bluuebunny/crossref_metadata_2025 huggingface dataset:
A Cell Number-Counting Factor Regulates Levels of a Novel Protein, SslA, as Part of a Group Size Regulation Mechanism in
Dictyostelium
Authors: Gao Tong , Roisin-Bouffay Celine , Hatton R. Diane , Tang Lei , Brock Debra A. , DeShazo Tiffany , Olson Laura , Hong Wan-Pyo , Jang Wonhee , Canseco Elvia , Bakthavatsalam Deenadayalan , Gomer Richard H.
Published: July 2007

Developing
Dictyostelium
cells form aggregation streams that break into groups of ∼2 × 10
4
cells. The breakup and subsequent group size are regulated by a secreted multisubunit counting factor (CF). To elucidate how CF regulates group size, we isolated second-site suppressors of
smlA
−
, a transformant that forms small groups due to oversecretion of CF.
smlA
−
sslA1
(
CR11
) cells form roughly wild-type-size groups due to an insertion in the beginning of the coding region of
sslA1
, one of two highly similar genes encoding a novel protein. The insertion increases levels of SslA. In wild-type cells, the
sslA1
(
CR11
) mutation forms abnormally large groups. Reducing SslA levels by antisense causes the formation of smaller groups. The
sslA
(
CR11
) mutation does not affect the extracellular accumulation of CF activity or the CF components countin and CF50, suggesting that SslA does not regulate CF secretion. However, CF represses levels of SslA. Wild-type cells starved in the presence of
smlA
−
cells, recombinant countin, or recombinant CF50 form smaller groups, whereas
sslA1
(
CR11
) cells appear to be insensitive to the presence of
smlA
−
cells, countin, or CF50, suggesting that the
sslA1
(
CR11
) insertion affects CF signal transduction. We previously found that CF reduces intracellular glucose levels. s
slA
(
CR11
) does not significantly affect glucose levels, while glucose increases SslA levels. Together, the data suggest that SslA is a novel protein involved in part of a signal transduction pathway regulating group size.
A
Toxoplasma gondii
Leucine-Rich Repeat Protein Binds Phosphatase Type 1 Protein and Negatively Regulates Its Activity
Authors: Daher Wassim , Oria Gabrielle , Fauquenoy Sylvain , Cailliau Katia , Browaeys Edith , Tomavo Stanislas , Khalife Jamal
Published: July 2007

We have characterized the
Toxoplasma gondii
protein phosphatase type 1 (TgPP1) and a potential regulatory binding protein belonging to the leucine-rich repeat protein family, designated TgLRR1. TgLRR1 is capable of binding to TgPP1 to inhibit its activity and to override a G
2
/M cell cycle checkpoint in
Xenopus
oocytes. In the parasite, TgLRR1 mRNA and protein are both highly expressed in the rapidly replicating and virulent tachyzoites, while only low levels are detected in the slowly dividing and quiescent bradyzoites. TgPP1 mRNA and protein levels are equally abundant in tachyzoites and bradyzoites. Affinity pull down and immunoprecipitation experiments reveal that the TgLRR1-TgPP1 interaction takes place in the nuclear subcompartment of tachyzoites. These results are consistent with those of localization studies using both indirect immunofluorescence with specific polyclonal antibody and transient transfection of
T. gondii
vector expressing TgLRR1 and TgPP1. The inability to obtain stable transgenic tachyzoites suggested that overexpression of TgLRR1 and TgPP1 may impair the parasite's growth. Together with the activation of
Xenopus
oocyte meiosis reinitiation, these data indicate that TgLRR1 protein could play a role in the regulation of the
T. gondii
cell cycle through the modulation of phosphatase activity.
Transcriptional and Physiological Responses of
Bradyrhizobium japonicum
to Desiccation-Induced Stress
Authors: Cytryn Eddie J. , Sangurdekar Dipen P. , Streeter John G. , Franck William L. , Chang Woo-suk , Stacey Gary , Emerich David W. , Joshi Trupti , Xu Dong , Sadowsky Michael J.
Published: July 2007

The growth and persistence of rhizobia and bradyrhizobia in soils are negatively impacted by drought conditions. In this study, we used genome-wide transcriptional analyses to obtain a comprehensive understanding of the response of
Bradyrhizobium japonicum
to drought. Desiccation of cells resulted in the differential expression of 15 to 20% of the 8,480
B. japonicum
open reading frames, with considerable differentiation between early (after 4 h) and late (after 24 and 72 h) expressed genes. While 225 genes were universally up-regulated at all three incubation times in response to desiccation, an additional 43 and 403 up-regulated genes were common to the 4/24- and 24/72-h incubation times, respectively. Desiccating conditions resulted in the significant induction (>2.0-fold) of the trehalose-6-phosphate synthetase (
otsA
), trehalose-6-phosphate phosphatase (
otsB
), and trehalose synthase (
treS
) genes, which encode two of the three trehalose synthesis pathways found in
B. japonicum
. Gene induction was correlated with an elevated intracellular concentration of trehalose and increased activity of trehalose-6-phosphate synthetase, collectively supporting the hypothesis that this disaccharide plays a prominent and important role in promoting desiccation tolerance in
B. japonicum
. Microarray data also indicated that σ
54
- and σ
24
-associated transcriptional regulators and genes encoding isocitrate lyase, oxidative stress responses, the synthesis and transport of exopolysaccharides, heat shock response proteins, enzymes for the modification and repair of nucleic acids, and the synthesis of pili and flagella are also involved in the response of
B. japonicum
to desiccation. Polyethylene glycol-generated osmotic stress induced significantly fewer genes than those transcriptionally activated by desiccation. However, 67 genes were commonly induced under both conditions. Taken together, these results suggest that
B. japonicum
directly responds to desiccation by adapting to changes imparted by reduced water activity, such as the synthesis of trehalose and polysaccharides and, secondarily, by the induction of a wide variety of proteins involved in protection of the cell membrane, repair of DNA damage, stability and integrity of proteins, and oxidative stress responses.
Anaerobic Regulation of
Shigella flexneri
Virulence: ArcA Regulates
fur
and Iron Acquisition Genes
Authors: Boulette Megan L. , Payne Shelley M.
Published: July 2007

