bluuebunny/crossref_metadata_2025 huggingface dataset:
Differences of the porcine amelogenin X and Y chromosome genes (AMELX and AMELY) and their application for sex determination in pigs
Authors: Fontanesi Luca , Scotti Emilio , Russo Vincenzo
Published: April 2008

Molecular sexing in wild and domestic animals has becoming an important issue in several fields including reproduction. X and Y chromosome‐specific sequence differences of the amelogenin genes (AMELX and AMELY) have been described in different mammalian species and used for sex determination. We studied the possibility to use sequence variability between the porcine AMELX and AMELY genes for sex determination in pigs. Sequence analysis of about 400 bp of intron 3 of the porcine amelogenin genes showed the presence of a 9–10 bp deletion in AMELY gene compared to AMELX sequences. Moreover, one single nucleotide polymorphism (SNP) was detected for the AMELY sequence. Four other SNPs and 1 bp insertion differentiated three AMELX haplotypes indicating an unexpected quite high nucleotide diversity for a chromosome X region. Two sex determination assays targeting the 9–10 bp difference between AMELX and AMELY were developed. Assessment of the accuracy of the amelogenin assays to correctly sex individuals was tested on 329 pigs belonging to different breeds/lines. All analysed animals were correctly sexed with the new designed amelogenin tests. No amplification was obtained in human, cattle, goat, sheep, and horse genomic DNA. These assays can be used for sex diagnosis of small amounts of genomic DNA (20 pg) obtained from different sources including embryo biopsies, hair, meat, and other biological specimens. Thus, apart from the application in the reproduction field, these tests can be useful in several other sectors including forensics, archaeozoology, meat production, and processing as well as for quality control in sample identification. Mol. Reprod. Dev. 75: 1662–1668, 2008. © 2008 Wiley‐Liss, Inc.
Association of TGIFLX/Y mRNA expression with azoospermia in infertile men
Authors: Aarabi M. , Ousati‐Ashtiani Z. , Nazarian A. , Modarressi M.H. , Heidari M.
Published: April 2008

HOX genes are well‐known to encode transcriptional regulatory proteins that play essential roles in directing embryonic development. TGIFLX/Y contains two genes, TGIFLX (X‐linked) and TGIFLY (Y‐linked), which are specifically expressed in human adult testes. The function(s) of these genes in normal and abnormal development are unknown. To investigate the potential role(s) of the TGIFLX/Y gene in infertile males, a nested reverse transcriptase polymerase chain reaction (RT‐PCR) was performed on testicular samples from 110 patients with nonobstructive azoospermia. Although the only 51 (46.4%) of the 110 patients had detectable levels of TGIFLY expression, none of the patients with various spermatogenesis defects showed any of the TGIFLX gene expression found in normal testes. These results suggest that the function of TGIFLX may be required for the regulation of spermatogonial stem cell specification and proliferation. While functional similarity has been demonstrated among some homeobox genes, these results may refute the suggestion of redundancy between TGIFLX and TGIFLY. Furthermore, TGIFLX might be a potential biomarker candidate for male infertility assessment. Mol. Reprod. Dev. 75: 1761–1766, 2008. © 2008 Wiley‐Liss, Inc.
Investigating the role of murine epididymosomes and uterosomes in GPI‐linked protein transfer to sperm using SPAM1 as a model
Authors: Griffiths Genevieve S. , Galileo Deni S. , Reese Kristen , Martin‐DeLeon Patricia A.
Published: April 2008

Sperm uptake of glycosyl phosphatidylinositol (GPI)‐linked proteins from luminal fluids has been shown to occur in male and estrous female reproductive tracts. In males, this is attributed to membranous vesicles secreted into the epididymis and prostate. While epididymosomes have been characterized, there have been no reports of the presence of vesicles in female luminal fluids. Here we report the presence of vesicles, characterized as “uterosomes,” in the murine estrous female reproductive fluid; and use Sperm Adhesion Molecule 1 (SPAM1/PH‐20), a well‐known hyaluronidase found in male and female fluids, as a model to investigate vesicle‐mediated GPI‐linked protein transfer to sperm. Epididymosomes and uterosomes isolated after ultracentrifugation of epididymal (ELF) and uterine luminal fluid (ULF) were analyzed by electron microscopy and shown to be ∼10–70 and ∼15–50 nm in diameter. The structural integrity of uterosomes was confirmed by their resistance to hypo‐osmotic and freeze/thaw stresses; and immunogold labeling localized SPAM1 to their outer membrane surface, as was the case for epididymosomes. SPAM1 was acquired by caudal sperm during incubation in epididymosomes and uterosomes; uptake was abolished when the GPI anchor was enzymatically cleaved. Sperm analyzed by confocal and transmission electron microscopy (TEM) after incubation in fluorescently labeled vesicles revealed the label on the membrane over the acrosome and midpiece of the flagella, where SPAM1 normally resides. High magnification TEM images demonstrated vesicles juxtaposed to the sperm plasma membrane potentially transferring SPAM1. Taken together, these results implicate vesicular docking as the mechanism of vesicle‐mediated GPI‐linked protein transfer to sperm from murine reproductive fluids. Mol. Reprod. Dev. 75: 1627–1636, 2008. © 2008 Wiley‐Liss, Inc.
Detection and characterization of gamete‐specific molecules in Mytilus edulis using selective antibody production
Authors: Stuckas Heiko , Messerschmidt Katrin , Putzler Sascha , Baumann Otto , Schenk Jörg A. , Tiedemann Ralph , Micheel Burkhard
Published: April 2008

