bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emerging topics in human tumor virology
Authors: Hoppe‐Seyler Felix , Hoppe‐Seyler Karin 
Published: March 2011

AbstractAfter a long period of scepticism and disbelief, tumor viruses are today recognized as a significant cancer risk factor for humans. Much has been learned about the viral transforming mechanisms and prophylactic vaccines have been developed against 2 major tumor viruses, HBV and HPV. Yet, many important issues of tumor virology remain unresolved and exciting new ones are emerging from recent discoveries. They define future research directions for the field and include (i) novel strategies for tumor virus hunting, (ii) tumor viruses as experimental tools to study human carcinogenesis, (iii) the interplay between viruses and the world of small noncoding RNAs, (iv) epigenetic interactions between tumor viruses and the host cell, (v) the role of virus/virus interactions for viral carcinogenesis and (vi) novel strategies for prevention and therapy of virus‐associated cancers. These topics are discussed by summarizing recent developments, pointing out unresolved issues and suggesting possible strategies for their solution.
VEGF directly suppresses activation of T cells from ovarian cancer patients and healthy individuals via VEGF receptor Type 2
Authors: Ziogas Apostolos C. , Gavalas Nikos G. , Tsiatas Marinos , Tsitsilonis Ourania , Politi Ekaterini , Terpos Evangelos , Rodolakis Alexandros , Vlahos George , Thomakos Nikolaos , Haidopoulos Dimitrios , Antsaklis Aristidis , Dimopoulos Meletios A. , Bamias Aristotle 
Published: March 2011

AbstractThe role of vascular endothelial growth factor (VEGF) in tumor angiogenesis is well characterized; nevertheless, it is also a key element in promoting tumor evasion of the immune system by downregulating dendritic cell maturation and thus T cell activation. We sought to investigate the possible direct effect of VEGF on T cell activation and through which type of VEGF receptor (VEGFR) it exerts this effect. Circulating T cells from healthy donors and ovarian cancer patients were expanded in cultures with anti‐CD3 and IL‐2 with or without VEGF for 14 days, and the number of T cells was assessed. Cultured T cells were also tested for their cytotoxic activity in a standard 4‐hr 51Cr‐release assay, and the expression of VEGFRs 1, 2 and 3 was assayed by flow cytometry, immunocytochemistry and Western blotting. To assess the ability of activated T cells to secrete VEGF, levels in culture supernatants were measured by enzyme linked immunosorbent assay. The addition of VEGF in cultures significantly reduced T cell proliferation in a dose‐dependent manner. Protein expression studies demonstrated that CD3+ T cells express VEGFR‐2 on their surface upon activation. Experiments with anti‐VEGFR‐2 antibodies showed that the direct suppressive effect of VEGF on T cell proliferation is mediated by VEGFR‐2. We also showed that VEGF significantly reduced the cytotoxic activity of T cells and that activated T cells secrete VEGF in the culture environment. Overall, our study shows that T cells secret VEGF and expresses VEGFR‐2 upon activation. VEGF directly suppresses T cell activation via VEGF receptor type 2.
LINE‐1 hypomethylation is associated with bladder cancer risk among nonsmoking Chinese
Authors: Cash Haley L. , Tao Li , Yuan Jian‐Min , Marsit Carmen J. , Houseman E. Andres , Xiang Yong‐Bing , Gao Yu‐Tang , Nelson Heather H. , Kelsey Karl T. 
Published: March 2011

AbstractReduced levels of global DNA methylation, assessed in peripheral blood, have been associated with bladder cancer risk in European and American populations. Similar data are lacking in Asian populations where genetic differences, lifestyle factors and different environmental exposures may affect DNA methylation and its risk relationship with bladder cancer. The association between global DNA methylation measured at long interspersed nuclear element (LINE‐1) repeat regions through bisulfite pyrosequencing in lymphocyte DNA and bladder cancer risk was examined in a case–control study of 510 bladder cancer patients and 528 healthy control subjects in Shanghai, China. In an initial analysis restricted to control subjects, LINE‐1 methylation was elevated among men, those who frequently consumed cruciferous vegetables and those with a null genotype for either glutathione S‐transferase M1 (GSTM1) or GSTT1. In contrast, reduced LINE‐1 methylation was found in current smokers with a high‐cytochrome P450 1A2 (CYP1A2) phenotype index. In a case–control analysis, there was no significant association of LINE‐1 methylation with case status, although reduced LINE‐1 methylation was associated with increased risk of bladder cancer among never smokers (p for trend = 0.03); analysis by tertile revealed odds ratios (ORs) of 1.91 (lowest tertile; 95% CI = 1.17–3.13) and 1.34 (middle tertile; 95% CI = 0.79–2.28) when compared with the highest tertile. This association was strongest among nonsmokers null for either the GSTM1 or GSTT1 genotype (p for trend = 0.006). Further research is needed to understand the relationships between methyl group availability and LINE‐1 methylation in relation to bladder cancer risk.
Side‐necked turtle (Pleurodira, Chelonia, reptilia) hemoglobin: cDNA‐derived primary structures and X‐ray crystal structures of Hb A
Authors: Hasegawa Tomokazu , Shishikura Fumio , Kuwada Takao 
Published: March 2011

