bluuebunny/crossref_metadata_2025_split huggingface dataset:
Compartmentalized DCC signalling is distinct from DCC localized to lipid rafts
Authors: Petrie Ryan J. , Zhao Beibei , Bedford Fiona , Lamarche‐Vane Nathalie 
Published: July 2008

Background information. Netrin‐1 is a bi‐functional cue that attracts or repels different classes of neurons during development. The netrin‐1 receptor DCC (deleted in colorectal cancer) acts as a tyrosine kinase‐associated receptor to mediate the attractive response towards netrin‐1. The lipid raft‐localized Src family kinase Fyn is required for DCC‐mediated axon guidance. DCC functions are also dependent on lipid rafts, membrane microdomains corresponding to a low‐density, detergent‐resistant membrane fraction. However, it remains unclear how the association of DCC with lipid rafts controls netrin‐1 signalling.Results. DCC targeted to lipid rafts represented a minor proportion of total DCC inside the cell, but predominated on the cell surface of both IMR‐32 human neuroblastoma cells and embryonic cortical neurons. Netrin‐1 accumulated in lipid rafts, but had no effect on the targeting of DCC to that compartment, with DCC remaining on the cell surface in lipid rafts through 60 min post‐treatment. However, DCC was able to interact with Fyn, both in the lipid rafts and soluble compartments isolated from embryonic E19 rat brains, whereas early downstream signalling components such as Nck‐1, and total and active focal adhesion kinase were mainly localized to the non‐lipid raft compartment.Conclusions. Together, these results suggest that DCC can be found in raft and non‐raft portions of the plasma membrane, with early signalling events propagated by non‐raft associated DCC.
Structure–function relationships in Escherichia coli adenylate cyclase
Authors: Linder Jürgen U. 
Published: July 2008

Class I adenylate cyclases are found in γ- and δ-proteobacteria. They play central roles in processes such as catabolite repression in Escherichia coli or development of full virulence in pathogens such as Yersinia enterocolitica and Vibrio vulnificus. The catalytic domain (residues 2–446) of the adenylate cyclase of E. coli was overexpressed and purified. It displayed a Vmax of 665 nmol of cAMP·mg−1·min−1 and a Km of 270 μM. Titration of the metal cofactor Mg2+ against the substrate ATP showed a requirement for free metal ions in addition to the MgATP complex, suggesting a two-metal-ion mechanism as is known for class II and class III adenylate cyclases. Twelve residues which are essential for catalysis were identified by mutagenesis of a total of 20 polar residues conserved in all class I adenylate cyclases. Five essential residues (Ser103, Ser113, Asp114, Asp116 and Trp118) were part of a region which is found in all members of the large DNA polymerase β-like nucleotidyltransferase superfamily. Alignment of the E. coli adenylate cyclase with the crystal structure of a distant member of the superfamily, archaeal tRNA CCA-adding enzyme, suggested that Asp114 and Asp116 are the metal-cofactor-ion-binding residues. The S103A mutant had a 17-fold higher Km than wild-type, demonstrating its important role in substrate binding. In comparison with the tRNA CCA-adding enzyme, Ser103 of the E. coli adenylate cyclase apparently binds the γ-phosphate group of ATP. Consistent with this function, the S103A mutation caused a marked reduction of discrimination between ATP- and ADP- or AMP-derived inhibitors.
Nutritional considerations for captive Charadriiformes (shorebirds, gulls and alcids).
Authors: McWilliams D. A. 
Published: July 2008

Abstract
A progressive decline in Charadriiforme populations prioritizes appropriate life-stage nutrition for captive Charadriiformes as conservation efforts continue to develop. These species are opportunistic feeders on fish and aquatic invertebrates. Appropriate life-stage nutrition for captive Charadriiformes requires nutrient provision beyond simple piscivory. This review presents existing data on relevant dietary components (protein, fat, carotenoids, minerals and vitamins) and examines the importance of these components in life-stage nutrition (embryonic development, neonates (chicks), juveniles, adults, breeding, incubation and chick rearing). The issue of determining metabolic rates of captive Charadriiformes populations is briefly presented. Eight recommendations for the amelioration of diet deficiencies are outlined.
On the superrigidity of malleable actions with spectral gap
Authors: Popa Sorin 
Published: July 2008