Invasion and plaque formation in epithelial monolayers are routinely used to assess the virulence of
Shigella flexneri
, a causative agent of dysentery. A modified plaque assay was developed to identify factors contributing to the virulence of
S. flexneri
under the anaerobic conditions present in the colon. This assay demonstrated the importance of the ferrous iron transport system Feo, as well as the global transcription factors Fur, ArcA, and Fnr, for
Shigella
plaque formation in anoxic environments. Transcriptional analyses of
S. flexneri
iron transport genes indicated that anaerobic conditions activated
feoABC
while repressing genes encoding two other iron transport systems, the ABC transporter Sit and the Iuc/Iut aerobactin siderophore synthesis and transport system. The anaerobic transcription factors ArcA and Fnr activated expression of
feoABC
, while ArcA repressed
iucABCD iutA
. Transcription of
fur
, encoding the iron-responsive transcriptional repressor of bacterial iron acquisition, was also repressed anaerobically in an ArcA-dependent manner.
Hydroxyatrazine
N
-Ethylaminohydrolase (AtzB): an Amidohydrolase Superfamily Enzyme Catalyzing Deamination and Dechlorination
Authors: Seffernick Jennifer L. , Aleem Asma , Osborne Jeffrey P. , Johnson Gilbert , Sadowsky Michael J. , Wackett Lawrence P.
Published: July 2007

Hydroxyatrazine [2-(
N
-ethylamino)-4-hydroxy-6-(
N
-isopropylamino)-1,3,5-triazine]
N
-ethylaminohydrolase (AtzB) is the sole enzyme known to catalyze the hydrolytic conversion of hydroxyatrazine to
N
-isopropylammelide. AtzB, therefore, serves as the point of intersection of multiple
s
-triazine biodegradative pathways and is completely essential for microbial growth on
s
-triazine herbicides. Here,
atzB
was cloned from
Pseudomonas
sp. strain ADP and its product was purified to homogeneity and characterized. AtzB was found to be dimeric, with subunit and holoenzyme molecular masses of 52 kDa and 105 kDa, respectively. The
k

cat

and
K

m

of AtzB with hydroxyatrazine as a substrate were 3 s
−1
and 20 μM, respectively. Purified AtzB had a 1:1 zinc-to-subunit stoichiometry. Sequence analysis revealed that AtzB contained the conserved mononuclear amidohydrolase superfamily active-site residues His74, His76, His245, Glu248, His280, and Asp331. An intensive in vitro investigation into the substrate specificity of AtzB revealed that 20 of the 51 compounds tested were substrates for AtzB; this allowed for the identification of specific substrate structural features required for catalysis. Substrates required a monohydroxylated
s
-triazine ring with a minimum of one primary or secondary amine substituent and either a chloride or amine leaving group. AtzB catalyzed both deamination and dechlorination reactions with rates within a range of one order of magnitude. This differs from AtzA and TrzN, which do not catalyze deamination reactions, and AtzC, which is not known to catalyze dechlorination reactions.
Alterations in the Two Globular Domains or in the Connecting α-Helix of Bacterial Ribosomal Protein L9 Induces +1 Frameshifts
Authors: Leipuviene Ramune , Björk Glenn R.
Published: July 2007

The ribosomal 50S subunit protein L9, encoded by the gene
rplI
, is an elongated protein with an α-helix connecting the N- and C-terminal globular domains. We isolated
rplI
mutants that suppress the +1 frameshift mutation
hisC3072
in
Salmonella enterica
serovar Typhimurium. These mutants have amino acid substitutions in the N-terminal domain (G24D) or in the C-terminal domain (I94S, A102D, G126V, and F132S) of L9. In addition, different one-base deletions in
rplI
altered either the final portion of the C terminus or removed the C-terminal domain with or without the connecting α-helix. An alanine-to-proline substitution at position 59 (A59P), which breaks the α-helix between the globular domains, induced +1 frameshifting, suggesting that the geometrical relationship between the N and C domains is important to maintain the reading frame. Except for the alterations G126V in the C terminus and A59P in the connecting α-helix, our results confirm earlier results obtained by using the phage T4 gene
60
-based system to monitor bypassing. The way
rplI
mutations suppress various frameshift mutations suggests that bypassing of many codons from several takeoff and landing sites occurred instead of a specific frameshift forward at overlapping codons.
Characterization of the Osmoprotectant Transporter OpuC from
Pseudomonas syringae
and Demonstration that Cystathionine-β-Synthase Domains Are Required for Its Osmoregulatory Function
Authors: Chen Chiliang , Beattie Gwyn A.
Published: July 2007

