bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel disulfide engineering in human carbonic anhydrase II using the PAIRWISE side‐chain geometry database
Authors: Burton Randall E. , Oas Terrence G. , Fterke Carol A. , Hunt Jennifer A. 
Published: October 2010

AbstractAn analysis of the pairwise side‐chain packing geometries of cysteine residues observed in high‐resolution protein crystal structures indicates that cysteine pairs have pronounced orientational preferences due to the geometric constraints of disulfide bond formation. A potential function was generated from these observations and used to evaluate models for novel disulfide bonds in human carbonic anhydrase II (HCAII). Three double‐cysteine variants of HCAII were purified and the effective concentrations of their thiol groups were determined by titrations with glutathione and dithiothreitol. The effects of the cysteine mutations on the native state structure and stability were characterized by circular dichroism, enzymatic activity, sulfonamide binding, and guanidine hydrochloride titration. These analyses indicate that the PAIRWISE potential is a good predictor of the strength of the disulfide bond itself, but the overall structural and thermodynamic effects on the protein are complicated by additional factors. In particular, the effects of cysteine substitutions on the native state and the stabilization of compact nonnative states by the disulfide can override any stabilizing effect of the cross‐link.
Chemical denaturation and elevated folding temperatures are required for wild‐type activity and stability of recombinant Methanococcus jannaschii 20S proteasome
Authors: Frankenberg Rob J. , Hsu Tina S. , Yakota Hisao , Kim Rosalind , Clark Douglas S. 
Published: October 2010

AbstractThe 20S proteasome from the extreme thermophile Methanococcus jannaschii (Mj) was purified and sequenced to facilitate production of the recombinant proteasome in E. coli. The recombinant proteasome remained in solution at a purity level of 80–85% (according to SDS PAGE) following incubation of cell lysates at 70°C. Temperature–activity profiles indicated that the temperature optima of the wild‐type and recombinant enzymes differed substantially, with optimal activities occurring at 119°C and 95°C, respectively. To ameliorate this discrepancy, two recombinant enzyme preparations were produced, each of which included denaturation of the proteasome by 4 M urea followed by high‐temperature (85°C) dialysis. The wild‐type temperature optimum was restored, but only if proteasome subunits were denatured and refolded prior to assembly (a preparation designated as α & β). In contrast, when proteasome assembly preceded denaturation (designated α + β) the optimum temperature was raised to a lesser degree. Moreover, the α & β and α + β preparations had apparent thermal half‐lives at 114°C of 54.2 and 26.2 min, respectively, and the thermostability of the less stable enzyme was more sensitive to a reduction in pH. Attainment of wild‐type activity and stability thus required the proper folding of both the α‐ and β‐subunits prior to proteasome assembly. Consistent with this behavior, dual‐scanning calorimetry (DSC) measurements revealed differences in the reassembly efficiency of the two proteasome preparations. The ability to produce structural conformers with dramatically different thermal optima and thermostabilities may facilitate the determination of molecular forces and structural motifs responsible for enzyme thermostablity and high‐temperature activity.
Aberrant mobility phenomena of the DNA repair protein XPA
Authors: Iakoucheva Lilia M. , Kimzey Amy L. , Masselon Christophe D. , Smith Richard D. , Dunker A. Keith , Ackerman Eric J. 
Published: October 2010

