bluuebunny/crossref_metadata_2025_split huggingface dataset:
‘Crystal lattice engineering,’ an approach to engineer protein crystal contacts by creating intermolecular symmetry: Crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines
Authors: Yamada Hidenori , Tamada Taro , Kosaka Megumi , Miyata Kohei , Fujiki Shinya , Tano Masaru , Moriya Masayuki , Yamanishi Mamoru , Honjo Eijiro , Tada Hiroko , Ino Takeshi , Yamaguchi Hiroshi , Futami Junichiro , Seno Masaharu , Nomoto Takashi , Hirata Tomoko , Yoshimura Motonobu , Kuroki Ryota 
Published: June 2007

AbstractA protein crystal lattice consists of surface contact regions, where the interactions of specific groups play a key role in stabilizing the regular arrangement of the protein molecules. In an attempt to control protein incorporation in a crystal lattice, a leucine zipper‐like hydrophobic interface (comprising four leucine residues) was introduced into a helical region (helix 2) of the human pancreatic ribonuclease 1 (RNase 1) that was predicted to form a suitable crystallization interface. Although crystallization of wild‐type RNase 1 has not yet been reported, the RNase 1 mutant having four leucines (4L‐RNase 1) was successfully crystallized under several different conditions. The crystal structures were subsequently determined by X‐ray crystallography by molecular replacement using the structure of bovine RNase A. The overall structure of 4L‐RNase 1 is quite similar to that of the bovine RNase A, and the introduced leucine residues formed the designed crystal interface. To characterize the role of the introduced leucine residues in crystallization of RNase 1 further, the number of leucines was reduced to three or two (3L‐ and 2L‐RNase 1, respectively). Both mutants crystallized and a similar hydrophobic interface as in 4L‐RNase 1 was observed. A related approach to engineer crystal contacts at helix 3 of RNase 1 (N4L‐RNase 1) was also evaluated. N4L‐RNase 1 also successfully crystallized and formed the expected hydrophobic packing interface. These results suggest that appropriate introduction of a leucine zipper‐like hydrophobic interface can promote intermolecular symmetry for more efficient protein crystallization in crystal lattice engineering efforts.
Immune regulation by CD4+CD25+ T cells and interleukin‐10 in birch pollen‐allergic patients and non‐allergic controls
Authors: Thunberg S. , Akdis M. , Akdis C. A. , Grönneberg R. , Malmström V. , Trollmo C. , Van Hage M. , Gafvelin G. 
Published: June 2007

SummaryBackground
CD4+CD25+ regulatory T (Treg) cells and the cytokines IL‐10 or TGF‐β play key roles in the maintenance of T cell homeostasis and tolerance to infectious and non‐infectious antigens such as allergens.Objective
To investigate the regulation of immune responses to birch pollen allergen compared with influenza antigen by Treg cells obtained from birch pollen‐allergic patients and non‐allergic controls.Methods
Peripheral blood was collected from 10 birch pollen‐allergic patients and 10 non‐allergic healthy controls. CD4+CD25+ and CD4+CD25− cells isolated by magnetic‐activated cell sorting were co‐cultured and stimulated with birch pollen extract or influenza vaccine in the absence or presence of anti‐IL‐10 or soluble TGF‐βRII.Results
CD4+CD25+ cells from non‐allergic controls were able to suppress influenza antigen and birch pollen stimulated effector cell proliferation, whereas CD4+CD25+ cells from allergic patients suppressed influenza antigen‐, but not birch pollen‐stimulated proliferation. The production of Th1 cytokines, but not Th2 cytokines, was suppressed by CD4+CD25+ cells from both allergic patients and controls, upon stimulation with birch pollen extract. Neutralization of IL‐10 led to significantly increased production of IFN‐γ in cultures with CD4+CD25− T effector cells. In addition, six‐fold higher concentrations of TNF‐α were detected after neutralization of IL‐10 in both CD4+CD25− and CD4+CD25+ cell cultures from allergic patients and controls.Conclusion
We demonstrate that the allergen‐specific suppressive function of CD4+CD25+ cells from allergic patients is impaired compared with non‐allergic controls. Moreover, neutralization of IL‐10 enhances the production of TNF‐α, suggesting counter‐acting properties of IL‐10 and TNF‐α, where IL‐10 promotes tolerance and suppression by Treg cells and TNF‐α promotes inflammatory responses.
Overexpression of the phosphoprotein enriched in diabetes gene product (Ped/pea‐15) in women with polycystic ovary syndrome
Authors: Savastano Silvia , Orio Francesco , Palomba Stefano , Cascella Teresa , Manguso Francesco , Lupoli Gelsy Arianna , Formisano Pietro , Lombardi Gaetano , Colao Annamaria , Beguinot Francesco , Valentino Rossella 
Published: June 2007

