bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of crystal phase from an electron backscatter diffraction pattern
Authors: Dingley David J. , Wright Stuart I.
Published: January 2009

Electron backscatter diffraction (EBSD) is a scanning electron microscope-based technique principally used for the determination and mapping of crystal orientation. This work describes an adaptation of the EBSD technique into a potential tool for crystal phase determination. The process can be distilled into three steps: (1) extracting a triclinic cell from a single EBSD pattern, (2) identifying the crystal symmetry from an examination of the triclinic cell, and (3) determining the lattice parameters. The triclinic cell is determined by finding the bands passing through two zone axes in the pattern including a band connecting the two. A three-dimensional triclinic unit cell is constructed based on the identified bands. The EBSD pattern is indexed in terms of the triclinic cell thus formed and the crystal orientation calculated. The pattern indexing results in independent multiple orientations due to the symmetry the crystal actually possesses. By examining the relationships between these multiple orientations, the crystal system is established. By comparing simulated Kikuchi bands with the pattern the lattice parameters can be determined. Details of the method are given for a test case of EBSD patterns obtained from the hexagonal phase of titanium.
Chord length distribution of pentagonal and hexagonal rods: relation to small-angle scattering
Authors: Gille Wilfried , Aharonyan Narine G. , Harutyunyan Hrachya S.
Published: January 2009

Based on explicit formulas of chord length density functions (CLDs) for a regular pentagon and a hexagon, the CLDs of infinitely long regular homogeneous pentagonal/hexagonal cylinders are discussed. Characteristic properties of the small-angle scattering of these cylinders are studied.
Population pharmacokinetics of intravenous pantoprazole in paediatric intensive care patients
Authors: Pettersen Géraldine , Mouksassi Mohamad‐Samer , Théorêt Yves , Labbé Line , Faure Christophe , Nguyen Bao , Litalien Catherine
Published: January 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• The use of intravenous pantoprazole, a proton pump inhibitor, has been increasing in the paediatric intensive care unit.

• Despite this increased use, data on the disposition of intravenous pantoprazole in paediatric intensive care patients are very scarce.

WHAT THIS STUDY ADDS

• Our population approach has determined the pharmacokinetic parameters of intravenous pantoprazole in paediatric intensive care patients and the relative importance of factors influencing its disposition.

• Pantoprazole clearance was significantly influenced by developmental changes and by the presence of systemic inflammatory syndrome, hepatic dysfunction and CYP2C19 inhibitors.

AIMS

To characterize the pharmacokinetics of intravenous pantoprazole in a paediatric intensive care population and to determine the influence of demographic factors, systemic inflammatory response syndrome (SIRS), hepatic dysfunction and concomitantly used CYP2C19 inducers and inhibitors on the drug's pharmacokinetics.

METHODS

A total of 156 pantoprazole concentration measurements from 20 patients (10 days to 16.4 years of age) at risk for or with upper gastrointestinal bleeding, who received pantoprazole doses ranging from 19.9 to 140.6 mg/1.73 m2/day, were analysed using a population pharmacokinetic approach (nonmem program).

RESULTS

The best structural model for pantoprazole was a two‐compartment model with zero order infusion and first‐order elimination. Body weight, SIRS, age, hepatic dysfunction and presence of CYP2C19 inhibitors were significant covariates affecting clearance (CL), accounting for 75% of interindividual variability. Only body weight significantly influenced central volume of distribution (Vc). In the final population model, the estimated CL and Vc were 5.28 l h−1 and 2.22 l, respectively, for a typical 5‐year‐old child weighing 20 kg. Pantoprazole CL increased with weight and age, whereas the presence of SIRS, CYP2C19 inhibitors and hepatic dysfunction, when present separately, significantly decreased pantoprazole CL by 62.3, 65.8 and 50.5%, respectively. For patients aged between 6 months and 5 years without SIRS, CYP2C19 inhibitor or hepatic dysfunction, the predicted pantoprazole CL is faster than that reported in adults.

CONCLUSION

These results provide important information for physicians regarding selection of a starting dose and dosing regimens of pantoprazole for paediatric intensive care patients based on factors frequently encountered in this population.
Lack of age and gender effects on single‐dose pharmacokinetics of tomopenem (RO4908463/CS‐023), a novel carbapenem
Authors: Mallalieu Navita L. , Lennon Siân , Guy Thorold , Liu Mei , Luedin Eric , Davies Brian E.
Published: January 2009

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• This compound belongs to a well‐described class of antibacterials, the carbapenems, which are characterized by excellent bactericidal activity.

• This compound is unique in that it has activity against methicillin‐resistant Staphylococcus aureus and Pseudomonas aeruginosa.

• The pharmacokinetics (PK) of all molecules in this class is characterized by short plasma half‐lives and renal elimination as the major source of clearance.

• Age‐ and gender‐related effects on renal and hepatic function have been shown to necessitate adjustments in dosing regimens to ensure safe and efficacious exposures to drugs.

WHAT THIS STUDY ADDS

• The extent of changes in PK of tomopenem in the elderly and women is minor when compared with healthy male volunteers, so dose adjustments are not necessary.

• Instead of age or gender, creatinine clearance can be used to explain the slight effect of these variables on PK.

AIMS To investigate the effect of age and gender on the tolerability, safety and pharmacokinetics (PK) of tomopenem (RO4908463/CS‐023), a novel carbapenem antibiotic, and its major metabolite.

METHODS Forty‐two subjects were assigned to one of the following three groups: young men, elderly men and elderly women. The PK, safety and tolerability of an intravenous infusion of 1500 mg tomopenem and its resultant major metabolite (open beta‐lactam ring) were assessed.

