bluuebunny/crossref_metadata_2025_split huggingface dataset:
Photo‐activity induced by amyloidogenesis
Authors: Tcherkasskaya Olga 
Published: February 2007

AbstractAccumulation of chemically altered proteins is a noted characteristic of biological aging, and increasing evidence suggests a variety of deleterious cellular developments associated with senescence. Concomitantly, the “aging” of protein deposits associated with numerous neurological disorders may involve covalent modifications of their constituents. However, the link between disease‐related protein aggregation and chemical alterations of its molecular constituents has yet to be established. The present study of amyloidogenic α‐synuclein protein points to a decisive change in the biophysical behavior of growing protein aggregates with progressive photo‐activity in the visible range of the electromagnetic spectrum. I hypothesize that the photo‐activity induced by filament formation is governed by the same mechanism as seen for the intrinsic chromophore of 4‐(p‐hydroxybenzylidene)‐5‐imidazolinone‐type in the family of green fluorescent proteins. This type of the covalent alterations is initiated concurrently with amyloid elongation and involves a complex multi‐step process of chain cyclization, amino acid dehydration, and aerial oxidation. Given that different stages in filament formation yield distinct optical characteristics, the photo‐activity induced by amyloidogenesis may have application in molecular biology by enabling in vivo visualization of protein aggregation and its impact on cellular function.
The Abl SH2‐kinase linker naturally adopts a conformation competent for SH3 domain binding
Authors: Chen Shugui , Brier Sébastien , Smithgall Thomas E. , Engen John R. 
Published: February 2007

AbstractThe core of the Abelson tyrosine kinase (c‐Abl) is structurally similar to Src‐family kinases where SH3 and SH2 domains pack against the backside of the kinase domain in the down‐regulated conformation. Both kinase families depend upon intramolecular association of SH3 with the linker joining the SH2 and kinase domains for suppression of kinase activity. Hydrogen deuterium exchange (HX) and mass spectrometry (MS) were used to probe intramolecular interaction of the c‐Abl SH3 domain with the linker in recombinant constructs lacking the kinase domain. Under physiological conditions, the c‐Abl SH3 domain undergoes partial unfolding, which is stabilized by ligand binding, providing a unique assay for SH3:linker interaction in solution. Using this approach, we observed dynamic association of the SH3 domain with the linker in the absence of the kinase domain. Truncation of the linker before W254 completely prevented cis‐interaction with SH3, while constructs containing amino acids past this point showed SH3:linker interactions. The observation that the Abl linker sequence exhibits SH3‐binding activity in the absence of the kinase domain is unique to Abl and was not observed with Src‐family kinases. These results suggest that SH3:linker interactions may have a more prominent role in Abl regulation than in Src kinases, where the down‐regulated conformation is further stabilized by a second intramolecular interaction between the C‐terminal tail and the SH2 domain.
X‐ray crystallographic analysis of the sulfur carrier protein SoxY from Chlorobium limicola f. thiosulfatophilum reveals a tetrameric structure
Authors: Stout Jan , Van Driessche Gonzalez , Savvides Savvas N. , Van Beeumen Jozef 
Published: February 2007

AbstractDissimilatory oxidation of thiosulfate in the green sulfur bacterium Chlorobium limicola f. thiosulfatophilum is carried out by the ubiquitous sulfur‐oxidizing (Sox) multi‐enzyme system. In this system, SoxY plays a key role, functioning as the sulfur substrate‐binding protein that offers its sulfur substrate, which is covalently bound to a conserved C‐terminal cysteine, to another oxidizing Sox enzyme. Here, we report the crystal structures of a stand‐alone SoxY protein of C. limicola f. thiosulfatophilum, solved at 2.15 Å and 2.40 Å resolution using X‐ray diffraction data collected at 100 K and room temperature, respectively. The structure reveals a monomeric Ig‐like protein, with an N‐terminal α‐helix, that oligomerizes into a tetramer via conserved contact regions between the monomers. The tetramer can be described as a dimer of dimers that exhibits one large hydrophobic contact region in each dimer and two small hydrophilic interface patches in the tetramer. At the tetramer interface patch, two conserved redox‐active C‐terminal cysteines form an intersubunit disulfide bridge. Intriguingly, SoxY exhibits a dimer/tetramer equilibrium that is dependent on the redox state of the cysteines and on the type of sulfur substrate component bound to them. Taken together, the dimer/tetramer equilibrium, the specific interactions between the subunits in the tetramer, and the significant conservation level of the interfaces strongly indicate that these SoxY oligomers are biologically relevant.
Conformational stability and differential structural analysis of LcrV, PcrV, BipD, and SipD from type III secretion systems
Authors: Espina Marianela , Ausar S. Fernando , Middaugh C. Russell , Baxter M. Aaron , Picking William D. , Picking Wendy L. 
Published: February 2007