SummaryObjective  To evaluate Ped/pea‐15 (phosphoprotein enriched in diabetes) expression in polycystic ovary syndrome (PCOS) women.Design and patients  Thirty PCOS women were studied and compared with other 30 age‐ and body mass index (BMI)‐matched women, considered as the control group. Both patients and controls were divided according to BMI. All subjects underwent endocrine and metabolic investigation and Ped/pea‐15 expression was evaluated by western blot analysis. Insulin resistance was assessed by HOMA model and insulin sensitivity index (ISI) composite.Results  Insulin resistance, evaluated by HOMA‐R and ISI composite, was significantly higher in PCOS women and in obese controls than in normal weight controls. Ped/pea‐15 expression (%) was higher in PCOS women than in controls (440·4 ± 220·7 vs. 163·0 ± 45·5; P < 0·001; range 145·5–987% and 97–281%, respectively), and was positively correlated with insulin, BMI, total testosterone, HOMA index, and family history (P < 0·001). In patients with PCOS univariate analysis of variance showed no effect of BMI variation (P = 0·13) on Ped/pea‐15 expression levels. On multiple linear regression analysis, the major determinants of Ped/pea‐15 overexpression were family history, insulin, and PCOS status independent of BMI.Conclusion  These preliminary data (1) highlight the overexpression of Ped/pea‐15 in PCOS compared to normal controls, independent of obesity; (2) suggest that Ped/pea‐15 overexpression might be an early component of the metabolic syndrome in PCOS; and (3) support the hypothesis that Ped/pea‐15 represents a possible useful tool to assess the presence of a genetic condition associated with insulin resistance in PCOS.
Molecular dynamics simulation of cationic complexation with natural organic matter
Authors: Kalinichev A. G. , Kirkpatrick R. J. 
Published: June 2007

SummaryMolecular computer modelling of natural organic matter (NOM) and its interactions with metal cations in aqueous solution is a highly effective tool for helping to understand and quantitatively predict the molecular mechanisms of metal‐NOM complexation. This paper presents the results of molecular dynamics (MD) computations of the interaction of NOM with dissolved Na+, Cs+, Mg2+ and Ca2+. They show that Na+ forms only very weak outer‐sphere complexes with NOM, whereas Cs+ interacts somewhat more strongly, but also mainly via outer‐sphere association. Mg2+ interacts little with NOM due to its strongly held hydration shell. Ca2+ has the strongest association with NOM and forms inner‐sphere complexes with NOM carboxylate groups. This last result supports the idea of supramolecular, Ca‐mediated NOM aggregation. Cation‐NOM binding occurs principally with carboxylate groups, and to a lesser extent with phenolic and other –R‐OH groups. The contributions of other NOM functional groups are minimal. The diffusional mobility of NOM‐bound cations is ∼20% (NOM‐Na+ outer‐sphere complex) to ∼95% (NOM‐Ca2+ inner‐sphere complex) less than in aqueous solutions without NOM. The MD simulation results are in good agreement with NMR spectroscopic measurements for Cs‐NOM solutions.
Enhancing rigour in qualitative health research: exploring subjectivity through Peshkin's I's
Authors: Bradbury‐Jones Caroline 
Published: June 2007