The mussel Mytilus edulis can be used as model to study the molecular basis of reproductive isolation because this species maintains its species integrity, despite of hybridizing in zones of contact with the closely related species M. trossulus or M. galloprovincialis. This study uses selective antibody production by means of hybridoma technology to identify molecules which are involved in sperm function of M. edulis. Fragmented sperm were injected into mice and 25 hybridoma cell clones were established to obtain monoclonal antibodies (mAb). Five clones were identified producing mAb targeting molecules putatively involved in sperm function based on enzyme immunoassays, dot and Western blotting as well as immunostaining of tissue sections. Specific localization of these mAb targets on sperm and partly also in somatic tissue suggests that all five antibodies bind to different molecules. The targets of the mAb obtained from clone G26‐AG8 were identified using mass spectrometry (nano‐LC‐ESI‐MS/MS) as M6 and M7 lysin. These acrosomal proteins have egg vitelline lyses function and are highly similar (76%) which explains the cross reactivity of mAb G26‐AG8. Furthermore, M7 lysin was recently shown to be under strong positive selection suggesting a role in interspecific reproductive isolation. This study shows that M6 and M7 lysin are not only found in the sperm acrosome but also in male somatic tissue of the mantle and the posterior adductor muscle, while being completely absent in females. The monoclonal antibody G26‐AG8 described here will allow elucidating M7/M6 lysin function in somatic and gonad tissue of adult and developing animals. Mol. Reprod. Dev. 76: 4–10, 2009. © 2008 Wiley‐Liss, Inc.
Synergistic effect between a char forming agent (CFA) and microencapsulated ammonium polyphosphate on the thermal and flame retardant properties of polypropylene
Authors: Nie Shibin , Hu Yuan , Song Lei , He Qingliang , Yang Dandan , Chen Hao
Published: April 2008

The synergistic effect between a char forming agent (CFA) and microencapsulated ammonium polyphosphate (MAPP) on the thermal and flame retardancy of polypropylene (PP) are investigated by limiting oxygen index (LOI), UL‐94 test, cone calorimetry, thermogravimetric analysis (TGA), scanning electron micrograph (SEM), and water resistance test. The results of cone calorimetry show that heat release rate peak (PHRR), total heat release (THR), and the mass loss of PP with 30 wt% intumescent flame retardant (IFR, CFA/MAPP = 1:2) decreases remarkably compared with that of pure PP. The HRR, THR, and mass loss decrease, respectively from 1140 to 100 kW/m2, from 96 to 16.8 MJ/m2, and from 100 to 40%. The PP composite with CFA/MAPP = 1:2 has the best water resistance, and it can still obtain a UL‐94 V‐0 rating after 168 hr soaking in water. Copyright © 2008 John Wiley & Sons, Ltd.
Helical arrangement of a hydrogen‐bonded columnar liquid crystal induced by a centered triphenylene derivative bearing chiral side‐chains
Authors: Ishihara Shinsuke , Furuki Yusuke , Takeoka Shinji
Published: April 2008

A hydrogen‐bonded helical columnar liquid crystal was synthesized, in which the helical structure is induced by a centered triphenylene derivative bearing chiral side‐chains. The triphenylene derivative, 2,6,10‐tris(carboxymethoxy)‐3,7,11‐tris((S)‐(‐)‐2‐methyl‐1‐butanoxy)triphenylene (TPC4(S)), and a dendric amphiphile, 3,5‐bis‐(3,4‐bis‐dodecyloxy‐benzyloxy)‐N‐pyridine‐4‐yl‐benzamide (DenC12), were mixed in a 1:3 ratio to obtain a complex, TPC4(S)‐DenC12. Analyses by 1H‐NMR spectroscopy, diffusion ordered spectroscopy (DOSY), CD spectroscopy, infrared (IR) spectroscopy, polarized optical microscopy (POM), differential scanning calorimetry (DSC), and X‐ray diffractometry revealed that TPC4(S)‐DenC12 self‐assembles to form helical columnar stacks in solution and a helical columnar liquid crystal in bulk. The hydrogen bonding between TPC4(S) and DenC12 is essential for the helical columnar organization, and the preference for a one‐handed helical conformation is likely derived from the steric interaction between the chiral side‐chains and the dendric amphiphiles in the packing of the hydrogen‐bonded columnar assemblies. Copyright © 2008 John Wiley & Sons, Ltd.
Proteomic analysis of the venom from the fish eating coral snake Micrurus surinamensis: Novel toxins, their function and phylogeny
Authors: Olamendi‐Portugal Timoteo , Batista Cesar V. F. , Restano‐Cassulini Rita , Pando Victoria , Villa‐Hernandez Oscar , Zavaleta‐Martínez‐Vargas Alfonso , Salas‐Arruz Maria C. , de la Vega Ricardo C. Rodríguez , Becerril Baltazar , Possani Lourival D.
Published: April 2008