AbstractThe DNA repair protein XPA recognizes a wide variety of bulky lesions and interacts with several other proteins during nucleotide excision repair. We recently identified regions of intrinsic order and disorder in full lengthXenopusXPA (xXPA) protein using an experimental approach that combined time‐resolved trypsin proteolysis and electrospray ionization interface coupled to a Fourier transform ion cyclotron resonance (ESI‐FTICR) mass spectrometry (MS). MS data were consistent with the interpretation that xXPA contains no post‐translational modifications. Here we characterize the discrepancy between the calculated molecular weight (31 kDa) for xXPA and its apparent molecular weight on SDS‐PAGE (multiple bands from ∼40–45 kDa) and gel filtration chromatography (∼92 kDa), as well as the consequences of DNA binding on its anomalous mobility. Iodoacetamide treatment of xXPA prior to SDS‐PAGE yielded a single 42‐kDa band, showing that covalent modification of Cys did not correct aberrant mobility. Determination of sulfhydryl content in xXPA with Ellman's reagent revealed that all nine Cys in active protein are reduced. Unexpectedly, structural constraints induced by intramolecular glutaraldehyde crosslinks in xXPA produced a ∼32‐kDa monomer in closer agreement with its calculated molecular weight. To investigate whether binding to DNA alters xXPA's anomalous migration, we used gel filtration chromatography. For the first time, we purified stable complexes of xXPA and DNA ± cisplatin ± mismatches. xXPA showed at least 10‐fold higher affinity for cisplatin DNA ± mismatches compared to undamaged DNA ± mismatches. In all cases, DNA binding did not correct xXPA's anomalous migration. To test predictions that a Glu‐rich region (EEEEAEE) and/or disordered N‐ and C‐terminal domains were responsible for xXPA's aberrant mobility, the molecular weights of partial proteolytic fragments from ∼5 to 25 kDa separated by reverse‐phase HPLC and precisely determined by ESI‐FTICR MS were correlated with their migration on SDS‐PAGE. Every partial tryptic fragment analyzed within this size range exhibited 10%–50% larger molecular weights than expected. Thus, both the disordered domains and the Glu‐rich region in xXPA are primarily responsible for the aberrant mobility phenomena.
Dopamine release in ventral striatum during Iowa Gambling Task performance is associated with increased excitement levels in pathological gambling
Authors: Linnet Jakob , Møller Arne , Peterson Ericka , Gjedde Albert , Doudet Doris 
Published: September 2010

ABSTRACTAims  Gambling excitement is believed to be associated with biological measures of pathological gambling. Here, we tested the hypothesis that dopamine release would be associated with increased excitement levels in Pathological Gamblers compared with Healthy Controls.Design  Pathological Gamblers and Healthy Controls were experimentally compared in a non‐gambling (baseline) and gambling condition.Measurements  We used Positron Emission Tomography (PET) with the tracer raclopride to measure dopamine D 2/3 receptor availability in the ventral striatum during a non‐gambling and gambling condition of the Iowa Gambling Task (IGT). After each condition participants rated their excitement level.Setting  Laboratory experiment.Participants  18 Pathological Gamblers and 16 Healthy Controls.Findings  Pathological Gamblers with dopamine release in the ventral striatum had significantly higher excitement levels than Healthy Controls despite lower IGT performance. No differences in excitement levels and IGT performance were found between Pathological Gamblers and Healthy Controls without dopamine release. Pathological Gamblers showed a significant correlation between dopamine release and excitement level, while no such interaction was found in Healthy Controls.Conclusions  In pathological gamblers dopamine release in the ventral striatum appears to be associated with increased excitement levels despite lower IGT performance. The results might suggest a ‘double deficit’ function of dopamine in pathological gambling, where dopamine release reinforces maladaptive gambling through increasing excitement levels, reducing inhibition of risky decisions, or a combination of both. These findings may have implications for the understanding of dopamine in pathological gambling and other forms of addiction.
Identification of potential host plant mimics of CLAVATA3/ESR (CLE)‐like peptides from the plant‐parasitic nematode Heterodera schachtii
Authors: WANG JIANYING , REPLOGLE AMY , HUSSEY RICHARD , BAUM THOMAS , WANG XIAOHONG , DAVIS ERIC L. , MITCHUM MELISSA G. 
Published: October 2010