Abstract Title. Enhancing rigour in qualitative health research: exploring subjectivity through Peshkin's I's Aim.  This paper is a discussion of the use of a systematic approach to explore researcher subjectivity and how this enhanced the rigour of a qualitative study.Background.  The need for rigour in qualitative research is widely documented; the means by which it is enhanced are varied and numerous. Although most qualitative health researchers espouse the notion of being aware of their own subjectivity, the methods by which their self‐awareness is developed is seldom made explicit.Method.  This paper draws on the work of Peshkin from the discipline of education, who articulated the need for researchers to identify their subjectivity systematically throughout the course of their research by searching for their subjective I's. I share my experience of adopting this approach by using a reflexive journal as data. I recorded the journal as an integral part of a study in which I explored the meaning of empowerment for nursing students during the period 2005–2006.Findings.  This systematic approach to exploring my subjectivity revealed four subjective I's that had potential for influence throughout the entire study. I argue that cognisance of my subjective I's improved the trustworthiness of the research.Conclusions.  I offer this approach for consideration by healthcare researchers as a robust means of illuminating researcher subjectivity. This is not intended as a narcissistic process; it is one that is advocated for use as part of an audit trail as a means of enhancing the rigour of qualitative research.
Patients’ experiences of having chemotherapy in a day hospital setting
Authors: McIlfatrick Sonja , Sullivan Kate , McKenna Hugh , Parahoo Kader 
Published: June 2007

AbstractTitle. Patients’ experiences of having chemotherapy in a day hospital settingAim. This paper is a report of a study to explore patients’ experiences of having chemotherapy in a day hospital.Background. The nature of cancer care has changed dramatically in recent years with most patients receiving chemotherapy in a day hospital. Despite recognition of the need to explore patients’ experience of cancer treatment, little research has been undertaken in this specific area.Method. A qualitative approach was adopted with a convenience sample of 30 patients diagnosed with cancer and receiving chemotherapy in a day hospital. Data were collected from January 2002 to March 2003 using unstructured tape‐recorded interviews and analysed using a narrative framework.Findings. Participants viewed their experiences of chemotherapy treatment from the initial perspective of having to face their need to have chemotherapy. Their experiences in the day hospital had both positive and negative dimensions. Positive aspects related to maintaining a sense of normality and absence of the sick role, whilst negative aspects were related to the dehumanizing, factory‐like system in the day hospital. Organizational issues also influenced experiences, including the sense of comradeship with other patients. Participants indicated the need to remain positive about the future and to learn to ‘work around’ the treatment.Conclusion. More effective methods are needed to develop patients’ confidence and motivation to realize their self‐care potential, together with increased awareness of organizational influences on patient experiences. Nurses need to focus on the ‘here and now’ concerns of patients as opposed to a biomedical perspective relating to treatment regimes, survival and prognosis.
Life‐history traits are correlated with geographical distribution patterns of western European forest herb species
Authors: Van der Veken Sebastiaan , Bellemare Jesse , Verheyen Kris , Hermy Martin 
Published: June 2007

AbstractAim To investigate whether six plant life‐history traits that have been related to colonization ability at local scales are also related to the geographical range characteristics of 273 forest plant species.Location Continental western Europe, five countries in particular: France, Luxemburg, Belgium, the Netherlands and Germany. The region is situated between 42° and 55°N and 5°W and 15°E and has a summed total area of 971,404 km2.Methods Distribution data were compiled from five national data bases and converted to a 10′ grid. Life‐history traits were taken from existing compilations of autecological information of European species. The spatial arrangement of occupied grid cells was investigated using Ripley'sK. Cross‐species correlations and phylogenetically independent contrasts were used to investigate the relationships between plant life‐history traits and three range characteristics: area of occupancy, latitudinal extent and centroid latitude.Results For herbaceous species, seed dispersal mode, seed production and seed bank longevity exhibited significant associations with geographical range characteristics, including area of occupancy. Woody plant species exhibited fewer significant associations, although maximum height was positively associated with range centroid latitude within the study area. Furthermore, the ranges of species with limited dispersal ability were found to be more clustered than the ranges of species with morphological adaptations for long‐distance seed dispersal.Main conclusions For western European forest plant species, life‐history traits that are related to colonization ability at local scales are associated with variation in large‐scale geographical range characteristics. This finding implies that the distributions of some forest plant species in the study area may be limited by seed dispersal and colonization capacity rather than climate or other environmental factors.
Candidate genes and thermal phenotypes: identifying ecologically important genetic variation for thermotolerance in the Australian Drosophila melanogaster cline
Authors: RAKO LEA , BLACKET MARK J. , McKECHNIE STEPHEN W. , HOFFMANN ARY A. 
Published: June 2007