We prove that if a countable group

Γ
\Gamma

contains infinite commuting subgroups

H
,

H
′

⊂
Γ

H, H’\subset \Gamma

with

H
H

non-amenable and

H
′

H’

“weakly normal” in

Γ
\Gamma

, then any measure preserving

Γ
\Gamma

-action on a probability space which satisfies certain malleability, spectral gap and weak mixing conditions (e.g. a Bernoulli

Γ
\Gamma

-action) is cocycle superrigid. If in addition

H
′

H’

can be taken non-virtually abelian and

Γ
↷
X

\Gamma \curvearrowright X

is an arbitrary free ergodic action while

Λ
↷
Y
=

T

Λ

\Lambda \curvearrowright Y=\mathbb {T}^{\Lambda }

is a Bernoulli action of an arbitrary infinite conjugacy class group, then any isomorphism of the associated II

1

_{1}

factors

L

∞

X
⋊
Γ
≃

L

∞

Y
⋊
Λ

L^{\infty }X \rtimes \Gamma \simeq L^{\infty }Y \rtimes \Lambda

comes from a conjugacy of the actions.
Stable self-similar blow up dynamics for the three dimensional relativistic gravitational Vlasov-Poisson system
Authors: Lemou Mohammed , Méhats Florian , Raphaël Pierre 
Published: July 2008

The three dimensional gravitational Vlasov-Poisson system

∂
t

f
+
v
⋅

∇
x

f
−

E
f

⋅

∇
v

f
=
0

\partial _tf+v\cdot \nabla _x f-E_f\cdot \nabla _vf=0

, where

E
f

(
x
)
=

∇
x

ϕ
f

(
x
)

E_f(x)=\nabla _x \phi _f(x)

,

Δ
x

ϕ
f

=

ρ
f

(
x
)

\Delta _x\phi _f=\rho _f(x)

,

ρ
f

(
x
)
=

∫

R

N

f
(
x
,
v
)
d
v

\rho _f(x)=\int _{\mathbb {R}^N} f(x,v)dv

, describes the mechanical state of a stellar system subject to its own gravity. Smooth initial data yield unique global in time solutions from a celebrated result by Pfaffelmoser. There exists a hierarchy of physical models which aim at taking into account further relativistic effects. The simplest one is the three dimensional relativistic gravitational Vlasov-Poisson system

∂
t

f
+

v

1
+

|

v

|

2

⋅

∇
x

f
−

E
f

⋅

∇
v

f
=
0

\partial _tf+\frac {v}{\sqrt {1+|v|^2}}\cdot \nabla _x f-E_f\cdot \nabla _vf=0

which we study here. A striking feature as observed by Glassey and Schaeffer is that this system now admits finite blow up solutions. Nevertheless, the existence argument is purely obstructive and provides no insight into the description of the singularity formation. We exhibit in this paper a family of finite time blow up self-similar solutions and prove that their blow up dynamic is stable with respect to radially symmetric perturbations. Our analysis applies to the four dimensional gravitational Vlasov-Poisson system as well.
Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies
Authors: Homer Nils , Tembe Waibhav D. , Szelinger Szabolcs , Redman Margot , Stephan Dietrich A. , Pearson John V. , Nelson Stanley F. , Craig David 
Published: July 2008

Abstract
Summary: For many genome-wide association (GWA) studies individually genotyping one million or more SNPs provides a marginal increase in coverage at a substantial cost. Much of the information gained is redundant due to the correlation structure inherent in the human genome. Pooling-based GWA studies could benefit significantly by utilizing this redundancy to reduce noise, improve the accuracy of the observations and increase genomic coverage. We introduce a measure of correlation between individual genotyping and pooling, under the same framework that r2 provides a measure of linkage disequilibrium (LD) between pairs of SNPs. We then report a new non-haplotype multimarker multi-loci method that leverages the correlation structure between SNPs in the human genome to increase the efficacy of pooling-based GWA studies. We first give a theoretical framework and derivation of our multimarker method. Next, we evaluate simulations using this multimarker approach in comparison to single marker analysis. Finally, we experimentally evaluate our method using different pools of HapMap individuals on the Illumina 450S Duo, Illumina 550K and Affymetrix 5.0 platforms for a combined total of 1 333 631 SNPs. Our results show that use of multimarker analysis reduces noise specific to pooling-based studies, allows for efficient integration of multiple microarray platforms and provides more accurate measures of significance than single marker analysis. Additionally, this approach can be extended to allow for imputing the association significance for SNPs not directly observed using neighboring SNPs in LD. This multimarker method can now be used to cost-effectively complete pooling-based GWA studies with multiple platforms across over one million SNPs and to impute neighboring SNPs weighted for the loss of information due to pooling.
Contact: dcraig@tgen.org
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Begonia Chlorotic Ringspot Caused by Zucchini yellow mosaic virus in Taiwan
Authors: Chen Y. K. , Hong Y. H. 
Published: July 2008

