bluuebunny/crossref_metadata_2025_split huggingface dataset:
Site‐2 protease regulated intramembrane proteolysis: Sequence homologs suggest an ancient signaling cascade
Authors: Kinch Lisa N. , Ginalski Krzysztof , Grishin Nick V. 
Published: December 2005

AbstractSite‐2 proteases (S2Ps) form a large family of membrane‐embedded metalloproteases that participate in cellular signaling pathways through sequential cleavage of membrane‐tethered substrates. Using sequence similarity searches, we extend the S2P family to include remote homologs that help define a conserved structural core consisting of three predicted transmembrane helices with traditional metalloprotease functional motifs and a previously unrecognized motif (GxxxN/S/G). S2P relatives were identified in genomes from Bacteria, Archaea, and Eukaryota including protists, plants, fungi, and animals. The diverse S2P homologs divide into several groups that differ in various inserted domains and transmembrane helices. Mammalian S2P proteases belong to the major ubiquitous group and contain a PDZ domain. Sequence and structural analysis of the PDZ domain support its mediating the sequential cleavage of membrane‐tethered substrates. Finally, conserved genomic neighborhoods of S2P homologs allow functional predictions for PDZ‐containing transmembrane proteases in extra‐cytoplasmic stress response and lipid metabolism.
An examination of dynamics crosstalk between SH2 and SH3 domains by hydrogen/deuterium exchange and mass spectrometry
Authors: Hochrein James M. , Lerner Edwina C. , Schiavone Anthony P. , Smithgall Thomas E. , Engen John R. 
Published: December 2005

AbstractThe ability of proteins to regulate their own enzymatic activity can be facilitated by changes in structure or protein dynamics in response to external regulators. Because many proteins contain SH2 and SH3 domains, transmission of information between the domains is a potential method of allosteric regulation. To determine if ligand binding to one modular domain may alter structural dynamics in an adjacent domain, allowing potential transmission of information through the protein, we used hydrogen exchange and mass spectrometry to measure changes in protein dynamics in the SH3 and SH2 domains of hematopoietic cell kinase (Hck). Ligand binding to either domain had little or no effect on hydrogen exchange in the adjacent domain, suggesting that changes in protein structure or dynamics are not a means of SH2/SH3 crosstalk. Furthermore, ligands of varying affinity covalently attached to SH3/SH2 altered dynamics only in the domain to which they bind. Such results demonstrate that ligand binding may not structurally alter adjacent SH3/SH2 domains and implies that other aspects of protein architecture contribute to the multiple levels of regulation in proteins containing SH3 and SH2 domains.
A structural model of an amyloid protofilament of Transthyretin
Authors: Correia Bruno E. , Loureiro‐Ferreira Nuno , Rodrigues J. Rui , Brito Rui M.M. 
Published: December 2005

AbstractA docking‐and‐alignment protocol was devised in order to build amyloid protofilaments of Transthyretin (TTR), starting from partially disrupted TTR monomeric subunits and based on experimentally available information. The docking approach is driven by a combination of shape complementarity and energetic criteria, and uses constraints derived from experimental data obtained for the fibrillar state. The dimeric structures obtained were then subjected to an alignment scheme followed by clustering analysis, producing a collection of protofilaments with distinct geometric properties. The selected protofilament model presented here does agree with known experimental data and general amyloid properties; it is formed by two extended continuous β‐sheets with the β‐strands perpendicular to the main axis of the protofilament and a helical twist with a period of ∼48 β‐strands. This TTR proto‐filament model may be an important step in the understanding of the molecular mechanisms of TTR aggregation, as well as, a valuable instrument in drug design strategies against amyloid diseases.
Crystal structure of TBP‐interacting protein (Tk‐TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA‐DNA
Authors: Yamamoto Takahiko , Matsuda Tomoki , Inoue Tsuyoshi , Matsumura Hiroyoshi , Morikawa Masaaki , Kanaya Shigenori , Kai Yasushi 
Published: December 2005

