bluuebunny/crossref_metadata_2025_split huggingface dataset:
The 1.7 Å resolution structure of At2g44920, a pentapeptide-repeat protein in the thylakoid lumen ofArabidopsis thaliana
Authors: Ni Shuisong , McGookey Michael E. , Tinch Stuart L. , Jones Alisha N. , Jayaraman Seetharaman , Tong Liang , Kennedy Michael A. 
Published: November 2011

At2g44920 belongs to a diverse family (Pfam PF00805) of pentapeptide-repeat proteins (PRPs) that are present in all known organisms except yeast. PRPs contain at least eight tandem-repeating sequences of five amino acids with an approximate consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Recent crystal structures show that PRPs adopt a highly regular four-sided right-handed β-helical structure consisting mainly of type II and type IV β-turns, sometimes referred to as a repeated five-residue (or Rfr) fold. Among sequenced genomes, PRP genes are most abundant in cyanobacteria, leading to speculation that PRPs play an important role in the unique lifestyle of photosynthetic cyanobacteria. Despite the recent structural characterization of several cyanobacterial PRPs, most of their functions remain unknown. Plants, whose chloroplasts are of cyanobacterial origin, have only four PRP genes in their genomes. At2g44920 is one of three PRPs located in the thylakoid lumen. Here, the crystal structure of a double methionine mutant of residues 81–224 of At2g44920, the naturally processed fragment of one of its full-length isoforms, is reported at 1.7 Å resolution. The structure of At2g44920 consists of the characteristic Rfr fold with five uninterrupted coils made up of 25 pentapeptide repeats and α-helical elements capping both termini. A disulfide bridge links the two α-helices with a conserved loop between the helical elements at its C-terminus. This structure represents the first structure of a PRP protein whose subcellular location has been experimentally confirmed to be the thylakoid lumen in a plant species.
Cloning, expression, purification and crystallization of dihydrodipicolinate synthase from the grapevine Vitis vinifera
Authors: Atkinson Sarah C. , Dogovski Con , Newman Janet , Dobson Renwick C. J. , Perugini Matthew A. 
Published: November 2011

Dihydrodipicolinate synthase (DHDPS) catalyses the first committed step of the lysine-biosynthesis pathway in bacteria, plants and some fungi. This study describes the cloning, expression, purification and crystallization of DHDPS from the grapevine Vitis vinifera (Vv-DHDPS). Following in-drop cleavage of the hexahistidine tag, cocrystals of Vv-DHDPS with the substrate pyruvate were grown in 0.1 M Bis-Tris propane pH 8.2, 0.2 M sodium bromide, 20%(w/v) PEG 3350. X-ray diffraction data in space group P1 at a resolution of 2.2 Å are presented. Preliminary diffraction data analysis indicated the presence of eight molecules per asymmetric unit (V
M = 2.55 Å3 Da−1, 52% solvent content). The pending crystal structure of Vv-DHDPS will provide insight into the molecular evolution in quaternary structure of DHDPS enzymes.
Crystallization and preliminary X-ray analysis of crinumin, a chymotrypsin-like glycosylated serine protease with thrombolytic and antiplatelet activity
Authors: Singh Kunwar Awaneesh , Jagannadham M. V. , Rao G. R. K. , Celie Patrick H. N. 
Published: November 2011

Crinumin, a novel glycosylated serine protease with chymotrypsin-like catalytic specificity, was purified from the medicinally important plant Crinum asiaticum. Crinumin is a 67.7 kDa protease with an extraordinary stability and activity over a wide range of pH and temperature and is functional in aqueous, organic and chaotropic solutions. The purified protease has thrombolytic and antiplatelet activity. The use of C. asiaticum extracts has also been reported for the treatment of a variety of disorders such as injury, joint inflammation and arthritis. In order to understand its structure–function relationship, the enzyme was purified from the plant latex and crystallized by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected from a single crystal and processed to 2.8 Å resolution. The crystal belonged to the monoclinic space group C2, with unit-cell parameters a = 121.61, b = 95.00, c = 72.10 Å, α = γ = 90, β = 114.19°. The Matthews coefficient was 2.81 Å3 Da−1, corresponding to a solvent content of 56%, assuming one molecule in the asymmetric unit. Structure determination of the enzyme is in progress.
Engineered tryptophan in the adenine-binding pocket of catalytic subunit A of A-ATP synthase demonstrates the importance of aromatic residues in adenine binding, forming a tool for steady-state and time-resolved fluorescence spectroscopy
Authors: Tadwal Vikeramjeet Singh , Manimekalai Malathy Sony Subramanian , Grüber Gerhard 
Published: November 2011