AbstractRed blood cells of yellow‐spotted river turtles (Podocnemis unifilis, Pleurodira, Chelonia, REPTILIA) have two hemoglobin (Hb) components, Hb A and Hb D. We purified the hemoglobin component homologous to amniote (reptiles, birds, and mammals) adult Hb A which comprises two identical αA‐globin polypeptides and two identical β‐globin polypeptides. To establish the crystal structure of Podocnemis Hb A, we first determined the globin primary structures using cDNA nucleotide sequencing with the assistance of protein sequencing. The purified Podocnemis Hb A produced a different form of crystal for each of the two different buffer systems used: form A, tetragonal crystals (space group, P41212), produced under neutral pH (pH 7–8) conditions; and form B, hexagonal crystals (space group, P6122), produced under high alkaline pH (pH 11–13) conditions. Single crystals of the two forms were examined by Raman microscopy with an excitation of 532 nm, indicating their structural differences. The crystal structures of the two forms were constructed by X‐ray crystallographic diffraction at a resolution of 2.20 Å for form A and 2.35 Å for form B. The differences of the tertiary and quaternary structures of the two forms were marginal; however, one clear difference was found in helix structure. When comparing Podocnemis Hb A with Hb A from specimens in other taxa, such as Anser
indicus (birds) and Homo
sapiens (mammals) by SHELXPRO, the root mean square deviation (RMSD) between the corresponding Cα atoms of the two globins does not exceed 2.0 Å. These low values indicate the crystal structures resemble each other. Our data on X‐ray crystal structures and Raman spectra not only reveal the first findings on the two crystal forms of Podocnemis
unifilis Hb A but also provide the first refined models for reptilian adult Hb A. © 2011 IUBMB IUBMB Life, 63(3): 188–196, 2011
Structural properties of 2/2 hemoglobins: The group III protein from Helicobacter hepaticus
Authors: Nothnagel Henry J. , Winer Benjamin Y. , Vuletich David A. , Pond Matthew P. , Lecomte Juliette T. J. 
Published: March 2011

AbstractThe ε‐proteobacterium Helicobacter hepaticus (Hh) contains a gene coding for a hemoglobin (Hb). The protein belongs to the 2/2 Hb lineage and is representative of group III, a set of Hbs about which little is known. An expression and purification procedure was developed for Hh Hb. Electronic absorption and nuclear magnetic resonance (NMR) spectra were used to characterize ligation states of the ferric and ferrous protein. The pKa of the acid/alkaline transition of ferric Hh Hb was 7.3, an unusually low value. NMR analysis of the cyanomet complex showed the orientation of the heme group to be reversed when compared with most group I and group II 2/2 Hbs. Ferrous Hh Hb formed a stable cyanide complex that yielded NMR spectra similar to those of the carbonmonoxy complex. All forms of Hh Hb were self‐associated at NMR concentrations. Comparison was made to the related Campylobacter jejuni 2/2 Hb (Ctb), and the amino acid conservation pattern of group III was reinspected to help in the generalization of structure–function relationships. © 2011 IUBMB IUBMB Life, 63(3): 197–205, 2011
Protonation of histidine 55 affects the oxygen access to heme in the alpha chain of the hemoglobin from the Antarctic fish Trematomus bernacchii
Authors: Boechi Leonardo , Martì Marcelo A. , Vergara Alessandro , Sica Filomena , Mazzarella Lelio , Estrin Dario A. , Merlino Antonello 
Published: March 2011

