bluuebunny/crossref_metadata_2025_split huggingface dataset:
Redox‐related conformational changes in Rhodobacter capsulatus cytochrome c2
Authors: Zhao Dezheng , Hutton Harold M. , Gooley Paul R. , Mackenzie Neil E. , Cusanovich Michael A. 
Published: February 2009

AbstractWEFT‐NOESY and transfer WEFT‐NOESY NMR spectra were used to determine the heme proton assignments for Rhodobacter capsulatus ferricytochrome c2. The Fermi contact and pseudo‐contact contributions to the paramagnetic effect of the unpaired electron in the oxidized state were evaluated for the heme and ligand protons. The chemical shift assignments for the 1H and 15N NMR spectra were obtained by a combination of 1H‐1H and 1H‐15N two‐dimensional NMR spectroscopy. The short‐range nuclear Overhauser effect (NOE) data are consistent with the view that the secondary structure for the oxidized state of this protein closely approximates that of the reduced form, but with redox‐related conformational changes between the two redox states. To understand the decrease in stability of the oxidized state of this cytochrome c2 compared to the reduced form, the structural difference between the two redox states were analyzed by the differences in the NOE intensities, pseudo‐contact shifts and the hydrogen‐deuterium exchange rates of the amide protons. We find that the major difference between redox states, although subtle, involve heme protein interactions, orientation of the heme ligands, differences in hydrogen bond networks and, possible alterations in the position of some internal water molecules. Thus, it appears that the general destabilization of cytochrome c2, which occurs on oxidation, is consistent with the alteration of hydrogen bonds that result in changes in the internal dynamics of the protein.
Change in dimerization mode by removal of a single unsatisfied polar residue located at the interface
Authors: Pokkuluri P. R. , Cai X. , Johnson G. , Stevens F. J. , Schiffer M. 
Published: February 2009

AbstractThe importance of unsatisfied hydrogen bonding potential on protein‐protein interaction was studied. Two alternate modes of dimerization (conventional and flipped form) of an immunoglobulin light chain variable domain (VL) were previously identified. In the flipped form, interface residue Gln89 would have an unsatisfied hydrogen bonding potential. Removal of this Gln should render the flipped dimer as the more favorable quaternary form. High resolution crystallographic studies of the Q89A and Q89L mutants show, as we predicted, that these proteins indeed form flipped dimers with very similar interfaces. A small cavity is present in the Q89A mutant that is reflected in the ∼100 times lower association constant than found for the Q89L mutant. The association constant of Q89A and Q89L proteins (4 × 106 M−1 and > 108 M−1) are 10‐ and 1,000‐fold higher than that of the wild‐type protein that forms conventional dimers clearly showing the energetic reasons for the flipped dimer formation.
The route to development of myelodysplastic syndrome/acute myeloid leukaemia in Shwachman‐Diamond syndrome: the role of ageing, karyotype instability, and acquired chromosome anomalies
Authors: Maserati Emanuela , Pressato Barbara , Valli Roberto , Minelli Antonella , Sainati Laura , Patitucci Francesco , Marletta Cristina , Mastronuzzi Angela , Poli Furio , Lo Curto Francesco , Locatelli Franco , Danesino Cesare , Pasquali Francesco 
Published: February 2009

SummaryAn investigation of 22 new patients with Shwachman‐Diamond syndrome (SDS) and the follow‐up of 14 previously reported cases showed that (i) clonal chromosome changes of chromosomes 7 and 20 were present in the bone marrow (BM) of 16 out of 36 cases, but if non‐clonal changes were taken into account, the frequency of anomalies affecting these chromosomes was 20/36: a specific SDS karyotype instability was thus confirmed; (ii) the recurrent isochromosome i(7)(q10) did not include short arm material, whereas it retained two arrays of D7Z1 alphoid sequences; (iii) the deletion del(20)(q11) involved the minimal region of deletion typical of myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML); (iv) only one patient developed MDS, during the rapid expansion of a BM clone with a chromosome 7 carrying additional material on the short arms; (v) the acquisition of BM clonal chromosome anomalies was age‐related. We conclude that karyotype instability is part of the natural history of SDS through a specific mutator effect, linked to lacking SBDS protein, with consequent clonal anomalies of chromosomes 7 and 20 in BM, which may eventually promote MDS/AML with the patients’ ageing.
Unrelated donor and HLA‐identical sibling haematopoietic stem cell transplantation cure chronic granulomatous disease with good long‐term outcome and growth
Authors: Soncini Elena , Slatter Mary A. , Jones Laura B. K. R. , Hughes Stephen , Hodges Stephen , Flood Terence J. , Barge Dawn , Spickett Gavin P. , Jackson Graham H. , Collin Matthew P. , Abinun Mario , Cant Andrew J. , Gennery Andrew R. 
Published: February 2009