RESULTS Minor differences in exposure of both tomopenem and the major metabolite were seen. The area under the curve (AUC) of tomopenem was 22% higher in elderly men compared with young men, and 19% higher in elderly women relative to the elderly men. Total clearance of tomopenem decreased with decreasing creatinine clearance. In the two male groups, renal clearance values of tomopenem were similar (3.52 and 3.67 l h−1) and higher than in the elderly female group (2.83 l h−1). The mean half‐lives ranged from 2.03 (healthy young men) to 2.41 h (elderly men). The difference in AUC of tomopenem can be explained by differences in the mean creatinine clearances of 116 (young men), 101 (elderly men) and 84.7 (elderly women) ml min−1 1.73 m−2, respectively.

CONCLUSIONS While some PK parameters were statistically different among the three groups, the differences were mostly minor and unlikely to be clinically meaningful. The difference in the PK can be largely attributed to the difference in creatinine clearance of these groups.
Airway angiogenesis in patients with rhinitis and controlled asthma
Authors: Kristan S. S. , Malovrh M. M. , Silar M. , Kern I. , Flezar M. , Kosnik M. , Suskovic S. , Korosec P.
Published: January 2009

Background
Airway angiogenesis may be an important part of structural remodelling in the pathogenesis of asthma. The development of asthma is frequently preceded by rhinitis.

Objective
We sought to determine whether the levels of angiogenesis‐related factors are elevated in airways of patients with rhinitis or controlled asthma.

Methods
We analysed the induced sputum of 18 rhinitis patients, 16 asthmatic patients, and 15 healthy controls. The concentrations of angiogenin, vascular endothelial growth factor (VEGF), IL‐8, fibroblast growth factor (bFGF), and TNF‐α were measured by cytometric bead arrays.

Results
We found significantly increased angiogenin and VEGF concentrations in the induced sputum supernatant of both rhinitis and asthma patients compared with that of the healthy control group (P0.0005). With the exception of TNF‐α, there was no difference in the other angiogenic factors; TNF‐α levels were higher in the rhinitis group than in the control group (P=0.02).

Conclusion
These in vivo results suggest increased airway angiogenesis in patients with rhinitis without asthma as well as in corticosteroid‐treated and well‐controlled asthma patients.
Beta lactam allergy and resensitization in children with suspected beta lactam allergy
Authors: Hershkovich J. , Broides A. , Kirjner L. , Smith H. , Gorodischer R.
Published: January 2009

Background
In patients who were clinically diagnosed as having beta lactam allergy and had negative skin tests, the rates of reported resensitization to beta lactams after subsequent exposures, vary significantly. Some allergists advocate skin testing before every exposure to beta lactams.

Objective
We sought to determine the true rate of beta lactam allergy and of resensitization in children with a positive history for suspected beta lactam allergy.

Methods
The study was conducted from July 1998 to May 2004, with follow‐up during 2007. Beta lactam allergy tests with the major determinant and freshly prepared minor determinant mixtures were offered to history positive children. Negative skin tests were followed by oral challenge. The tests were performed again 1–5 months later in order to address the possibility of resensitization.

Results
Tests were performed on 166 children: 150 for penicillins alone, 14 for penicillin in combination with cephalosporins, and an additional 2 patients solely for cephalosporins. Only 10 children (6%) were positive in the initial evaluation, four by skin test and six by oral challenge. A second set of tests was performed in 98 children with a negative initial evaluation; only two children (2%) were resensitized. On a follow‐up survey of 71 of the 96 patients, 59 (83%) had received beta lactams; only one had developed a minor rash after subsequent exposure to amoxicillin.

Conclusions
Most children with suspected beta lactam allergy were not allergic to beta lactams. Resensitization to beta lactam antibiotics in children in this study was infrequent. In children with a clinical diagnosis of beta lactam allergy and negative skin tests, repeated skin testing before every exposure is usually unnecessary.
Animal models of protein allergenicity: potential benefits, pitfalls and challenges
Authors: Dearman R. J. , Kimber I.
Published: January 2009

Food allergy is an important health issue. With an increasing interest in novel foods derived from transgenic crop plants, there is a growing need for the development of approaches suitable for the characterization of the allergenic potential of proteins. There are methods available currently (such as homology searches and serological testing) that are very effective at identifying proteins that are likely to cross‐react with known allergens. However, animal models may play a role in the identification of truly novel proteins, such as bacterial or fungal proteins, that have not been experienced previously in the diet. We consider here the potential benefits, pitfalls and challenges of the selection of various animal models, including the mouse, the rat, the dog and the neonatal swine. The advantages and disadvantages of various experimental end‐points are discussed, including the measurement of specific IgE by ELISA, Western blotting or functional tests such as the passive cutaneous anaphylaxis assay, and the assessment of challenge‐induced clinical symptoms in previously sensitized animals. The experimental variables of route of exposure to test proteins and the incorporation of adjuvant to increase the sensitivity of the responses are considered also. It is important to emphasize that currently none of these approaches has been validated for the purposes of hazard identification in the context of a safety assessment. However, the available evidence suggests that the judicious use of an accurate and robust animal model could provide important additional data that would contribute significantly to the assessment of the potential allergenicity of novel proteins.
The impact of chemokine receptor CX3CR1 deficiency during respiratory infections with Mycobacterium tuberculosis or Francisella tularensis
Authors: Hall J D , Kurtz S L , Rigel N W , Gunn B M , Taft-Benz S , Morrison J P , Fong A M , Patel D D , Braunstein M , Kawula T H
Published: January 2009