AbstractTATA‐binding protein (TBP)‐interacting protein from the hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1 (Tk‐TIP26) is a possible transcription regulatory protein in Thermococcales. Here, we report the crystal structure of Tk‐TIP26 determined at 2.3 Å resolution with multiple‐wavelength anomalous dispersion (MAD) method. The overall structure of Tk‐TIP26 consists of two domains. The N‐terminal domain forms an α/β structure, in which three α‐helices enclose the central β‐sheet. The topology of this domain is similar to that of holliday junction resolvase Hjc from Pyrococcus furiosus. The C‐terminal domain comprises three α‐helices, six β‐strands, and two 310‐helices. In the dimer structure of Tk‐TIP26, two molecules are related with the crystallographic twofold axis, and these molecules rigidly interact with each other via hydrogen bonds. The complex of Tk‐TIP26/Tk‐TBP is isolated and analyzed by SDS‐PAGE and gel filtration column chromatography, resulting in a stoichiometric ratio of the interaction between Tk‐TIP26 and Tk‐TBP of 4:2, i.e., two dimer molecules of Tk‐TIP26 formed a complex with one dimeric TBP. The electrostatic surfaces of Tk‐TIP26 and TBP from Pyrocuccus woesei (PwTBP) allowed us to build a model of the Tk‐TIP26/TBP complex, and to propose the inhibition mechanism where two dimer molecules of Tk‐TIP26 bind to a dimeric TBP, preventing its binding to TATA‐DNA.
Diagnostic cross‐linking of paired cysteine pairs demonstrates homologous structures for two chemoreceptor domains with low sequence identity
Authors: Lai Wing‐Cheung , Peach Megan L. , Lybrand Terry P. , Hazelbauer Gerald L. 
Published: December 2005

AbstractHundreds of bacterial chemoreceptors from many species have periplasmic, ligand‐recognition domains of approximately the same size, but little or no sequence identity. The only structure determined is for the periplasmic domain of chemoreceptor Tar from Salmonella and Escherichia coli. Do sequence‐divergent but similarly sized chemoreceptor periplasmic domains have related structures? We addressed this issue for the periplasmic domain of chemoreceptor TrgE from E. coli, which has a low level of sequence similarity to Tar, by combining homology modeling and diagnostic cross‐linking between pairs of introduced cysteines. A homology model of the TrgE domain was created using the homodimeric, four‐helix bundle structure of the TarS domain from Salmonella. In this model, we chose four pairs of positions at which introduced cysteines would be sufficiently close to form disulfides across each of four different helical interfaces. For each pair we chose a second pair, in which one cysteine of the original pair was shifted by one position around the helix and thus would be less favorably placed for disulfide formation. We created genes coding for proteins containing four such pairs of cysteine pairs and investigated disulfide formation in vivo as well as functional consequences of the substitutions and disulfides between neighboring helices. Results of the experimental tests provided strong support for the accuracy of the model, indicating that the TrgE periplasmic domain is very similar to the TarS domain. Diagnostic cross‐linking of paired pairs of introduced cysteines could be applied generally as a stringent test of homology models.
Use of a probiotic to control lactococcosis and streptococcosis in rainbow trout, Oncorhynchus mykiss (Walbaum)
Authors: Brunt J , Austin B 
Published: December 2005

AbstractFrom a comparison of 125 bacterial isolates recovered from the digestive tract of rainbow trout, Oncorhynchus mykiss, and carp, Cyprinus sp., a culture was obtained which was effective at preventing clinical disease caused by Lactococcus garvieae and Streptococcus iniae when used as a feed additive. The culture, Aeromonas sobria GC2, was incorporated into the feed and fed to rainbow trout (average weight = 20 g) for 14 days at a dose equivalent to 5 × 107 cells g−1 of feed. Whereas the untreated controls experienced losses of 75–100% when challenged intraperitoneally with L. garvieae and S. iniae, the probiotic‐treated groups remained healthy with total mortalities of only 0–6%. Formalized and sonicated preparations of GC2 and cell‐free supernatant fared less well. The mode of action reflected stimulation of innate immunity, namely an increased number of leucocytes and enhanced phagocytic and respiratory burst activity.
Engulfed pathogen‐induced apoptosis in haemocytes of giant freshwater prawn,Macrobrachium rosenbergii
Authors: Hsu J‐P , Huang C , Liao C‐M , Hsuan S‐L , Hung H‐H , Chien M‐S 
Published: December 2005