Begonia (Begonia semperflorens) showing symptoms of systemic chlorotic ringspots were observed in the central part of Taiwan in May 2006. Infected begonia plants showed faint ringspots in leaves at the early stage of infection. Symptoms turned chlorotic and coalesced as the disease progressed. Electron microscopic examination revealed filamentous virus particles approximately 750 × 13 nm in the crude sap of infected begonia. Typical pinwheel inclusion bodies of potyvirus infection were observed in the ultrathin sections of infected begonia. A virus culture was isolated via mechanical inoculations in Chenopodium quinoa and serologically identified as Zucchini yellow mosaic virus (ZYMV) (1) by ELISA, western blotting, and immunoelectron microscopy. Complementary DNA fragments of viral genomic RNA were cloned, sequenced, and the full-length sequence was submitted to the EMBL database (Accession No. AM422386). The genomic RNA consists of 9,591 nucleotides excluding the poly-A tail and has an identical genome organization to that reported for members of the genus, Potyvirus. The nucleotide sequence of the full-length genome and the deduced amino acid sequence of coat protein share 98% identity to those of ZYMV-CU (Accession No. AJ307036), ZYMV-SG (Accession No. AJ316228), and ZYMV-TW-TN3 (Accession No. AF127929). The virus caused local lesions on the inoculated leaves of C. quinoa, systemic mosaic in cucumber (Cucumis sativus), zucchini (Cucurbita pepo), and Cucumis metuliferus, and chlorotic ringspots in begonia. Symptoms caused by the begonia isolate in cucurbits were much milder than those caused by ZYMVs of cucurbit origin. A ringspot disease with symptoms similar to those caused by ZYMV is also produced on begonia by an Ilarvirus, Prunus necrotic ringspot virus (PNRSV), which was previously identified in begonia (2). To our knowledge, this is the first report of natural infection of ZYMV in begonia. References: (1) V. Lisa et al. Phytopathology 71:667, 1981. (2) N. Verma et al. Plant Pathol. 51:800, 2002.
First Report of Anthracnose Fruit Rot Caused by Colletotrichum acutatum on Strawberry in Korea
Authors: Nam M. H. , Kim T. I. , Gleason M. L. , Song J. Y. , Kim H. G. 
Published: July 2008