Recruitment of immune cells to infection sites is a critical component of the host response to pathogens. This process is facilitated partly through interactions of chemokines with cognate receptors. Here, we examine the importance of fractalkine (CX3CL1) receptor, CX3CR1, which regulates function and trafficking of macrophages and dendritic cells, in the host's ability to control respiratory infections with Mycobacterium tuberculosis or Francisella tularensis. Following low-dose aerosol challenge with M. tuberculosis, CX3CR1−/− mice were no more susceptible to infection than wild-type C57BL/6 mice as measured by organ burden and survival time. Similarly, following inhalation of F. tularensis, CX3CR1−/− mice displayed similar organ burdens to wild-type mice. CX3CR1−/− mice had increased recruitment of monocytes and neutrophils in the lung; however, this did not result in increased abundance of infected monocytes or neutrophils. We conclude that CX3CR1-deficiency affects immune-cell recruitment; however, loss of CX3CR1 alone does not render the host more susceptible to M. tuberculosis or F. tularensis.
Involvement of functional polymorphisms in theTNFAgene in the pathogenesis of autoimmune thyroid diseases and production of anti-thyrotropin receptor antibody
Authors: Inoue N , Watanabe M , Nanba T , Wada M , Akamizu T , Iwatani Y
Published: January 2009

The severity of Hashimoto's disease (HD) and intractability of Graves' disease (GD) varies among patients. Severity of HD is associated with the functional +874A/T polymorphism for interferon-γ, an inflammatory cytokine. To clarify the association between functional polymorphisms in two other inflammatory cytokine genes [tumour necrosis factor (TNF)-α and interleukin (IL)-2] and the severity of autoimmune thyroid disease (AITD), we examined the TNF-α−1031T/C, TNF-α−857C/T and IL-2 −330T/G polymorphisms in genomic DNA samples. We genotyped 41 patients with intractable GD, 34 patients with GD in remission, 41 patients with severe HD, 36 patients with mild HD and 70 healthy controls. The frequency of carriers of TNF-α−1031C (CT + CC), which correlates with higher TNF-α production, was significantly higher in HD and GD patients than in controls, but was not associated with the severity of HD. In GD patients, the levels of anti-thyrotropin receptor antibody (TRAb) at onset of the disease was higher in patients with the TNF-α−857T (CT + TT) genotype, which correlates with higher TNF-α production, than in those with the −857CC genotype. We found no differences in the IL-2 −330T/G polymorphism among groups of AITD patients. In conclusion, the functional −1031T/C polymorphism of the TNFA gene is associated with the development of AITD and the functional −857C/T polymorphism is associated with the levels of TRAb in active GD patients.
Translating transplantation tolerance in the clinic: where are we, where do we go?
Authors: Goldman M , Wood K
Published: January 2009

Research networks dedicated to translation of immune tolerance in the clinic currently support pilot trials aiming at immunosuppression withdrawal in kidney or liver allograft recipients. Although results obtained so far indicate that significant hurdles still need to be overcome before organ transplant recipients can be weaned off drugs safely and routinely, recent advances suggest that immunosuppression minimization on the basis of validated biomarkers might become standard practice in a near future.
Immune characterization of an individual with an exceptionally high natural killer T cell frequency and her immediate family
Authors: Chan A C , Serwecinska L , Cochrane A , Harrison L C , Godfrey D I , Berzins S P
Published: January 2009

Natural killer T cells (NKT) are a regulatory subset of T lymphocytes whose frequency in peripheral blood is highly variable within the human population. Lower than normal NKT frequencies are associated with increased predisposition to a number of diseases, including type 1 diabetes and some forms of cancer, raising the possibility that an increased frequency may be protective. However, there is little or no understanding of how high NKT frequencies arise or, most importantly, whether the potential exists to boost and maintain NKT levels for therapeutic advantage. Here, we provide a detailed functional and phenotypic characterization of the NKT compartment of a human donor with NKT levels approximately 50 times greater than normal, including an analysis of NKT in her immediate family members. The study focuses upon the characteristics of this donor and her family, but demonstrates more broadly that the size and flexibility of the NKT niche is far greater than envisioned previously. This has important implications for understanding how the human NKT compartment is regulated, and supports the concept that the human NKT compartment might be expanded successfully for therapeutic benefit.
A new class of tissue‐specifically methylated regions involving entire CpG islands in the mouse
Authors: Suzuki Masako , Sato Shun , Arai Yoshikazu , Shinohara Takashi , Tanaka Satoshi , Greally John M. , Hattori Naka , Shiota Kunio
Published: January 2009

CpG islands, which have higher GC content and CpG frequencies compared to the genome as a whole, are generally believed to be unmethylated in tissues except at promoters of genes undergoing X chromosome inactivation or genomic imprinting. Recent studies, however, have shown that CpG islands at promoters of a number of genes contain tissue‐dependent, differentially methylated regions (T‐DMRs). In general, the tissue‐specific methylation is restricted to a part of the promoter CpG island, with hypomethylation of the remaining sequence. In the current study, using comparison between Restriction Landmark Genomic Scanning (RLGS) and in silico RLGS, we identified ten sperm‐specific unmethylated NotI sites, T‐DMRs located in CpG islands that were hypomethylated in sperm but near‐completely methylated in the kidney and brain. Unusually, these T‐DMRs involve the whole CpG island at each of these loci. We characterized one of these genes, adenine nucleotide translocator 4 (Ant4), which is expressed in germ cells. Using a promoter assay, we demonstrated that expression of Ant4 gene is controlled by DNA methylation at the CpG island sequences within the promoter region. Ant4 and other sperm‐specific hypomethylated loci represent a new class of CpG islands that become completely methylated in different cell lineages. T‐DMRs at CpG islands are functionally important gene regulatory elements that may now be categorized into two classes: T‐DMRs involving a subregion of the CpG island and those that occupy the whole CpG island.
Regulation of the interaction of Disabled‐1 with CIN85 by phosphorylation with Cyclin‐dependent kinase 5
Authors: Sato Yutaka , Taoka Masato , Sugiyama Nami , Kubo Ken‐ichiro , Fuchigami Takahiro , Asada Akiko , Saito Taro , Nakajima Kazunori , Isobe Toshiaki , Hisanaga Shin‐ichi
Published: January 2009

