‐SAP.
Immunochemistry showed that, 2 weeks after intracerebroventricular injection of the toxin, 5‐HT expression was strikingly attenuated in the brain, whereas values of BRS, BPV and BP were similar to those in the sham group. In intact SHR, 0.3 mg/kg ketanserin significantly improved BRS (191% control) and reduced BPV without affecting BP; at 3.0 mg/kg, ketanserin significantly increased BRS (197% control) and decreased BPV and BP. In toxin‐pretreated SHR, only the high dose of ketanserin improved BRS (132% control), neither of the ketanserin doses reduced BPV, but both significantly decreased BP.
We conclude that the BRS‐enhancing effects of ketanserin are mediated largely by central 5‐HT2A receptors, whereas the antihypertensive effect of ketanserin persists even after destruction of serotonergic neurons in the central nervous system.