bluuebunny/crossref_metadata_2025 huggingface dataset:
Multicomponent reactive transport modeling of acid neutralization reactions in mine tailings
Authors: Jurjovec Jasna , Blowes David W. , Ptacek Carol J. , Mayer K. Ulrich
Published: November 2004

Multicomponent reactive transport modeling was conducted to analyze and quantify the acid neutralization reactions observed in a column experiment. Experimental results and the experimental procedures have been previously published. The pore water geochemistry was described by dissolution and precipitation reactions involving primary and secondary mineral phases. The initial amounts of the primary phases ankerite‐dolomite, siderite, chlorite, and gypsum were constrained by mineralogical analyses of the tailings sample used in the experiment. Secondary gibbsite was incorporated into the model to adequately explain the changes in pH and concentration changes of Al in the column effluent water. The results of the reactive transport modeling show that the pH of the column effluent water can be explained by dissolution reactions of ankerite‐dolomite, siderite, chlorite, and secondary gibbsite. The modeling results also show that changes in Eh can be explained by dissolution of ferrihydrite during the experiment. In addition, the modeling results show that the kinetically limited dissolution of chlorite contributes the largest mass of dissolved Mg and Fe (II) in the effluent water, followed by ankerite‐dolomite, which contributes substantially less. In summary, reactive transport modeling based on detailed geochemical and mineralogical data was successful to quantitatively describe the changes in pH and major ions in the column effluent.
Monthly CO surface sources inventory based on the 2000–2001 MOPITT satellite data
Authors: Pétron Gabrielle , Granier Claire , Khattatov Boris , Yudin Valery , Lamarque Jean‐François , Emmons Louisa , Gille John , Edwards David P.
Published: November 2004

This paper presents results of the inverse modeling of carbon monoxide surface sources on a monthly and regional basis using the MOPITT (Measurement Of the Pollution In The Troposphere) CO retrievals. The targeted time period is from April 2000 to March 2001. A sequential and time‐dependent inversion scheme is implemented to correct an a priori set of monthly mean CO sources. The a posteriori estimates for the total anthropogenic (fossil fuel + biofuel + biomass burning) surface sources of CO in TgCO/yr are 509 in Asia, 267 in Africa, 140 in North America, 90 in Europe and 84 in Central and South America. Inverting on a monthly scale allows one to assess a corrected seasonality specific to each source type and each region. Forward CTM simulations with the a posteriori emissions show a substantial improvement of the agreement between modeled CO and independent in situ observations.
Solar wind interaction with the ionosphere/atmosphere and crustal magnetic fields at Mars: Mars Global Surveyor Magnetometer/Electron Reflectometer, radio science, and accelerometer data
Authors: Krymskii A. M. , Ness N. F. , Crider D. H. , Breus T. K. , Acuña M. H. , Hinson D. P.
Published: November 2004

The solar wind (SW) mainly interacts with the Martian ionosphere/atmosphere. However, the intense crustal magnetization creates localized minimagnetospheres above the surface. The interplanetary magnetic field (IMF) can reconnect with these crustal fields and this allows SW and more energetic particles to precipitate into and heat the neutral atmosphere in localized regions, especially in the southern hemisphere. A study of 907 electron density profiles obtained by the MGS Radio Science (RS) experiment at latitudes from +63° to +77° and 219 profiles at latitudes −69° to −64.5° has been conducted. The role of the magnetic field as a driving force of the cross‐terminator convection is discussed. Longitudinal variations of neutral atmosphere scale height Hpeak derived from the MGS RS data have been analyzed. Ionospheric parameters are found to be more variable in the southern than in the northern hemisphere. This correlates well with the variability of the magnetic field direction from local zenith. The scale height of neutral atmosphere density HACC derived from the MGS accelerometer data is also found to be more variable in the southern than in the northern hemisphere.
Field‐aligned current distribution in the transition current system
Authors: Belenkaya Elena S. , Alexeev Igor I. , Clauer C. Robert
Published: November 2004

The interactions of coronal mass ejections with the Earth's magnetosphere are interesting because they often lead to extreme forcing of magnetospheric convection. Here we consider the initial interaction of a CME with the magnetosphere for the specific case in which there is a sharp increase in the dynamic pressure (interplanetary shock) that is associated with a simultaneous northward turning of the interplanetary magnetic field (IMF). The magnetospheric response to such conditions has been observed to be atypical to that expected for the compression of the magnetosphere. The sudden magnetic field increase observed at low‐latitude ground stations in response to such an event is asymmetric, with the largest field enhancement observed on the nightside and little or no field increase observed near local noon. We explain this response in terms of a temporary transition current system that is generated in the high‐latitude magnetosphere in response to the northward turning of the IMF. In this paper we consider the dependence of the distribution of field‐aligned currents in the transition current system to the radial and azimuthal components of the IMF. Model results are compared with the onground magnetometer data during 31 March 2001 storm sudden commencement (SSC).
Flow burst–induced large‐scale plasma sheet oscillation
Authors: Volwerk M. , Glassmeier K.‐H. , Runov A. , Nakamura R. , Baumjohann W. , Klecker B. , Richter I. , Balogh A. , Rème H. , Yumoto K.
Published: November 2004

