bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nitric oxide levels regulate macrophage commitment to apoptosis or necrosis during pneumococcal infection
Authors: Marriott Helen M. , Ali Farzana , Read Robert C. , Mitchell Tim J. , Whyte Moira K. B. , Dockrell David H. 
Published: May 2004

ABSTRACTMacrophages are resistant to constitutive apoptosis, but infectious stimuli can induce either microbial or host‐mediated macrophage apoptosis. Phagocytosis and killing of opsonized pneumococci by macrophages are potent stimuli for host‐mediated apoptosis, but the link between pneumococcal killing and apoptosis induction remains undefined. We now show phagocytosis of pneumococci by differentiated human monocyte‐derived macrophages (MDM) results in up‐regulation of inducible nitric oxide synthase (iNOS) and increased production of NO and reactive nitrogen species. NO accumulation in macrophages initiates an apoptotic program that involves NO‐dependent mitochondrial membrane permeabilization, Mcl‐1 down‐ regulation, and caspase activation and results in nuclear condensation and fragmentation. An inhibitor of mitochondrial permeability transition, bongkrekic acid, decreases pneumococcal‐ associated macrophage apoptosis. Conversely, inhibition of NO production using iNOS inhibitors decreases bacterial killing and shifts the cell death program from apoptosis to necrosis. Pneumolysin contributes to both NO production and apoptosis induction. After initial microbial killing, NO accumulation switches the macrophage phenotype from an activated cell to a cell susceptible to apoptosis. These results illustrate important roles for NO in the integration of host defense and regulation of inflammation in human macrophages.
Production of a fully functional, permuted single‐chain penicillin G acylase
Authors: Flores Gabriela , Soberón Xavier , Osuna Joel 
Published: May 2004

AbstractPenicillin G acylase (PGA) is a heterodimeric enzyme synthesized as a single‐polypeptide precursor that undergoes an autocatalytic processing to remove an internal spacer peptide to produce the active enzyme. We constructed a single‐chain PGA not dependent on autoproteolytic processing. The mature sequence of the β‐domain was expressed as the N terminus of a new polypeptide, connected by a random tetra‐peptide to the α‐domain, to afford a permuted protein. We found several active enzymes among variants differing in their linker peptides. Protein expression analysis showed that the functional single‐chain variants were produced when using a Sec‐dependent leader peptide, or when expressed inside the bacterial cytoplasm. Active‐site titration experiments showed that the single‐chain proteins displayed similar kcat values to the ones obtained with the wild‐type enzyme. Interestingly, the single‐chain proteins also displayed close to 100% of functional active sites compared to 40% to 70% functional yield usually obtained with the heterodimeric protein.
Modification of halogen specificity of a vanadium‐dependent bromoperoxidase
Authors: Ohshiro Takashi , Littlechild Jennifer , Garcia‐Rodriguez Esther , Isupov Michail N. , Iida Yasuaki , Kobayashi Takushi , Izumi Yoshikazu 
Published: May 2004

AbstractThe halide specificity of vanadium‐dependent bromoperoxidase (BPO) from the marine algae, Corallina pilulifera, has been changed by a single amino acid substitution. The residue R397 has been substituted by the other 19 amino acids. The mutant enzymes R397W and R397F showed significant chloroperoxidase (CPO) activity as well as BPO activity. These mutant enzymes were purified and their properties were investigated. The maximal velocities of CPO activities of the R397W and R397F enzymes were 31.2 and 39.2 units/mg, and the Km values for Cl− were 780 mM and 670 mM, respectively. Unlike the native enzyme, both mutant enzymes were inhibited by NaN3. In the case of the R397W enzyme, the incorporation rate of vanadate into the active site was low, compared with the R397F and the wild‐type enzyme. These results supported the existence of a specific halogen binding site within the catalytic cleft of vanadium haloperoxidases.
Pressure dissociation studies provide insight into oligomerization competence of temperature‐sensitive folding mutants of P22 tailspike
Authors: Lefebvre Brian G. , Comolli Noelle K. , Gage Matthew J. , Robinson Anne Skaja 
Published: May 2004