Symptoms typical of anthracnose fruit rot; sunken, dark brown lesions on maturing fruits, were found in a commercial field of strawberry (Fragaria × ananassa) cv. Cal Giant in Yangyang County, Korea in May 2007. Masses of conidia were produced in acervuli in the center of lesions. The fungus was isolated on potato dextrose agar (PDA). Colonies grown on PDA were pale to mouse gray and became dark green to black in reverse. Conidia were formed in orange-to-salmon pink masses in the center of the culture. The average size of conidia on PDA was 15.2 × 4.6 μm, and they were hyaline, straight, cylindrical, with pointed ends, and aseptate (1). The fungus did not form an ascigerous stage in culture. Mycelial growth rate was 7.5 mm per day at 25°C on PDA. The identity of two isolates was confirmed as Colletotrichum acutatum J.H. Simmonds by PCR amplification using species-specific primers TBCA and TB5 (2), resulting in a characteristic 330-bp band on agarose gel. Morphological characters were in accordance with previous reports on C. acutatum. A pathogenicity test was conducted with five healthy plants of cvs. Cal Giant, Maehyang, Seolhyang, Kumhyang, Akihime, and Redpearl. After fruits and flowers were sprayed with a conidia suspension (105 conidia per ml), the plants were maintained at 10 to 25°C and 100% relative humidity in a greenhouse. As a control, five healthy plants were sprayed with sterile distilled water and incubated under the same conditions. Dark brown, water-soaked spots appeared on mature fruits of all cultivars after 5 days, and lesions on green fruits appeared on individual achenes. Flowers developed dark lesions, dried out, and died. No symptoms were found on the control plants. After the pathogen was reisolated from fruits and flowers lesions, the morphological characters developed in culture as described above. To our knowledge, this is the first report of C. acutatum causing strawberry anthracnose in Korea. References: (1) B. J. Smith and L. L. Black. Plant Dis. 74:69, 1990. (2) P. Talhinhas et al. Appl. Environ. Microbiol. 71:2987, 2005.
First Report of Xylella fastidiosa in Nerium oleander in Costa Rica
Authors: Montero-Astúa M. , Saborío-R. G. , Chacón-Díaz C. , Villalobos W. , Rodríguez C. M. , Moreira L. , Rivera C. 
Published: July 2008

Oleander (Nerium oleander L.) shrubs presenting mottling, leaf tip and margin scorch, short internodes, defoliation, and branch dieback were observed at different localities in the Central Valley in Costa Rica. Severity of the symptoms ranged widely, and most plants showed both diseased and healthy branches. In severe cases, entire sections of the plant were defoliated. Symptoms resembled those described for oleander leaf scorch (OLS) caused by the bacterium Xylella fastidiosa in the United States (3). This bacterium has been reported in coffee and citrus plants in Costa Rica. Sixty plants from five different places were sampled and tested using ELISA (Agdia Inc., Elkhart, IN) against X. fastidiosa. Thirty-five plants showed absorbance mean value of duplicate wells greater than the mean of control wells plus three times the standard deviation, and therefore were considered positive. Thirty-three of the sixty samples were processed for an immunofluorescence assay modified from Carbajal et al. (1) with antibody to X. fastidiosa (Agdia Inc.). Thirteen samples showed fluorescent rod-shaped bacilli with morphology similar to those observed from a pure culture of X. fastidiosa obtained from coffee. Ten of these thirteen samples were positive by ELISA. DNA extracts (2) from three of the oleander plants with high ELISA absorbance values were tested by nested PCR with primer pair 272-1/272-2 followed by the pair 272-1 int/272-2 int (4). Two of the samples were positive for the bacterium and one of the PCR products was cloned and sequenced in both directions (GenBank Accession No. EU009615). The negative (PCR mix) and positive (pure culture of X. fastidiosa isolated from grapevine) controls for nested-PCR were indeed negative and positive, respectively. The BLAST program was used to compare the sequence to the nucleotide collection (nr/nt) and Microbe Assembled Genomes databases in GenBank. All matches corresponded to X. fastidiosa sequences. The sequence showed 97% similarity with strains Found-4 (coffee strain from Brazil) and Found-5 (citrus strain from Brazil) and 96% similarity with strain Ann-1 from oleander in California. On the basis of serological, microscopic, and molecular detection of X. fastidiosa from oleander exhibiting symptoms of OLS similar to those reported in the literature, this pathogen likely is causing the symptoms we observed in Costa Rica. References: (1) D. Carbajal et al. Curr. Microbiol. 49:372, 2004. (2) M. J. Green et al. Plant Dis. 83:482, 1999. (3) Q. Huang et al. Plant Dis. 88:1049, 2004. (4) M. R. Pooler and J. S. Hartung. Curr. Microbiol. 31:377, 1995.
First Report of the Occurrence of Grapevine fanleaf virus in Washington State Vineyards
Authors: Mekuria T. , Martin R. R. , Naidu R. A. 
Published: July 2008