Disabled‐1 (Dab1) is an adaptor protein mediating Reelin signaling in neuronal migration during brain development. Cyclin‐dependent kinase 5 (Cdk5)–p35 is a proline‐directed Ser/Thr kinase also involved in neuronal migration. The interaction between Dab1 and Cdk5 is in need of investigation. Dab1 was phosphorylated at Ser400 and Ser491 by Cdk5 in vivo. We search for proteins that interact with Dab1 in a phosphorylation‐dependent manner at these sites, and identified CIN85, an SH3‐containing adaptor protein involved in endocytosis, and CPα/CPβ, which are subunits of barbed end F‐actin‐capping proteins (CP), as proteins bound to unphosphorylated Dab1 by mass spectrometric analysis. It was shown that the PTPAPR sequence of Dab1, conforming to the PxxxPR atypical SH3‐binding motif, was the binding site for SH3 domains of CIN85. The results that phosphorylation at Ser491 close to the PTPAPR sequence inhibited association with CIN85 may provide a mechanism regulating the interaction between the PxxxPR motif proteins and SH3 domains of CIN85 family proteins. Together with previous results that CIN85 regulates actin assembly, present results raise the possibility that Cdk5 modulates actin dynamics through regulation of CIN85–Dab1 interaction by the Dab1 phosphorylation.
Tel2: a common partner of PIK‐related kinases and a link between DNA checkpoint and nutritional response?
Authors: Kanoh Junko , Yanagida Mitsuhiro
Published: January 2009

A recent paper (Hayashi et al. 2007) in this issue of Genes to Cells shows that the fission yeast Schizosaccharomyces pombe Tel2, a homologue of mammalian/worm CLK2/Clk‐2/Rad‐5, physically interacts with all the phosphoinositide 3‐kinase‐related kinases (PIKKs) that include Rad3/Tel1 (ATR/ATM homologues), Tor1/Tor2 (TOR kinases) and Tra1/Tra2 (TRRAP homologues), raising the possibility that Tel2 family proteins link various PIKK‐related cellular processes by interacting with PIKK family proteins. In this minireview, implications and impact of the findings, and a possibility that PIKKs are functionally related through Tel2, are discussed.
Sp1‐mediated transcriptional regulation of NFBD1/MDC1 plays a critical role in DNA damage response pathway
Authors: Bu Youquan , Suenaga Yusuke , Ono Sayaka , Koda Tadayuki , Song Fangzhou , Nakagawara Akira , Ozaki Toshinori
Published: January 2009

NFBD1/MDC1 is a large nuclear protein with an anti‐apoptotic potential which participates in DNA damage response. Recently, we have demonstrated that NFBD1 has an inhibitory effect on pro‐apoptotic p53 and DNA damage‐induced transcriptional repression of NFBD1 plays an important role in p53‐dependent apoptotic response. In this study, we have found that NFBD1 promoter region contains canonical Sp1‐, STAT‐1‐ and NF‐Y‐binding sites and finally we have identified Sp1 as a transcriptional activator for NFBD1. The 5′‐RACE and bioinformatic analyses revealed that NFBD1 encodes at least four transcriptional variants arising from distinct transcriptional start sites. Luciferase reporter assays using a series of NFBD1 promoter deletion mutants demonstrated that the proximal Sp1‐binding site is required for the transcriptional activation of NFBD1. Indeed, the endogenous Sp1 was recruited onto the proximal Sp1‐binding site as examined by chromatin immunoprecipitation (ChIP) assay and siRNA‐mediated knockdown of the endogenous Sp1 in HeLa cells reduced the expression levels of NFBD1, which renders cells sensitive to adriamycin (ADR). In support of this notion, mithramycin A (MA, Sp1 inhibitor) treatment resulted in a significant down‐regulation of NFBD1. Taken together, our present findings suggest that Sp1‐mediated transcriptional regulation of NFBD1 plays an important role in the regulation of DNA damage response.
Caenorhabditis elegans DYF‐11, an orthologue of mammalian Traf3ip1/MIP‐T3, is required for sensory cilia formation
Authors: Kunitomo Hirofumi , Iino Yuichi
Published: January 2009

Cilia and flagella play critical roles in cell motility, development and sensory perception in animals. Formation and maintenance of cilia require a conserved protein transport system called intraflagellar transport (IFT). Here, we show that Caenorhabditis elegans dyf‐11 encodes an evolutionarily conserved protein required for cilium biogenesis. dyf‐11 is expressed in most of the ciliated neurons and is regulated by DAF‐19, a crucial transcription factor for ciliary genes in C. elegans. dyf‐11 mutants exhibit stunted cilia, fluorescent dye‐filling defects (Dyf) of sensory neurons, and abnormal chemotaxis (Che). Cell‐ and stage‐specific rescue experiments indicated that DYF‐11 is required for formation and maintenance of sensory cilia in cell‐autonomous manner. Fluorescent protein‐tagged DYF‐11 localizes to cilia and moves antero‐ and retrogradely via IFT. Analysis of DYF‐11 movement in bbs mutants further suggested that DYF‐11 is likely associated with IFT complex B. Domain analysis using DYF‐11 deletion constructs revealed that the coiled‐coil region is required for proper localization and ciliogenesis. We further show that Traf3ip1/MIP‐T3, the mammalian orthologue of DYF‐11, localizes to cilia in the MDCK renal epithelial cells.
Ribosomal stress induces processing of Mybbp1a and its translocation from the nucleolus to the nucleoplasm
Authors: Yamauchi Tomohiro , Keough Rebecca A. , Gonda Thomas J. , Ishii Shunsuke
Published: January 2009