On 12 August 2001 the Cluster spacecraft measured a rapid flux transport event, consisting of a strong perpendicular earthward flow burst combined with a dipolarization of the magnetic field after a strong compression of the magnetotail. Combining the Cluster data with those from ground‐based magnetometers, we find that this event is related to patchy reconnection taking place in the tail. After the event the magnetotail is locally evacuated of magnetic field, and an increased plasma pressure takes over from the magnetic pressure. This situation lasts for 15 min, after which a new equilibrium is sought, resulting in an oscillating magnetic field with a period of 20 min. The rapid flux transport observed with Bz and vx is shown to be in agreement with Bx variation using Maxwell's equations. The oscillation period agrees well with what is theoretically predicted. Our results show how a damped eigenoscillation of the magnetotail can be initiated by fast flows.
Empirical cotidal charts of the Bohai, Yellow, and East China Seas from 10 years of TOPEX/Poseidon altimetry
Authors: Fang Guohong , Wang Yonggang , Wei Zexun , Choi Byung Ho , Wang Xinyi , Wang Ji
Published: November 2004

Harmonic analysis of 10 years of TOPEX/Poseidon (TP) along‐track altimetry is performed to derive the semidiurnal, diurnal, long‐period, and quarter‐diurnal tides in the Bohai, Yellow, and East China Seas. The TP solutions are evaluated through intercomparison for crossover points and comparison with the ground truth, showing that the accuracy of TP solutions in the study area has achieved levels of 2–4 cm in amplitudes and 5° in phase lags for principal constituents (M2, S2, K1, O1, and Sa). The TP‐derived Sa amplitudes have a systematic bias of about −10% as compared with the ground truth, indicating the possible importance of loading effect of this constituent in the study area, which is generally not considered in geodetic surveys. The tidal harmonics from TP altimetry and at coastal and island stations are used to give a new set of empirical cotidal charts for principal constituents (M2, S2, K1, O1, and Sa). The accuracy of these new charts is believed to be significantly higher than the previous charts for the offshore area.
Biases in the estimation of transfer function prediction errors
Authors: Telford R. J. , Andersson C. , Birks H. J. B. , Juggins S.
Published: November 2004

In the quest for more precise sea‐surface temperature reconstructions from microfossil assemblages, large modern training sets and new transfer function methods have been developed. Realistic estimates of the predictive power of a transfer function can only be calculated from an independent test set. If the test set is not fully independent, the error estimate will be artificially low. We show that the modern analogue technique using a similarity index (SIMMAX) and the revised analogue method (RAM), both derived from the modern analogue technique, achieve apparently lower root mean square error of prediction (RMSEP) by failing to ensure statistical independence of samples during cross validation. We also show that when cross validation is used to select the best artificial neural network or modern analogue model, the RMSEP based on cross validation is lower than that for a fully independent test set.
Inhibition of calcium‐calmodulin kinase restores nitric oxide production and signaling in submandibular glands of a mouse model of salivary dysfunction
Authors: Rosignoli Florencia , Roca Valeria , Meiss Roberto , Pregi Nicolás , Leirós Claudia Pérez
Published: November 2004

Nitric oxide is an intracellular and diffusible messenger of neurotransmitters involved in salivary secretion, as well as an inflammatory mediator in salivary gland diseases. It is synthesized by three different isoforms of nitric oxide synthase (NOS), each subject to a fine transcriptional, post‐transcriptional and/or post‐translational regulation. Our purpose was to study the possible mechanisms leading to NOS downregulation in submandibular glands of normal mice and in the nonobese diabetic (NOD) mouse model of salivary dysfunction with lower NOS activity.

NOS activity and cGMP accumulation were determined by radioassays in submandibular glands of both mice in the presence of the protein kinase inhibitors KN‐93 and bisindolylmaleimide. NOS I mRNA and protein expression and localization were assessed by RT–PCR, Western blot and immunohistochemistry.

A downregulatory effect of calcium–calmodulin kinase II (CaMK II) on NOS activity in submandibular glands of both NOD and BALB/c mice was observed. Our results are consistent with a physiological regulation of NOS activity by this kinase but not by PKC in normal BALB/c mice. They are also supportive of a role for CaMK II in the lack of detectable NOS activity in submandibular glands of NOD mice. KN‐93 also restored cGMP accumulation in NOD submandibular glands.

The downregulation of NOS in NOD mice seems to be mainly mediated by this kinase rather than the result of a lower expression or different cellular localization of the enzyme. It was not related to different substrate or cofactors availability either.

British Journal of Pharmacology (2004) 143, 1058–1065. doi:10.1038/sj.bjp.0705952
Platelet–leukocyte aggregation induced by PAR agonists: regulation by nitric oxide and matrix metalloproteinases
Authors: Chung Ada W Y , Radomski Anna , Alonso‐Escolano David , Jurasz Paul , Stewart Michael W , Malinski Tadeusz , Radomski Marek W
Published: November 2004

Platelet–leukocyte aggregation (PLA) links haemostasis to inflammation. The role of nitric oxide (NO) and matrix metalloproteinases (MMP‐1, ‐2, ‐3, ‐9) in PLA regulation was studied.

Homologous human platelet–leukocyte suspensions were stimulated with thrombin (0.1–3 nM) and other proteinase activated receptor‐activating peptides (PAR‐AP), including PAR1AP (0.5–10 μM), PAR4AP (10–70 μM), and thrombin receptor‐activating peptide (1–35 μM).

PLA was studied using light aggregometry with simultaneous measurement of oxygen‐derived free radicals, dual colour flow cytometry, and phase‐contrast microscopy.

The release of NO was measured using a porphyrinic nanosensor, while MMPs were investigated by Western blot, substrate degradation assays, immunofluorescence microscopy, and flow cytometry. The levels of P‐selectin and microparticles (MP) in PLA were measured by flow cytometry.