The protein composition of the soluble venom from the South American fish‐eating coral snake Micrurus surinamensis surinamensis, here abbreviated M. surinamensis, was separated by RP‐HPLC and 2‐DE, and their components were analyzed by automatic Edman degradation, MALDI‐TOF and ESI‐MS/MS. Approximately 100 different molecules were identified. Sixty‐two components possess molecular masses between 6 and 8 kDa, are basically charged molecules, among which are cytotoxins and neurotoxins lethal to fish (Brachidanios rerio). Six new toxins (abbreviated Ms1–Ms5 and Ms11) were fully sequenced. Amino acid sequences similar to the enzymes phospholipase A2 and amino acid oxidase were identified. Over 20 additional peptides were identified by sequencing minor components of the HPLC separation and from 2‐DE gels. A functional assessment of the physiological activity of the six toxins was also performed by patch clamp using muscular nicotinic acetylcholine receptor assays. Variable degrees of blockade were observed, most of them reversible. The structural and functional data obtained were used for phylogenetic analysis, providing information on some evolutionary aspects of the venom components of this snake. This contribution increases by a factor of two the total number of α‐neurotoxins sequenced from the Micrurus genus in currently available literature.
The 6th East Midlands Proteomics Workshop supported by the BSPR and BMSS 14 November 2007, Nottingham, UK
Authors: Layfield Robert , Matharoo‐Ball Balwir
Published: April 2008

Now in its 6th year, the East Midlands Proteomics workshop held in November 2007 brought together over 200 scientists with a common interest in proteomic techniques and their application to complex biological and biomedical problems. For the first time, this meeting was jointly supported by the British Society for Proteome Research (BSPR) and British Mass Spectrometry Society (BMSS).
JunD mediates androgen‐induced oxidative stress in androgen dependent LNCaP human prostate cancer cells
Authors: Mehraein‐Ghomi Farideh , Lee Elyse , Church Dawn R. , Thompson Todd A. , Basu Hirak S. , Wilding George
Published: April 2008

BACKGROUND

Numerous and compelling evidence shows that high level of reactive oxygen species (ROS) plays a key role in prostate cancer occurrence, recurrence and progression. The molecular mechanism of ROS overproduction in the prostate gland, however, remains mostly unknown. Unique AP‐1 transcription factor JunD has been shown to inhibit cell proliferation, promote differentiation and mediate stress responses in a variety of eukaryotic cells. We previously reported that androgen–androgen receptor induced ROS production in androgen‐dependent LNCaP human prostate cancer cells is associated with increased JunD level/AP‐1 transcriptional activity.

METHODS

LNCaP cells constitutively overexpressing a functionally inactive form of JunD (JunDΔTA) or stably transfected with JunD siRNA (siJunD) to suppress JunD protein expression were established. Overexpression of JunD in LNCaP cells using transient transfection method was applied to assess the induction of ROS production in LNCaP cells. DCF assay was used to measure the ROS concentrations in the transfected as well as non‐transfected control cells. RT‐PCR and Western blot analyses were used to confirm silencing or overexpression of JunD in the transfected cells.

RESULTS

In the absence of androgen, LNCaP cells transiently transfected with a JunD overexpressing vector have relatively enhanced cellular ROS levels as compared to LNCaP cells transfected with a vector control. LNCaP cells that fail to express functional JunD (JunDΔTA or siJunD) do not exhibit any increase in ROS production in response to androgen.

CONCLUSION

Based on these data, we conclude that JunD is an essential mediator of the androgen‐induced increase in ROS levels in LNCaP cells. Prostate 68:924–934, 2008. © 2008 Wiley‐Liss, Inc.
Restoration of PTEN expression alters the sensitivity of prostate cancer cells to EGFR inhibitors
Authors: Wu Z. , Gioeli D. , Conaway M. , Weber M. J. , Theodorescu D.
Published: April 2008

Introduction

Prostate cancer (CaP) progression from an androgen‐dependent to an androgen‐independent state is associated with overexpression of EGFR family members or activation of their downstream signaling pathways, such as PI3K‐Akt and MAPK. Although there are data implicating PI3K‐Akt or MAPK pathway activation with resistance to EGFR inhibitors in CaP, the potential cross‐talk between these pathways in response to EGFR or MAPK inhibitors remains to be examined.

Methods

Cross‐talk between PTEN and MAPK signaling and its effects on CaP cell sensitivity to EGFR or MAPK inhibitors were examined in a PTEN‐null C4‐2 CaP cell, pTetOn PTEN C4‐2, where PTEN expression was restored conditionally.

Results

Expression of PTEN in C4‐2 cells exposed to EGF or serum was associated with increased phospho‐ERK levels compared to cells without PTEN expression. Similar hypersensitivity of MAPK signaling was observed when cells were treated with a PI3K inhibitor LY294002. This enhanced sensitivity of MAPK signaling in PTEN‐expressing cells was associated with a growth stimulatory effect in response to EGF. Furthermore, EGFR inhibitors gefitinib and lapatinib abrogated hypersensitivity of MAPK signaling and cooperated with PTEN expression to inhibit cell growth in both monolayer and anchorage‐independent conditions. Similar cooperative growth inhibition was observed when cells were treated with the MEK inhibitor, CI1040, in combination with PTEN expression suggesting that inhibition of MAPK signaling could mediate the cooperation of EGFR inhibitors with PTEN expression.

Conclusions

Our results suggest that signaling cross‐talk between the PI3K‐Akt and MAPK pathways occurs in CaP cells, highlighting the potential benefit of targeting both the PI3K‐Akt and MAPK pathways in CaP treatment. Prostate 68:935–944, 2008. © 2008 Wiley‐Liss, Inc.
Structural characterization and anti‐angiogenic properties of prostate‐specific antigen isoforms in seminal fluid
Authors: Mattsson Johanna M. , Valmu Leena , Laakkonen Pirjo , Stenman Ulf‐Håkan , Koistinen Hannu
Published: April 2008

BACKGROUND

The prostate produces high levels of prostate‐specific antigen (PSA), which has been shown to exert anti‐angiogenic properties and thus might slow down prostate tumor growth. It has been suggested that the protease activity of PSA is not needed for its anti‐angiogenic function. We have previously shown that seminal fluid contains both active and inactive, internally cleaved forms of PSA. The precise structural differences between these isoforms and their function are not known.