AbstractHaemocytes of the giant freshwater prawn,Macrobrachium rosenbergii, were investigated for the induction of apoptosis after phagocytosis of pathogenic yeasts, bacteria and non‐pathogenic latex beadsin vitro. Isolated haemocytes ofM. rosenbergiiwere cultured at a ratio of 1:50 haemocytes to pathogen with the yeastDebaryomyces hansenii, the bacteriaAeromonas hydrophilaorEnterococcus faecium, or with latex beads at 25 °C for 2 h, followed by washing to remove free particles. At least 200 haemocytes were counted to determine the phagocytosis rate, and the results showed that haemocytes engulfed latex beads at a higher rate than the aquatic pathogens. By transmission electron microscopy, the yeast‐ or bacterium‐engulfing haemocytes displayed morphological changes characteristic of apoptosis, including formation of cytoplasmic vacuoles, chromatin condensation and fragmentation of nuclei. This pathogen‐induced apoptosis was further confirmed by DNA laddering and TUNEL (terminal deoxynucleotidyl transferase‐mediated deoxy‐UTP nick‐end‐labelling) assays. Neither haemocytes treated with latex beads nor uninfected haemocytes (control group) showed signs of apoptosis after 48 h in culture.
Task‐dependent differences in subjective fatigue scores
Authors: RICHTER S. , MARSALEK K. , GLATZ C. , GUNDEL A. 
Published: December 2005

SummaryThe aim of the present study was to evaluate time‐on‐task effects on subjective fatigue in two different tasks of varying monotony during night‐time testing (20:00 to 4:00 hours) in a sleep deprivation intervention. The experiment included eight test runs separated by breaks of approximately 20 min. Twenty healthy volunteers performed a driving simulator and the Mackworth clock vigilance task in four of the test runs each. Sequence of tasks was varied across subjects. Before and after each task, subjective sleepiness was assessed by means of the Karolinska sleepiness scale and subjective fatigue was rated on the Samn‐Perelli checklist. Fatigue and sleepiness significantly increased over the course of the night. Both tasks led to an increase in fatigue and sleepiness across test runs. However, this time‐on‐task effect was larger in the vigilance than in the driving simulator task. It is important to note that fatigue and sleepiness in one test run were not influenced by the task performed in the preceding test run, that is there were no cross‐over effects. The results suggest that time‐on‐task effects superimpose circadian and sleep‐related factors affecting fatigue. They depend on the monotony of the task and can be quantified by means of a design including separate test runs divided by breaks.
Event‐related potential measures of the disruptive effects of trains of auditory stimuli during waking and sleeping states
Authors: CAMPBELL K. , MICHAUD D. S. , KEITH S. E. , MULLER‐GASS A. , WIEBE S. 
Published: December 2005

SummaryAcoustic backup alarms have been reported to particularly disrupt sleep. The present study simulated backup alarms by presenting trains of five consecutive 500 ms duration audible tones, with the time between the onset of each tone being 1 s and the time between trains (offset to onset) between 15 and 20 s. In different conditions, the tones were set at either 80 or 60 dB sound pressure level (SPL). Twelve young adults spent two consecutive nights in the laboratory. Stimuli were presented only on the second night. Measures of traditional sleep architecture (sleep stages) were not affected by the acoustic trains. Event‐related potentials were also measured following presentation of the stimuli. In the waking state, the initial 80 dB stimulus elicited a large amplitude N1, peaking at about 100 ms, followed by a positive peak, P3, peaking at about 325 ms. N1 was attenuated following presentation of the 60 dB stimulus. The amplitude of N1 was much reduced following presentation of the subsequent second to fifth stimuli in the train. During non‐rapid eye movement (NREM) sleep, the initial 80 dB stimulus elicited a large and later negativity (N350) that was reduced in amplitude for the 60 dB stimulus. A K‐Complex (a composite N350 and a much larger N550) was elicited following 35% of the initial 80 dB tones and 12% of the initial 60 dB tones. The amplitude of N550 did not, however, significantly vary as a function of stimulus SPL. During REM sleep, N1 continued to be elicited by the initial louder stimulus, but the later positive wave was not apparent. A late negativity peaking at about 350 ms was, however, apparent. When queried the next morning, subjects rarely indicated that the stimulus presentations disturbed their sleep. This might be because of the absence of the late positivity. The presence of the long latency negativities (N350 and N550) might serve to protect sleep from obtrusive sound during sleep.
Diurnal spectral EEG fluctuations in narcoleptic patients during rest and reaction time tasks
Authors: SMIT ANNIKA S. , DROOGLEEVER FORTUYN HAL A. , ELING PAUL A. T. M. , COENEN ANTON M. L. 
Published: December 2005