AbstractThe Root effect describes the drastic drop of oxygen affinity and loss of cooperativity at acidic pH expressed in the hemoglobins (Hb) of certain fish. The comparison between the deoxy structures of the Root effect Hb from the Antarctic fish Trematomus bernacchii (HbTb) at different pHs (pH = 6.2 and pH = 8.4) shows that the most significant differences are localized at the CDα region, where a salt bridge between Asp48 and His55 breaks during the low‐to‐high pH transition. In order to shed light on the relationship between pH, CDα loop structure and dynamics, and oxygen access to the active site in the alpha chain of HbTb, different computer simulation techniques were performed. Our results highlight the importance of the protonation of His55 in regulating oxygen access, underscoring its pivotal role in the structural and functional properties of HbTb. These data provide further support to the hypothesis that this residue might contribute to the release of Root protons in HbTb and underline the fact that an efficient transport of molecular oxygen in Hbs relies on a subtle balance of tertiary structure and protein conformational flexibility. © 2011 IUBMB IUBMB Life, 63(3): 175–182, 2011
Structural and functional properties of class 1 plant hemoglobins
Authors: Igamberdiev Abir U. , Bykova Natalia V. , Hill Robert D. 
Published: March 2011

AbstractNonsymbiotic class 1 plant hemoglobins are induced under hypoxia. Structurally they are protein dimers consisting of two identical subunits, each containing heme iron in a weak hexacoordinate state. The weak hexacoordination of heme‐iron binding to the distal histidine results in an extremely high avidity to oxygen, with a dissociation constant in the nanomolar range. This low dissociation constant is due to rapid oxygen binding resulting in protein conformational changes that slow dissociation from the heme site. Class 1 hemoglobins are characterized by an increased rate of Fe3+ reduction which is likely mediated by cysteine residue. This cysteine can form a reversible covalent bond between two monomers as shown by mass spectrometry analysis and, in addition to its structural role, prevents the molecule from autoxidation. The structural properties of class 1 hemoglobins allow them to serve as soluble electron transport proteins in the enzymatic system scavenging nitric oxide produced in low oxygen via reduction of nitrite. During oxygenation of nitric oxide to nitrate, oxidized ferric hemoglobin is formed (methemoglobin), which can be reduced by an associated reductase. The identified candidate for this reduction is monodehydroascorbate reductase. It is suggested that hemoglobin functions as a terminal electron acceptor during the hypoxic turnover of nitrogen, the process aided by its extremely high affinity for oxygen. © 2011 IUBMB IUBMB Life, 63(3): 146–152, 2011
Structure and dynamics of Antarctic fish neuroglobin assessed by computer simulations
Authors: Boron Ignacio , Russo Roberta , Boechi Leonardo , Cheng C.‐H. Christina , di Prisco Guido , Estrin Darío A. , Verde Cinzia , Nadra Alejandro D. 
Published: March 2011

AbstractNeuroglobin (Ngb) is a heme protein, highly conserved along evolution, predominantly found in the nervous system. It is upregulated by hypoxia and ischemia and may have a neuroprotective role under hypoxic stress. Although many other roles have been proposed, the physiological function is still unclear. Antarctic icefishes lack hemoglobin and some species also lack myoglobin, but all have Ngb and thus may help the elucidation of Ngb function. We present the first theoretically derived structure of fish Ngb and describe its behavior using molecular dynamics simulations. Specifically, we sequenced and analyzed Ngbs from a colorless‐blooded Antarctic icefish species Chaenocephalus aceratus and a related red‐blooded species (Dissostichus mawsoni). Both fish Ngbs are 6‐coordinated but have some peculiarities that differentiate them from mammalian counterparts: they have extensions in the N and C termini that can interact with the EF loop, and a gap in the alignment that changes the CD‐region structure/dynamics that has been found to play a key role in human neuroglobin. Our results suggest that a single mutation between both fish Ngbs is responsible for significant difference in the behavior of the proteins. The functional role of these characteristics is discussed. © 2011 IUBMB IUBMB Life, 63(3): 206–213, 2011
Hutchinson-gilford progeria is a skeletal dysplasia
Authors: Gordon Catherine M , Gordon Leslie B , Snyder Brian D , Nazarian Ara , Quinn Nicolle , Huh Susanna , Giobbie-Hurder Anita , Neuberg Donna , Cleveland Robert , Kleinman Monica , Miller David T , Kieran Mark W 
Published: March 2011

Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare segmental premature aging disorder that affects bone and body composition, among other tissues. We sought to determine whether bone density and structural geometry are altered in children with HGPS and whether relationships exist among these parameters and measures of skeletal anthropometry, body composition, and nutrition. We prospectively enrolled 26 children with HGPS (ages 3.1 to 16.2 years). Outcomes included anthropometric data; bone age; areal bone mineral density (aBMD) and body composition by dual-energy X-ray absorptiometry (DXA); volumetric bone mineral density (vBMD), strength-strain index (SSI), and bone structural rigidity calculated from radial transaxial peripheral quantitative computed tomographic (pQCT) images; serum bone biomarkers and hormonal measures; and nutrition assessments. Children with HGPS had low axial aBMD Z-scores by DXA, which improved after adjustment for height age, whereas differences in radial vBMD by pQCT were less striking. However, pQCT revealed distinct abnormalities in both novel measures of bone structural geometry and skeletal strength at the radius compared with healthy controls. Dietary intake was adequate, confirming that HGPS does not represent a model of malnutrition-induced bone loss. Taken together, these findings suggest that the phenotype of HGPS represents a unique skeletal dysplasia. © 2011 American Society for Bone and Mineral Research.
Protein folding and the order/disorder paradox
Authors: Kulkarni Prakash , Rajagopalan Krithika , Yeater David , Getzenberg Robert H. 
Published: March 2011

AbstractMost proteins encoded by the nuclear genome are synthesized in the cytoplasm and fold into precise 3D structures. During synthesis, the nascent polypeptide begins to fold as it traverses the large subunit of the ribosome and is assisted by molecular chaperones in attaining its precise folded/highly ordered state efficiently and in a biologically relevant timescale. Proteins that are misfolded are culled, re‐routed, and marked by mechanisms such as ubiquitinylation for degradation ensuring strict quality control (QC). In addition to the highly ordered “globular” proteins, emerging evidence indicates that a large fraction of the proteome also comprises the so‐called “Intrinsically Disordered Proteins” (IDPs). IDPs are proteins that lack rigid 3D structures and instead, exist as dynamic ensembles. The dynamic structures in the IDPs have many similarities with “normal” globular proteins such as the native (ordered), and non‐native (molten globule, pre‐molten globule, and coil‐like) states seen during folding of “normal” globular proteins. However, unlike the case of the nascent globular proteins, IDPs evade being detected as “misfolded” and degraded by the cell's QC system. We refer to this paradox as the order/disorder paradox and postulate that the IDPs capitalize on their intrinsic promiscuity and ability to undergo disorder‐to‐order transitions upon binding to biological targets (coupled folding and binding) to escape the cell's surveillance machinery. Understanding the mechanism by which the IDPs evade the quality check has wide implications from protein folding to disease biology since the aggregation of misfolded proteins underlies several debilitating illnesses such as many neurodegenerative diseases and cancer. J. Cell. Biochem. 112: 1949–1952, 2011. © 2011 Wiley‐Liss, Inc.
Survival, development, and gonadal differentiation in Rana dalmatina chronically exposed to chlorpyrifos
Authors: Bernabò Ilaria , Gallo Luisa , Sperone Emilio , Tripepi Sandro , Brunelli Elvira 
Published: March 2011

AbstractChlorpyrifos is an organophosphate pesticide among the most widely used in the world, which is suspected to be an endocrine‐disrupting compound. To determine the capacity of chlorpyrifos to affect gonadal differentiation in Rana dalmatina, tadpoles were exposed to this pesticide during larval development until completion of metamorphosis at ecologically relevant concentrations (0.025 and 0.05 mg/L). No effects of chlorpyrifos exposure on survival, development, or metamorphosis were observed. After a 1 month metamorphosis, the gonadal phenotype was determined by gross morphology and histological examination. Morphological and histological analysis revealed normal ovaries or testes in froglets belonging to control group, whereas testes from several froglets exposed to chlorpyrifos were interspersed with testicular oocytes in histological sections. Chlorpyrifos exposure during the entire larval period did not affect sex ratio, but reduced the percentage of males with histologically normal testes. The findings suggest that chlorpyrifos exposure has significant effects on gonadal differentiation in some animals by inducing an intersex condition and alterations to testicular morphology, and that R. dalmatina is sensitive to endocrine disruption. Thereby, this study provides evidence that the ecologically relevant concentrations of chlorpyrifos, although not adversely affect the survival, development, or metamorphosis, may interfere with sex differentiation and reproductive development of R. dalmatina via endocrine‐disrupting mechanisms. J. Exp. Zool. 315:314–327, 2011.. © 2011 Wiley‐Liss, Inc.
Simple efficient synthesis of 4‐aminoquinazoline via amidine of N‐arylamidoxime
Authors: Patil Sachin S. , Mhaske Pravin C. , Patil Sachin V. , Bobade Vivek D. 
Published: March 2011