AbstractSeveral temperature‐sensitive folding (tsf) mutants of the tailspike protein from bacteriophage P22 have been found to fold with lower efficiency than the wild‐type sequence, even at lowered temperatures. Previous refolding studies initiated from the unfolded monomer have indicated that the tsf mutations decrease the rate of structured monomer formation. We demonstrate that pressure treatment of the tailspike aggregates provides a useful tool to explore the effects of tsf mutants on the assembly pathway of the P22 tailspike trimer. The effects of pressure on two different tsf mutants, G244R and E196K, were explored. Pressure treatment of both G244R and E196K aggregates produced a folded trimer. E196K forms almost no native trimer in in vitro refolding experiments, yet it forms a trimer following pressure in a manner similar to the native tailspike protein. In contrast, trimer formation from pressure‐treated G244R aggregates was not rapid, despite the presence of a G244R dimer after pressure treatment. The center‐of‐mass shifts of the fluorescence spectra under pressure are nearly identical for both tsf aggregates, indicating that pressure generates similar intermediates. Taken together, these results suggest that E196K has a primary defect in formation of the β‐helix during monomer collapse, while G244R is primarily an assembly defect.
Sequence‐structure mapping errors in the PDB: OB‐fold domains
Authors: Venclovas Česlovas , Ginalski Krzysztof , Kang Chulhee 
Published: May 2004

AbstractThe Protein Data Bank (PDB) is the single most important repository of structural data for proteins and other biologically relevant molecules. Therefore, it is critically important to keep the PDB data, as much as possible, error‐free. In this study, we have analyzed PDB crystal structures possessing oligonucleotide/oligosaccharide binding (OB)‐fold, one of the highly populated folds, for the presence of sequence‐structure mapping errors. Using energy‐based structure quality assessment coupled with sequence analyses, we have found that there are at least five OB‐structures in the PDB that have regions where sequences have been incorrectly mapped onto the structure. We have demonstrated that the combination of these computation techniques is effective not only in detecting sequence‐structure mapping errors, but also in providing guidance to correct them. Namely, we have used results of computational analysis to direct a revision of X‐ray data for one of the PDB entries containing a fairly inconspicuous sequence‐structure mapping error. The revised structure has been deposited with the PDB. We suggest use of computational energy assessment and sequence analysis techniques to facilitate structure determination when homologs having known structure are available to use as a reference. Such computational analysis may be useful in either guiding the sequence‐structure assignment process or verifying the sequence mapping within poorly defined regions.
Accessibility of introduced cysteines in chemoreceptor transmembrane helices reveals boundaries interior to bracketing charged residues
Authors: Boldog Thomas , Hazelbauer Gerald L. 
Published: May 2004

AbstractTwo hydrophobic sequences, 24 and 30 residues long, identify the membrane‐spanning segments of chemoreceptor Trg from Escherichia coli. As in other related chemoreceptors, these helical sequences are longer than the minimum necessary for an α‐helix to span the hydrocarbon region of a biological membrane. Thus, the specific positioning of the segments relative to the hydrophobic part of the membrane cannot be deduced from sequence alone. With the aim of defining the positioning for Trg experimentally, we determined accessibility of a hydrophilic sulfhydryl reagent to cysteines introduced at each position within and immediately outside the two hydrophobic sequences. For both sequences, there was a specific region of uniformly low accessibility, bracketed by regions of substantial accessibility. The two low‐accessibility regions were each 19 residues long and were in register in the three‐dimensional organization of the transmembrane domain deduced from independent data. None of the four hydrophobic–hydrophilic boundaries for these two membrane‐embedded sequences occurred at a charged residue. Instead, they were displaced one to seven residues internal to the charged side chains bracketing the extended hydrophobic sequences. Many hydrophobic sequences, known or predicted to be membrane‐spanning, are longer than the minimum necessary helical length, but precise membrane boundaries are known for very few. The cysteine‐accessibility approach provides an experimental strategy for determining those boundaries that could be widely applicable.
External cephalic version: a safe procedure? A systematic review of version‐related risks
Authors: Collaris Ronald J. , Oei S. Guid 
Published: May 2004