PLA was also characterized using pharmacological agents: S‐nitroso‐glutathione (GSNO, 0.01–10 μM), 1H‐Oxadiazole quinoxalin‐1‐one (ODQ, 1 μM), NG‐L‐nitro‐L‐arginine methyl ester (L‐NAME, 100 μM) and compounds that modulate the actions of MMPs such as phenanthroline (100 μM), monoclonal anti‐MMP antibodies, and purified MMPs.

PAR agonists concentration‐dependently induced PLA, an effect associated with the release of microparticles (MP) and the translocation of P‐selectin to the platelet surface.

NO and radicals were also released during PLA. Inhibition of NO bioactivity by the concomitant release of free radicals or by the treatment with L‐NAME or ODQ stimulated PLA, while pharmacological administration of GSNO decreased PLA.

PAR agonist‐induced PLA resulted in the liberation of MMP‐1, ‐2, ‐3, and ‐9.

During PLA, MMPs were present on the cell surface, as shown by flow cytometry and immunofluorescence.

PLA led to the activation of latent MMPs to active MMPs, as shown by Western blot and substrate degradation assays.

Inhibition of MMPs actions by phenanthroline and by the antibodies attenuated PLA. In contrast, purified active, but not latent, MMPs amplified thrombin‐induced PLA.

It is concluded that NO and MMP‐1, ‐2, ‐3, and ‐9 play an important role in regulation of PAR agonist‐induced PLA.

British Journal of Pharmacology (2004) 143, 845–855. doi:10.1038/sj.bjp.0705997
Erythromycin exerts in vivo anti‐inflammatory activity downregulating cell adhesion molecule expression
Authors: Sanz María‐Jesús , Nabah Yafa Naim Abu , Cerdá‐Nicolás Miguel , O'Connor José‐Enrique , Issekutz Andrew C , Cortijo Julio , Morcillo Esteban J
Published: November 2004

Macrolides have long been used as anti‐bacterial agents; however, there is some evidence that may exert anti‐inflammatory activity. Therefore, erythromycin was used to characterize the mechanisms involved in their in vivo anti‐inflammatory activity.

Erythromycin pretreatment (30 mg kg−1 day−1 for 1 week) reduced the lipopolysaccharide (LPS; intratracheal, 0.4 mg kg−1)‐induced increase in neutrophil count and elastase activity in the bronchoalveolar lavage fluid (BALF) and lung tissue myeloperoxidase activity, but failed to decrease tumor necrosis factor‐α and macrophage‐inflammatory protein‐2 augmented levels in BALF. Erythromycin pretreatment also prevented lung P‐selectin, E‐selectin, intercellular adhesion molecule‐1 (ICAM‐1) and vascular cell adhesion molecule‐1 (VCAM‐1) mRNA upregulation in response to airway challenge with LPS.

Mesentery superfusion with LPS (1 μg ml−1) induced a significant increase in leukocyte–endothelial cell interactions at 60 min. Erythromycin pretreatment abolished the increases in these parameters.

LPS exposure of the mesentery for 4 h caused a significant increase in leukocyte rolling flux, adhesion and emigration, which were inhibited by erythromycin by 100, 93 and 95%, respectively.

Immunohistochemical analysis showed that LPS exposure of the mesentery for 4 h caused a significant enhancement in P‐selectin, E‐selectin, ICAM‐1 and VCAM‐1 expression that was downregulated by erythromycin pretreatment.

Flow cytometry analysis indicated that erythromycin pretreatment inhibited LPS‐induced CD11b augmented expression in rat neutrophils.

In conclusion, erythromycin inhibits leukocyte recruitment in the lung and this effect appears mediated through downregulation of CAM expression. Therefore, macrolides may be useful in the control of neutrophilic pulmonary diseases.

British Journal of Pharmacology (2005) 144, 190–201. doi:10.1038/sj.bjp.0706021
A newly identified zona pellucida glycoprotein, ZPD, and dimeric ZP1 of chicken egg envelope are involved in sperm activation on sperm–egg interaction
Authors: OKUMURA Hiroki , KOHNO Yoshinori , IWATA Yuki , MORI Hitoshi , AOKI Naohito , SATO Chihiro , KITAJIMA Ken , NADANO Daita , MATSUDA Tsukasa
Published: November 2004

Fertilization begins with interaction between the sperm and the egg. The surface of the vertebrate oocyte is covered with the egg envelope, which is composed of ZP (zona pellucida) glycoproteins. We have identified two glycoproteins, ZP1/gp97 and ZPC/gp42, as the major components of the chicken egg envelope. In the present study, another 42 kDa protein, designated ZPD, has been found as a new major component of the chicken egg envelope. ZPD was specifically released from the egg envelope by ultrasonication treatment without urea. ZPD cDNA was cloned using a chicken granulosa cell cDNA pool. The deduced amino acid sequence showed that preproprotein of ZPD is composed of 418 amino acid residues with four potential N-glycosylation sites and includes a ZP domain, common in vertebrate ZP glycoproteins, and a transmembrane domain. ZPD belongs phylogenetically to a distinct group from known ZP glycoprotein subfamilies, ZPA, ZPB, and ZPC. In two-dimensional gel electrophoresis ZPD proteins were identified to be several isoforms with different pI values between 5 and 7. ZP1, ZPC and the newly identified ZPD were confirmed to be the major components of chicken egg envelope by MS of proteolytic digests of whole egg envelope. The in vitro incubation of chicken sperm with calcium ionophore A23187 induced sperm activation, resulting in the fragmentation and release of a 41 kDa PNA (peanut agglutinin)-positive glycoprotein and the decrease or loss of sperm PNA-stainability. The incubation with ZPD and dimeric ZP1, but not ZPC and monomeric ZP1, also induced the decrease or loss of sperm PNA-stainability, suggesting the in vitro sperm activation by these ZP components. Collectively, ZPD might bind loosely to egg envelope matrix and play a key role in the sperm activation on avian sperm–egg interaction.
Proteomic characterization of two snake venoms: Naja naja atra and Agkistrodon halys
Authors: LI Shuting , WANG Jingqiang , ZHANG Xumin , REN Yan , WANG Ning , ZHAO Kang , CHEN Xishu , ZHAO Caifeng , LI Xiaolei , SHAO Jianmin , YIN Jianning , WEST Matthew B. , XU Ningzhi , LIU Siqi
Published: November 2004