AbstractDiverse Gram‐negative bacteria use type III secretion systems (T3SS) to translocate effector proteins into the cytoplasm of eukaryotic cells. The type III secretion apparatus (T3SA) consists of a basal body spanning both bacterial membranes and an external needle. A sensor protein lies at the needle tip to detect environmental signals that trigger type III secretion. The Shigella flexneri T3SA needle tip protein, invasion plasmid antigen D (IpaD), possesses two independently folding domains in vitro. In this study, the solution behavior and thermal unfolding properties of IpaD's functional homologs SipD (Salmonella spp.), BipD (Burkholderia pseudomallei), LcrV (Yersinia spp.), and PcrV (Pseudomonas aeruginosa) were examined to identify common features within this protein family. CD and FTIR data indicate that all members within this group are α‐helical with properties consistent with an intramolecular coiled‐coil. SipD showed the most complex unfolding profile consisting of two thermal transitions, suggesting the presence of two independently folding domains. No evidence of multiple folding domains was seen, however, for BipD, LcrV, or PcrV. Thermal studies, including DSC, revealed significant destabilization of LcrV, PcrV, and BipD after N‐terminal deletions. This contrasted with SipD and IpaD, which behaved like two‐domain proteins. The results suggest that needle tip proteins share significant core structural similarity and thermal stability that may be the basis for their common function. Moreover, IpaD and SipD possess properties that distinguish them from the other tip proteins.
An analysis of the molecular origin of osmolyte‐dependent protein stability
Authors: Rösgen Jörg , Pettitt B. Montgomery , Bolen David Wayne 
Published: February 2007

AbstractProtein solvation is the key determinant for isothermal, concentration‐dependent effects on protein equilibria, such as folding. The required solvation information can be extracted from experimental thermodynamic data using Kirkwood‐Buff theory. Here we derive and discuss general properties of proteins and osmolytes that are pertinent to their biochemical behavior. We find that hydration depends very little on osmolyte concentration and type. Strong dependencies on both osmolyte concentration and type are found for osmolyte self‐solvation and protein–osmolyte solvation changes upon unfolding. However, solvation in osmolyte solutions does not involve complex concentration dependencies as found in organic molecules that are not used as osmolytes in nature. It is argued that the simple solvation behavior of naturally occurring osmolytes is a prerequisite for their usefulness in osmotic regulation in vivo.
Changes in element concentrations during Andosol formation on tephra in Japan
Authors: Nanzyo M. , Yamasaki S. , Honna T. , Yamada I. , Shoji S. , Takahashi T. 
Published: February 2007

SummaryAndosol formation involves the rapid, abundant and in situ formation of non‐crystalline materials from tephra deposits. A large amount of humus complexed with Al also accumulates in the A horizons. As these materials are rich in Al or Fe compared to the parent tephra, the concentrations of the major and minor elements change significantly during Andosol formation. The objectives of this study were to examine how the rock type of the tephra and its weight loss during the formation process affect the changes in the element concentrations of Andosols. A total of 95 samples with different rock types from 18 pedons of Andosols in Japan were used to determine the total concentrations of 54 elements. Principal component analysis suggested that the degree of weathering and the rock types of parent tephra are the important factors in the variation of the element concentrations in Andosols. Three rock types, dacitic, andesitic and basaltic‐andesitic, were identified from the V and Zn contents of ferromagnetic minerals separated from the Andosol samples. Basaltic Andosols were identified from the abundant coloured volcanic glass and olivine in the sand fraction. Regarding concentrations of 41 elements, at least one group based on rock type was significantly different from one to three other groups at the P= 0.05 level. The content of oxalate‐extractable Si (Sio), Al (Alo) and Fe (Feo) was used as an index to show the extent of Andosol development. Relatively strong correlations between the element concentrations and Sio, Alo and Feo as well as other weathering indices were found in the andesitic samples. Among these elements, at least 27 (Be, Al, Ti, Fe, Y, Zr, Nb, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, Tl, Pb, Th and U) were enriched in the Andosols and the increases in these concentrations were related to total weight loss due to soil formation processes.
The effect of the El Niño Southern Oscillation on the reproductive frequency of eastern Pacific leatherback turtles
Authors: SABA VINCENT S. , SANTIDRIÁN‐TOMILLO PILAR , REINA RICHARD D. , SPOTILA JAMES R. , MUSICK JOHN A. , EVANS DAVID A. , PALADINO FRANK V. 
Published: February 2007