Background.  The Term Breech Trial has considerably increased the number of cesareans. External cephalic version (ECV) might be an effective method of lowering the rate of cesareans; its efficacy has been well established. However, although in the absence of anesthesia the risks are thought to be low, most studies have used populations too small to allow definite conclusions on version‐related risks.Methods.  In an attempt to make an inventory of these risks, we have systematically analyzed 44 studies, covering a total of 7377 patients from 1990 to 2002. The studies used were derived from a Medline and Embase search.Results.  The most frequently reported complications were transient abnormal cardiotocography (CTG) patterns (5.7%). Persisting pathological CTG readings (0.37%) and vaginal bleeding occur rarely (0.47%). The incidence of placental abruption was even lower, at 0.12%. Fetomaternal transfusion was absent in five out of seven studies, with a mean incidence of 3.7%. Emergency cesareans were performed in 0.43% of all versions. Perinatal mortality was 0.16%.Conclusions.  External cephalic version seems to be a safe procedure.
On maintaining and extending contrasts: notker's anlautgesetz
Authors: Lahiri Aditi , Kraehenmann Astrid 
Published: May 2004

AbstractNative speakers deal with their phonological system without any knowledge of a lost contrast. To avoid neutralisations, speakers can only make use of their present phonological system of contrasts. Speakers of Old Alemannic (the dialect of Notker der Deutsche) had no contrast in voicing or fortis/lenis after the Second Consonant Shift had reduced the pre‐OHG voiceless stops to fricatives and affricates. They had instead a quantity contrast, which they utilised to distinguish between an old coronal stop and a new one developed from *þ, thereby introducing a word‐initial contrast only in coronal stops. This contrast was again later extended to other places of articulation through generations while adapting loans from donor languages which had a contrast in voicing. No new contrast was added due to loans. As a result, modern Alemannic dialects such as Thurgovian have a quantity contrast in stops in all positions of a word.
Definiteness effects: evidence from Sardinian
Authors: Bentley Delia 
Published: May 2004

AbstractIn this paper I consider the definiteness effects which are found in Sardinian presentational structures. I argue that they result from well‐formedness conditions on the encoding of information structure. In particular, two kinds of information are encoded in morphosyntax: on the one hand, the pragmatic relations between the denotata of the sentence constituents and the propositions in which they are arguments and predicates, and, on the other hand, the status of such denotata in the minds of the discourse participants (see Lambrecht 1994: 49). An RRG analysis in terms of non‐derivational linking between semantics and syntax suggests that the syntax of existentials and locatives is irrelevant to agreement and the definiteness value of the nominal. The Sardinian evidence suggests that agreement can be subject to pragmatic constraints in dependent‐marking languages, regardless of pro drop. Finally, Sardinian presentationals with activity predicates, which are allegedly rare across languages, are analysed in terms of pragmatically motivated exceptional mapping between semantics and syntax. This analysis is likely to apply to analogous constructions which occur in Romance.
Assumptions Behind Grammatical Approaches To Code‐Switching: When The Blueprint Is A Red Herring
Authors: Gardner‐Chloros Penelope , Edwards Malcolm 
Published: May 2004

AbstractMany of the so‐called ‘grammars’ of code‐switching are based on various underlying assumptions, e.g. that informal speech can be adequately or appropriately described in terms of ‘‘grammar’’; that deep, rather than surface, structures are involved in code‐switching; that one ‘language’ is the ‘base’ or ‘matrix’; and that constraints derived from existing data are universal and predictive. We question these assumptions on several grounds. First, ‘grammar’ is arguably distinct from the processes driving speech production. Second, the role of grammar is mediated by the variable, poly‐idiolectal repertoires of bilingual speakers. Third, in many instances of CS the notion of a ‘base’ system is either irrelevant, or fails to explain the facts. Fourth, sociolinguistic factors frequently override ‘grammatical’ factors, as evidence from the same language pairs in different settings has shown. No principles proposed to date account for all the facts, and it seems unlikely that ‘grammar’, as conventionally conceived, can provide definitive answers. We conclude that rather than seeking universal, predictive grammatical rules, research on CS should focus on the variability of bilingual grammars.
The pathogenic activation of calpain: a marker and mediator of cellular toxicity and disease states
Authors: Vanderklish Peter W. , Bahr Ben A. 
Published: May 2004