A reporter tryptophan residue was individually introduced by site-directed mutagenesis into the adenine-binding pocket of the catalytic subunit A (F427W and F508W mutants) of the motor protein A1AO ATP synthase from Pyrococcus horikoshii OT3. The crystal structures of the F427W and F508W mutant proteins were determined to 2.5 and 2.6 Å resolution, respectively. The tryptophan substitution caused the fluorescence signal to increase by 28% (F427W) and 33% (F508W), with a shift from 333 nm in the wild-type protein to 339 nm in the mutant proteins. Tryptophan emission spectra showed binding of Mg-ATP to the F427W mutant with a K
d of 8.5 µM. In contrast, no significant binding of nucleotide could be observed for the F508W mutant. A closer inspection of the crystal structure of the F427W mutant showed that the adenine-binding pocket had widened by 0.7 Å (to 8.70 Å) in comparison to the wild-type subunit A (8.07 Å) owing to tryptophan substitution, as a result of which it was able to bind ATP. In contrast, the adenine-binding pocket had narrowed in the F508W mutant. The two mutants presented demonstrate that the exact volume of the adenine ribose binding pocket is essential for nucleotide binding and even minor narrowing makes it unfit for nucleotide binding. In addition, structural and fluorescence data confirmed the viability of the fluorescently active mutant F427W, which had ideal tryptophan spectra for future structure-based time-resolved dynamic measurements of the catalytic subunit A of the ATP-synthesizing enzyme A-ATP synthase.
Comprehensive taxon sampling reveals unaccounted diversity and morphological plasticity in a group of dimitic polypores (Polyporales, Basidiomycota)
Authors: Miettinen Otto , Larsson Ellen , Sjökvist Elisabet , Larsson Karl‐Henrik 
Published: November 2011

AbstractThe phylogeny of the poroid and hydnoid genera Antrodiella, Junghuhnia, and Steccherinum (Polyporales, Basidiomycota) was studied utilizing sequences of the gene regions ITS, nLSU, mtSSU, atp6, rpb2, and tef1. Altogether 148 taxa, represented by 549 sequences, were included in analyses. Results show that most species of these genera form a well supported clade in the Polyporales, called Steccherinaceae, along with 12 other hydnoid and poroid genera. Within the Steccherinaceae, generic concepts need to be revised: no fewer than 15 new genera are needed to accommodate existing and new species. At least 16 transitions have taken place between poroid and hydnoid hymenophore types within the Steccherinaceae, and similar plasticity can be seen in microscopic characters. Nevertheless, natural genera revealed in the analysis can mostly be characterized morphologically and, with few exceptions, poroid and hydnoid species belong to separate genera. The genus Steccherinum is shown to contain both hydnoid and poroid species. Species of the former Antrodiella belong to at least 10 genera within the Steccherinaceae.© The Willi Hennig Society 2011.
Chronic fatigue syndrome: acute infection and history of physical activity affect resting levels and response to exercise of plasma oxidant/antioxidant status and heat shock proteins
Authors: Jammes Y. , Steinberg J. G. , Delliaux S. 
Published: November 2011