AbstractClinal variation in traits often reflects climatic adaptation; in Drosophila melanogaster clinal variation provides an opportunity to link variation in chromosomal inversions, microsatellite loci and various candidate genes to adaptive variation in traits. We undertook association studies with crosses from a single population of D. melanogaster from eastern Australia to investigate the association between genetic markers and traits showing clinal variation. By genotyping parents and phenotyping offspring, we minimized genotyping costs but had the power to detect association between markers and quantitative traits. Consistent with prior studies, we found strong associations between the clinal chromosomal inversion In(3R)Payne and markers within it, as well as among these markers. We also found an association between In(3L)Payne and one marker located within this inversion. Of the five predicted associations between markers and traits, four were detected (increased heat, decreased cold resistance and body size with the heat shock gene hsr‐omega S, increased cold resistance with the inversion In(3L)Payne), while one was not detected (heat resistance and the heat shock gene hsp68). In a set of eight exploratory tests, we detected one positive association (between hsp23a and heat resistance) but no associations of heat resistance with alleles at the hsp26, hsp83, Desat 2, α‐Gpdh, hsp70 loci, while cold resistance was not associated with Frost and Dca loci. These results confirm interactions between hsr‐omega and thermal resistance, as well as between In(3L)Payne and cold resistance, but do not provide evidence for associations between thermal responses and alleles at other clinally varying marker genes.
Living on the edge: demographic and phylogeographical patterns in the woodlouse‐hunter spider Dysdera lancerotensis Simon, 1907 on the eastern volcanic ridge of the Canary Islands
Authors: BIDEGARAY‐BATISTA LETICIA , MACÍAS‐HERNÁNDEZ NURIA , OROMÍ PEDRO , ARNEDO MIQUEL A. 
Published: June 2007

AbstractThe Eastern Canary Islands are the emerged tips of a continuous volcanic ridge running parallel to the northeastern African coast, originated by episodic volcanic eruptions that can be traced back to the Miocene and that, following a major period of quiescence and erosion, continued from the Pliocene to the present day. The islands have been periodically connected by eustatic sea‐level changes resulting from Pleistocene glacial cycles. The ground‐dwelling spider Dysdera lancerotensis Simon, 1907 occurs along the entire ridge, except on recent barren lavas and sand dunes, and is therefore an ideal model for studying the effect of episodic geological processes on terrestrial organisms. Nested clade and population genetic analyses using 39 haplotypes from 605 base pairs of mitochondrial DNA cytochrome c oxidase I sequence data, along with phylogenetic analyses including two additional mitochondrial genes, uncover complex phylogeographical and demographic patterns. Our results indicate that D. lancerotensis colonized the ridge from north to south, in contrast to what had been expected given the SSW‐NNE trend of volcanism and to what had been reported for other terrestrial arthropods. The occurrence of several episodes of extinction, recolonization and expansion are hypothesized for this species, and areas that act as refugia during volcanic cycles are identified. Relaxed molecular clock methods reveal divergence times between main haplotype lineages that suggest an older origin of the northern islets than anticipated based on geological evidence. This study supports the key role of volcanism in shaping the distribution of terrestrial organisms on oceanic islands and generates phylogeographical predictions that warrant further research into other terrestrial endemisms of this fascinating region.
Variable expression of the 235 kDa rhoptry protein of Plasmodium yoelii mediate host cell adaptation and immune evasion
Authors: Iyer Jayasree Kaveri , Amaladoss Anburaj , Ganesan Saraswathy , Preiser Peter Rainer 
Published: June 2007

SummaryThe severity of infections caused by the malaria parasite Plasmodium is in part due to the rapid multiplication cycles in the blood of an infected individual. A fundamental step in this phenomenon is the invasion of selected erythrocytes of the host by the parasite. The py235 rhoptry protein multigene family of the rodent malaria parasite Plasmodium yoelii has been implicated in mediating host cell selection during erythrocyte invasion and virulence. Here we show using quantitative real‐time polymerase chain reaction and Western blot analysis that variations in the amounts of py235 may be a mechanism that the parasite uses to define its host cell repertoire. High levels of py235 expression leads to a wider range of erythrocytes invaded and therefore increased virulence. In contrast, to evade PY235‐specific immunity, the parasite downregulates py235 thereby decreasing the host cell repertoire and virulence. These results demonstrate a new mechanism where variations in the amounts of parasite ligand define the parasite host cell repertoire and enable it to evade host immunity.
RNase E‐dependent processing stabilizes MicX, a Vibrio cholerae sRNA
Authors: Davis Brigid M. , Waldor Matthew K. 
Published: June 2007