AbstractNarcolepsy is associated with lowered vigilance. Diurnal variation in vigilance appears altered, but the exact nature of this change is unclear. It was hypothesized that the homeostatic sleep drive is increased in narcolepsy. Decreased levels of vigilance are reflected in low frequency band power in the electroencephalogram (EEG), so these frequencies were expected to be increased in the narcolepsy group. Furthermore, it was expected that low frequency power should increase over the day. Narcoleptic patients and healthy controls participated (36 participants in total); they were not allowed to take medication or naps on the experimental day. EEG was measured at 9:00, 11:00, 13:00, 15:00, and 17:00 hours, during rest and during reaction time tasks. In the narcolepsy group, alpha power was lower at rest at all times. Delta and theta power during rest and task performance increased steadily over the day in this group, from 11:00 hours onwards. Additionally, in the narcolepsy group beta1 and beta2 power during rest appeared increased at the end of the day. The effects in the lower frequency bands strongly suggest that vigilance is low at all times. The progressive increase in low frequency power indicates that the sleep drive is enhanced. It is not clear whether this pattern reflects an extreme state of low vigilance, or a pathological brain condition. The effects in the higher frequencies suggest that narcoleptic patients may make an effort to counteract their low vigilance level.
Prevalence of Cryptosporidium spp. in asymptomatic sheep in family flocks from Mexico State
Authors: Alonso‐Fresán M. U. , García‐Álvarez A. , Salazar‐García F. , Vázquez‐Chagoyán J. C. , Pescador‐Salas N. , Saltijeral‐Oaxaca J. 
Published: December 2005

SummaryTo determine Cryptosporidium spp. prevalence in faeces from asymptomatic sheep, 37 family flocks in Mexico State were sampled. Data were collected by the interview method and Ziehl‐Neelsen stain of faecal samples for Cryptosporidium identification. The independent group proportion hypothesis test was used for differences in prevalences between sheep farms. A 34.3% general prevalence was found, and prevalence in herds with >100 animals was significantly higher (40.6%). Correlation was found between flock size and Cryptosporidium spp. presence (odds ratio, OR, 2.57; confidence interval, IC95%, 1.84–3.60).
Long‐Term Studies on Maternal Immunity for Aujeszky's Disease and Classical Swine Fever in Wild Boar Piglets
Authors: Müller T. , Teuffert J. , Staubach C. , Selhorst T. , Depner K. R. 
Published: December 2005

SummaryThe aim of the studies was to fathom the duration and the role of maternal immunity for Aujeszky's disease (AD) and classical swine fever (CSF) in wild boar offspring. In one experiment, two wild boar sows were infected with a low pathogenic pseudorabies virus (PRV) in 1999. A total of 51 offspring was born between 1999 and 2002 and was monitored for PRV maternal antibodies. In a second experiment, the maternal immunity for CSF was analysed. Therefore, a sow was orally vaccinated against CSF using vaccine baits containing the live‐attenuated C‐strain vaccine. The vaccination took place in January 1999. The sow gave birth to four piglets in 2001 and to two piglets in 2002. With respect to maternal immunity for AD, some piglets reacted positive in the ELISA up to 27‐week post‐partum while in the neutralization test antibodies were detected up to 15‐week post‐partum. The calculated half‐life of neutralizing antibodies was 21 days. Regarding CSF, the neutralization titres of maternal antibodies dropped continuously reaching values of ≤10 ND50 20‐week post‐partum. After the 12th week post‐partum, most of the sera reacted negative in the ELISA. However, after the third month, low levels of neutralization titres were still detectable. The results are discussed with respect to the epidemiology and control of both diseases in wild boar populations.
Comparative Study of the Effects of Several Chemical and Physical Treatments on the Activity of Protease Resistance and Infectivity of Scrapie Strain 263K
Authors: Yao H.‐L. , Han J. , Gao J.‐M. , Zhang J. , Zhang B.‐Y. , Guo Y.‐J. , Nie K. , Gao C. , Wang X.‐F. , Dong X.‐P. 
Published: December 2005