Abstract.  Jammes Y, Steinberg JG, Delliaux S (Aix‐Marseille University, Marseille, France). Chronic fatigue syndrome: acute infection and history of physical activity affect resting levels and response to exercise of plasma oxidant/antioxidant status and heat shock proteins. J Intern Med 2012; 272: 74–84.Objectives.  A history of high‐level physical activity and/or acute infection might constitute stress factors affecting the plasma oxidant–antioxidant status and levels of heat shock proteins (HSPs) in patients with chronic fatigue syndrome (CFS).Design.  This case–control study compared data from 43 CFS patients to results from a matched control group of 23 healthy sedentary subjects.Setting and subjects.  Five patients had no relevant previous history (group I). Eighteen had practised high‐level sport (group II), and severe acute infection had been diagnosed in nine patients (group III). A combination of sport practice and infection was noted in 11 patients (group IV).Interventions.  After examination at rest, all subjects performed a maximal cycling exercise test. Plasma levels of two markers of oxidative stress [thiobarbituric acid reactive substances (TBARS) and reduced ascorbic acid (RAA)] and both HSP27 and HSP70 were measured.Results.  At rest, compared with the control group, the TBARS level was higher in groups II, III and IV patients, and the RAA level was lower in groups III and IV. In addition, HSP70 levels were significantly lower in all CFS groups, compared with controls, but negative correlations were found between resting HSP27 and HSP70 levels and the history of physical activity. After exercise, the peak level of TBARS significantly increased in groups II, III and IV, and the variations in HSP27 and HSP70 were attenuated or suppressed, with the greatest effects in groups III and IV.Conclusion.  The presence of stress factors in the history of CFS patients is associated with severe oxidative stress and the suppression of protective HSP27 and HSP70 responses to exercise.
QTL linkage mapping of wing length in zebra finch using genome‐wide single nucleotide polymorphisms markers
Authors: SCHIELZETH HOLGER , FORSTMEIER WOLFGANG , KEMPENAERS BART , ELLEGREN HANS 
Published: November 2011

AbstractAvian wing length is an important trait that covaries with the ecology and migratory behaviour of a species and tends to change rapidly when the conditions are altered. Long‐distance migrants typically have longer wings than short‐distance migrants and sedentary species, and long‐winged species also tend to be more dispersive. Although the substantial heritability of avian wing length is well established, the identification of causal genes has remained elusive. Based on large‐scale genotyping of 1404 informative single nucleotide polymorphisms (SNP) in a captive population of 1067 zebra finches, we here show that the within‐population variation of relative wing length (h2 = 0.74 ± 0.05) is associated with standing genetic variation in at least six genomic regions (one genome‐wide significant and five suggestive). The variance explained by these six quantitative trait loci (QTL) sums to 36.8% of the phenotypic variance (half of the additive genetic variance), although this likely is an overestimate attributable to the Beavis effect. As avian wing length is primarily determined by the length of the primary feathers, we then searched for candidate genes that are related to feather growth. Interestingly, all of the QTL signals co‐locate withWntgrowth factors and closely interacting genes (Wnt3a,Wnt5a,Wnt6,Wnt7a,Wnt9a,RhoUandRhoV). Our findings therefore suggest that standing genetic variation in theWntgenes might be linked to avian wing morphology, although there are many other genes that also fall within the confidence regions.
Interaction between FliI ATPase and a flagellar chaperone FliT during bacterial flagellar protein export
Authors: Minamino Tohru , Kinoshita Miki , Imada Katsumi , Namba Keiichi 
Published: November 2011

SummaryFliT is a flagellar type III export chaperone specific for the filament‐capping protein FliD. The FliT/FliD complex binds to the FliI ATPase of the flagellar export apparatus. The C‐terminal α4 helix of FliT controls its interaction with FliI but it remains unknown how it does so. Here, we analysed the FliI–FliT interaction by pull‐down assays using GST affinity chromatography. FliT94, missing the C‐terminal α4 helix, bound to the extreme N‐terminal region of FliI (FliIEN) with high affinity and to the C‐terminal ATPase domain (FliICAT) with low affinity. The C‐terminal α4 helix of FliT suppressed the interaction with FliIEN. FliH and FliT94 bound to a common binding site on FliIEN and hence FliH induced the release of FliI from FliT94 in an ATP‐independent manner. FliD increased the binding affinity of FliICAT for FliT. These results raise a possible hypothesis that the FliH/FliI complex binds to the FliT/FliD complex through FliICAT to escort it from the cytoplasm to the export gate made up of six integral membrane proteins and that, upon dissociation of FliD from FliT, FliT94 may bind to FliIEN and then FliI may transfer from FliT94 to FliH by the direct competition of FliT94 and FliH for FliIEN.
Effect of kidney transplantation on heart conduction disturbances in children treated with chronic hemodialysis – A pilot study
Authors: Polak‐Jonkisz Dorota , Laszki‐Szcząchor Krystyna , Sobieszczańska Małgorzata , Makulska Irena , Pilecki Witold , Rusiecki Lesław , Zwolińska Danuta 
Published: November 2011