METHODS

To elucidate the structures, we purified PSA from seminal fluid and separated it by anion‐exchange chromatography into six different isoforms, which were characterized by mass spectrometry. The anti‐angiogenic activity of these PSA‐isoforms was analyzed by human umbilical vein endothelial cell (HUVEC) tube formation assay.

RESULTS

The enzymatically active PSA‐isoforms had an intact peptide moiety but could be separated into three isoforms based on differences in glycosylation. The major isoform contained PSA with a biantennary carbohydrate with terminal sialic acids on both antennae. The other active isoforms showed significant carbohydrate heterogeneity, containing one or no sialic acid. The inactive isoforms were internally cleaved at several different positions, but the fragments were held together by disulphide bonds. The enzymatic activity of PSA correlated with its inhibitory effect on the endothelial cell tube formation and the inhibition was dose‐dependent at physiological concentrations, whereas enzymatically inactive internally cleaved PSA‐isoforms had no effect.

CONCLUSIONS

Our results show that the anti‐angiogenic effect of PSA is based on its proteolytic activity. Prostate 68:945–954, 2008. © 2008 Wiley‐Liss, Inc.
Prediction of lymphatic invasion by peritumoral lymphatic vessel density in prostate biopsy cores
Authors: Kuroda Kenji , Horiguchi Akio , Asano Takako , Asano Tomohiko , Hayakawa Masamichi
Published: April 2008

BACKGROUND

Lymphatic invasion in radical prostatectomy specimens has been suggested to be an unfavorable prognostic factor in clinically localized prostate cancer. Lymphangiogenesis detected by antibodies specific for lymphatic endothelial cells has been associated with lymphatic invasion and lymph node metastasis in prostate cancer. This study was designed to examine whether lymphangiogenesis in prostate biopsy could predict lymphatic spread in radical prostatectomy specimens.

METHODS

Paraffin‐embedded positive biopsy cores obtained from 99 patients who underwent radical prostatectomy at our institution were immunostained with D2‐40 monoclonal antibody, which specifically recognizes lymphatic endothelium. The association between lymphatic parameters in prostate biopsy and pathological parameters in radical prostatectomy specimens was analyzed.

RESULTS

Peritumoral and intratumoral lymphatic (ITL) vessels were observed in 90 (90.9%) and 23 cases (23.2%). Average and maximal peritumoral lymphatic vessel density (PTLD) and the presence of ITL in positive biopsy cores were significantly associated with positive biopsy core rates (P = 0.0015 for average PTLD, P < 0.0001 for maximal PTLD, and P = 0.0038 for ITL) and lymphatic vessel invasion (P < 0.0001 for average PTLD, P < 0.0001 for maximal PTLD, and P = 0.0322 for ITL). Among preoperative parameters, the biopsy Gleason score (P = 0.0092, HR = 6.108) and average PTLD (P = 0.0034, HR = 1.860) were significant predictors of lymphatic invasion in radical prostatectomy specimens in multivariate analysis.

CONCLUSIONS

PTLD in prostate biopsy specimens assessed by immunohistochemistry using D2‐40 antibody could be a useful parameter for predicting lymphatic spread of clinically localized prostate cancer. Prostate 68:1057–1063, 2008. © 2008 Wiley‐Liss, Inc.
Region‐specific role of water in collagen unwinding and assembly
Authors: Ravikumar Krishnakumar M. , Hwang Wonmuk
Published: April 2008

Conformational stability of the collagen triple helix affects its turnover and determines tissue homeostasis. Although it is known that the presence of imino acids (prolines or hydroxyprolines) confer stability to the molecule, little is known regarding the stability of the imino‐poor region lacking imino acids, which plays a key role in collagen cleavage. In particular, there have been continuing debates about the role of water in collagen stability. We addressed these issues using molecular dynamics simulations on 30‐residue long collagen triple helices, including a structure that has a biologically relevant 9‐residue imino‐poor region from type III collagen (PDB ID: 1BKV). A torsional map approach was used to characterize the conformational motion of the molecule that differ between imino‐rich and imino‐poor regions. At temperatures 300 K and above, unwinding initiates at a common cleavage site, the glycine‐isoleucine bond in the imino‐poor region. This provides a linkage between previous observations that unwinding of the imino‐poor region is a requirement for collagenase cleavage, and that isolated collagen molecules are unstable at body temperature. We found that unwinding of the imino‐poor region is controlled by dynamic water bridges between backbone atoms with average lifetimes on the order of a few picoseconds, as the degree of unwinding strongly correlated with the loss of water bridges, and unwinding could be either prevented or enhanced, respectively by enforcing or forbidding water bridge formation. While individual water bridges were short‐lived in the imino‐poor region, the hydration shell surrounding the entire molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 Å, in good agreement with the experimentally measured inter‐collagen distances. These results elucidate the general role of water in collagen turnover: water not only affects collagen cleavage by controlling its torsional motion, but it also forms a larger‐scale lubrication layer mediating collagen self‐assembly. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Insights from the energetics of water binding at the domain‐ligand interface of the Src SH2 domain
Authors: Fabritiis Gianni De , Geroult Sebastien , Coveney Peter V. , Waksman Gabriel
Published: April 2008