The plant pathogen
Pseudomonas syringae
may cope with osmotic stress on plants, in part, by importing osmoprotective compounds. In this study, we found that
P. syringae
pv. tomato strain DC3000 was distinct from most bacterial species in deriving greater osmoprotection from exogenous choline than from glycine betaine. This superior osmoprotection was correlated with a higher capacity for uptake of choline than for uptake of glycine betaine. Of four putative osmoregulatory ABC transporters in DC3000, one, designated OpuC, functioned as the primary or sole transporter for glycine betaine and as one of multiple transporters for choline under high osmolarity. Surprisingly, the homolog of the well-characterized ProU transporter from
Escherichia coli
and
Salmonella enterica
serovar Typhimurium did not function in osmoprotection. The
P. syringae
pv. tomato OpuC transporter was more closely related to the
Bacillus subtilis
and
Listeria monocytogenes
OpuC transporters than to known osmoprotectant transporters in gram-negative bacteria based on sequence similarity and genetic arrangement. The
P. syringae
pv. tomato OpuC transporter had a high affinity for glycine betaine, a low affinity for choline, and a broad substrate specificity that included acetylcholine, carnitine, and proline betaine. Tandem cystathionine-β-synthase (CBS) domains in the ATP-binding component of OpuC were required for transporter function. The presence of these CBS domains was correlated with osmoregulatory function among the putative transporters examined in DC3000 and was found to be predictive of functional osmoregulatory transporters in other pseudomonads. These results provide the first functional evaluation of an osmoprotectant transporter in a
Pseudomonas
species and demonstrate the usefulness of the CBS domains as predictors of osmoregulatory activity.
Salicylic Acid, Yersiniabactin, and Pyoverdin Production by the Model PhytopathogenPseudomonas syringaepv. tomato DC3000: Synthesis, Regulation, and Impact on Tomato andArabidopsisHost Plants
Authors: Jones Alexander M. , Lindow Steven E. , Wildermuth Mary C.
Published: July 2007

A genetically tractable model plant pathosystem,Pseudomonas syringaepv. tomato DC3000 on tomato andArabidopsis thalianahosts, was used to investigate the role of salicylic acid (SA) and iron acquisition via siderophores in bacterial virulence. Pathogen-induced SA accumulation mediates defense in these plants, and DC3000 contains the genes required for the synthesis of SA, the SA-incorporated siderophore yersiniabactin (Ybt), and the fluorescent siderophore pyoverdin (Pvd). We found that DC3000 synthesizes SA, Ybt, and Pvd under iron-limiting conditions in culture. Synthesis of SA and Ybt by DC3000 requirespchA, an isochorismate synthase gene in the Ybt genomic cluster, and exogenous SA can restore Ybt production by thepchAmutant. Ybt was also produced by DC3000 in planta, suggesting that Ybt plays a role in DC3000 pathogenesis. However, thepchAmutant did not exhibit any growth defect or altered virulence in plants. This lack of phenotype was not attributable to plant-produced SA restoring Ybt production, as thepchAmutant grew similarly to DC3000 in anArabidopsisSA biosynthetic mutant, and in planta Ybt was not detected inpchA-infected wild-type plants. In culture, no growth defect was observed for thepchAmutant versus DC3000 for any condition tested. Instead, enhanced growth of thepchAmutant was observed under stringent iron limitation and additional stresses. This suggests that SA and Ybt production by DC3000 is costly and that Pvd is sufficient for iron acquisition. Further exploration of the comparative synthesis and utility of Ybt versus Pvd production by DC3000 found siderophore-dependent amplification ofybtgene expression to be absent, suggesting that Ybt may play a yet unknown role in DC3000 pathogenesis.
Expression and Association of Group IV Nitrogenase NifD and NifH Homologs in the Non-Nitrogen-Fixing ArchaeonMethanocaldococcus jannaschii
Authors: Staples Christopher R. , Lahiri Surobhi , Raymond Jason , Von Herbulis Lindsay , Mukhophadhyay Biswarup , Blankenship Robert E.
Published: July 2007

Using genomic analysis, researchers previously identified genes coding for proteins homologous to the structural proteins of nitrogenase (J. Raymond, J. L. Siefert, C. R. Staples, and R. E. Blankenship, Mol. Biol. Evol. 21:541-554, 2004). The expression and association of NifD and NifH nitrogenase homologs (named NflD and NflH for “Nif-like” D and H, respectively) have been detected in a non-nitrogen-fixing hyperthermophilic methanogen,Methanocaldococcus jannaschii. These homologs are expressed constitutively and do not appear to be directly involved with nitrogen metabolism or detoxification of compounds such as cyanide or azide. The NflH and NflD proteins were found to interact with each other, as determined by bacterial two-hybrid studies. Upon immunoisolation, NflD and NflH copurified, along with three other proteins whose functions are as yet uncharacterized. The apparent presence of genes coding for NflH and NflD in all known methanogens, their constitutive expression, and their high sequence similarity to the NifH and NifD proteins or the BchL and BchN/BchB proteins suggest that NflH and NflD participate in an indispensable and fundamental function(s) in methanogens.
Mutational Analysis of Active Site Residues Essential for Sensing of Organic Hydroperoxides by
Bacillus subtilis
OhrR
Authors: Soonsanga Sumarin , Fuangthong Mayuree , Helmann John D.
Published: July 2007

Bacillus subtilis
OhrR is the prototype for the one-Cys family of organic peroxide-sensing regulatory proteins. Mutational analyses indicate that the high sensitivity of the active site cysteine (C15) to peroxidation requires three Tyr residues. Y29 and Y40 from the opposing subunit of the functional dimer hydrogen bond with the reactive Cys thiolate, and substitutions at these positions reduce or eliminate the ability of OhrR to respond to organic peroxides. Y19 is also critical for peroxide sensing, and the Ala substitution mutant (OhrR Y19A) is less susceptible to oxidation at the active site C15 in vivo. The Y19A protein also displays decreased sensitivity to peroxide-mediated oxidation in vitro. Y19 is in van der Waals contact with two residues critical for protein function, F16 and R23. The latter residue makes critical contact with the DNA backbone in the OhrR-operator complex. These results indicate that the high sensitivity of the OhrR C15 residue to oxidation requires interactions with the opposed Tyr residues. Oxidative modification of C15 likely disrupts the C15-Y29′-Y40′ hydrogen bond network and thereby initiates conformational changes that reduce the ability of OhrR to bind to its operator site.
Docking of the Periplasmic FecB Binding Protein to the FecCD Transmembrane Proteins in the Ferric Citrate Transport System ofEscherichia coli
Authors: Braun Volkmar , Herrmann Christina
Published: July 2007