Polak‐Jonkisz D, Laszki‐Szcząchor K, Sobieszczańska M, Makulska I, Pilecki W, Rusiecki L, Zwolińska D. Effect of kidney transplantation on heart conduction disturbances in children treated with chronic hemodialysis – A pilot study.  Pediatr Transplantation 2011: 15: 835–843. © 2011 John Wiley & Sons A/S.Abstract:  Aim of the study was to assess the effect of KT on heart conduction in HD children. Non‐invasive electrocardiographic method of BSPM was used. Isochrone maps, presenting a VAT distribution, were taken from eight HD patients and 26 normal subjects. Patients were divided into two groups: I – three children were HD <12 months prior to KT; II – five children were HD >12 months prior to KT. After KT, the groups were marked as IP and IIP. Serum iPTH and phosphate levels were significantly higher in both HD groups than in controls, with a considerable normalization after transplantation. HD patients demonstrated neither conduction abnormalities on ECG nor left ventricular hypertrophy. Group‐mean VAT maps revealed: I and II – similar patterns of complete LBBB; IP – partial normalization to a pattern of anterior fascicle block; IIP – preserved pattern of LBBB. Intraventricular conduction disturbances found in HD children using BSPM were alleviated by KT. Short HD therapy increases a chance of conduction disturbances regression after KT, contrary to the longer HD treatment. BSPM is more sensitive than standard ECG in detecting heart conduction impairments in the HD patients.
Chronic malnutrition favours smaller critical size for metamorphosis initiation in Drosophila melanogaster
Authors: VIJENDRAVARMA R. K. , NARASIMHA S. , KAWECKI T. J. 
Published: November 2011

AbstractCritical size at which metamorphosis is initiated represents an important checkpoint in insect development. Here, we use experimental evolution in Drosophila melanogaster to test the long‐standing hypothesis that larval malnutrition should favour a smaller critical size. We report that six fly populations subject to 112 generations of laboratory natural selection on an extremely poor larval food evolved an 18% smaller critical size (compared to six unselected control populations). Thus, even though critical size is not plastic with respect to nutrition, smaller critical size can evolve as an adaptation to nutritional stress. We also demonstrate that this reduction in critical size (rather than differences in growth rate) mediates a trade‐off in body weight that the selected populations experience on standard food, on which they show a 15–17% smaller adult body weight. This illustrates how developmental mechanisms that control life history may shape constraints and trade‐offs in life history evolution.
Discovery of curcumin, a component of golden spice, and its miraculous biological activities
Authors: Gupta Subash C , Patchva Sridevi , Koh Wonil , Aggarwal Bharat B 
Published: November 2011

Summary1. Curcumin is the active ingredient of the dietary spice turmeric and has been consumed for medicinal purposes for thousands of years. Modern science has shown that curcumin modulates various signalling molecules, including inflammatory molecules, transcription factors, enzymes, protein kinases, protein reductases, carrier proteins, cell survival proteins, drug resistance proteins, adhesion molecules, growth factors, receptors, cell cycle regulatory proteins, chemokines, DNA, RNA and metal ions.2. Because of this polyphenol’s potential to modulate multiple signalling molecules, it has been reported to possess pleiotropic activities. First demonstrated to have antibacterial activity in 1949, curcumin has since been shown to have anti‐inflammatory, anti‐oxidant, pro‐apoptotic, chemopreventive, chemotherapeutic, antiproliferative, wound healing, antinociceptive, antiparasitic and antimalarial properties as well. Animal studies have suggested that curcumin may be active against a wide range of human diseases, including diabetes, obesity, neurological and psychiatric disorders and cancer, as well as chronic illnesses affecting the eyes, lungs, liver, kidneys and gastrointestinal and cardiovascular systems.3. Although many clinical trials evaluating the safety and efficacy of curcumin against human ailments have already been completed, others are still ongoing. Moreover, curcumin is used as a supplement in several countries, including India, Japan, the US, Thailand, China, Korea, Turkey, South Africa, Nepal and Pakistan. Although inexpensive, apparently well tolerated and potentially active, curcumin has not been approved for the treatment of any human disease.4. In the present article, we discuss the discovery and key biological activities of curcumin, with a particular emphasis on its activities at the molecular and cellular levels, as well as in animals and humans.
Characteristics of the short children referred to an academic paediatric endocrine clinic in Greece
Authors: Papadimitriou Anastasios , Douros Konstantinos , Papadimitriou Dimitrios T , Kleanthous Kleanthis , Karapanou Olga , Fretzayas Andreas 
Published: November 2011