SH2 domains play important roles in signal transduction by binding phosphorylated tyrosine residues on cell surface receptors. In an effort to understand the mechanism of ligand binding and more specifically the role of water, we have designed a general computational protocol based on the potential of mean force to compute the thermodynamics of water molecules at the protein–ligand interface for two SH2 domain complexes of the Src kinase, those bound to the two peptides Ac‐PQpYEpYI‐NH2 and Ac‐PQpYIpYV‐NH2 where pY indicates a phosphotyrosine. These two peptides were chosen because they have similar binding affinities but very different entropic/enthalpic thermodynamic binding signatures, indicating different interactions with solvent. We find that the isoleucine to valine mutation at position +3 (the third amino acid C‐terminal to pY) in the ligand has only limited impact on the water structure. By contrast, the glutamic acid to isoleucine mutation at position +1 has a significant impact by not only abrogating a local hydrophilic binding site but, more importantly and surprisingly, inducing a favorable nonlocal entropic contribution from the water molecules around the phophorylated tyrosine at the +2 position. Our study demonstrates the validity of the method reported here for exploring the thermodynamic solvation landscape of protein–protein interactions. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Structural studies of prephenate dehydratase from Mycobacterium tuberculosis H37Rv by SAXS, ultracentrifugation, and computational analysis
Authors: Vivan Ana Luiza , Caceres Rafael Andrade , Beltran Abrego Jose Ramon , Borges Júlio César , Neto João Ruggiero , Ramos Carlos H.I , de Azevedo Walter Filgueira , Basso Luiz Augusto , Santos Diógenes Santiago
Published: April 2008

Tuberculosis (TB) is one of the most common infectious diseases known to man and responsible for millions of human deaths in the world. The increasing incidence of TB in developing countries, the proliferation of multidrug resistant strains, and the absence of resources for treatment have highlighted the need of developing new drugs against TB. The shikimate pathway leads to the biosynthesis of chorismate, a precursor of aromatic amino acids. This pathway is absent from mammals and shown to be essential for the survival of Mycobacterium tuberculosis, the causative agent of TB. Accordingly, enzymes of aromatic amino acid biosynthesis pathway represent promising targets for structure‐based drug design. The first reaction in phenylalanine biosynthesis involves the conversion of chorismate to prephenate, catalyzed by chorismate mutase. The second reaction is catalyzed by prephenate dehydratase (PDT) and involves decarboxylation and dehydratation of prephenate to form phenylpyruvate, the precursor of phenylalanine. Here, we describe utilization of different techniques to infer the structure of M. tuberculosis PDT (MtbPDT) in solution. Small angle X‐ray scattering and ultracentrifugation analysis showed that the protein oligomeric state is a tetramer and MtbPDT is a flat disk protein. Bioinformatics tools were used to infer the structure of MtbPDT. A molecular model for MtbPDT is presented and molecular dynamics simulations indicate that MtbPDT is stable. Experimental and molecular modeling results were in agreement and provide evidence for a tetrameric state of MtbPDT in solution. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Analysis of the structure of human apo‐S100B at low temperature indicates a unimodal conformational distribution is adopted by calcium‐free S100 proteins
Authors: Malik Shahid , Revington Matthew , Smith Steven P. , Shaw Gary S.
Published: April 2008

S100B is one of the best‐characterized members of the calcium‐signaling S100 protein family. Most S100 proteins are dimeric, with each monomer containing two EF‐hand calcium‐binding sites (EF1, EF2). S100B and other S100 proteins respond to calcium increases in the cell by coordinating calcium and undergoing a conformational change that allows them to interact with a variety of cellular targets. Although several three dimensional structures of S100 proteins are available in the calcium‐free (apo‐) state it has been observed that these structures appear to adopt a wide range of conformations in the EF2 site with respect to the positioning of helix III, the helix that undergoes the most dramatic calcium‐induced conformational change. In this work, we have determined the structure of human apo‐S100B at 10°C to examine whether temperature might be responsible for these structural differences. Further, we have used this data, and other available apo‐S100 structures, to show that despite the range of interhelical angles adopted in the apo‐S100 structures, normal Gaussian distributions about the mean angles found in the structure of human apo‐S100B are observed. This finding, only obvious from the analysis of all available apo‐S100 proteins, provides direct structural evidence that helix III is a loosely packed helix. This is likely a necessary functional property of the S100 proteins that facilitates the calcium‐induced conformational change of helix III. In contrast, the calcium‐bound structures of the S100 proteins show significantly smaller variability in the interhelical angles. This shows that calcium binding to the S100 proteins causes not only a conformational change but results in a tighter distribution of helices within the EF2 calcium binding site required for target protein interactions. Proteins 2008. © 2008 Wiley‐Liss, Inc.
Evaluation of the environmental fate of thymol and phenethyl propionate in the laboratory
Authors: Hu Dingfei , Coats Joel
Published: April 2008

BACKGROUND: The natural monoterpenoid pesticides thymol and phenethyl propionate (PEP) are used indoors and outdoors, but their fate in the environment has not been reported. In order better to understand their impact on the environment, water metabolism and soil metabolism studies were conducted with thymol and PEP at a concentration of 10 µg g−1 in water and in soil under laboratory conditions.

RESULTS: Dissipation half‐lives of thymol and PEP were 16 and 5 days in water and 5 and 4 days in soil. 2‐Phenylethanol and 2‐(4‐hydroxyphenyl)ethanol were detected as primary degradation products of PEP. Over time, a considerable volatilization loss of thymol, but not of phenethyl propionate, was found in the 1 month study under the experimental conditions used. Less than 6% of thymol and PEP were detected as bound residues, and less than 3% were mineralized during the 30 day study.