Myb‐binding protein 1a (Mybbp1a) was originally identified as a c‐myb proto‐oncogene product (c‐Myb)‐interacting protein, and also binds to various other transcription factors. The 160‐kDa Mybbp1a protein (p160MBP) is ubiquitously expressed and is post‐translationally processed in some types of cells to generate an amino‐terminal 67 kDa fragment (p67MBP). Despite its interaction with various transcription factors, Mybbp1a is localized predominantly, but not exclusively, in nucleoli. Here, we have purified the two Mybbp1a‐containing complexes. The smaller complex contained p67MBP and p140MBP, which lacked the C‐terminal region of p160MBP containing the nucleolar localization sequences. The larger complex contained the intact p160MBP and various ribosomal subunits. Treatment of cells with actinomycin D (ActD), cisplatin or UV, all of which inhibit ribosome biogenesis, induced processing of p160MBP into p140MBP and p67MBP. ActD, cisplatin and UV also induced a translocation of Mybbp1a from the nucleolus to the nucleoplasm. Both small and large Mybbp1a complexes contained nucleophosmin and nucleolin. In contrast, nucleostemin was detected only in the large complex, while the cell cycle‐regulated protein EBP1 was only in the small complex. These results suggest that Mybbp1a may connect the ribosome biogenesis and the Myb‐dependent transcription, which controls cell cycle progression and proliferation.
Defining the function of β‐catenin tyrosine phosphorylation in cadherin‐mediated cell–cell adhesion
Authors: Tominaga Junji , Fukunaga Yoshitaka , Abelardo Edgardo , Nagafuchi Akira
Published: January 2009

β‐catenin is a key protein in cadherin–catenin cell adhesion complex and its tyrosine phosphorylation is believed to cause destruction of junctional apparatus. The broad spectrum of substrates for kinases and phosphatases, however, does not rule out tyrosine phosphorylation of other junctional proteins as the main culprit in reduction of cell adhesion activity. Further, the endogenous β‐catenin perturbs detailed functional analysis of phosphorylated mutant β‐catenin in living cells. To directly evaluate the effect of β‐catenin tyrosine phosphorylation in cell adhesion, we utilized F9 cells in which expression of endogenous β‐catenin and its closely related protein plakoglobin were completely shut down. We also used α‐catenin‐deficient (αD) cells to evaluate the role of α‐catenin on β‐catenin tyrosine phosphorylation. We show that β‐catenin with phosphorylation mutation at 654th tyrosine forms functional cadherin–catenin complex to mediate strong cadherin‐mediated cell adhesion. Moreover, we show that 64th and 86th tyrosines are mainly phosphorylated in F9 cells, especially in the absence of α‐catenin. Phosphorylation of these tyrosine residues, however, does not affect cadherin‐mediated cell adhesion activity. Our data identified a novel site phosphorylated by endogenous tyrosine kinases in β‐catenin. We also demonstrate that tyrosine phosphorylation of β‐catenin might regulate cadherin‐mediated cell adhesion in a more complicated way than previously expected.
Establishment of cell polarity by afadin during the formation of embryoid bodies
Authors: Komura Hitomi , Ogita Hisakazu , Ikeda Wataru , Mizoguchi Akira , Miyoshi Jun , Takai Yoshimi
Published: January 2009

Afadin directly links nectin, an immunoglobulin‐like cell–cell adhesion molecule, to actin filaments (F‐actin) at adherens junctions (AJs). The nectin–afadin complex is important for the formation of not only AJs but also tight junctions (TJs) in epithelial cells. Studies using afadin‐knockout mice have revealed that afadin is indispensable for embryonic development by organizing the formation of cell–cell junctions. However, the molecular mechanism of cell–cell junction disorganization during embryonic development in afadin‐knockout mice is poorly understood. To address this, we took advantage of embryoid bodies (EBs) as a model system. The formation of cell–cell junctions including AJs and TJs was impaired in afadin‐null EBs. The proper accumulation of the Par complex and the activation of Cdc42 and atypical PKC (aPKC), which are crucial for the formation of cell polarity, were also inhibited by knockout of afadin. In addition, the disruption of afadin caused the abnormal deposition of laminin and the dislocalization of its receptors integrin α6 and integrin β1. These results indicate that afadin organizes the formation of cell–cell junctions by regulating cell polarization in early embryonic development.
Quantifying photosynthetic capacity and its relationship to leaf nitrogen content for global‐scale terrestrial biosphere models
Authors: KATTGE JENS , KNORR WOLFGANG , RADDATZ THOMAS , WIRTH CHRISTIAN
Published: January 2009