Over‐activation of calpain, a ubiquitous calcium‐sensitive protease, has been linked to a variety of degenerative conditions in the brain and several other tissues. Dozens of substrates for calpain have been identified and several of these have been used to measure activation of the protease in the context of experimentally induced and naturally occurring pathologies. Calpain‐mediated cleavage of the cytoskeletal protein spectrin, in particular, results in a set of large breakdown products (BDPs) that are unique in that they are unusually stable. Over the last 15 years, measurements of BDPs in experimental models of stroke‐type excitotoxicity, hypoxia/ischemia, vasospasm, epilepsy, toxin exposure, brain injury, kidney malfunction, and genetic defects, have established that calpain activation is an early and causal event in the degeneration that ensues from acute, definable insults. The BDPs also have been found to increase with normal ageing and in patients with Alzheimer's disease, and the calpain activity may be involved in related apoptotic processes in conjunction with the caspase family of proteases. Thus, it has become increasingly clear that regardless of the mode of disturbance in calcium homeostasis or the cell type involved, calpain is critical to the development of pathology and therefore a distinct and powerful therapeutic target. The recent development of antibodies that recognize the site at which spectrin is cleaved has greatly facilitated the temporal and spatial resolution of calpain activation in situ. Accordingly, sensitive spectrin breakdown assays now are utilized to identify potential toxic side‐effects of compounds and to develop calpain inhibitors for a wide range of indications including stroke, cerebral vasospasm, and kidney failure.
Diverging diversity patterns of vascular plants and geometrid moths during forest regeneration on Mt Kilimanjaro, Tanzania
Authors: Axmacher Jan C. , Tünte Henry , Schrumpf Marion , Müller‐Hohenstein Klaus , Lyaruu Herbert V. M. , Fiedler Konrad 
Published: May 2004

AbstractAim  This study investigates diversity patterns of vascular plants and plant‐feeding geometrid moths during montane rain forest regeneration in relation to the biogeographical and historical conditions of Mt Kilimanjaro.Location  Investigations were undertaken on the south‐western slopes of Mt Kilimanjaro at altitudes between 2075 and 2265 m.Methods  Thirteen plots were selected for this study. Four of these were situated in the middle of large clearings (> 1000 m2), three in secondary forest, two in mature forest remnants surrounded by secondary forest and four plots within continuous closed mature forest. Vascular plant species were recorded in an area of 20 × 20 m2. Geometrid moths were attracted using lamps placed inside reflective gauze cylinders.Results  Ninety‐three species of vascular plants were recorded on the plots. Plant diversity increased in the course of forest regeneration from clearings and secondary forest to mature forest remnants and mature forest. This increase was visible in all vegetation strata as well as in the species number of Dicotyledoneae. The diversity of geometrid moths conversely decreased from early to late successional stages. A total of 2276 Geometridae representing 114 morphospecies were included in the study. Local values of Fisher's α varied from 10.3 to 18.3 on clearings and in secondary forest, whereas they remained below 8.0 in mature forest and mature forest remnants. There was a significant negative correlation between the diversity of Geometridae and the number of dicots, and of plant species in the shrub layer.Main conclusions  Contrary to an expected positive correlation between the diversity of vascular plants and herbivorous geometrid moths, diversity patterns of these two groups are strongly diverging due to biogeographical and ecological factors differently affecting the two groups. The increase in plant diversity can chiefly be explained with an increase in epiphyte diversity which is related to the occurrence of suitable habitats in extensive moss layers on huge Ocotea usambarensis (Engl.) trees in the mature forest. The low diversity of geometrid moths in these forests may be connected to the isolation and relatively young age of the montane rain forests on Mt Kilimanjaro. Hence only a small number of moth species adapted to the cool and perhumid conditions within moist mature forest have so far immigrated into these habitats, and time was insufficient for the evolution of many new species.
Assessing spatial variation in browsing history by means of fraying scars
Authors: Vila Bruno , Guibal Frédéric , Torre Franck , Martin Jean‐Louis 
Published: May 2004