Citrate-mediated iron transport across the cytoplasmic membrane is catalyzed by an ABC transporter that consists of the periplasmic binding protein FecB, the transmembrane proteins FecC and FecD, and the ATPase FecE. Salt bridges between glutamate residues of the binding protein and arginine residues of the transmembrane proteins are predicted to mediate the positioning of the substrate-loaded binding protein on the transmembrane protein, based on the crystal structures of the ABC transporter for vitamin B12, consisting of the BtuF binding protein and the BtuCD transmembrane proteins (E. L. Borths et al., Proc. Natl. Acad. Sci. USA 99:16642-16647, 2002). Here, we examined the role of the residues predicted to be involved in salt-bridge formation between FecB and FecCD by substituting these residues with alanine, cysteine, arginine, and glutamate and by analyzing the citrate-mediated iron transport of the mutants. Replacement of E93 in FecB with alanine [FecB(E93A)], cysteine, or arginine nearly abolished citrate-mediated iron transport. Mutation FecB(E222R) nearly eliminated transport, and FecB(E222A) and FecB(E222C) strongly reduced transport. FecD(R54C) and FecD(R51E) abolished transport, whereas other R-to-C mutations in putative interaction sites between FecCD and FecB substantially reduced transport. The introduced cysteine residues in FecB and FecCD also served to examine the formation of disulfide bridges in place of salt bridges between the binding protein and the transmembrane proteins. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis results suggest cross-linking of FecB(E93C) to FecD(R54C) and FecB(E222C) to FecC(R60C). The data are consistent with the proposal that FecB(E93) is contained in the region that binds to FecD and FecB(E222) in the region that binds to FecC.
The Amino Terminus of
Bacillus subtilis
TagB Possesses Separable Localization and Functional Properties
Authors: Bhavsar Amit P. , D'Elia Michael A. , Sahakian Tiffany D. , Brown Eric D.
Published: July 2007

The function(s) of gram-positive wall teichoic acid is emerging with recent findings that it is an important virulence factor in the pathogen
Staphylococcus aureus
and that it is crucial to proper rod-shaped cell morphology of
Bacillus subtilis
. Despite its importance, our understanding of teichoic acid biosynthesis remains incomplete. The TagB protein has been implicated in the priming step of poly(glycerol phosphate) wall teichoic acid synthesis in
B. subtilis.
Work to date indicates that the TagB protein is localized to the membrane, where it adds a single glycerol phosphate residue to the nonreducing end of the undecaprenol-phosphate-linked
N
-acetylmannosamine-β(1,4)-
N
-acetylglucosamine-1-phosphate. Thus, membrane association is critical to TagB function. In this work we elucidate the mechanism of TagB membrane localization. We report the identification of a membrane targeting determinant at the amino terminus of TagB that is necessary and sufficient for membrane localization. The putative amphipathicity of this membrane targeting determinant was characterized and shown to be required for TagB function but not localization. This work shows for the first time that the amino terminus of TagB mediates membrane targeting and protein function.
Cryptococcus neoformans
Typing by PCR Fingerprinting Using (GACA)
4
Primers Based on
C. neoformans
Genome Project Data
Authors: Cogliati Massimo , Esposto Maria Carmela , Liberi Giordano , Tortorano Anna Maria , Viviani Maria Anna
Published: August 2007

Four (GACA)
4
PCR fingerprinting sequences, used as markers to identify serotypes A and D and AD hybrids, were retrieved in four
Cryptococcus neoformans
genome databases. Their locations, both in serotype A and D genomes, were confirmed by chromosomal hybridization with specific probes. Two sequences were recognized to code for hypothetical functional proteins.
Serine/Arginine-Rich Proteins Contribute to Negative Regulator of Splicing Element-Stimulated Polyadenylation in Rous Sarcoma Virus
Authors: Maciolek Nicole L. , McNally Mark T.
Published: August 2007

Rous sarcoma virus (RSV) requires large amounts of unspliced RNA for replication. Splicing and polyadenylation are coupled in the cells they infect, which raises the question of how viral RNA is efficiently polyadenylated in the absence of splicing. Optimal RSV polyadenylation requires a far-upstream splicing control element, the negative regulator of splicing (NRS), that binds SR proteins and U1/U11 snRNPs and functions as a pseudo-5′ splice site that interacts with and sequesters 3′ splice sites. We investigated a link between NRS-mediated splicing inhibition and efficient polyadenylation. In vitro, the NRS alone activated a model RSV polyadenylation substrate, and while the effect did not require the snRNP-binding sites or a downstream 3′ splice site, SR proteins were sufficient to stimulate polyadenylation. Consistent with this, SELEX-binding sites for the SR proteins ASF/SF2, 9G8, and SRp20 were able to stimulate polyadenylation when placed upstream of the RSV poly(A) site. In vivo, however, the SELEX sites improved polyadenylation in proviral clones only when the NRS-3′ splice site complex could form. Deletions that positioned the SR protein-binding sites closer to the poly(A) site eliminated the requirement for the NRS-3′ splice site interaction. This indicates a novel role for SR proteins in promoting RSV polyadenylation in the context of the NRS-3′ splice site complex, which is thought to bridge the long distance between the NRS and poly(A) site. The results further suggest a more general role for SR proteins in polyadenylation of cellular mRNAs.
West Nile Virus-Induced Neuroinflammation: Glial Infection and Capsid Protein-Mediated Neurovirulence
Authors: van Marle Guido , Antony Joseph , Ostermann Heather , Dunham Christopher , Hunt Tracey , Halliday William , Maingat Ferdinand , Urbanowski Matt D. , Hobman Tom , Peeling James , Power Christopher
Published: August 2007