SummaryChronic granulomatous disease (CGD) causes recurrent infection and inflammatory disease. Despite antimicrobial prophylaxis, patients experience frequent hospitalisations and 50% mortality by 30 years. Haematopoietic stem cell transplantation (HSCT) can cure CGD with resolution of infection and colitis. This study reports the survival and long‐term outcome in 20 conditioned patients treated between 1998 and 2007, using 10 matched sibling (MSD) and 10 unrelated donors (URD). Age at HSCT, graft‐versus‐host disease (GvHD), growth, and outcome were analysed. Fourteen had ≥1 invasive infection, 10 had colitis and seven had growth failure before HSCT. Median age at transplantation was 75 months (range 15 months–21 years). Eighteen (90%) were alive 4–117 months (median 61) after HSCT with normal neutrophil function. Two died from disseminated fungal infection. Two experienced significant chronic GvHD, with continuing sequelae in 1. Colitis resolved within 8 weeks of HSCT. Mean weight and height for age Z scores on recovery from HSCT rose significantly (P < 0·001). HSCT with MSD or URD gave excellent engraftment and survival, remission of colitis and catch‐up growth, with low incidence of significant GvHD. Transplant‐associated complications were restricted to those with pre‐existing infection or inflammation, supporting the argument for early HSCT for more CGD patients with a well matched donor.
Spatial and temporal dynamics of habitat selection across canopy gradients generates patterns of species richness and composition in aquatic beetles
Authors: BINCKLEY CHRISTOPHER A. , RESETARITS WILLIAM J. 
Published: February 2009

Abstract1. Colonisation is a critical ecological process influencing both population and community level dynamics by connecting spatially discrete habitat patches. How communities respond to both natural and anthropogenic disturbances, furthermore, requires a basic understanding of how any environmental change modifies colonisation rates. For example, disturbance‐induced shifts in the quantity of forest cover surrounding aquatic habitats have been associated with the distribution and abundance of numerous aquatic taxa. However, the mechanisms generating these broad and repeatable field patterns are unclear.2. Such patterns of diversity could result from differential spatial mortality post colonisation, or from colonisation alone if species select sites non‐randomly along canopy coverage gradients. We examined the colonisation/oviposition dynamics of aquatic beetles in experimental ponds placed under both open and closed forest canopies.3. Canopy coverage imposed a substantial behavioural filter on the colonisation and reproduction of aquatic beetles representing multiple trophic levels, and resulted in significantly higher abundance, richness, and oviposition activity in open canopy ponds. These patterns strengthened overtime; although early in the experiment, the most abundant beetle had similar abundance in open and closed ponds. However, its abundance subsequently declined and then most other species heavily colonised open canopy ponds.4. The primary response of many aquatic species to disturbances that generate canopy coverage gradients surrounding aquatic ecosystems is behavioural. The magnitude of the colonisation responses reported here rivals, if not exceeds, those produced by predators, suggesting that aquatic landscapes are behaviourally assessed and partitioned across multiple environmental gradients. The community level structure produced solely by selective colonisation, is predicted to strongly modify how patch area and isolation affect colonisation rates and the degree to which communities are linked by the flux of individuals and species.
Species and site differences in Neotropical army ant emigration behaviour
Authors: O’DONNELL SEAN , LATTKE JOHN , POWELL SCOTT , KASPARI MICHAEL 
Published: February 2009