Snake venom is a complex mixture of proteins and peptides, and a number of studies have described the biological properties of several venomous proteins. Nevertheless, a complete proteomic profile of venom from any of the many species of snake is not available. Proteomics now makes it possible to globally identify proteins from a complex mixture. To assess the venom proteomic profiles from Naja naja atra and Agkistrodon halys, snakes common to southern China, we used a combination strategy, which included the following four different approaches: (i) shotgun digestion plus HPLC with ion-trap tandem MS, (ii) one-dimensional SDS/PAGE plus HPLC with tandem MS, (iii) gel filtration plus HPLC with tandem MS and (iv) gel filtration and 2DE (two-dimensional gel electrophoresis) plus MALDI–TOF (matrix-assisted laser desorption ionization–time-of-flight) MS. In the present paper, we report the novel identification of 124 and 74 proteins and peptides in cobra and viper venom respectively. Functional analysis based upon toxin categories reveals that, as expected, cobra venom has a high abundance of cardio- and neurotoxins, whereas viper venom contains a significant amount of haemotoxins and metalloproteinases. Although approx. 80% of gel spots from 2DE displayed high-quality MALDI-TOF-MS spectra, only 50% of these spots were confirmed to be venom proteins, which is more than likely to be a result of incomplete protein databases. Interestingly, these data suggest that post-translational modification may be a significant characteristic of venomous proteins.
Two-dimensional IR correlation spectroscopy of mutants of the β-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus identifies the mechanism of quaternary structure stabilization and unravels the sequence of thermal unfolding events
Authors: AUSILI Alessio , DI LAURO Barbara , COBUCCI-PONZANO Beatrice , BERTOLI Enrico , SCIRÈ Andrea , ROSSI Mosè , TANFANI Fabio , MORACCI Marco
Published: November 2004

β-Glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus is a homotetramer with a higher number of ion pairs compared with mesophilic glycoside hydrolases. The ion pairs are arranged in large networks located mainly at the tetrameric interface of the molecule. In the present study, the structure and thermal stability of the wild-type β-glycosidase and of three mutants in residues R488 and H489 involved in the C-terminal ionic network were examined by FTIR (Fourier-transform IR) spectroscopy. The FTIR data revealed small differences in the secondary structure of the proteins and showed a lower thermostability of the mutant proteins with respect to the wild-type. Generalized 2D-IR (two-dimensional IR correlation spectroscopy) at different temperatures showed different sequences of thermal unfolding events in the mutants with respect to the wild-type, indicating that punctual mutations affect the unfolding and aggregation process of the protein. A detailed 2D-IR analysis of synchronous maps of the proteins allowed us to identify the temperatures at which the ionic network that stabilizes the quaternary structure of the native and mutant enzymes at the C-terminal breaks down. This evidence gives support to the current theories on the mechanism of ion-pair stabilization in proteins from hyperthermophilic organisms.
Synergistic role of specificity proteins and upstream stimulatory factor 1 in transactivation of the mouse carboxylesterase 2/microsomal acylcarnitine hydrolase gene promoter
Authors: FURIHATA Tomomi , HOSOKAWA Masakiyo , SATOH Tetsuo , CHIBA Kan
Published: November 2004

Mouse carboxylesterase 2 (mCES2), a microsomal acylcarnitine hydrolase, is thought to play some important roles in fatty acid (ester) metabolism, and it is therefore thought that the level of transcription of the mCES2 gene is under tight control. Examination of the tissue expression profiles revealed that mCES2 is expressed in the liver, kidney, small intestine, brain, thymus, lung, adipose tissue and testis. When the mCES2 promoter was cloned and characterized, it was revealed that Sp1 (specificity protein 1) and Sp3 could bind to a GC box, that USF (upstream stimulatory factor) 1 could bind to an E (enhancer) box, and that Sp1 could bind to an NFκB (nuclear factor κB) element in the mCES2 promoter. Co-transfection assays showed that all of these transcription factors contributed synergistically to transactivation of the mCES2 promoter. Taken together, our results indicate that Sp1, Sp3 and USF1 are indispensable factors for transactivation of the mCES2 gene promoter. To our knowledge, this is the first study in which transcription factors that interact with a CES2 family gene have been identified. The results of the present study have provided some clues for understanding the molecular mechanisms regulating mCES2 gene expression, and should be useful for studies aimed at elucidation of physiological functions of mCES2.
Studies of SpoIIAB mutant proteins elucidate the mechanisms that regulate the developmental transcription factor σF in Bacillus subtilis
Authors: SHU Jwu-Ching , CLARKSON Joanna , YUDKIN Michael D.
Published: November 2004