SummaryTo study the influences of chemical and physical factors on the protease resistant activity in vitro and the infectivity in vivo of scrapie strain 263K, PrPSc from the hamsters infected intracerebrally with scrapie strain 263K were treated with several commonly used disinfection methods, including sodium hydroxide (NaOH), sodium hypochlorite (NaOCl), heating or autoclaving at 80, 100, 121 and 134°C in the solutions with or without 3% sodium dodecyl sulphate (SDS). The protease resistance of PrPSc was analysed by a proteinase K (PK) digesting Western blot and the infectivity of PrPSc was analysed by intracerebral (i.c.) inoculation into experimental hamsters. The results showed that PrPSc signals were removed in the preparations treated with NaOH higher than 0.05 mol/l, NaOCl higher than 0.1%, autoclaved over 121°C, or heated over 80°C in the presence of 3% SDS. Animal challenges revealed that mixing with 2 mol/l NaOH or 2% NaOCl, autoclaving at 134°C, as well as heating at 100°C or autoclaving at 121°C in the solutions with 3% SDS completely blocks the transmission of scrapie 263K in this experimental situation. It is obvious that the removal of PK resistance of PrPSc happened at relatively lower concentration chemicals or lower temperature, while elimination of the infectivity needs more vigorous conditions. Our data provide the useful evidences for several commonly used methods to inactivate TSEs agent and suggest that it is inappropriate to use PrPSc as a surrogate for TSEs infectivity in inactivation experiments.
Analysis of the learning context, perceptions of the learning environment and approaches to learning accounting: a longitudinal study
Authors: Jackling Beverley 
Published: December 2005

AbstractThis study investigates student approaches to learning over the 3 years of an undergraduate degree course in accounting. The objective of the study was, first, to identify changes in learning approaches over the course duration. Second, the study examined whether any changes in learning approaches were consistent with changes in the context of learning as well as students' perceptions of the teaching/learning environment. The results show that students made greater use of sophisticated learning approaches over time linked to their more favourable perceptions of the teaching/learning environment as they progressed in their course. However, there were no significant changes in learning approach attributable to the learning context. Implications for accounting educators drawn from the findings are discussed.
Is ‘benchmark beating’ by Australian firms evidence of earnings management?
Authors: Coulton Jeff , Taylor Sarah , Taylor Stephen 
Published: December 2005

AbstractWe investigate the extent to which Australian firms that report small profits and/or small increases in earnings (i.e. benchmark beaters) have done so by the upward manipulation of these earnings. Although evidence of an unusually large number of firms managing to just beat such earnings benchmarks has been interpreted as evidence of earnings management, this approach fails to identify those firms that are the manipulators from those where unbiased earnings fall naturally into the benchmark beating group. Our results suggest that caution is required in interpreting benchmark beating as an indicator of the extent of earnings management. Using several methods for estimating the unexpected accrual component of earnings, we show that although benchmark beaters have larger positive unexpected accruals than other firms, a similar result holds when firms with small losses or earnings declines (i.e. ‘just miss’ firms) are compared with other firms. Moreover, there is no statistically significant difference between unexpected accruals for the benchmark beating and just miss groups. At a minimum, we reject the joint hypothesis that unexpected accruals capture earnings management and that an unusual kink around zero in the distribution of earnings levels or earnings changes is caused by earnings management.
Integrating consumer information with the new product development process: the development of lighter dairy products
Authors: Bogue Joe , Ritson Christopher 
Published: December 2005

AbstractIn highly competitive markets, research methodologies need to be adapted to understand end‐users’ needs with greater clarity than hitherto when new products were developed. Integrating marketing and sensory analysis to measure end‐users’ preferences for the extrinsic and intrinsic attributes of food products can help understand end‐users’ perceptions of product quality. This research identified the extrinsic and intrinsic attributes that determined end‐users’ preferences for a range of full‐fat and lighter dairy products. Six focus groups revealed end‐users’ perceptions of lighter dairy products while Descriptive Sensory Analysis was used to profile the sensory characteristics of the full‐fat and lighter dairy products. Preference Mapping and Hierarchical Cluster Analysis were then used to identify clusters of end‐users with similar preferences for lighter dairy products. End‐users had a higher preference for lighter strawberry yoghurts, than lighter Cheddar‐type cheeses. Integrating marketing and sensory information promotes a market‐oriented approach to the development of new food products.