Abstract1. Along with large wingless queens and group foraging raids, periodic colony movements or emigrations are a defining feature of army ant behaviour. Emigrations are important because they regulate spacing among colonies, and provide access to new foraging sites.2. Raid and emigration activity of army ant communities was measured at four Neotropical sites using a standardised sampling protocol. Sampling of emigration activity was carried out throughout the diel cycle.3. Both raid and emigration activity occurred throughout the day and night. Emigration activity was highest under cover of darkness, but sites and species differed in the diel timing of emigrations. These site and species differences have implications for the evolution of emigration behaviour, as well as for the community ecology of army ants.
Biodiversity of Belgian groundwater fauna in relation to environmental conditions
Authors: MARTIN PATRICK , DE BROYER CLAUDE , FIERS FRANK , MICHEL GEORGES , SABLON ROSE , WOUTERS KAREL 
Published: February 2009

Summary1. The Pleistocene glaciations during the Quaternary appear to have resulted in an impoverished groundwater fauna in northern Europe. Re‐colonisation may have occurred either through long‐distance dispersal from unglaciated southern areas or from local refugia.2. The Belgian groundwater fauna was sampled at multiple sites, and its habitats characterised, to assess whether the composition of present‐day stygobiotic assemblages can be attributed to either of these mechanisms.3. A total of 202 sampling sites were selected in four hydrogeographic units of the Meuse River catchment. Sites were equally divided among the saturated and unsaturated zones of fractured aquifers (karst) and within the hyporheic and phreatic zones of porous aquifers. Seventeen environmental parameters were determined in parallel.4. More than 140 species were recorded, including representatives of the Amphipoda, Cladocera, Copepoda, Hydrachnidia, Isopoda, Oligochaeta, Ostracoda, Mollusca, Syncarida and Nematoda. Thirty stygobiont species were identified, of which 10 species were new to the Belgian fauna, raising the total number of stygobiotic species in Belgium to 41.5. The frequency of occurrences of stygobiotic species was always low, with 37% of the sampled sites lacking stygobionts. A few species were exclusive to one hydrological zone, although no statistically significant differences were detected in species richness at any of the four hierarchial levels considered (Meuse catchment = region, hydrogeographic units, aquifer type and hydrological zone).6. Overall, results suggest that the stygobiotic fauna of Belgium is species‐poor and mostly comprises widely distributed species with broad ecological tolerances. This supports the view that eurytopic species re‐colonised the area by long‐distance dispersal from refugia in southern Europe. The virtual absence of endemic species further suggests that the scenario of an ancient fauna that survived in local refugia is of minor importance.
Abundance and production of bacteria, and relationship to phytoplankton production, in a large tropical lake (Lake Tanganyika)
Authors: STENUITE STEPHANE , PIRLOT SAMUEL , TARBE ANNE‐LAURE , SARMENTO HUGO , LECOMTE MÉLANIE , THILL SOPHIE , LEPORCQ BRUNO , SINYINZA DANNY , DESCY JEAN‐PIERRE , SERVAIS PIERRE 
Published: February 2009

Summary1. Abundance and bacterial production (BP) of heterotrophic bacteria (HBact) were measured in the north and south basins of Lake Tanganyika, East Africa, during seasonal sampling series between 2002 and 2007. The major objective of the study was to assess whether BP can supplement phytoplankton particulate primary production (particulate PP) in the pelagic waters, and whether BP and particulate PP are related in this large lake. HBact were enumerated in the 0–100 m surface layer by epifluorescence microscopy and flow cytometry; BP was quantified using3H‐thymidine incorporation, usually in three mixolimnion layers (0–40, 40–60 and 60–100 m).2. Flow cytometry allowed three subpopulations to be distinguished: low nucleic acid content bacteria (LNA), high nucleic acid content bacteria (HNA) andSynechococcus‐like picocyanobacteria (PCya). The proportion of HNA was on average 67% of total bacterial abundance, and tended to increase with depth. HBact abundance was between 1.2 × 105and 4.8 × 106 cells mL−1, and was maximal in the 0–40 m layer (i.e. roughly, the euphotic layer). Using a single conversion factor of 15 fg C cell−1, estimated from biovolume measurements, average HBact biomass (integrated over a 100‐m water column depth) was 1.89 ± 1.05 g C m−2.3. Significant differences in BP appeared between seasons, especially in the south basin. The range of BP integrated over the 0–100 m layer was 93–735 mg C m−2 day−1, and overlapped with the range of particulate PP (150–1687 mg C m−2 day−1) measured in the same period of time at the same sites.4. Depth‐integrated BP was significantly correlated to particulate PP and chlorophyll‐a, and BP in the euphotic layer was on average 25% of PP.5. These results suggest that HBact contribute substantially to the particulate organic carbon available to consumers in Lake Tanganyika, and that BP may be sustained by phytoplankton‐derived organic carbon in the pelagic waters.
Nitrogen effects on net ecosystem carbon exchange in a temperate steppe
Authors: NIU SHULI , WU MINGYU , HAN YI , XIA JIANGYANG , ZHANG ZHE , YANG HAIJUN , WAN SHIQIANG 
Published: February 2009