σF, the first compartment-specific sigma factor of sporulation, is regulated by an anti-sigma factor, SpoIIAB (AB) and its antagonist SpoIIAA (AA). AB can bind to σF in the presence of ATP or to AA in the presence of ADP; in addition, AB can phosphorylate AA. The ability of AB to switch between its two binding partners regulates σF. Early in sporulation, AA activates σF by releasing it from its complex with AB. We have previously proposed a reaction scheme for the phosphorylation of AA by AB which accounts for AA's regulatory role. A crucial feature of this scheme is a conformational change in AB that accompanies its switch in binding partner. In the present study, we have studied three AB mutants, all of which have amino-acid replacements in the nucleotide-binding region; AB-E104K (Glu104→Lys) and AB-T49K (Thr49→Lys) fail to activate σF, and AB-R105A (Arg105→Ala) activates it prematurely. We used techniques of enzymology, surface plasmon resonance and fluorescence spectroscopy to analyse the defects in each mutant. AB-E104K was deficient in binding to AA, AB-T49K was deficient in binding to ADP and AB-R105A bound ADP exceptionally strongly. Although the release of σF from all three mutant proteins was impaired, and all three failed to undergo the wild-type conformational change when switching binding partners, the phenotypes of the mutant cells were best accounted for by the properties of the respective AB species in forming complexes with AA and ADP. The behaviour of the mutants enables us to propose convincing mechanisms for the regulation of σF in wild-type bacteria.
Activation of PPARγ is required for curcumin to induce apoptosis and to inhibit the expression of extracellular matrix genes in hepatic stellate cells in vitro
Authors: ZHENG Shizhong , CHEN Anping
Published: November 2004

During liver fibrogenesis, quiescent HSC (hepatic stellate cells) become active, a transformation that is associated with enhanced cell proliferation and overproduction of ECM (extracellular matrix). Inhibition of cell proliferation and induction of apoptosis are potential strategies to block the activation of HSC for the prevention and treatment of liver fibrosis. Levels of PPARγ (peroxisome proliferator-activated receptor γ) are dramatically diminished in parallel with HSC activation. Stimulation of PPARγ by its agonists inhibits HSC activation in vitro and in vivo. We demonstrated recently that curcumin, the yellow pigment in curry, inhibited HSC activation in vitro, reducing cell proliferation, inducing apoptosis and inhibiting ECM gene expression. Further studies indicated that curcumin induced the gene expression of PPARγ and stimulated its activity in activated HSC in vitro, which was required for curcumin to inhibit HSC proliferation. The aims of the present study were to evaluate the roles of PPARγ activation in the induction of apoptosis and suppression of ECM gene expression by curcumin in activated HSC, and to elucidate the underlying mechanisms. Our results demonstrated that blocking PPARγ activation abrogated the effects of curcumin on the induction of apoptosis and inhibition of the expression of ECM genes in activated HSC in vitro. Further experiments demonstrated that curcumin suppressed the gene expression of TGF-β (transforming growth factor-β) receptors and interrupted the TGF-β signalling pathway in activated HSC, which was mediated by PPARγ activation. Taken together, our results demonstrate that curcumin stimulated PPARγ activity in activated HSC in vitro, which was required for curcumin to reduce cell proliferation, induce apoptosis and suppress ECM gene expression. These results provide novel insight into the mechanisms responsible for the inhibition of HSC activation by curcumin. The characteristics of curcumin, which has no adverse health effects, make it a potential candidate for prevention and treatment of hepatic fibrosis.
Distinct classes of glyoxalase I: metal specificity of the Yersinia pestis, Pseudomonas aeruginosa and Neisseria meningitidis enzymes
Authors: SUKDEO Nicole , CLUGSTON Susan L. , DAUB Elisabeth , HONEK John F.
Published: November 2004

The metalloisomerase glyoxalase I (GlxI) catalyses the conversion of methylglyoxal-glutathione hemithioacetal and related derivatives into the corresponding thioesters. In contrast with the previously characterized GlxI enzymes of Homo sapiens, Pseudomonas putida and Saccharomyces cerevisiae, we recently determined that Escherichia coli GlxI surprisingly did not display Zn2+-activation, but instead exhibited maximal activity with Ni2+. To investigate whether non-Zn2+ activation defines a distinct, previously undocumented class of GlxI enzymes, or whether the E. coli GlxI is an exception to the previously established Zn2+-activated GlxI, we have cloned and characterized the bacterial GlxI from Yersinia pestis, Pseudomonas aeruginosa and Neisseria meningitidis. The metal-activation profiles for these additional GlxIs firmly establish the existence of a non-Zn2+-dependent grouping within the general category of GlxI enzymes. This second, established class of metal activation was formerly unidentified for this metalloenzyme. Amino acid sequence comparisons indicate a more extended peptide chain in the Zn2+-dependent forms of GlxI (H. sapiens, P. putida and S. cerevisiae), compared with the GlxI enzymes of E. coli, Y. pestis, P. aeruginosa and N. meningitidis. The longer sequence is due in part to the presence of additional regions situated fairly close to the metal ligands in the Zn2+-dependent forms of the lyase. With respect to sequence alignments, these inserts may potentially contribute to defining the metal specificity of GlxI at a structural level.
A misassembled transmembrane domain of a polytopic protein associates with signal peptide peptidase
Authors: CRAWSHAW Samuel G. , MARTOGLIO Bruno , MEACOCK Suzanna L. , HIGH Stephen
Published: November 2004

The endoplasmic reticulum (ER) exerts a quality control over newly synthesized proteins and a variety of components have been implicated in the specific recognition of aberrant or misfolded polypeptides. We have exploited a site-specific cross-linking approach to search for novel ER components that may specifically recognize the misassembled transmembrane domains present in truncated polytopic proteins. We find that a single probe located in the transmembrane domain of a truncated opsin fragment is cross-linked to several ER proteins. These components are distinct from subunits of the Sec61 complex and represent a ‘post-translocon’ environment. In this study, we identify one of these post-translocon cross-linking partners as the signal peptide peptidase (SPP). We find that the interaction of truncated opsin chains with SPP is mediated by its second transmembrane domain, and propose that this interaction may contribute to the recognition of misassembled transmembrane domains during membrane protein quality control at the ER.
Filopodia formation and Disabled degradation downstream of Reelin
Authors: WINDER Steven J.
Published: November 2004