West Nile virus (WNV) infection causes neurological disease at all levels of the neural axis, accompanied by neuroinflammation and neuronal loss, although the underlying mechanisms remain uncertain. Given the substantial activation of neuroinflammatory pathways observed in WNV infection, we hypothesized that WNV-mediated neuroinflammation and cell death occurred through WNV infection of both glia and neurons, which was driven in part by WNV capsid protein expression. Analysis of autopsied neural tissues from humans with WNV encephalomyelitis (WNVE) revealed WNV infection of both neurons and glia. Upregulation of proinflammatory genes, CXCL10, interleukin-1β, and indolamine-2′,3′-deoxygenase with concurrent suppression of the protective astrocyte-specific endoplasmic reticulum stress sensor gene, OASIS (for old astrocyte specifically induced substance), was evident in WNVE patients compared to non-WNVE controls. These findings were supported by increased ex vivo expression of these proinflammatory genes in glia infected by WNV-NY99. WNV infection caused endoplasmic reticulum stress gene induction and apoptosis in neurons but did not affect glial viability. WNV-infected astrocytic cells secreted cytotoxic factors, which caused neuronal apoptosis. The expression of the WNV-NY99 capsid protein in neurons and glia by a Sindbis virus-derived vector (SINrep5-WNVc) caused neuronal death and the release of neurotoxic factors by infected astrocytes, coupled with proinflammatory gene induction and suppression of OASIS. Striatal implantation of SINrep5-WNVCinduced neuroinflammation in rats, together with the induction of CXCL10 and diminished OASIS expression, compared to controls. Moreover, magnetic resonance neuroimaging showed edema and tissue injury in the vicinity of the SINrep5-WNVc implantation site compared to controls, which was complemented by neurobehavioral abnormalities in the SINrep5-WNVc-implanted animals. These studies underscore the important interactions between the WNV capsid protein and neuroinflammation in the pathogenesis of WNV-induced neurological disorders.
D2-40 is a sensitive and specific marker in differentiating primary adrenal cortical tumours from both metastatic clear cell renal cell carcinoma and phaeochromocytoma
Authors: Browning L , Bailey D , Parker A
Published: July 2007

Background:

The morphological similarities between the cells of clear cell renal cell carcinoma (CCRCC) and those of the adrenal cortex impose diagnostic difficulties, for example in the context of a solitary nodule in the adrenal gland in a patient with renal cell carcinoma (RCC). This problem is confounded by the variable and patchy staining seen with the established panel of antibodies utilised in this context, namely EMA, cytokeratins, vimentin, inhibin, melan-A, and RCC marker; particularly on biopsy material. D2-40, an antibody commonly used to highlight lymphatic endothelial cells, is consistently positive in the normal adrenal cortex.

Aims:

To investigate the utility of D2-40 in distinguishing neoplastic and non-neoplastic adrenal cortical cells from those of CCRCC, and from phaeochromocytoma.

Methods:

D2-40 antibody was applied to tissue sections from 10 normal adrenal glands, 15 renal carcinomas (13 clear cell, 2 papillary variants), 1 metastatic CCRCC in the adrenal gland, 6 adrenal cortical hyperplasias, 5 adrenal cortical adenomas, 3 adrenal cortical carcinomas, and 4 phaeochromocytomas.

Results:

D2-40 was strongly and diffusely positive in the cells of the neoplastic and non-neoplastic adrenal cortex, but negative in the cells of the CCRCC, both primary and metastatic, in 100% of the cases. The cells of the adrenal medulla, and those of the phaeochromocytomas, were negative for D2-40.

Conclusions:

D2-40 may be a useful marker for distinguishing primary adrenal cortical neoplasms from both metastatic CCRCC and phaeochromocytoma.
The soil seed bank of a montane meadow: consequences of conifer encroachment and implications for restoration
Authors: Lang Nicole L. , Halpern Charles B.
Published: August 2007

We examined changes in the soil seed bank associated with conifer encroachment of montane meadows in the western Cascade Range of Oregon. We asked whether, and over what period of time, meadow species maintain viable seeds in the soil, and by implication, whether the seed bank can contribute to restoration if conifers are removed. Seed bank composition, ground vegetation, and forest age structure were quantified for 209 samples representing a chronosequence of open meadow, young forest (<75 years), and old forest (95 to >200 years). The seed bank was substantial (44 taxa and 2332 germinants/m2), but dominated by native ruderals (16 species comprising 71% of germinants). Greater than 70% of meadow species were absent from the seed bank. Thirteen meadow species accounted for 21% of all germinants, but most of these were the dominant sedge, Carex pensylvanica Lam.. Seed density, richness, and composition showed weak relationships to forest age, and little resemblance to the ground vegetation, which changed markedly with forest development. Our results suggest that there is limited potential for recovery of most meadow species via the seed bank. Natural reestablishment of these species will require seed dispersal or gradual vegetative spread from existing openings, but competitive interactions with ruderal or forest species may limit recruitment or recovery.
THE LUKASH PLANE-WAVE ATTRACTOR AND RELATIVE ENERGY
Authors: KORUNUR MURAT , SALTI MUSTAFA , AYDOGDU OKTAY
Published: August 2007