AbstractIt has widely been documented that nitrogen (N) enrichment stimulates plant growth and net primary production. However, there is still dispute on how N addition affects net ecosystem CO2 exchange (NEE), which represents the balance between ecosystem carbon (C) uptake and release. We conducted an experimental study to examine effects of N addition on NEE in a temperate steppe in northern China from 2005 to 2008. N was added at a rate of 10 g N m−2 yr−1 with NH4NO3 alone or in combination with phosphorous (P, 5 g P2O5 m−2 yr−1) in both clipped and unclipped plots. Over the 4 years, N addition significantly stimulated growing‐season NEE, on average, by 27%. Neither the main effects of P addition or clipping nor their interactions with N addition were statistically significant on NEE in any of the 4 years. However, the magnitude of N stimulation on NEE declined over time. N addition significantly increased NEE by 60% in 2005 and 21% in 2006, but its effect was not significant in 2007 and 2008. N‐induced shift in species composition was primarily responsible for the declined N stimulation over time. The gradually increasing coverage of the upper canopy species (Stipa krylovii) and standing litter accumulation induced light limitation on the lower canopy species (Artemisia frigida). Thus, N‐induced shifts in plant species composition strongly regulated the direct effects of N addition on C sequestration in the temperate steppe.
Arctic alpine vegetation change over 20 years
Authors: WILSON SCOTT D. , NILSSON CHRISTER 
Published: February 2009

AbstractRecent arctic warming experiments have recorded significant vegetation responses, typically an increase in shrub cover and a loss of species richness. We report similar changes in vegetation along an arctic mountainside in northern Sweden over 20 years. During this time mean annual temperature increased by 2.0 °C, and growing season temperature by 2.3 °C. Growing season length increased by 28% at the bottom of our study area, in birch forest, and by 175% on the mountaintop. Neither total vegetation cover nor the cover of bare ground changed. One common dwarf shrub, Empetrum hermaphroditum, and two common forbs, Viola biflora and Geranium sylvaticum, increased in abundance over time, but no common species moved up the gradient. Species richness declined significantly over time, with an average loss of two species per 50 cm × 100 cm plot. The richness of herbaceous species at intermediate altitudes decreased significantly with increasing shrub cover. In spite of large changes in temperature, the type and magnitude of vegetation change along this mountainside were relatively modest and consistent with those from wide‐spread warming experiments.
Potential effects of elevated atmospheric carbon dioxide on benthic autotrophs and consumers in stream ecosystems: a test using experimental stream mesocosms
Authors: HARGRAVE CHAD W. , GARY KAITLEN P. , ROSADO SAMIR K. 
Published: February 2009