During Drosophila embryogenesis, Abl (Abelson tyrosine kinase) is localized in the axons of the CNS (central nervous system). Mutations in Abl have a subtle effect on the morphology of the embryonic CNS, and the mutant animals survive to the pupal and adult stages. However, genetic screens have identified several genes that, when mutated along with the Abl gene, modified the phenotypes. Two prominent genes that arose from these screens were enabled (Ena) and disabled (Dab). It has been known for some time that Enabled and its mammalian homologues are involved in the regulation of actin dynamics, and promote actin polymerization at the leading edge of motile cells. It was a defect in actin polymerization in migrating neurons in particular that resulted in the identification of Enabled as an important regulator of neuronal migration. Defects in Disabled, in both Drosophila and mammals, also gave rise to neuronal defects which, in mice, were indistinguishable from phenotypes observed in the reeler mouse. These observations suggested that mDab1 (mammalian Disabled homologue 1) acted in a pathway downstream of Reelin, the product of the reelin gene found to be defective in reeler mice. Now, in this issue of the Biochemical Journal, Takenawa and colleagues have demonstrated that Disabled also acts in a pathway to regulate actin dynamics through the direct activation of N-WASP (neuronal Wiskott–Aldrich syndrome protein). Furthermore, they were also able to link several lines of investigation from other groups to show that the ability of mDab1 to regulate actin dynamics during cell motility was under the negative control of tyrosine phosphorylation, leading to ubiquitin-mediated degradation of mDab1.
Ptychogyliauchen, a new genus of Gyliauchenidae (Platyhelminthes : Digenea) from siganid fishes of the Indo-West Pacific
Authors: Hall Kathryn A. , Cribb Thomas H.
Published: November 2004

We propose a new genus of the Gyliauchenidae Fukui, 1929 (Digenea), Ptychogyliauchen, gen. nov., for four new species that infect Indo-West Pacific siganid fishes. Ptychogyliauchen, gen. nov. is a morphologically distinctive genus, diagnosed principally by the presence of a highly convoluted oesophagus, which generally exceeds the total body length of the worm, and by the unusual folded structure of the ejaculatory duct. Ptychogyliauchen thetidis, sp. nov. is designated as the type species, and is described from the intestine of Siganus punctatus (Siganidae) from Heron Island, Great Barrier Reef, Queensland, Australia. Ptychogyliauchen himinglaeva, sp. nov. is described from the intestine of Siganus corallinus (Siganidae) from Lizard Island, Great Barrier Reef, Queensland, Australia. Ptychogyliauchen leucothea, sp. nov. is described from the intestine of S.�argenteus, and further recorded from S. fuscescens, off Ningaloo, Western Australia, Australia. Ptychogyliauchen thistilbardi, sp. nov. is described from the intestine of S. doliatus from Noumea, New Caledonia, and is also found in S. argenteus, S. canaliculatus, S. corallinus and S. spinus from Noumea, New Caledonia, and Moorea, Tahiti, French Pacific. Ptychogyliauchen thistilbardi, sp. nov. also occurs in the intestine of Chaetodon citrinellus (Chaetodontidae) from Moorea. A key to species is provided. All species have been described following morphological examination using light microscopy, and specimens of P. thetidis, sp. nov., P. leucothea, sp. nov. and P. thistilbardi, sp. nov. have been characterised using molecular methods. Sequences were obtained for a combination of nuclear ribosomal (28S (D1–D3) and ITS2) and mitochondrial (ND1) genes. A phylogenetic analysis of sequenced specimens of Ptychogyliauchen, gen. nov. was conducted using species of Petalocotyle Ozaki, 1934 for outgroup comparison. This analysis, based on alignments of the ITS2 and 28S (D1–D3) rDNA genes, supports monophyly of the geographically widespread P. thistilbardi, sp. nov., which is known from both siganid and chaetodontid hosts. We discuss the taxonomy of the genus and the host associations of each species and the group.
High levels of spatial and temporal recruitment variability in the temperate sparid Pagrus auratus
Authors: Hamer Paul A. , Jenkins Gregory P.
Published: November 2004

Knowledge of spatial and temporal variation in the abundance of early life stages is important to developing an understanding of juvenile recruitment processes and, ultimately, the dynamics and demographics of fish populations. In Victoria, south-eastern Australia, snapper, Pagrus auratus, supports an important fishery characterised by high variability in year-class strength. We investigated spatial and temporal variation in the recruitment of small juvenile (0+) snapper by monitoring their abundance in four bay and inlet nursery areas during four consecutive summer/autumn recruitment periods (2000–2003). We found considerable spatial variability in the abundance of recruits, both within and among inlets. Interannual recruitment variation, however, differed among inlets. Recruitment into the largest nursery area and most important fishery, Port Phillip Bay, varied by ~10-fold across years, whereas variation for the other inlets was low or not significant. There were also clear differences in size distributions of recruits among both inlets and years. Strong recruitment in Port Phillip Bay during 2001 was related to a longer period of spawning and successful larval settlement and was associated with above average water temperatures. Future monitoring of 0+ recruitment in Victoria and studies of the recruitment processes should be specific to individual nursery areas.
Iron precipitate accumulations associated with waterways in drained coastal acid sulfate landscapes of eastern Australia
Authors: Sullivan L. A. , Bush R. T.
Published: November 2004