We study energy distribution in the context of teleparallel theory of gravity, due to matter and fields including gravitation, of the universe based on the plane-wave Bianchi VIIδ spacetimes described by the Lukash metric. For this calculation, we consider the teleparallel gravity analogs of the energy–momentum formulations of Einstein, Bergmann–Thomson and Landau–Lifshitz. We find that Einstein and Bergmann–Thomson prescriptions agree with each other and give the same results for the energy distribution in a given spacetime, but the Landau–Lifshitz complex does not. Energy density turns out to be nonvanishing in all of these prescriptions. It is interesting to mention that the results can be reduced to the already available results for the Milne universe when we write ω = 1 and Ξ2 = 1 in the metric of the Lukash spacetime, and for this special case, we get the same relation among the energy–momentum formulations of Einstein, Bergmann–Thomson and Landau–Lifshitz as obtained for the Lukash spacetime. Furthermore, our results support the hypothesis by Cooperstock that the energy is confined to the region of nonvanishing energy–momentum tensor of matter and all non-gravitational fields, and also sustain the importance of the energy–momentum definitions in the evaluation of the energy distribution associated with a given spacetime.
THE EFFECT OF Z′-MEDIATED FLAVOR-CHANGING NEUTRAL CURRENT ON Bd→ℓ+ℓ- DECAY
Authors: SAHOO S. , MAHARANA L.
Published: August 2007

We study the effect of both Z and Z′-mediated flavor-changing neutral current (FCNC) on the Bd→ℓ+ℓ-, (ℓ = μ, τ) rare decay. We find that the branching ratio can be larger by order two from its Standard Model (SM) value due to the effect of both Z and Z′-mediated FCNC, though the major contribution comes from Z boson and provides signals for new physics beyond the SM.
NONPARAMETRIC DETERMINATION OF REDSHIFT EVOLUTION INDEX OF DARK ENERGY
Authors: ZIAEEPOUR HOURI
Published: August 2007

We propose a nonparametric method to determine the sign of γ — the redshift evolution index of dark energy. This is important for distinguishing between positive energy models, a cosmological constant, and what is generally called ghost models. Our method is based on geometrical properties and is more tolerant to uncertainties of other cosmological parameters than fitting methods in what concerns the sign of γ. The same parametrization can also be used for determining γ and its redshift dependence by fitting. We apply this method to SNLS supernovae and to gold sample of re-analyzed supernovae data from Riess et al. Both datasets show strong indication of a negative γ. If this result is confirmed by more extended and precise data, many of the dark energy models, including simple cosmological constant, standard quintessence models without interaction between quintessence scalar field(s) and matter, and scaling models are ruled out. We have also applied this method to Gurzadyan–Xue models with varying fundamental constants to demonstrate the possibility of using it to test other cosmologies.
THE TRANSVERSE IMPEDANCE OF NORMAL LIQUID 3He
Authors: SHAHZAMANIAN M. A. , YAVARY H.
Published: August 2007

The effect of the external velocity field on the transverse impedance of normal liquid 3 He has been considered. It is shown that there is an additional frequency dependent term proportional to the current-current correlation function. Vertex corrections to the collisional self-energy have to be treated in order to turn the simple relaxation time into viscous transport time, which is necessary for a quantitative description of the problem.
ONE-PHONON-ASSISTED ELECTRON RESONANT RAMAN SCATTERING IN FREE-STANDING QUANTUM WIRES
Authors: ZHAO XIANG-FU , LIU CUI-HONG
Published: August 2007

The scattering intensity (SI) for an electron resonant Raman scattering (ERRS) process in a free-standing semiconductor quantum wire of cylindrical geometry associated with bulk longitudinal optical (LO) phonon modes or the surface optical (SO) phonon modes is calculated for T=0 K . The Fröhlich interaction is considered to illustrate the theory for a GaAs system. Electron states are confined within a free-standing quantum wire (FSW). Single parabolic conduction and valence bands are assumed. The selection rules are studied. Numerical results and a discussion are also presented for various radii of the cylindrical quantum wires.
OPTICAL SOLITARY WAVES FOR THE GENERALIZED HIGHER-ORDER NONLINEAR SCHRÖDINGER EQUATION WITH VARIABLE COEFFICIENTS
Authors: DAI CHAO-QING , ZHOU GUO-QUAN , ZHANG JIE-FANG
Published: August 2007

In this paper, four kinds of optical solitary wave solutions, including bright, dark optical solitary waves and new types of solitary waves (W-shaped and M-shaped), for the generalized higher-order nonlinear Schrödinger equation (GHONLSE) with variable coefficients are considered under certain parametric conditions. Among these solutions, the W-shaped and M-shaped solitary waves, which cannot exist in the variable-coefficient nonlinear Schrödinger equation (vNLSE), are first given for the GHONLSE with variable coefficients. As examples, we analyze the properties of these solitary wave solutions in some periodic distributed amplification systems. When α1(z)=0, these bright and dark optical solitary wave solutions agree with the corresponding solutions in Refs. 25, 26 and 27, and the W-shaped solitary wave is in agreement with the corresponding result in Ref. 29. When α3(z)–α7(z) are constants and α1(z)=α2(z)=0, the W-shaped and M-shaped solitary waves in Refs. 14 and 15 can be recovered, respectively. Under the absence of the higher-order terms (α4(z), α6(z), α7(z)) and α1(z)=0, we provide the same results as reported in Refs. 22 and 23. This means that our results have more general forms than the earlier reports.
PROBABILISTIC ANALYSIS OF STRONG GROUND MOTION AND TSUNAMI HAZARDS IN SOUTHEAST ASIA
Authors: THIO HONG KIE , SOMERVILLE PAUL , ICHINOSE GENE
Published: August 2007

The December 2004 Sumatra-Andaman earthquake emphasized the need for a consistent and comprehensive assessment of tsunami hazard. We have developed a method for Probabilistic Tsunami Hazard Analysis (PTHA) based on the traditional Probabilistic Seismic Hazard Analysis (PSHA) and therefore completely consistent with standard seismic practice. In lieu of attenuation relations, it uses the summation of finite-difference Green's functions that have been pre-computed for individual subfaults, which enables us to rapidly construct scenario tsunami waveforms from an aggregate of subfaults that comprise a single large event. For every fault system, it is then possible to integrate over sets of thousands of events within a certain magnitude range that represents a fully probabilistic distribution. Because of the enclosed nature of ports and harbors, effects of resonance need to be addressed as well, which is why we have extended this method to not only analyze exceedance levels of maximum wave height, but also of spectral amplitudes. As in PSHA, these spectral amplitudes can be matched with the spectral response of harbors, and thus allow a comprehensive probabilistic analysis of tsunami hazard in ports and harbors.
IIx myosin heavy chain promoter regulation cannot be characterized in vivo by direct gene transfer
Authors: Pandorf Clay E. , Haddad Fadia , Qin Anqi X. , Baldwin Kenneth M.
Published: August 2007