Summary

Pacific leatherback turtle Dermochelys coriacea populations have been declining precipitously. It has been suggested that fishery‐associated mortality is the leading factor causing the decline; however, the sensitivity of leatherbacks to climate variability relative to their population ecology is unknown.
We investigated the effects of interannual climate variability, as governed by the El Niño Southern Oscillation (ENSO), on leatherback nesting ecology. We used equatorial Pacific sea surface temperature (SST) anomaly data over various time scales derived from both moored buoys and remote satellites as signals of ENSO. We then incorporated these data into a remigration probability model for the largest nesting population of eastern Pacific leatherbacks at Parque Nacional Marino Las Baulas (PNMB), Costa Rica.
Our results showed that nesting females of PNMB exhibited a strong sensitivity to ENSO, as reflected in their nesting remigration probabilities. Cool La Niña events corresponded with a higher remigration probability and warm El Niño events corresponded with a lower remigration probability.
We suggest that productivity transitions at leatherback foraging areas in the eastern equatorial and south‐eastern Pacific in response to El Niño/La Niña events result in variable remigration intervals and thus variable annual egg production. This phenomenon may render the eastern Pacific leatherback population more vulnerable to anthropogenic mortality than other populations.
Synthesis and applications. Physical indices of environmental variation can be used to estimate the probability of leatherbacks remigrating to nest at PNMB. This type of modelling approach can be extremely useful for understanding the effects of climatic variation on the population dynamics of sea turtles. Our remigration probability model can be applied to any monitored sea turtle nesting population where nesting site fidelity and beach monitoring coverage remains high. This modelling approach can help nesting beach monitoring programmes forecast remigrant numbers based on prior climate data, and can further quantify anthropogenic mortality by validating survival estimates.
Realized climatic niches of deciduous trees: comparing western Eurasia and eastern North America
Authors: Manthey Michael , Box Elgene O. 
Published: February 2007

AbstractAim  Assessment of cross‐continental similarities and differences in climatic limiting values for deciduous tree species and of the possible deterministic influence of past and present climatic differences on the modern tree flora in two regions.Location  The deciduous forest regions of western Eurasia and eastern North America.Methods  Based on species distribution data (range maps) and climate site data, the realized climatic niches of 137 deciduous tree species from the two regions were quantified using climatic envelopes. To compare these envelopes on the two continents, a hierarchical cluster analysis was performed, and principal components analysis was used to check cluster consistency.Results  Significant differences do exist for upper limits of winter temperatures and for lower limits of summer temperatures between Western Eurasia and eastern North America. Lower limits for the annual water balance also appear different, suggesting that the deciduous trees may be more drought‐tolerant in western Eurasia than in eastern North America. Climatic range types generated by the cluster analysis can be characterized, according to the distribution of the species, as boreal‐temperate, northern temperate, temperate, southern temperate, and Appalachian. Five of the eight clusters contain trees from both regions, but three groups consist only of American species that have no European counterparts.Main conclusions  Differences in temperature limitations can be explained by location on the east versus west side of the continents and by the almost complete lack of warm moist areas in western Eurasia. The difference in drought tolerance, on the other hand, is more likely to be the product of a deterministic sorting process that occurred during the Plio‐Pleistocene.
Catchments catch all: long‐term population history of a giant springtail from the southeast Australian highlands — a multigene approach
Authors: GARRICK R. C. , SANDS C. J. , ROWELL D. M. , HILLIS D. M. , SUNNUCKS P. 
Published: February 2007