AbstractElevated atmospheric carbon dioxide (eCO2) has been shown to have a variety of ecosystem‐level effects in terrestrial systems, but few studies have examined how eCO2 might affect aquatic habitats. This limits broad generalizations about the effects of a changing climate across biomes. To broaden this generalization, we used free air CO2 enrichment to compare effects of eCO2 (i.e., double ambient ∼720 ppm) relative to ambient CO2 (aCO2∼360 ppm) on several ecosystem properties and functions in large, outdoor, experimental mesocosms that mimicked shallow sand‐bottom prairie streams. In general, we showed that eCO2 had strong bottom‐up effects on stream autotrophs, which moved through the food web and indirectly affected consumer trophic levels. These general effects were likely mediated by differential CO2 limitation between the eCO2 and aCO2 treatments. For example, we found that eCO2 decreased water‐column pH and increased dissolved CO2 in the mesocosms, reducing CO2‐limitation at times of intense primary production (PP). At these times, PP of benthic algae was about two times greater in the eCO2 treatment than aCO2 treatment. Elevated PP enhanced the rate of carbon assimilation relative to nutrient uptake, which reduced algae quality in the eCO2 treatment. We predicted that reduced algae quality would negatively affect benthic invertebrates. However, density, biomass and average individual size of benthic invertebrates increased in the eCO2 treatment relative to aCO2 treatment. This suggested that total PP was a more important regulator of secondary production than food quality in our experiment. This study broadens generalizations about ecosystem‐level effects of a changing climate by providing some of the first evidence that the global increase in atmospheric CO2 might affect autotrophs and consumers in small stream ecosystems throughout the southern Great Plains and Gulf Coastal slope of North America.
Endosomal processing for antigen presentation mediated by CD1 and Class I major histocompatibility complex: roads to display or destruction
Authors: Boes Marianne , Stoppelenburg Arie J. , Sillé Fenna C. M. 
Published: February 2009

SummaryThe presentation of antigen in a form that can be recognized by T lymphocytes of the immune system requires antigen processing and association of antigen‐derived fragments with molecules encoded by the major histocompatibility complex (MHC) locus or by the CD1 locus. Much emphasis on antigen processing and presentation in the last decades has focused on what we consider ‘conventional routes’ of antigen processing and presentation, whereby extracellular antigens are processed for presentation via Class II MHC complexes and cytosolic antigens are presented as peptide–Class I MHC complexes. We here highlight two other pathways in myeloid dendritic cells, those of lipid antigen presentation in association with CD1 and of peptide cross‐presentation via Class I MHC complexes. Some pathogens evade immune recognition through inhibition of antigen presentation of phagosomal origin. Deviations in endosomal antigen processing and presentation are also seen in individuals suffering from glycosphingolipid lysosomal lipid storage diseases. We summarize recent developments in the endosomal antigen processing and presentation pathway, for display as lipid–CD1 complexes to natural killer T cells and as peptide–Class I MHC complexes to CD8 T cells.
T‐cell reconstitution without T‐cell immunopathology in two models of T‐cell‐mediated tissue destruction
Authors: Penaloza‐MacMaster Pablo , Masopust David , Ahmed Rafi 
Published: February 2009

SummaryAntigen‐specific T cells play a pivotal role in adaptive immune responses. However, they also contribute to the progression of a variety of diseases including autoimmune disorders, graft rejection and graft‐versus‐host disease (GVHD). Non‐specific immune‐ablation treatments compromise the ability of the host to respond to infection, whereas the selective removal of epitope‐specific T cells could theoretically ameliorate T‐cell‐mediated pathology while preserving the rest of the host immune function. In this study we investigated whether it is possible to destroy specific unwanted antigen‐specific T cells by incubating polyclonal T‐cell populations with major histocompatibility complex (MHC) tetramers that are conjugated to the ribosomal‐inactivating toxin, saporin. This strategy resulted in a dramatic reduction in the number of targeted antigen (Ag)‐specific CD8 T cells with no observable bystander toxicity in vitro. Moreover, in a model of transferable T‐cell‐dependent neurological disease induced by intracerebral (i.c.) lymphocytic choriomeningitis virus (LCMV) infection, the targeted killing of LCMV‐specific CD8 T cells extended the survival of mice or fully prevented their death, depending on the dose of cells transferred. In addition, the tetramer– saporin conjugate also reduced liver damage in a model of donor T‐cell‐mediated hepatic destruction. These data provide a proof of principle that MHC tetramers could be exploited for the elimination or clinical manipulation of T‐cell responses by linking effector molecules (a toxin in this case) to MHC tetramers. Also, the results suggest that it may be feasible to remodel T‐cell responses, especially in immunocompromised hosts who receive adoptive cell transfers with many potential alloreactive cells.