AbstractPreparation of 4‐amino‐2‐aryl quinazolines by reduction of N‐(2‐cyanoaryl) amidoximes via amidines using SnCl2 in ethanol. J. Heterocyclic Chem., (2011).
Piping plover habitat selection and nest success on natural, managed, and engineered sandbars
Authors: Catlin Daniel H. , Fraser James D. , Felio Joy H. , Cohen Jonathan B. 
Published: March 2011

AbstractLoss of breeding habitat and nest predation have contributed to the decline of many shorebird species. The United States Army Corps of Engineers (USACE) initiated a piping plover (Charadrius melodus) habitat creation and augmentation program on the Missouri River in the summer of 2004. The USACE increased unvegetated sandbar habitat by depositing dredged material (engineered sandbars) and by clearing vegetation from existing sandbars (managed sandbars). We evaluated the effects of this increase in nesting and foraging habitat on habitat selection and nest daily survival rate (DSR) of piping plovers on Lewis and Clark Lake and the Gavins Point Reach of the Missouri River from 2005 to 2007 (n = 623 nests). Piping plovers selected engineered sandbars more often than expected based on area and selected natural and managed habitats less than expected based on area. Daily survival rate on engineered sandbars was significantly higher than on natural or managed sandbars (log odds: 2.50, 95% CI: 1.05–5.94). Thus, plovers' habitat selection may have increased their nesting success. Our results suggest that habitat augmentation may stave off declines in piping plover populations limited by insufficient habitat and low nesting success. © 2011 The Wildlife Society.
Trap style influences wild pig behavior and trapping success
Authors: Williams Brian L. , Holtfreter Robert W. , Ditchkoff Stephen S. , Grand James B. 
Published: March 2011

AbstractDespite the efforts of many natural resource professionals, wild pig (Sus scrofa) populations are expanding in many areas of the world. Although many creative techniques for controlling pig populations are being explored, trapping has been and still is the most commonly used method of population control for many public and private land managers. We conducted an observational study to examine the efficiency of 2 frequently used trap styles: a small, portable box‐style trap and a larger, semi‐permanent, corral‐style trap. We used game cameras to examine patterns of trap entry by wild pigs around each style of trap, and we conducted a trapping session to compare trapping success between trap styles. Adult female and juvenile wild pigs entered both styles of trap more readily than did adult males, and adult males seemed particularly averse to entering box traps. Less than 10% of adult male visits to box traps resulted in entries, easily the least percentage of any class at any style of trap. Adult females entered corral traps approximately 2.2 times more often per visit than box traps and re‐entered corral traps >2 times more frequently. Juveniles entered and re‐entered both box and corral traps at similar rates. Overall (all‐class) entry‐per‐visit rates at corral traps (0.71) were nearly double that of box traps (0.37). Subsequent trapping data supported these preliminary entry data; the capture rate for corral traps was >4 times that of box traps. Our data suggest that corral traps are temporally and economically superior to box traps with respect to efficiency; that is, corral traps effectively trap more pigs per trap night at a lower cost per pig than do box traps. © 2011 The Wildlife Society.
Constrained estimation of the arterial input function for myocardial perfusion cardiovascular magnetic resonance
Authors: Fluckiger Jacob U. , Schabel Matthias C. , DiBella Edward V. R. 
Published: March 2011

AbstractAccurate quantification of myocardial perfusion remains challenging due to saturation of the arterial input function at high contrast concentrations. A method for estimating the arterial input function directly from tissue curves in the myocardium that avoids these difficulties is presented. In this constrained alternating minimization with model (CAMM) algorithm, a portion of the left ventricular blood pool signal is also used to constrain the estimation process. Extensive computer simulations assessing the accuracy of kinetic parameter estimation were performed. In 5000 noise realizations, the use of the AIF given by the estimation method returned kinetic parameters with mean Ktrans error of −2% and mean kep error of 0.4%. Twenty in vivo resting perfusion datasets were also processed with this method, and pharmacokinetic parameter values derived from the blind AIF were compared with those derived from a dual‐bolus measured AIF. For 17 of the 20 datasets, there were no statistically significant differences in Ktrans estimates, and in aggregate the kinetic parameters were not significantly different from the dual‐bolus method. The cardiac constrained alternating minimization with model method presented here provides a promising approach to quantifying perfusion of myocardial tissue with a single injection of contrast agent and without a special pulse sequence though further work is needed to validate the approach in a clinical setting. Magn Reson Med, 2010. © 2011 Wiley‐Liss, Inc.