Photosynthetic capacity and its relationship to leaf nitrogen content are two of the most sensitive parameters of terrestrial biosphere models (TBM) whose representation in global‐scale simulations has been severely hampered by a lack of systematic analyses using a sufficiently broad database. Here, we use data of qualitative traits, climate and soil to subdivide the terrestrial vegetation into functional types (PFT), and then assimilate observations of carboxylation capacity, Vmax (723 data points), and maximum photosynthesis rates, Amax (776 data points), into the C3 photosynthesis model proposed by Farquhar et al. to constrain the relationship of (Vmax normalised to 25 °C) to leaf nitrogen content per unit leaf area for each PFT. In a second step, the resulting functions are used to predict per PFT from easily measurable values of leaf nitrogen content in natural vegetation (1966 data points). Mean values of thus obtained are implemented into a TBM (BETHY within the coupled climate–vegetation model ECHAM5/JSBACH) and modelled gross primary production (GPP) is compared with independent observations on stand scale. Apart from providing parameter ranges per PFT constrained from much more comprehensive data, the results of this analysis enable several major improvements on previous parameterisations. (1) The range of mean between PFTs is dominated by differences of photosynthetic nitrogen use efficiency (NUE, defined as divided by leaf nitrogen content), while within each PFT, the scatter of values is dominated by the high variability of leaf nitrogen content. (2) We find a systematic depression of NUE on certain tropical soils that are known to be deficient in phosphorous. (3) of tropical trees derived by this study is substantially lower than earlier estimates currently used in TBMs, with an obvious effect on modelled GPP and surface temperature. (4) The root‐mean‐squared difference between modelled and observed GPP is substantially reduced.
Drought turns a Central European Norway spruce forest soil from an N2O source to a transient N2O sink
Authors: GOLDBERG STEFANIE DANIELA , GEBAUER GERHARD
Published: January 2009

Based on current climate scenarios, a higher frequency of summer drought periods followed by heavy rainfall events is predicted for Central Europe. It is expected that drying/rewetting events induce an increased matter cycling in soils and may contribute considerably to increased emissions of the greenhouse gas N2O on annual scales. To investigate the influence of drying/rewetting events on N2O emissions in a mature Norway spruce forest in the Fichtelgebirge area (NE Bavaria, Germany), a summer drought period of 46 days was induced by roof installations on triplicate plots, followed by a rewetting event of 66 mm experimental rainfall in 2 days. Three nonmanipulated plots served as controls. The experimentally induced soil drought was accompanied by a natural drought. During the drought period, the soil of both the throughfall exclusion and control plots served as an N2O sink. This was accompanied by subambient N2O concentrations in upper soil horizons. The sink strength of the throughfall exclusion plots was doubled compared with the control plots. We conclude that the soil water status together with the soil nitrate availability was an important driving factor for the N2O sink strength. Rewetting quickly turned the soil into a source for atmospheric N2O again, but it took almost 4 months to turn the cumulative soil N2O fluxes from negative (sink) to positive (source) values. N2O concentration and isotope analyses along soil profiles revealed that N2O produced in the subsoil was subsequently consumed during upward diffusion along the soil profile throughout the entire experiment. Our results show that long drought periods can lead to drastic decreases of N2O fluxes from soils to the atmosphere or may even turn forest soils temporarily to N2O sinks. Accumulation of more field‐scale data on soil N2O uptake as well as a better understanding of underlying mechanisms would essentially advance our knowledge of the global N2O budget.
Pharyngeal airway dimensions after chin cup treatment in Class III malocclusion subjects
Authors: TUNCER B. BALOŞ , KAYGISIZ E. , TUNCER C. , YÜKSEL S.
Published: January 2009

Summary  The objective of this study was to examine if chin cup therapy have any adverse effect on the sagittal pharyngeal dimensions in Class III malocclusion patients. Twenty patients (10 girls and 10 boys; mean age 10·31 ± 1·15 years) with skeletal Class III malocclusion, and an untreated control group (8 girls and 10 boys, mean age 9·89 ± 1·55 years) were evaluated. The chin cup appliance and an occlusal bite plate with 600 grams totally was used for 9·78 ± 0·93 months. Linear, angular and area measurements were evaluated on the cephalometric radiographs taken before and after observation and treatment periods. Treatment changes showed significant increases in maxillary forward position, effective length of the maxilla and the mandible, and vertical facial height measurements. The mandible showed a clockwise rotation revealed by the decrease in SNB and the increase in mandibular plane angles. Significant increase in the nasopharyngeal area was found when the treatment and control groups were compared. The nasopharyngeal airway area was affected by chin cup treatment, without any adverse effect on the pharyngeal airway dimensions in the short term.
The relationship between lingual‐palatal pressures and submental surface electromyographic signals
Authors: LENIUS K. , CARNABY‐MANN G. , CRARY M.
Published: January 2009

Summary  This study investigated the relationship between lingual‐palatal pressures and submental surface electromyographic (sEMG) signals. During isometric and isotonic tongue press tasks, lingual‐palatal pressures from the anterior, middle and posterior hard palate and submental sEMG signals were recorded. Peak values of both tasks and mean values of the isotonic task were analyzed using Pearson’s correlations. The correlations ranged from slightly negative (r = −0·103) between the posterior tongue bulb and sEMG peaks in the isotonic condition, to positive (r = 0·360) between the posterior tongue bulb and sEMG peaks in the isometric condition. None of the correlations were statistically significant. Overall, the correlations between submental sEMG signals and lingual‐palatal pressures were low. These results suggest that sEMG signals obtained from the submental region measure some of muscle activation during tongue press tasks, but are unable to capture discrete variations in lingual‐palatal pressure.
Threonine phosphorylation prevents promoter DNA binding of the Group B Streptococcus response regulator CovR
Authors: Lin Wan‐Jung , Walthers Don , Connelly James E. , Burnside Kellie , Jewell Kelsea A. , Kenney Linda J. , Rajagopal Lakshmi
Published: January 2009