AbstractAim  We used fraying scars to understand spatial variation in browsing history. Information on browsing history is an essential background in studies on the long‐term effect of deer browsing on the flora and fauna and of its variation in space.Location  We focused on two small neighbouring islands of Haida Gwaii (British Columbia, Canada), Reef Island and South‐Skedans Island, colonized by introduced black‐tailed deer (Odocoileus hemionus sitkensis).Methods  We searched for sites where trees with fraying scars were clustered. We studied the trees that deer selected (species, size) and the characteristics of scars (number, position, size). Using a cross‐dating procedure, we dated fraying scars with dendrochronology, obtaining an accurate estimate of the year the scar was formed.Results  On Reef Island, Thuja plicata was the tree species chosen for fraying. On South‐Skedans Island, where Thuja plicata is missing, deer chose Salix sp. and Alnus rubra. Deer chose only trees with a circumference of less than 50 cm. About two to three fraying scars were recorded per tree. All of them extended between 30–40 and 70–80 cm from the ground and were between 5 and 6 cm in width. On Reef Island, 95% of the scars were formed during the last 50 years. On South‐Skedans Island, 95% were formed over the last 10 years. Age distribution of scars showed a constant increase of the number of scars over time. It indicated that deer had colonized Reef Island 53 years prior to this study but were absent or rare on South‐Skedans Island until 13 years prior to this study.Main conclusions  These results indicate different colonization dates and thus different length of browsing histories for the islands studied and provide the historical background necessary to analyse the involvement of deer in the current differences in the flora and fauna observed between islands.
Seed removal by small mammals, birds and ants in semi‐arid Chile, and comparison with other systems
Authors: Kelt Douglas A. , Meserve Peter L. , Gutiérrez Julio R. 
Published: May 2004

AbstractAim  This study aims to evaluate the relative importance of birds, small mammals, and ants as seed predators at a semi‐arid site in northern Chile.Location  Northern Chile, in Parque Nacional Bosque Fray Jorge (30°41′ N, 71°40′ W, c. 80 m elevation).Methods  We studied the relative abilities of birds, small mammals, and ants to find and remove millet seeds either singly (i.e. background seed removal) or in bulk. Single seeds were set in shallow depressions in Plexiglas trays which were established in long and arbitrary transects, and were available either to birds (diurnally) or small mammals (nocturnally) or were covered by hardware cloth and therefore available only to ants. Bulk removal was evaluated with seeds in Petri dishes that also were established in long and arbitrary transects, and trays were either open diurnally (birds) or nocturnally (small mammals); a third set of trays was covered with hardware cloth cages to excluded vertebrates, and ants were given access to Petri dishes with twigs that were arranged across the edge of the dishes. All experiments lasted four days and nights, and trays and dishes were checked and replenished as needed in the morning and evening. In the former study vertebrate consumption was determined as the mean number of seeds removed from trays (within a given transect) minus the number removed from ant‐only trays. Because ants were rarely seen in vertebrate access Petri dishes, however, we did not correct consumption there. Treatments were compared using repeated measures mixed model analysis of variance. In addition to evaluating patterns within this community, we compared our results against those obtained in similar studies in various arid regions.Results  Diurnal seed consumption was significantly greater than nocturnal seed consumption, which in turn was significantly greater than consumption by ants. Diurnal consumption was highly seasonal, evidently corresponding to the seasonal arrival and departure of migratory birds. In general, South American sites exhibit much lower levels of seed predation than sites in the northern hemisphere, but removal at our site appears to be much greater and more strongly avian‐dominated than at other sites in South America. Our results are consistent with predictions based on a hypothesis relating precipitation to seed predictability.Main conclusions  Both birds and small mammals were much more important seed consumers at our site than elsewhere in South America, whereas ants have been relatively unimportant at all South American sites studied to date. Although the dominant seed consumers differ across sites, overall levels of seed removal appear similar in South America and Australia, and substantially lower than reported from sites in the northern hemisphere and Africa.