SUMMARYIn this article, we present the cloning of two CLAVATA3/ESR (CLE)‐like genes, HsCLE1 and HsCLE2, from the beet cyst nematode Heterodera schachtii, a plant‐parasitic cyst nematode with a relatively broad host range that includes the model plant Arabidopsis. CLEs are small secreted peptide ligands that play important roles in plant growth and development. By secreting peptide mimics of plant CLEs, the nematode can developmentally reprogramme root cells for the formation of unique feeding sites within host roots for its own benefit. Both HsCLE1 and HsCLE2 encode small secreted polypeptides with a conserved C‐terminal CLE domain sharing highest similarity to Arabidopsis CLEs 1–7. Moreover, HsCLE2 contains a 12‐amino‐acid CLE motif that is identical to AtCLE5 and AtCLE6. Like all other plant and nematode CLEs identified to date, HsCLEs caused wuschel‐like phenotypes when overexpressed in Arabidopsis, and this activity was abolished when the proteins were expressed without the CLE motif. HsCLEs could also function in planta without a signal peptide, highlighting the unique, yet conserved function of nematode CLE variable domains in trafficking CLE peptides for secretion. In a direct comparison of HsCLE2 overexpression phenotypes with those of AtCLE5 and AtCLE6, similar shoot and root phenotypes were observed. Exogenous application of 12‐amino‐acid synthetic peptides corresponding to the CLE motifs of HsCLEs and AtCLE5/6 suggests that the function of this class of CLEs may be subject to complex endogenous regulation. When seedlings were grown on high concentrations of peptide (10 µm), root growth was suppressed; however, when seedlings were grown on low concentrations of peptide (0.1 µm), root growth was stimulated. Together, these findings indicate that AtCLEs1–7 may be the target peptides mimicked by HsCLEs to promote parasitism.
Level of psychological distress and social support among patients with limb fractures in Hong Kong
Authors: Lam Kin , Chan Sally WC , Lam Simon C 
Published: October 2010

Aims.  To explore the relationship between psychological distress and social support and examine its association with various socio‐demographic and clinical characteristics.Background.  Psychological distress is a common experience in patients after limb fractures. In this regard, a lower level of psychological distress is associated with better social support among patients with various types of diseases. However, there is a paucity of studies examining the relationship between social support and psychological distress among patients with limb fractures. More so, no such study has been conducted in the Chinese population.Design.  A cross‐sectional and correlational design.Method.  A convenience sample of participants with upper limb fractures (n = 43) or lower limb fractures (n = 43) was recruited from two orthopaedic wards of a regional acute public hospital in Hong Kong. Data were obtained through face‐to‐face interview. The Impact of Event Scale was used to measure the level of psychological distress, while the Social Support Questionnaire Short‐Form (SSQ6) was used to measure social support.Results.  Approximately two‐thirds of the participants (n = 54) suffered from medium to high level of psychological distress. Majority of them were fairly satisfied with their social support, with their children being the most common support persons. Furthermore, there was no significant difference in the level of distress between the participants with lower or upper limb fractures. No significant correlation was found between psychological distress and social support. Those who were women, had lower education level and lower monthly income were significantly associated with a higher level of psychological distress.Relevance to clinical practice.  Patients with fractured limb suffered from a high level of psychological distress. Therefore, a comprehensive assessment of psychological distress should be incorporated as routine assessment. Also, assessing the socio‐demographic characteristics of patients should enable nurses to identify patients at risk of developing a high level of psychological distress.
Managing invasive weeds under climate change: considering the current and potential future distribution of Buddleja davidii
Authors: KRITICOS D J , WATT M S , POTTER K J B , MANNING L K , ALEXANDER N S , TALLENT‐HALSELL N 
Published: October 2010