SummaryIn Vibrio cholerae, bioinformatic approaches have been used to predict the locations of numerous small RNA (sRNA)‐encoding genes, but biological roles have been determined for very few. Here, we describe the expression, processing and biological role of an sRNA (previously known as A10) that was identified through such analyses. We have renamed this sRNA MicX as, like the Escherichia coli sRNAs MicA, MicC and MicF, it regulates expression of an outer membrane protein (OMP). MicX appears to be a direct negative regulator of vc0972, which encodes an uncharacterized OMP, and vc0620, which encodes the periplasmic component of a peptide ABC transporter. Hfq is apparently not required for MicX's interactions with and regulation of these targets. The sequence encoding MicX overlaps with vca0943; however, primary transcripts of MicX are processed in an RNase E‐ and Hfq‐dependent fashion to a shorter, still active and much more stable form consisting largely of the vca0943 3′ untranslated region. Our data suggest that processing of MicX enhances its effectiveness, and that sRNA cleavage is not simply a means to sRNA inactivation and clearance.
Insights into the complex regulation of rpoS in Borrelia burgdorferi
Authors: Burtnick Mary N. , Downey Jennifer S. , Brett Paul J. , Boylan Julie A. , Frye Jonathan G. , Hoover Timothy R. , Gherardini Frank C. 
Published: June 2007

SummaryCo‐ordinated regulation of gene expression is required for the transmission and survival of Borrelia burgdorferi in different hosts. The sigma factor RpoS (σS), as regulated by RpoN (σ54), has been shown to regulate key virulence factors (e.g. OspC) required for these processes. As important, multiple signals (e.g. temperature, pH, cell density, oxygen) have been shown to increase the expression of σS‐dependent genes; however, little is known about the signal transduction mechanisms that modulate the expression of rpoS. In this report we show that: (i) rpoS has a σ54‐dependent promoter that requires Rrp2 to activate transcription; (ii) Rrp2Δ123, a constitutively active form of Rrp2, activated σ54‐dependent transcription of rpoS/P‐lacZ reporter constructs in Escherichia coli; (iii) quantitative reverse transcription polymerase chain reaction (QRT‐PCR) experiments with reporter cat constructs in B. burgdorferi indicated that Rrp2 activated transcription of rpoS in an enhancer‐independent fashion; and finally, (iv) rpoN is required for cell density‐ and temperature‐dependent expression of rpoS in B. burgdorferi, but histidine kinase Hk2, encoded by the gene immediately upstream of rrp2, is not essential. Based on these findings, a model for regulation of rpoS has been proposed which provides mechanisms for multiple signalling pathways to modulate the expression of the σS regulon in B. burgdorferi.
Symplastic connection is required for bud outgrowth following dormancy in potato (Solanum tuberosum L.) tubers
Authors: VIOLA ROBERTO , PELLOUX JÉRÔME , VAN DER PLOEG ANKE , GILLESPIE TRUDI , MARQUIS NICOLA , ROBERTS ALISON G. , HANCOCK ROBERT D. 
Published: June 2007

ABSTRACTTo gain greater insight into the mechanism of dormancy release in the potato tuber, an investigation into physiological and biochemical changes in tuber and bud tissues during the transition from bud dormancy (immediately after harvest) to active bud growth was undertaken. Within the tuber, a rapid shift from storage metabolism (starch synthesis) to reserve mobilization within days of detachment from the mother plant suggested transition from sink to source. Over the same period, a shift in the pattern of [U‐14C]sucrose uptake by tuber discs from diffuse to punctate accumulation was consistent with a transition from phloem unloading to phloem loading within the tuber parenchyma. There were no gross differences in metabolic capacity between resting and actively growing tuber buds as determined by [U‐14C]glucose labelling. However, marked differences in metabolite pools were observed with large increases in starch and sucrose, and the accumulation of several organic acids in growing buds. Carboxyfluorescein labelling of tubers clearly demonstrated strong symplastic connection in actively growing buds and symplastic isolation in resting buds. It is proposed that potato tubers rapidly undergo metabolic transitions consistent with bud outgrowth; however, growth is initially prevented by substrate limitation mediated via symplastic isolation.