All living organisms communicate with the external environment for their survival and existence. In prokaryotes, communication is achieved by two‐component systems (TCS) comprising histidine kinases and response regulators. In eukaryotes, signalling is accomplished by serine/threonine and tyrosine kinases. Although TCS and serine/threonine kinases coexist in prokaryotes, direct cross‐talk between these families was first described in Group B Streptococcus (GBS). A serine/threonine kinase (Stk1) and a TCS (CovR/CovS) co‐regulate toxin expression in GBS. Typically, promoter binding of regulators like CovR is controlled by phosphorylation of the conserved active site aspartate (D53). In this study, we show that Stk1 phosphorylates CovR at threonine 65. The functional consequence of threonine phosphorylation of CovR in GBS was evaluated using phosphomimetic and silencing substitutions. GBS encoding the phosphomimetic T65E allele are deficient for CovR regulation unlike strains encoding the non‐phosphorylated T65A allele. Further, compared with wild‐type or T65A CovR, the T65E CovR is unable to bind promoter DNA and is decreased for phosphorylation at D53, similar to Stk1‐phosphorylated CovR. Collectively, we provide evidence for a novel mechanism of response regulator control that enables GBS (and possibly other prokaryotes) to fine‐tune gene expression for environmental adaptation.
The importance of biological samples in longitudinal birth cohort studies
Authors: Jones Richard
Published: January 2009

Here we describe how measurements in biological samples can be used to provide direct measures of exposures to environmental pollutants, nutrients, infectious organisms and drugs of abuse, and to validate other less direct measures of exposure such as questionnaire responses. They can also be used as measures of outcome traits or intermediate phenotypes which may lie on the pathways to disease.
Taking and storing biological samples for longitudinal birth cohorts
Authors: Jones Richard
Published: January 2009

Biological samples collected as part of a longitudinal birth cohort study can add a wealth of detailed information on environmental exposures and outcome traits, and the mechanisms by which they occur. Here we advise on methods for collecting, labelling and storing different types of sample so that they can be retrieved for analysis in the future.
Array‐based genotype–phenotype correlation in a case of supernumerary ring chromosome 12
Authors: Davidsson J , Collin A , Öreberg M , Gisselsson D
Published: January 2009

Supernumerary ring chromosomes (SRC) account for approximately 10% of prenatal marker chromosomes and 60% of these SRCs are associated with an abnormal phenotype of the patient carrying them. SRCs have, with few exceptions, not been characterized at the molecular genetic level. Here, we present the first case of a SRC 12 thoroughly investigated with tiling resolution array‐based comparative genomic hybridization (array CGH); multicolor, centromere, subtelomeric and whole chromosome painting fluorescence in situ hybridization. In addition, to be able to correlate phenotypic manifestations with a possible pathogenetic outcome of the SRC 12, we retrospectively compared and reviewed all 14 cases of SRC 12 reported, including our present case. Our analyses revealed that the SRC comprised 25.53–46.40 Mb of chromosome 12, a region known to harbor 47 annotated genes of which nine were of putative pathogenetic relevance. Reviewing the previously described cases of SRC 12, we could not establish any specific recurrent features associated with this type of SRC. This most probably reflects heterogeneity in break‐point distribution among the reported cases, resulting in differently sized ring chromosomes and hence varying phenotypic traits of the patients. Detailed genomic evaluation, by array CGH or similar techniques may thus be of importance to predict the clinical course in individual cases.
Two novel functional mutations in the Na+,K+‐ATPase α2‐subunit ATP1A2 gene in patients with familial hemiplegic migraine and associated neurological phenotypes
Authors: Castro M‐J , Nunes B , De Vries B , Lemos C , Vanmolkot KRJ , Van Den Heuvel JJMW , Temudo T , Barros J , Sequeiros J , Frants RR , Koenderink JB , Pereira‐Monteiro JM , Van Den Maagdenberg AMJM
Published: January 2009

Mutations in the ATP1A2 gene, encoding the α2‐subunit of the Na+,K+‐ATPase, are associated with familial hemiplegic migraine type 2. The majority of ATP1A2 mutations were reported in patients with hemiplegic migraine without any additional neurological findings. Here, we report on two novel ATP1A2 mutations that were identified in two Portuguese probands with hemiplegic migraine and interesting additional clinical features. The proband’s of family 1 (with a V362E mutation) had mood alterations, classified as a borderline personality. The proband in family 2 (with a P796S mutation) had mild mental impairment, in addition to hemiplegic migraine; more severe mental retardation was observed in his brother, who also had hemiplegic migraine and carried the same mutation. Cell‐survival assays clearly showed abnormal functioning of mutant Na+,K+‐ATPase, indicating that both ATP1A2 mutants are disease causing. Additionally, our results suggest a possible causal relationship of the ATP1A2 mutations with the complex clinical phenotypes observed in the probands.
A life without pain? Hedonists take note
Authors: Young FBJ
Published: January 2009

An SCN9A channelopathy causes congenital inability to experience pain Cox et al. (2006) Nature 444: 894–898

Loss‐of‐function mutations in the Nav1.7 gene underlie congenital indifference to pain in multiple human populations Goldberg et al. (2007) Clin Genet 71: 311–319

A stop codon mutation in SCN9A causes lack of pain sensation Ahmad et al. (2007) Hum Mol Genet 16: 2114–2121

‘We cannot learn without pain.’– Aristotle
When adaptive processes go awry: gain‐of‐function in SCN9A
Authors: Young FBJ
Published: January 2009