CONCLUSION: In order to maximize the pesticidal effect, more attention should be paid to the temperature for thymol than for PEP when they are being applied, owing to the high volatility of the former. Thymol and PEP pose low risks to the ecosystem because of their rapid dissipation and low bound residues in the environment. Copyright © 2008 Society of Chemical Industry
Long term exposure effect of a unique metabolic nutrition system containing a diverse group of phytochemicals on serum chemistry and genomic and non‐genomic changes in the liver of female B6C3F1 mice
Authors: Ray Sidhartha D. , Parmar Mayur , Syed Ismail , Rathod Jasmine , Zinkovsky Daniel , Bulku Elida , Gigliotti Joseph , Hackman Robert M. , Stohs Sidney J.
Published: April 2008

The nutritional value and therapeutic benefits coupled with presumed safety have heightened interest in the use of custom designed dietary supplements. Their use has increased substantially since the passage of the 1994 Dietary Supplement Health Education Act. However, few well‐controlled studies have been conducted to assess the safety and potential adverse effects of dietary supplements. MNSO (MNS Orange‐AdvoCare®) is a unique combination of vitamins, minerals, omega‐3 fatty acids and herbal extracts designed to provide a strong foundation of nutritional support, enhance thermogenesis, heighten energy levels and improve immune status. This investigation was designed to explore the safety and toxic effects, if any, of 12 months of continuous exposure to the ephedra and caffeine containing MNSO on serum chemistry and histopathology of seven vital target organs in female B6C3F1 mice. MNSO is enriched with extracts of citrus, Ephedra, Ginkgo, green tea and Ocimum. In this study, mice were fed control (‐MNSO) or MNSO (1×–10×, 1× = daily human dose) diets. Blood was collected from all groups including the control every 4 months for serum chemistry analysis (enzyme, lipid, carbohydrate, electrolyte profiles), and liver tissue was collected for tissue biochemistry and histopathology. Multiple biochemical parameters included: (i) determination of oxidative stress via lipid peroxidation and (ii) assessment of genomic integrity via DNA fragmentation. In addition, food consumption and body weight changes were also monitored biweekly. The data showed that 12 months ingestion of 10×‐MNSO did not significantly influence organ histopathology, alter the normal serum chemistry profile or any of the crucial tissue biochemistry. MNSO‐exposed animals were more active, consumed more food and were relatively leaner compared with the controls. This study indicates that a caffeine and ephedra containing metabolic nutrition system is non‐toxic and non‐hepatotoxic in mice at up to 10× the human consumption dose of ephedra. Copyright © 2008 John Wiley & Sons, Ltd.
Biphasic effects of Morus alba leaves green tea extract on mice in chronic forced swimming model
Authors: Sattayasai Jintana , Tiamkao Siriporn , Puapairoj Prapawadee
Published: April 2008

In this study, the effects of an aqueous extract of Morus alba leaves green tea (ME) on mouse behaviors (depression, anxiety, climbing activity and thermal response), muscle coordination and muscle strength were studied. Male IRC mice received a single intraperitoneal injection of either the ME, desipramine or diazepam. Thirty minutes after injection, the mice were tested in all experimental models. A significant antidepressant‐like effect could be detected in the animals receiving either 100 or 200 mg/kg ME. The effect of 200 mg/kg ME in decreasing the immobility time was comparable to 10 mg/kg desipramine. With higher dose (1000 mg/kg), a significant increase in immobility time could be observed. In the elevated plus maze, no increase in time in the open arm could be observed in mice treated with ME at either 100 or 200 mg/kg. However, high doses of ME (500 or 1000 mg/kg) decreased both time in the open arm and the number of entries in the maze. No change in thermal response could be seen in mice treated with ME at doses up to 500 mg/kg, however, at 1000 mg/kg, the response time to heat was increased significantly. The ME at either 500 or 1000 mg/kg also decreased muscle coordination, strength and climbing activity significantly when compared with the control. This study suggests that ME possesses an antidepressant‐ without an anxiolytic‐like effect, however, at high doses, the extract might show the sedative effect and alter other functions such as muscle strength, animal activity in the maze and pain response. Copyright © 2008 John Wiley & Sons, Ltd.
Treatment of osteoarthritis with Pycnogenol®. The SVOS (San Valentino osteo‐arthrosis study). evaluation of signs, symptoms, physical performance and vascular aspects
Authors: Belcaro G. , Cesarone M. R. , Errichi S. , Zulli C. , Errichi B. M. , Vinciguerra G. , Ledda A. , Renzo A. Di , Stuard S. , Dugall M. , Pellegrini L. , Errichi S. , Gizzi G. , Ippolito E. , Ricci A. , Cacchio M. , Cipollone G. , Ruffini I. , Fano F. , Hosoi M. , Rohdewald P.
Published: April 2008

The aim of this double‐blind, placebo‐controlled study was to evaluate the efficacy of 100 mg Pycnogenol® daily (oral capsules) in a 3 month study in patients with osteoarthritis (OA). OA symptoms were evaluated by WOMAC scores, mobility by recording their walking performance (treadmill). Treatment (77 patients) and placebo group (79) were comparable for age, sex distribution, WOMAC scores, walking distances and use of antiinflammatory drugs. The global WOMAC score decreased by 56% (p < 0.05) in the treatment group versus 9.6% in the placebo group. Walking distance in the treadmill test was prolonged from 68 m at the start to 198 m after 3 months treatment (p < 0.05), under placebo, from 65 m to 88 m (NS). The use of drugs decreased by 58% in the treatment group (p < 0.05) versus 1% under placebo. Gastrointestinal complications decreased by 63% in the treatment group, but only 3% under placebo. Overall, treatment costs were reduced significantly compared with placebo. Foot edema was present in 76% of the patients of the treatment group at inclusion and in 79% of the controls. After 3 months edema decreased in 79% of Pycnogenol patients (p < 0.05) vs 1% in controls. In conclusion, Pycnogenol offers an option for reduction of treatment costs and side effects by sparing antiinflammatory drugs. Copyright © 2008 John Wiley & Sons, Ltd.
Convective inhibition beneath an upper‐level PV anomaly
Authors: Russell A. , Vaughan G. , Norton E. G. , Morcrette C. J. , Browning K. A. , Blyth A. M.
Published: April 2008