Kriticos DJ,Watt MS, Potter KJB, Manning LK,Alexander NS &Tallent‐Halsell N (2011). Managing invasive weeds under climate change: considering the current and potential future distribution of Buddleja davidii. Weed Research 51, 85–96.Summary Buddleja davidii is both a prized garden ornamental and an invasive shrub that rapidly colonises disturbed ground. Originally from China, B. davidii has been widely distributed by horticulturalists and has subsequently invaded much of Europe and New Zealand, and to a lesser degree the Americas and Australia. The present and future climate suitability for B. davidii was assessed using a process‐oriented climate suitability model. There appears to be a considerable scope for further invasion, with the most suitable areas occurring adjacent to existing naturalised populations in the north‐eastern United States, north‐eastern Europe, south‐eastern Australia and south‐eastern New Zealand. Under future climates, the potential distribution and climate suitability for B. davidii increases most noticeably in the northern United States and southern Canada, northern and eastern Europe, and to a lesser extent in the south‐western part of the South Island of New Zealand. Elsewhere, there are projected poleward range shifts (South America) or range contractions out of subtropical areas (Africa and Australia). Climate‐based potential distribution models can help adapt weed management programmes to expected climate changes by: (i) classifying areas for the different types of weed management, (ii) supporting strategic control initiatives to prevent the spread of a weed, (iii) informing the reallocation of resources away from controlling a weed where climate suitability is expected to diminish in the future and (iv) identifying opportunities for relatively inexpensive preventative management to be applied to minimise future weed impacts.
The Efficiency of In vitro Ovine Embryo Production Using an Undefined or a Defined Maturation Medium is Determined by the Source of the Oocyte
Authors: Cocero MJ , Alabart JL , Hammami S , Martí JI , Lahoz B , Sánchez P , Echegoyen E , Beckers JF , Folch J 
Published: October 2010

Contents In vitro oocyte maturation can be influenced by oocyte source and maturation media composition. The aim of the present study was to compare the efficiency of a defined in vitro maturation medium (TCM199 supplemented with cysteamine and epidermal growth factor; Cys + EGF) with an undefined medium (TCM199 supplemented with follicle‐stimulating hormone and follicular fluid; FSH + FF) for in vitro production (IVP) of ovine embryos, using oocytes obtained by laparoscopic ovum pick‐up from FSH‐stimulated [n = 11; 158 cumulus‐oocyte complexes (COCs)] and non‐stimulated (n = 16; 120 COCs) live ewes, as well as abattoir‐derived oocytes (170 COCs). The produced blastocysts were vitrified and some of them were transferred to synchronized recipients. The best and the worst final yields of embryo IVP observed in this study were obtained using oocytes from FSH‐stimulated ewes matured in FSH + FF (41.3%; 33/80) and in Cys + EGF (19.2%; 15/78) medium, respectively (p < 0.01). No significant differences between both media were attained in the blastocyst development rate or in the final yield of embryo IVP using oocytes from non‐stimulated ewes or abattoir‐derived oocytes. The overall in vivo survival rate of the transferred vitrified blastocysts was 13.1% (8/61), without significant differences between oocyte sources or maturation media. In conclusion, under the experimental conditions of the present study, TCM199 supplemented with cysteamine and EGF is a convenient defined maturation medium for IVP of embryos from oocytes of live non‐stimulated ewes or from oocytes of abattoir‐derived ovaries. However, the best final yield of embryo IVP observed in this study was attained when oocytes came from FSH‐stimulated donors and TCM199 was supplemented with FSH and follicular fluid.
How to read critically a prognostic cohort study
Authors: PALMER SUETONIA C , STRIPPOLI GIOVANNI FM 
Published: September 2010

ABSTRACTIn nephrology, cohort studies are an abundant source of information. They are the ideal study design to answer clinical questions about prevalence, prognosis and aetiology. In this study, the evaluation of a cohort study to guide decisions about prognosis in clinical nephrology is discussed.
Spontaneous twin cervico‐isthmic pregnancy in a grand multiparous woman
Authors: Cetin Meral , Yildiz Caglar , Yenicesu Ayse G. I. , Cetin Ali 
Published: September 2010

AbstractCervico‐isthmic pregnancy is a rare form of ectopic pregnancy and is defined as the implantation of a fertilized ovum in the cervico‐isthmic portion. The cause is unknown; local pathology related to previous cervical or uterine surgery may play a role, given an apparent association with a prior history of curettage or cesarean delivery. Transvaginal ultrasonography and β‐human chorionic gonadotrophin assays are useful for diagnosis. Here we report a case of spontaneous twin cervico‐isthmic pregnancy in a grand multiparous patient who was diagnosed early in the first trimester with transvaginal ultrasonography. The pregnancy was terminated successfully with methotrexate. Methotrexate seems to be most successful at early gestational ages.
The impact of systematic para‐aortic and pelvic lymphadenectomy on survival in patients with optimally debulked ovarian cancer
Authors: Abe Akiko , Furumoto Hiroyuki , Irahara Minoru , Ino Hiroyasu , Kamada Masaharu , Naka Osamu , Sasaki Masaru , Kagawa Toshiaki , Okitsu Osamu , Kushiki Norio 
Published: September 2010