SCN9A mutations in paroxysmal extreme pain disorder: allelic variants underlie distinct channel defects and phenotypes Fertleman et al. (2006) Neuron 52: 767–774
Dyskeratosis congenita: a genetic disorder of many faces
Authors: Kirwan M , Dokal I
Published: January 2009

Dyskeratosis congenita (DC) is an inherited syndrome exhibiting marked clinical and genetic heterogeneity. It is characterized by multiple features including mucocutaneous abnormalities, bone marrow failure and an increased predisposition to cancer. Three genetic subtypes are recognized: X‐linked recessive DC bears mutations in DKC1, the gene encoding dyskerin, a component of H/ACA small nucleolar ribonucleoprotein particles; autosomal dominant (AD) DC has heterozygous mutations in either TERC or TERT, the RNA and enzymatic components of telomerase, respectively, and autosomal recessive DC in which the genes involved remain largely elusive. Disease pathology is believed to be a consequence of chromosome instability because of telomerase deficiency due to mutations in DKC1, TERC and TERT; in patients with DKC1 mutations, defects in ribosomal RNA modification, ribosome biogenesis, translation control or mRNA splicing may also contribute to disease pathogenesis. The involvement of telomerase complex components in X‐linked and AD forms and the presence of short telomeres in DC patients suggest that DC is primarily a disease of defective telomere maintenance. Treatment is variable and complicated by the development of secondary cancers but, being a monogenic disorder, it could potentially be treated by gene therapy. DC overlaps both clinically and genetically with several other diseases including Hoyeraal–Hreidarsson syndrome, aplastic anaemia and myelodysplasia, among others and its underlying telomeric defect has implications for a broader range of biological processes including ageing and many forms of cancer.
Use of multiplex ligation‐dependent probe amplification increases the detection rate for 11p15 epigenetic alterations in Silver–Russell syndrome
Authors: Eggermann T , Schönherr N , Eggermann K , Buiting K , Ranke MB , Wollmann HA , Binder G
Published: January 2009

Silver–Russell syndrome (SRS) describes a malformation syndrome with severe intrauterine and postnatal growth retardation. Currently, two major (epi)mutations have been described: while approximately 10% of patients carry a maternal uniparental disomy of chromosome 7 (UPD7), 35–60% show a hypomethylation at the H19 differentially methylated regions (DMRs) in 11p15. Until recently, a Southern‐blot based test was routinely used to identify epimutation carriers. Nevertheless, this test was time consuming and hampered by the huge amount of genomic DNA needed. With the methylation‐specific multiplex ligation‐dependent probe amplification assay (MLPA) for SRS, a PCR‐based test is now available, allowing the analysis also of small amounts of DNA. Probes in this assay hybridize to the H19 DMRs but do not cover the genomic target of the Southern‐blot probe. We now screened 72 patients with SRS by MLPA. Hypomethylation of the H19 DMRs was confirmed in all patients analyzed by Southern blot. In addition, we identified six individuals with hypomethylation of the H19 DMR who had previously normal blot results. This discrepancy can be explained by the observed generally lower degree of demethylation in this group, possibly not detectable by the less sensitive Southern‐blot method but also with a varying degree of methylation at different DMRs in the same individual. Apart from hypomethylation in the H19 DMR, we observed a slight demethylation for one of the IGF2 probes. The total detection rate of 11p15 hypomethylation is now increased to >38%. Considering maternal UPD7 and chromosomal aberrations, (epi)genetic alterations now account for more than 50% of SRS patients. In summary, MLPA represents an easy, low cost and reliable system in the molecular diagnostics of SRS.
Mutation and phenotypic spectrum in patients with cardio‐facio‐cutaneous and Costello syndrome
Authors: Schulz AL , Albrecht B , Arici C , Van Der Burgt I , Buske A , Gillessen‐Kaesbach G , Heller R , Horn D , Hübner CA , Korenke GC , König R , Kress W , Krüger G , Meinecke P , Mücke J , Plecko B , Rossier E , Schinzel A , Schulze A , Seemanova E , Seidel H , Spranger S , Tuysuz B , Uhrig S , Wieczorek D , Kutsche K , Zenker M
Published: January 2009

Cardio‐facio‐cutaneous (CFC) and Costello syndrome (CS) are congenital disorders with a significant clinical overlap. The recent discovery of heterozygous mutations in genes encoding components of the RAS–RAF–MAPK pathway in both CFC and CS suggested a similar underlying pathogenesis of these two disorders. While CFC is heterogeneous with mutations in BRAF, MAP2K1, MAP2K2 and KRAS, HRAS alterations are almost exclusively associated with CS. We carried out a comprehensive mutation analysis in 51 CFC‐affected patients and 31 individuals with CS. Twelve different BRAF alterations were found in twenty‐four patients with CFC (47.0%), two MAP2K1 mutations in five (9.8%) and two MAP2K2 sequence variations in three CFC‐affected individuals (5.9%), whereas three patients had a KRAS alteration (5.9%). We identified four different missense mutations of HRAS in twenty‐eight cases with CS (90.3%), while KRAS mutations were detected in two infants with a phenotype meeting criteria for CS (6.5%). In 14 informative families, we traced the parental origin of HRAS alterations and demonstrated inheritance of the mutated allele exclusively from the father, further confirming a paternal bias in the parental origin of HRAS mutations in CS. Careful clinical evaluation of patients with BRAF and MAP2K1/2 alterations revealed the presence of slight phenotypic differences regarding craniofacial features in MAP2K1‐ and MAP2K2‐mutation positive individuals, suggesting possible genotype–phenotype correlations.