Upper‐level potential‐vorticity (PV) anomalies reduce the convective stability of the troposphere through their impact on the vertical potential‐temperature profile, thus reducing convective inhibition (CIN) and increasing convective available potential energy. Here, by contrast, we show the impact of a layer of stable air that was intrinsically linked with an upper‐level PV anomaly and that increased CIN. This layer descended and tracked beneath the small upper‐level PV anomaly, which in this case was a shallow upper‐level trough. This low‐humidity, relatively high‐PV layer originated from the tropopause fold, generated by a breaking Rossby wave, which also produced the upper‐level PV anomaly two days later. Despite conditions favourable for deep convection (as demonstrated by the development of a single storm), the CIN produced by this dry layer or lid was largely responsible for capping convection over much of southern England at around 2.5 km during the case presented here, which comes from the Convective Storm Initiation Project. Copyright © 2008 Royal Meteorological Society
A method for quantifying the impacts and interactions of potential‐vorticity anomalies in extratropical cyclones
Authors: Romero R.
Published: April 2008

The theory of potential vorticity (PV) allows us to describe the life cycle of mid‐latitude baroclinic systems in terms of the individual impacts and interactions of distinct PV anomalies embedded in the background flow. PV anomalies associated with the undulating tropopause, the low‐level thermal field, and key diabatic processes such as the latent‐heat release within the cloudy systems of the cyclone, are often considered as evolving features regulated by their lateral and vertical mutual interactions and their interaction with the stratospheric high‐latitude PV reservoir. Under some balance‐flow assumptions, PV inversion can be used to quantify the contribution of the PV anomalies to the cyclone depth (or other attributes) at various stages of its life cycle (astaticapproach); but it is less clear how to diagnose with similar quantitative detail the various types of time‐dependent interactions among the anomalies and mean flow that govern the processes of cyclogenesis and cyclolysis (adynamicapproach).

This paper presents a method that implements the concepts of ‘PV thinking’ quantitatively. The method first applies a piecewise PV‐inversion scheme formulated according to the Charney nonlinear mass–wind‐balance approximation. Then it combines a prognostic system of balance equations that are consistent with the applied inversion scheme with a factor‐separation technique. By switching on and off the PV anomalies of interest, various flow configurations are generated, and the corresponding solutions to the prognostic equations can be algebraically combined to isolate the magnitude of both the individual and the synergistic effects of the PV anomalies on the spatial pattern of geopotential‐height tendency (and vertical motion) around the cyclone, with low computational cost.

The potential of the method to elucidate the relative importance of physically‐meaningful PV anomalies for the growth or decay of baroclinic systems is illustrated for the intense Mediterranean cyclone of 10–12 November 2001, using the NCEP meteorological grid analyses at 12 h intervals.

The upper‐level PV anomalies contributed very significantly during the whole life cycle of this Mediterranean cyclone. Surface thermal anomalies were fundamental during the development period, and induced the general northeastward movement of the system during the later stages. During the mature stage of the cyclone, the interaction between the two types of anomalies became the dominant effect. All other contributions, including the individual and synergistic effects of diabatically‐generated PV, were generally most relevant during this mature stage. Copyright © 2008 Royal Meteorological Society
Semi‐Lagrangian advection scheme with controlled damping: An alternative to nonlinear horizontal diffusion in a numerical weather prediction model
Authors: Váňa Filip , Bénard Pierre , Geleyn Jean‐François , Simon André , Seity Yann
Published: April 2008

This paper proposes a nonlinear horizontal diffusion scheme for models using semi‐Lagrangian formulations. The scheme is made flow dependent and not entirely linked to the model levels. As an extension, the implementation of the scheme to the model Aladin is given. The damping abilities of interpolation are used for the diffusion filtering. The aim is to provide a horizontal diffusion scheme of similar stability and computational efficiency as the existing linear spectral diffusion scheme in Aladin. Preserving such qualities, the new scheme brings beneficial new skills to the model. The differences between the performances of the two diffusion schemes are examined and discussed. Finally, some interesting case‐studies simulated with both horizontal diffusion schemes are presented. Copyright © 2008 Royal Meteorological Society
Primary and successive events in the Madden–Julian Oscillation
Authors: Matthews Adrian J.
Published: April 2008