AbstractPhylogeography can reveal evolutionary processes driving natural genetic‐geographical patterns in biota, providing an empirical framework for optimizing conservation strategies. The long‐term population history of a rotting‐log‐adapted giant springtail (Collembola) from montane southeast Australia was inferred via joint analysis of mitochondrial and multiple nuclear gene genealogies. Contemporary populations were identified using multilocus nuclear genotype clustering. Very fine‐scale sampling combined with nested clade and coalescent‐based analyses of sequences from mitochondrial cytochrome oxidase I and three unlinked nuclear loci uncovered marked population structure, deep molecular divergences, and abrupt phylogeographical breaks over distances on the order of tens of kilometres or less. Despite adaptations that confer low mobility, rare long‐distance gene flow was implicated: novel computer simulations that jointly modelled stochasticity inherent in coalescent processes and that of DNA sequence evolution showed that incomplete lineage sorting alone was unable to explain the observed spatial‐genetic patterns. Impacts of Pleistocene or earlier climatic cycles were detected on multiple timescales, and at least three putative moist forest refuges were identified. Water catchment divisions predict phylogeographical patterning and present‐day population structure with high precision, and may serve as an excellent surrogate for biodiversity indication in sedentary arthropods from topographically heterogeneous montane temperate forests.
Deep 610-MHz Giant Metrewave Radio Telescope observations of the Spitzer extragalactic First Look Survey field – I. Observations, data analysis and source catalogue
Authors: Garn Timothy , Green David A. , Hales Sally E. G. , Riley Julia M. , Alexander Paul 
Published: February 2007

Abstract
Observations of the Spitzer extragalactic First Look Survey field taken at 610 MHz with the Giant Metrewave Radio Telescope are presented. Seven individual pointings were observed, covering a total area of ∼4 deg2 with a resolution of 5.8 × 4.7 arcsec2, PA 60°. The rms noise at the centre of the pointings is between 27 and 30 μJy before correction for the Giant Metrewave Radio Telescope (GMRT) primary beam. The techniques used for data reduction and production of a mosaicked image of the region are described, and the final mosaic, along with a catalogue of 3944 sources detected above ∼5σ, are presented. The survey complements existing radio and infrared data available for this region.
No genetic evidence of sex‐biased dispersal in a lekking bird, the capercaillie (Tetrao urogallus)
Authors: MÄKI‐PETÄYS H. , CORANDER J. , AALTO J. , LIUKKONEN T. , HELLE P. , ORELL M. 
Published: February 2007

AbstractSex‐biased dispersal is often connected to the mating behaviour of the species. Even if patterns of natal dispersal are reasonably well documented for monogamous birds, only a few data are available for polygynous and especially lekking species. We investigated the dispersal of the capercaillie (Tetrao urogallus) by examining sex‐specific gene flow among the leks. Genetic information was extracted using nuclear and mitochondrial molecular markers for sexed faecal samples and analysed by novel Bayesian statistical methods. Contrary to the traditional view that the males are highly philopatric and female is the dispersing sex, we found roughly equivalent gross and effective dispersal of the sexes. The level of polygamy has a strong influence on the effective population size and on the effective dispersal. The results do not support the theories that dispersal evolves solely as a result of resource competition or other advantages to males obtained through kin selection in lekking species.
Evaluation of direct versus non‐refluxing technique and functional results in orthotopic Y‐ileal neobladder after 12 years of follow up
Authors: Hassan Ayman A , Elgamal Samir A , Sabaa Magdy A , Salem Khalid A , Elmateet Mahmoud S 
Published: February 2007