AbstractAim:  The objective of this study was to verify the impact of systematic retroperitoneal lymphadenectomy on survival in patients with ovarian cancer.Material & Methods:  During 2001–2005, clinical records of 118 patients with epithelial ovarian cancer were collected in Tokushima prefecture. From a number of hospitals, patients in one group were treated without systematic lymphadenectomy, and in another group, patients were treated with routine systematic lymphadenectomy. Clinical records were reviewed retrospectively and progression‐free survival (PFS) and overall survival (OS) were compared.Results:  Sixty‐two patients were staged as I–II according to the macroscopic findings at surgery. Forty of these patients received systematic lymphadenectomy and 22 patients did not. The 5‐year OS was 100 and 80%, respectively (P = 0.07). The 5‐year PFS was 94 and 71%, respectively (P = 0.04). In patients with clear cell adenocarcinoma, 3‐year OS and PFS were significantly better in the lymphadenectomy group (P = 0.01, P = 0.046, respectively). The 56 patients staged as III–IV according to the macroscopic findings at surgery were optimally debulked. Twenty‐eight of these patients received systematic lymphadenectomy and 28 patients did not. There is no difference in the 5‐year OS (65 and 66%, respectively; P = 0.71) or the 5‐year PFS (30 and 52%, respectively; P = 0.48).Conclusion:  This study has demonstrated that the systematic lymphadenectomy had benefit only in patients with ovarian cancer macroscopically confined to the pelvis. In patients with clear cell adenocarcinoma, systematic lymphadenectomy was beneficial. To the contrary, systematic lymphadenectomy had no benefit on OS or PFS in patients with advanced ovarian cancer if optimally debulked.
Correlations between the detection of stress‐associated hormone/oxidative stress markers in umbilical cord blood and the physical condition of the mother and neonate
Authors: Chiba Takako , Omori Atsuko , Takahashi Kenji , Tanaka Kanako , Kudo Kaori , Manabe Mami , Mariya Yasushi , Kashiwakura Ikuo 
Published: September 2010

AbstractAim:  The objective of this study was to assess the correlations between the detection of stress‐associated hormone/oxidative stress markers in umbilical cord blood (CB) and the physical condition of the mother and neonate.Methods:  CB units collected from normal vaginal deliveries were analyzed for various biochemical markers, some stress‐associated hormones, such as progesterone, cortisol, adrenocorticotropic hormone (ACTH), corticotrophin releasing factor (CRF) and oxidative stress marker 8‐hydroxy‐deoxyguanosine (8‐OHdG), respectively.Results:  The progesterone concentration closely correlated with Apgar score, hemoglobin, maternal smoking and insulin concentration, respectively. In particular, its concentration in the non‐smoker group and Apgar score 10 points group was significantly lower in comparison to the smoker group and Apgar score 8 points group, respectively. Cortisol concentration correlated significantly with the number of parities, pre‐pregnancy body mass index (BMI), and increase of neonatal weight and height per day, respectively. In particular, its concentration in deliveries of males and first babies was significantly higher in comparison to female deliveries and second babies, respectively. In addition, a significant correlation was observed between the duration between spontaneous/artificial membrane rupture time and delivery time and the ACTH concentration. However, no significant relationship was observed between maternal/neonatal factors and CRF concentration and 8‐OHdG concentration, respectively. A significant negative correlation was observed between cortisol and 8‐OHdG concentration.Conclusion:  CB stress‐associated hormone/oxidative stress markers strongly reflect maternal and neonatal condition at the time of delivery.