Iron precipitate accumulations from surface environments surrounding waterways (such as the side of drains and soil surface horizons) in acid sulfate soil landscapes were analysed for their mineralogy, micromorphology and chemical properties. Schwertmannite (Fe8(OH)5.5(SO4)1.25) was the dominant mineral in these accumulations. Goethite (α-FeOOH) was the other iron precipitate mineral identified in these accumulations and the data indicate that this iron mineral was formed from schwertmannite, often as pseudomorphs after schwertmannite. The schwertmannite in these accumulations had similar morphology and chemical properties to schwertmannite reported for environments affected by acid mine drainage. The activity of Fe3+ in the drainage waters in these landscapes appears to be controlled by schwertmannite during both low flow (dry season) and flood conditions. Iron precipitate accumulations contained appreciable amounts of stored acidity (i.e. titratable actual acidity of between 164 and 443 mol (H+) t–1, and 1900 to 2580 mol (H+) t–1 of schwertmannite upon complete conversion to goethite) that tends to buffer these waters to very acidic conditions (i.e. pHs ~3.0–3.5). The relationship between water quality (i.e. pH and sulfate concentration) and type of iron precipitate mineral formed should enable the mineralogy of the iron precipitates in these surface environments to be used to help identify the degree of severity of degradation in these acid sulfate soil landscapes and to monitor the effectiveness of remediation programmes.
Microarrays of small molecules embedded in biodegradable polymers for use in mammalian cell-based screens
Authors: Bailey Steve N. , Sabatini David M. , Stockwell Brent R.
Published: November 2004

We developed a microarray-based system for screening small molecules in mammalian cells. This system is compatible with image-based screens and requires fewer than 100 cells per compound. Each compound is impregnated in a 200-μm-diameter disc composed of biodegradable poly-(d),(l)-lactide/glycolide copolymer. Cells are seeded on top of these discs, and compounds slowly diffuse out, affecting proximal cells. In contrast with microtiter-based screening, this system does not involve the use of wells or walls between each compound-treated group of cells. We demonstrate detection of the effects of a single compound in a large microarray, that diverse compounds can be released in this format, and that extended release over several days is feasible. We performed a small synthetic lethal screen and identified a compound (macbecin II) that has reduced activity in cells with RNA interference-mediated decrease in the expression of tuberous sclerosis 2. Thus, we have developed a microarray-based screening system for testing the effects of small molecules on mammalian cells by using an imaging-based readout. This method will be useful to those performing small-molecule screens to discover new chemical tools and potential therapeutic agents.
A crucial arginine residue is required for a conformational switch in NifL to regulate nitrogen fixation in
Azotobacter vinelandii
Authors: Martinez-Argudo Isabel , Little Richard , Dixon Ray
Published: November 2004

NifL is an antiactivator that tightly regulates transcription of genes required for nitrogen fixation in
Azotobacter vinelandii
by controlling the activity of its partner protein NifA, a member of the family of σ
54
-dependent transcriptional activators. Although the C-terminal region of
A. vinelandii
NifL shows homology to the transmitter domains of histidine protein kinases, signal transduction between NifL and NifA is conveyed by means of protein-protein interactions rather than by phosphorylation. Binding of the ligand 2-oxoglutarate to NifA plays a crucial role in preventing inhibition by NifL under conditions appropriate for nitrogen fixation. We have used a suppressor screen to identify a critical arginine residue (R306) in NifL that is required to release NifA from inhibition under appropriate environmental conditions. Amino acid substitutions at position 306 result in constitutive inhibition of NifA activity by NifL, thus preventing nitrogen fixation. Biochemical studies with one of the mutant proteins demonstrate that the substitution alters the conformation of NifL significantly and prevents the response of NifA to 2-oxoglutarate. We propose that arginine 306 is critical for the propagation of signals perceived by
A. vinelandii
NifL in response to the redox and fixed-nitrogen status and is required for a conformational switch that inactivates the inhibitory function of NifL under conditions appropriate for nitrogen fixation.
A combinatorial model for the Macdonald polynomials
Authors: Haglund J.
Published: November 2004

We introduce a polynomialC̃μ[Z;q, t], depending on a set of variablesZ=z1,z2,..., a partition μ, and two extra parametersq, t. The definition ofC̃μinvolves a pair of statistics (maj(σ, μ), inv(σ, μ)) on words σ of positive integers, and the coefficients of theziare manifestly in\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathbb{N}}[q,t]\end{equation*}\end{document}. We conjecture thatC̃μ[Z;q, t] is none other than the modified Macdonald polynomialH̃μ[Z;q, t]. We further introduce a general family of polynomialsFT[Z;q, S], whereTis an arbitrary set of squares in the first quadrant of thexyplane, andSis an arbitrary subset ofT. The coefficients of theFT[Z;q, S] are in\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathbb{N}}[q]\end{equation*}\end{document}, andC̃μ[Z;q, t] is a sum of certainFT[Z;q, S] times nonnegative powers oft. We proveFT[Z;q, S] is symmetric in theziand satisfies other properties consistent with the conjecture. We also show how the coefficient of a monomial inFT[Z;q, S] can be expressed recursively.maplecalculations indicate theFT[Z;q, S] are Schur-positive, and we present a combinatorial conjecture for their Schur coefficients when the setTis a partition with at most three columns.
Resolution and evolution of the duck-billed platypus karyotype with an X
1
Y
1
X
2
Y
2
X
3
Y
3
X
4
Y
4
X
5
Y
5
male sex chromosome constitution
Authors: Rens Willem , Grützner Frank , O'Brien Patricia C. M. , Fairclough Helen , Graves Jennifer A. M. , Ferguson-Smith Malcolm A.
Published: November 2004