Conventional analyses of the MJO tend to produce a repeating cycle, such that any particular feature cannot be unambiguously attributed to the current or previous event. We take advantage of the sporadic nature of the MJO and classify each observed Madden–Julian (MJ) event as either primary, with no immediately preceding MJ event, or successive, which does immediately follow a preceding event. 40% of MJ events are primary events. Precursor features of the primary events can be unambiguously attributed to that event. A suppressed convective anomaly grows and decays in situ over the Indian Ocean, prior to the start of most primary MJ events. An associated mid‐tropospheric temperature anomaly destabilises the atmosphere, leading to the generation of the active MJ event. Hence, primary MJ events appear to be thermodynamically triggered by a previous dry period, although stochastic forcing may also be important. Other theories predict that boundary‐layer convergence, humidity, propagation of dynamical structures around the Equator, sea surface temperatures, and lateral forcing by extratropical transients may all be important in triggering an event. Although precursor signals from these mechanisms are diagnosed from reanalysis and satellite observational data in the successive MJ events, they are all absent in the primary MJ events. Hence, it appears that these apparent precursor signals are part of the MJO once it is established, but do not play a role in the spontaneous generation of the MJO. The most frequent starting location of the primary events is the Indian Ocean, but over half of them start elsewhere, from the maritime continent to the western Pacific. Copyright © 2008 Royal Meteorological Society
Effects of wave function modifications on calculated HC and CC stretching frequencies
Authors: Lopes Kelson C. , Fragoso Wallace D. , Ramos Mozart N. , Pereira Arquimedes M. , Araújo Regiane C. M. U.
Published: April 2008

Two‐level factorial design (FD) and principal component (PC) models are used to determine the effects of wave function modifications on calculated HC and CC harmonic stretching frequencies for the HCCH, HCCF, HCCCl, HCCCCH, HCCCN and HCCCH3 molecules. Our results have shown that valence (val), diffuse (dif), polarization (pol), and electron correlation (corr) main effects as well as some second‐order interaction effects are significant to build factorial models for these vibrational frequencies. For instance, when valence and diffuse functions are introduced in the basis set, the calculated HC and CC stretching frequencies decrease. However, this reduction is much more accentuated when the electron correlation effect is introduced in the Hartree‐Fock wave functions. By far, the corr main effect is the most important one on the HC and CC frequency values. The MP2 electron correlation effect provokes an increment of −157.4 cm−1 and −283.8 cm−1 on the HC and CC stretching frequencies, respectively, whereas the dif effect produces only a reduction of −9.1 cm−1 and −12.9 cm−1 on these frequencies, respectively. The inclusion of Møller–Plesset 2 perturbation in the Hartree‐Fock wave functions also produces an important pol–corr interaction effect on the HC and CC stretching frequencies, increasing their values by +45.2 cm−1 and +17.3 cm−1, respectively. Algebraic models were then established to explain how calculated HC and CC stretching frequencies depend on characteristics of the molecular orbital wave functions. These models were successful in reproducing calculated HC and CC frequency values for the HCN and CH3CCCH3 molcules, which were not included in the training set. The principal component analysis has revealed that the calculated HC and CC stretching frequencies can be adequately described by a single principal component. It is capable of explaining more than 99% of the total data variance. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Three‐center Coulomb repulsion integrals with Slater functions
Authors: Fernández Rico J. , López R. , Ema I. , Ramírez G.
Published: April 2008

The translation method for products of two Slater functions is improved and combined with the short–long range separation in order to develop a robust and efficient algorithm for the evaluation of three‐center Coulomb integrals with Slater functions. Several tests are carried out showing that the algorithm reported here yields integrals with an absolute error below 10−12 hartree and a computational cost of a few microseconds per integral. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Unnatural parity states of helium with screened Coulomb potentials
Authors: Kar Sabyasachi , Ho Y. K.
Published: April 2008

Effect of screened Coulomb (Yukawa) potentials on the doubly excited meta‐stable bound states and the resonance states with unnatural parities of the helium atom have been investigated in the framework of stabilization method using CI‐type basis functions. A total of 54 resonances (6 each of 1Do and 3Do states, 12 each of 1Fe and 3Fe states, 9 each of 1Go and 3Go states) below the He+(3P) thresholds have been estimated by calculating the density of resonance states using a stabilization method. The resonances belong to the different 3lnl′ (n ≥ 3) series. We have also calculated the doubly excited 1,3Fe and 1,3Go meta‐stable bound states of He atom below the He+ (2P) thresholds. The resonance energies and widths along with the meta‐stable bound states energies are reported for various screening parameters. In free atom case, some of the F‐wave resonance states and most of the cases, F‐ and G‐wave resonance widths are reported for the first time. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Many‐electron atom confinement by a penetrable spherical box
Authors: Díaz‐García C. , Cruz S. A.
Published: April 2008

A confinement model for many‐electron atoms enclosed by a spherical boundary with finite‐barrier potential height is presented. The model is based on the Thomas–Fermi–Dirac–Weizsäcker (TFDλW) functional formalism using known properties of the orbital electron densities and constitutes a natural extension of a previously published report for the case of infinitely hard walls [Cruz et al., Int J Quantum Chem, 2005, 102, 897]. The confining barrier potential is considered as a step‐like function of finite height V0. This assumption demands of the appropriate description of the TFDλW energy functional for both the interior and exterior regions together with corresponding ansatz orbital density representations, subject to continuity boundary conditions at the wall. For a given cage radius R and confining barrier height V0, the total ground‐state energy is variationally optimized with respect to the characteristic parameters defining the interior and exterior orbital densities. The total ground‐state energy and corresponding electronic density are obtained as function of barrier height and cage radius for many‐electron atoms and ions. The model is explicitly applied to He, Li, C, and Ne and various ionic species for barrier heights (atomic units) V0 = 0, 5, and ∞. Given a barrier height V0, the results are presented for the critical cage size to produce one or more unbound electrons—yet, confined by the box—until reaching threshold size values for which electron escape from the confinement region take place. © 2008 Wiley Periodicals, Inc. Int. J. Quantum Chem, 2008