Aim:  To describe the characteristics of short children in relation to gender and the various diagnoses.Methods:  All new patients of Greek origin that were referred to our institution in the years 2007 and 2008 for evaluation of short stature were included in the study. Children were categorized according to the severity of their short stature in those with height standard deviation score (HSDS) ≤−3 and HSDS >−3.Results:  Two hundred ninety‐five children (162 boys and 133 girls, ratio 1.2) were referred. HSDS of boys was −2.3 (0.6) and of girls −2.1 (0.5), P= 0.004. Girls had shorter parents, and the predicted adult HSDS was also shorter for girls −1.7 (0.8) than for boys −1.35 (0.76), P= 0.003. Seventy per cent of the children of both sexes had familial short stature (FSS), constitutional delay of growth or a combination of the two conditions. About 10% presented the auxological and biochemical criteria for growth hormone deficiency (GHD). In addition, 11.8% had a HSDS ≤−3, the most common diagnosis being GHD (36.1%); the less severely short children most commonly presented FSS (41.2%).Conclusions:  There is no gender bias in referrals for short stature in Greece. About 70% of children of both sexes presented FSS or constitutional delay of growth or a combination of the two conditions, whereas GHD was diagnosed in about 10% of the children. Normal variants of growth were present in about 80% of children with HSDS >−3, but in only 40% when HSDS was ≤−3.
Peritoneal drainage versus laparotomy for perforated necrotising enterocolitis or spontaneous intestinal perforation: A retrospective cohort study
Authors: Rakshasbhuvankar Abhijeet , Rao Shripada , Minutillo Corrado , Gollow Ian , Kolar Satish 
Published: November 2011

Aim:  Perforated necrotising enterocolitis (NEC) and spontaneous intestinal perforation (SIP) in preterm infants are associated with high morbidity and mortality. The optimum surgical management during the acute stage remains unclear. The aim of the study was to compare the outcomes of preterm infants (gestational age at birth <30 weeks) with perforated NEC or SIP undergoing primary peritoneal drainage (PD) versus laparotomy.Methods:  This was a retrospective cohort study (January 2004 to February 2010). Initial search of hospital database followed by a review of the medical records was performed to identify eligible infants. Thirty‐nine infants were included in the study. Information regarding the baseline characteristics and outcomes of interest were recorded using the medical charts, radiology and laboratory databases. NEC was differentiated from SIP based on radiological, operative and clinical findings retrospectively for this study.Results:  Among 39 infants, 19 underwent primary PD while 20 had primary laparotomy. Gestational age and birthweight were similar between the two groups. The composite outcome of mortality before discharge or hospital stay longer than 3 months post‐term was significantly worse in PD group (74% vs. 40%, P= 0.038).Conclusions:  Preterm infants undergoing PD for NEC/SIP appeared to have increased risk of adverse outcome compared with laparotomy. More randomised controlled trials are necessary to confirm these findings.
Potential influence of sevelamer hydrochloride on responsiveness to erythropoiesis‐stimulating agents in haemodialysis patients
Authors: IKEE RYOTA , TSUNODA MASATAKA , SASAKI NAOMI , SATO NARITSUGU , HASHIMOTO NOBUO 
Published: November 2011

ABSTRACT:Aim:  Vitamin D analogues, cinacalcet, and sevelamer play pivotal roles in the management of chronic kidney disease‐mineral bone disorder, and are noted to have pleiotropic effects. We examined whether these agents might be associated with the responsiveness to erythropoiesis‐stimulating agents (ESA).Methods:  In this cross‐sectional study including haemodialysis patients treated with ESA, we searched for clinical parameters associated with the ESA resistance index, which was calculated as the weekly ESA dose divided by the patient's haemoglobin value.Results:  Among 45 patients (male: female = 28 : 17, age 68 ± 10 years, haemodialysis duration 84 ± 60 months), vitamin D analogue, cinacalcet, and sevelamer were used in 95.6%, 26.7%, and 84.4% of the patients, respectively. Univariate analysis showed significant association of the ESA resistance index with transferrin saturation rate (TSAT), vitamin D analogue dose, and sevelamer dose. In multivariate analysis, the sevelamer dose and TSAT were found to be independent determinants of the ESA resistance index.Conclusion:  Our preliminary data showed an independent association between sevelamer dose and the responsiveness to ESA in haemodialysis patients. Further studies are required to investigate the causal relationship between sevelamer and ESA responsiveness.