The platypus (2
n
= 52) has a complex karyotype that has been controversial over the last three decades. The presence of unpaired chromosomes and an unknown sex-determining system especially has defied attempts at conventional analysis. This article reports on the preparation of chromosome-specific probes from flow-sorted chromosomes and their application in the identification and classification of all platypus chromosomes. This work reveals that the male karyotype has 21 pairs of chromosomes and 10 unpaired chromosomes (E1-E10), which are linked by short regions of homology to form a multivalent chain in meiosis. The female karyotype differs in that five of these unpaired elements (E1, E3, E5, E7, and E9) are each present in duplicate, whereas the remaining five unpaired elements (E2, E4, E6, E8, and E10) are absent. This finding indicates that sex is determined by the alternate segregation of the chain of 10 during spermatogenesis so that equal numbers of sperm bear either one of the two groups of five elements, i.e., five X and five Y chromosomes. Chromosome painting reveals that these X and Y chromosomes contain pairing (XY shared) and differential (X- or Y-specific) segments. Y differential regions must contain male-determining genes, and X differential regions should be dosage-compensated in the female. Two models for the evolution of the sex-determining system are presented. The resolution of the longstanding debate over the platypus karyotype is an important step toward the understanding of mechanisms of sex determination, dosage compensation, and karyotype evolution.
Transgenic mice expressing a soluble form of porcine nectin-1/herpesvirus entry mediator C as a model for pseudorabies-resistant livestock
Authors: Ono Etsuro , Amagai Keiko , Taharaguchi Satoshi , Tomioka Yukiko , Yoshino Saori , Watanabe Yuki , Cherel Pierre , Houdebine Louis-Marie , Adam Micheline , Eloit Marc , Inobe Manabu , Uede Toshimitsu
Published: November 2004

An approach to genetically engineered resistance to pseudorabies virus (PRV) infection was examined by using a transgene encoding a soluble form of nectin-1, also known as herpesvirus entry mediator C. Nectin-1 is an α-herpesvirus receptor that binds to virion glycoprotein D. Nectin-1 mediates entry of PRV, herpes simplex virus types 1 and 2, and bovine herpesvirus type 1. To assess the antiviral potential of an ectopic expression of the nectin-1 ectodomain
in vivo
, six transgenic mouse lines expressing a soluble form of nectin-1, consisting of an extracellular domain of porcine nectin-1 and the Fc portion of human IgG1, were generated. All of the transgenic mouse lines showed nearly complete resistance to PRV infection by means of both i.p. and intranasal routes. These results suggest that the introduction into farm animals of a transgene encoding a soluble form of nectin-1 would offer a potent biological approach to generating α-herpesvirus-resistant livestock.
Integrated regulatory responses of
fimB
to
N
-acetylneuraminic (sialic) acid and GlcNAc in
Escherichia coli
K-12
Authors: Sohanpal Baljinder K. , El-Labany Sammia , Lahooti Maryam , Plumbridge Jacqueline A. , Blomfield Ian C.
Published: November 2004

Bacterial-host attachment by means of bacterial adhesins is a key step in host colonization. Phase variation (reversible on-off switching) of the type 1 fimbrial adhesin of
Escherichia coli
involves a DNA inversion catalyzed by FimB (switching in either direction) or FimE (mainly on-to-off switching).
fimB
is separated from the divergent
yjhATS
operon by a large (1.4 kbp) intergenic region. Short (≈28 bp) cis-active elements (regions 1 and 2) close to
yjhA
stimulate
fimB
expression and are required for sialic acid (Neu
5
Ac) sensitivity of its expression [El-Labany, S., Sohanpal, B. K., Lahooti, M., Akerman, R. & Blomfield, I. C. (2003)
Mol. Microbiol.
49, 1109-1118]. Here, we show that whereas NanR, a sialic acid-response regulator, binds to region 1, NagC, a GlcNAc-6P-responsive protein, binds to region 2 instead. The NanR- and NagC-binding sites lie adjacent to deoxyadenosine methylase (Dam) methylation sites (5′-GATC) that are protected from modification, and the two regulators are shown to be required for methylation protection at regions 1 and 2, respectively. Mutations in
nanR
and
nagC
diminish
fimB
expression, and both
fimB
expression and FimB recombination are inhibited by GlcNAc (3- and >35-fold, respectively). Sialic acid catabolism generates GlcNAc-6-P, and whereas GlcNAc disrupts methylation protection by NagC alone, Neu
5
Ac inhibits the protection mediated by both NanR and NagC as expected. Type 1 fimbriae are proinflammatory, and host defenses enhance the release of both Neu
5
Ac and GlcNAc by a variety of mechanisms. Inhibition of type 1 fimbriation by these amino sugars may thus help balance the interaction between
E. coli
and its hosts.
Tropical geometry of statistical models
Authors: Pachter Lior , Sturmfels Bernd
Published: November 2004

This article presents a unified mathematical framework for inference in graphical models, building on the observation that graphical models are algebraic varieties. From this geometric viewpoint, observations generated from a model are coordinates of a point in the variety, and the sum-product algorithm is an efficient tool for evaluating specific coordinates. Here, we address the question of how the solutions to various inference problems depend on the model parameters. The proposed answer is expressed in terms of tropical algebraic geometry. The Newton polytope of a statistical model plays a key role. Our results are applied to the hidden Markov model and the general Markov model on a binary tree.