In skeletal muscle of the adult mammal IIx is a pivotal myosin heavy chain (MHC) isoform that can be either up- or downregulated depending on both the fiber type of the target muscle and the type of external stimulus imposed. Since little is known about promoter elements of the IIx MHC gene that are important for its transcriptional regulation in vivo,the main goal of this study was to characterize IIx MHC promoter activity and identify potential regulatory elements on the IIx MHC promoter. A direct gene transfer approach was used, and this approach involved transfection of promoter-reporter constructs into intact rat soleus and plantaris muscle under control and denervated conditions, as well as hindlimb suspension (i.e., models to upregulate IIx MHC transcription). Fast-twitch (plantaris) muscle fibers were confirmed to have significantly greater IIx MHC transcriptional products (pre-mRNA and mRNA) than slow-twitch (soleus) muscle fibers. However, promoter sequences corresponding to −2671 to +1720, −1000 to +392, and −605/+392 relative to the IIx MHC transcription start site, plus an additional construct ligated to a putative embryonic MHC enhancer, failed to produce a fiber type-specific response that is characteristic of the endogenous IIx MHC promoter. Furthermore, the activity of these promoter constructs did not demonstrate the expected response to denervation or hindlimb suspension (i.e., marked upregulation), despite normal uptake and activity of a coinjected α-actin reference promoter. On the basis of these findings with IIx MHC promoter-reporters we conclude that the loss of the native chromatin environment as well as other necessary cis elements may preclude use of the gene transfer approach, thereby suggesting that there are hidden layers of regulation for the IIx MHC gene.
Bacterial symbionts induce a FUT2-dependent fucosylated niche on colonic epithelium via ERK and JNK signaling
Authors: Meng Di , Newburg David S. , Young Cheryl , Baker Amy , Tonkonogy Susan L. , Sartor R. Balfour , Walker W. Allan , Nanthakumar N. Nanda
Published: August 2007

The intestinal epithelium of the adult gut supports a complex, dynamic microbial ecosystem and expresses highly fucosylated glycans on its surface. Uncolonized gut contains little fucosylated glycan. The transition toward adult colonization, such as during recovery from germ-free status or from antibiotic treatment, increased expression of fucosylated epitopes in the colonic epithelium. This increase in fucosylation is accompanied by induction of fut2 mRNA expression and α1,2/3-fucosyltransferase activity. Colonization stimulates ERK and JNK signal transduction pathways, resulting in activation of transcription factors ATF2 and c-Jun, respectively. This increases transcription of fut2 mRNA and expression of α1,2/3-fucosyltransferase activity, resulting in a highly fucosylated intestinal mucosa characteristic of the adult mammalian gut. Blocking the ERK and JNK signaling cascade inhibits the ability of colonization to induce elevated fut2 mRNA and fucosyltransferase activity in the mature colon. Thus pioneer-mutualist symbiotic bacteria may utilize the ERK and JNK signaling cascade to induce the high degree of fucosylation characteristic of adult mammalian colon, and we speculate that this fucosylation facilitates colonization by adult microbiota.
COX-2-dependent and potentially cardioprotective effects of negative inotropic substances released after ischemia
Authors: Birkenmeier Katrin , Staudt Alexander , Schunck Wolf-Hagen , Janke Irka , Labitzke Corina , Prange Thomas , Trimpert Christiane , Krieg Thomas , Landsberger Martin , Stangl Verena , Felix Stephan B.
Published: July 2007

During reperfusion, cardiodepressive factors are released from isolated rat hearts after ischemia. The present study analyzes the mechanisms by which these substances mediate their cardiodepressive effect. After 10 min of global stop-flow ischemia, rat hearts were reperfused and coronary effluent was collected over a period of 30 s. We tested the effect of this postischemic effluent on systolic cell shortening and Ca2+ metabolism by application of fluorescence microscopy of field-stimulated rat cardiomyocytes stained with fura-2 AM. Cells were preincubated with various inhibitors, e.g., the cyclooxygenase (COX) inhibitor indomethacin, the COX-2 inhibitors NS-398 and lumiracoxib, the COX-1 inhibitor SC-560, and the potassium (ATP) channel blocker glibenclamide. Lysates of cardiomyocytes and extracts from whole rat hearts were tested for expression of COX-2 with Western blot analysis. As a result, in contrast to nonischemic effluent (control), postischemic effluent induced a reduction of Ca2+ transient and systolic cell shortening in the rat cardiomyocytes ( P < 0.001 vs. control). After preincubation of cells with indomethacin, NS-398, and lumiracoxib, the negative inotropic effect was attenuated. SC-560 did not influence the effect of postischemic effluent. The inducibly expressed COX-2 was detected in cardiomyocytes prepared for fluorescence microscopy. The effect of postischemic effluent was eliminated with applications of glibenclamide. Furthermore, postischemic effluent significantly reduced the intracellular diastolic and systolic Ca2+ increase ( P < 0.01 vs. control). In conclusion, the cardiodepressive effect of postischemic effluent is COX-2 dependent and protective against Ca2+ overload in the cells.
Moderate hypothermia (30°C) maintains myocardial integrity and modifies response of cell survival proteins after reperfusion
Authors: Ning Xue-Han , Chi Emil Y. , Buroker Norman E. , Chen Shi-Han , Xu Cheng-Su , Tien Ying-Tzang , Hyyti Outi M. , Ge Ming , Portman Michael A.
Published: July 2007