Objectives:  We report on the long‐term functional results of the orthotopic Y‐ileal neobladder and compare the outcome of the antireflux technique for ureteral implantation versus direct anastomosis.Patients and Methods:  Between 1990 and 2002, 120 patients underwent cystoprostatectomy and orthotopic Y‐shaped ileal neobladder for invasive bladder carcinoma. The direct Nesbit technique for ureteral reimplantation was applied in 58 patients (group 1) and in 62 patients the ureters were reimplanted using the Le Duc antirefluxing technique (group 2). The mean follow‐up period was 72 months (range, 36–144 months).Results:  Of 62 patients who underwent the Le Duc technique, six (9.7%) had unilateral uretero‐ileal anastomotic stricture and four (6.5%) had reflux. Of 58 patients who underwent direct anastomosis, six (10.3%) patients had unilateral reflux, four of them had dilated ureters preoperatively and no patient had uretero‐ileal anastomotic stricture. The incidence of stricture formation in the Le Duc technique is significantly higher than direct anastomosis (P = 0.04). There was no significant difference in the overall incidence of reflux in both groups. However, the incidence of reflux in preoperatively dilated ureters was significantly higher in direct ureteral anastomosis than Le Duc technique (40% in group 1 vs 16.7% in group 2; P = 0.045). The incidence of stone formation, azotemia, pyelonephritis and bacteriuria was comparable in both groups. The urodynamic findings showed a mean increase in the neobladder capacity at 6 and 18 months after surgery by 340 and 560 mL, respectively. The mean of the maximum pressure was 22 ± 10 cm H2O, 18 months after surgery. Daytime and nighttime continence was good or satisfactory in 93.3% and 85.5% of the patients, respectively, after 3 years of follow‐up.Conclusions:  The functional and voiding results of a Y‐shaped neobladder pouch using 40 cm of ileum are similar to the more sophisticated larger pouches. Direct uretero‐ileal anastomosis in orthotopic bladder replacement is more reasonable than the Le Duc antireflux technique in non‐dilated ureters. The benefit of the antireflux technique has been overestimated despite of the frequency of stricture formation.
First‐line high‐dose chemotherapy combined with peripheral blood stem cell transplantation for patients with advanced extragonadal germ cell tumors
Authors: Kumano Masafumi , Miyake Hideaki , Hara Isao , Furukawa Junya , Takenaka Atsushi , Fujisawa Masato 
Published: February 2007

Background:  The objective of this study was to evaluate the efficacy and safety of first‐line high‐dose chemotherapy (HDCT) combined with peripheral blood stem cell transplantation (PBSCT) for patients with advanced extragonadal germ cell tumors (EGGCT).Methods:  Six male patients with advanced non‐seminomatous EGGCT were treated with HDCT combined with PBSCT following 2–3 cycles of conventional‐dose induction chemotherapy. The regimens used for HDCT were carboplatin, etoposide and ifosfamide (ICE) in five patients and ICE plus paclitaxel (T‐ICE) in one patient, and that for induction therapy was cisplatin, etoposide and bleomycin (PEB) in all patients. As a rule, HDCT was continuously administered until α‐fetoprotein (AFP) and β‐human chorionic gonadotropin normalized (β‐HCG).Results:  Following 1–6 courses of HDCT (median, 4 courses), β‐HCG and AFP were normalized in all patients, and five and one patient were diagnosed as showing partial remission and stable disease, respectively. Five patients underwent surgical resection of residual tumors after HDCT, yielding necrotic tissue in two, mature teratoma in two, and viable cancer tissue in one, and the surgical margin was negative in all patients. At a median follow‐up of 36 months, five patients were alive and disease‐free, whereas the remaining one died of disease progression. Although all patients had grade 3 hematological toxicity, there was no treatment‐related death by combining PBSCT.Conclusions:  First‐line HDCT with PBSCT could be safely administered to patients with advanced EGGCT, and the antitumor effect of this treatment was comparatively favorable. First‐line HDCT therefore may represent an attractive option for patients with advanced EGGCT.
Long‐term results of tension‐free vaginal tape for female urinary incontinence: Follow up over 6 years
Authors: Deffieux Xavier , Donnadieu Anne Claire , Porcher Raphaël , Gervaise Amelie , Frydman Rene , Fernandez Herve 
Published: February 2007

Objective:  To describe the long‐term outcome of using tension‐free vaginal tape (TVT) with and without associated procedures.Methods:  A questionnaire was mailed to a population of 61 women who had undergone TVT surgery more than 6 years ago. Of this population, 41 (80%) had suffered from stress urinary incontinence (SUI). The questionnaire included questions about urinary symptoms, satisfaction and quality of life. The questionnaire was answered by 51 of the 61 women.Results:  Mean follow up was 83 months. The women with SUI had a persistent cure rate of 80% with a satisfaction rate of 97%. The cure rate after 6 years was 37% in women with mixed incontinence. Concomitant hysterectomy (relative risks = 0.87) and body mass index (BMI) do not alter the long‐term results of TVT procedure. Peroperative bladder injury is not associated with an increased risk of long‐term lower urinary tract symptoms (LUTS) or with a decreased satisfaction rate (relative risks = 0.85).Conclusions:  Concomitant hysterectomy, increased BMI and bladder injury do not alter good long‐term results of TVT.