Hypothermia preserves myocardial function, promotes signaling for cell survival, and inhibits apoptotic pathways during 45-min reperfusion. We tested the hypothesis that signaling at the transcriptional level is followed by corresponding proteomic response and maintenance of structural integrity after 3-h reperfusion. Isolated hearts were Langendorff perfused and exposed to mild (I group; n = 6, 34°C) or moderate (H group; n = 6, 30°C) hypothermia during 120-min total ischemia with cardioplegic arrest and 180-min 37°C reperfusion. Moderate hypothermia suppressed anaerobic metabolism during ischemia and significantly diminished left ventricular end-diastolic pressure at the end of ischemia from 52.7 ± 3.3 (I group) to 1.8 ± 0.9 (H group) mmHg. Unlike the I group, which showed poor cardiac function and high left ventricular pressure, the H group showed preservation of myocardial function, coronary flow, and oxygen consumption. Compared with normal control hearts without ischemia ( n = 5), histological staining in the I group showed marked disarray and fragmentation of collagen network ( score 4–5), while the H group showed preserved collagen integrity ( score 0–1). The apoptosis-linked tumor suppressor protein p53 was expressed throughout the I group only ( score 4–5). The H group produced elevated expression for hypoxia-inducible factor 1α and heme oxygenase 1, but minimally affected vascular endothelial growth factor expression. The H group also elevated expression for survival proteins peroxisomal proliferator-activated receptor-β and Akt-1. These results show in a constant left ventricular volume model that moderate hypothermia (30°C) decreases myocardial energy utilization during ischemia and subsequently promotes expression of proteins involved in cell survival, while inhibiting induction of p53 protein. These data also show that 34°C proffers less protection and loss of myocardial integrity.
Effects of metabolic inhibition on conduction, Ca transients, and arrhythmia vulnerability in embryonic mouse hearts
Authors: Chen Fuhua , De Diego Carlos , Xie Lai-Hua , Yang Jun-Hai , Klitzner Thomas S , Weiss James N
Published: July 2007

Developing myocardium is more dependent on glycolysis than adult myocardium, yet the effects of selectively inhibiting glycolysis versus oxidative phosphorylation on embryonic heart function have not been well characterized. Accordingly, we investigated how selective metabolic inhibition affects membrane voltage and intracellular Ca (Cai) transients in embryonic mouse hearts, including their susceptibility to arrhythmias. A total of 136 isolated embryonic mouse hearts were exposed to either 1) 2-deoxyglucose (2DG; 10 mM) or iodoacetate (IAA; 0.1 mM) with 10 mM pyruvate in place of glucose to selectively inhibit glycolysis or 2) the mitochondrial uncoupler protonophore carbonyl cyanide p-(trifluoromethoxy)phenylhydrazone (FCCP; 500 nM) with 10 mM glucose present to selectively inhibit oxidative phosphorylation. Using confocal imaging, we found that mitochondrial membrane potential monitored with tetramethylrhodamine methyl ester (200 nM) remained stable with 2DG or IAA but depolarized within 5 min after exposure to FCCP. IAA and FCCP decreased heart rate, inhibited Cai transient amplitude, shortened action potential duration at 80% repolarization (APD80), and prolonged atrioventricular conduction time to similar extents. Although 2DG decreased heart rate and Cai transient amplitude, it did not significantly affect APD80 and AV conduction time. In addition, spontaneous arrhythmias occurred in 77 of 136 embryonic hearts (57%) after exposure to IAA (28/53) or FCCP (49/83). There were no significant differences in the types or incidence of arrhythmias induced by IAA and FCCP. These data support the idea that both glycolysis and oxidative phosphorylation play critical metabolic roles in regulating cardiac function in the embryonic mouse heart.
Altered role of smooth muscle endothelin receptors in coronary endothelin-1 and α1-adrenoceptor-mediated vasoconstriction in Type 2 diabetes
Authors: Bender S. B. , Klabunde R. E.
Published: July 2007

Regulation of vascular tone and blood flow involves interactions between numerous local and systemic vascular control signals, many of which are altered by Type 2 diabetes (T2D). Vascular responses to endothelin-1 (ET-1) are mediated by endothelin type A (ETA) and type B (ETB) receptors that have been implicated in cross talk with α1-adrenoceptors (α1-AR). ETAand ETBreceptor expression and plasma ET-1 levels are elevated in T2D; however, whether this influences coronary α1-AR function has not been examined. Therefore, we examined the effect of ETAand ETBreceptor inhibition on coronary vasoconstriction to ET-1 and α1-AR activation in a mouse model of T2D. Coronary vascular responses were examined in isolated mouse hearts from control and diet-induced T2D C57BL/6J mice. Responses to ET-1 and the selective α1-AR agonist phenylephrine (PE) were examined alone and in the presence of the nitric oxide synthase inhibitor Nω-nitro-l-arginine methyl ester (l-NAME) alone or in combination with selective ETAor ETBreceptor inhibitors BQ-123 and BQ-788, respectively. Vasoconstriction to ET-1 was enhanced, whereas ETB, but not ETA, receptor blockade reduced basal coronary tone in T2D hearts. In the presence of l-NAME, ETAreceptor inhibition attenuated ET-1 vasoconstriction in both groups, whereas ETBinhibition abolished this response only in control hearts. In addition, ETAinhibition enhanced α1-AR-mediated vasoconstriction in T2D, but not control, hearts following l-NAME treatment. Therefore, in this model, enhanced coronary ET-1 responsiveness is mediated primarily through smooth muscle ETBreceptors, whereas the interaction with α1-ARs is mediated solely through the ETAreceptor subtype.