Grapevine fanleaf virus (GFLV; genus Nepovirus, family Comoviridae), responsible for fanleaf degeneration disease, is one of the most important viruses of grapevines worldwide (1). During our reconnaissance studies during 2007, dormant wood cuttings from individual grapevines of wine grape cv. Chardonnay were collected randomly from two geographically separate vineyards in eastern Washington State. Extracts made from cambial scrapings of these cuttings were tested separately for different viruses by single-tube reverse transcription (RT)-PCR using virus-specific primers. Two of the thirty-one grapevines in one vineyard tested positive for GLFV as mixed infection with Grapevine leafroll-associated virus (GLRaV)-3. In another vineyard, six of the twenty-six grapevines tested positive for GFLV as mixed infection with GLRaV-1, GLRaV-3, and Grapevine virus A (GVA) A forward primer (5′-ACCGGATTGACGTGGGTGAT, corresponding to nucleotides [nt] 2231–2250) and reverse primer (5′-CCAAAGTTGGTTTCCCAAGA, complementary to nt 2533–2552) specific to RNA-2 of GFLV-F13 isolate (GenBank Accession No. X16907) were used in RT-PCR assays for the detection of GFLV (4). Primers used for RT-PCR detection of GLRaV-1, GLRaV-2, and GVA were described in Martin et al (2) and Minafra et al (3). The RT-PCR results indicated mixed infection of GFLV with GLRaV-1, GLRaV-3, and GVA. To confirm the presence of GFLV, the 322-bp sequence representing a portion of the coat protein encoded by RNA-2 genomic segment was cloned into pCR2.1 (Invitrogen Corp., Carlsbad, CA). Amplicons obtained from six individual grapevines in the two vineyards were used for cloning. Three independent clones per amplicon were sequenced from both orientations. Pairwise comparison of these sequences showed 99 to 100% nucleotide sequence identity among themselves, indicating that GFLV isolates from the two vineyards may be identical. A comparison of the consensus sequence (GenBank Accession No. EU573307) with corresponding sequences of other GFLVs deposited in GenBank showed 89 to 91% identity at the nucleotide level and 95 to 99% identity at the amino acid level. However, mixed infection of GFLV with different viruses in the two vineyards suggests separate introduction of the planting material. ELISA with GFLV-specific antibodies further confirmed the presence of the virus in samples that were positive in RT-PCR. To our knowledge, this is the first report of GFLV in grapevines grown in the Pacific Northwest states of the United States. Further investigations are being carried out on the distribution, symptoms, molecular variability, and nematode vector transmission of GFLV. References: (1) P. Andret-Link et al. J. Plant Pathol. 86:183, 2004. (2) R. R. Martin et al. Plant Dis. 89:763, 2005. (3) A. Minafra et al. Arch. Virol. 142:417, 1997 (4) A. Rowhani et al. Phytopathology 83:749, 1993.
First Report of Sclerotinia sclerotiorum on Argyranthemum frutescens in Italy
Authors: Garibaldi A. , Pensa P. , Gullino M. L. 
Published: July 2008

Paris daisy (Argyranthemum frutescens (L.) Sch. Bip.) is an economically important crop on the Riviera Ligure (northern Italy), where approximately 10 million plants per year are produced for export. In the winter of 2007, extensive wilting was observed on 5-month-old potted plants of A. frutescens grown in a commercial greenhouse near Albenga. First symptoms included stem necrosis, darkening and withering of leaves, and wilting of young buds. As stem and foliar necrosis progressed, infected plants wilted and died. Wilt occurred a few days after the appearance of the first symptoms. Infected plants were characterized by the presence of soft, watery tissues. Lesions became covered with a whitish mycelium and dark sclerotia were produced on the mycelium. Diseased stem tissue was surface sterilized for 1 min in 1% NaOCl and plated on potato dextrose agar (PDA) amended with 100 mg/l streptomycin sulfate. Sclerotinia sclerotiorum (Lib.) de Bary (2) was consistently recovered from infected stem pieces. Sclerotia produced on PDA measured 1.4 to 5.2 × 2.3 to 6.7 (average 3.3 to 4.2) mm. The internal transcribed spacer (ITS) region of rDNA was amplified using primers ITS4/ITS6 and then sequenced. BLAST analysis (1) of the 531-bp segment showed a 100% homology with the sequence of S. sclerotiorum. The nucleotide sequence has been assigned GenBank Accession No. EU 556701. Pathogenicity of two isolates obtained from infected plants was confirmed by inoculating 10 90-day-old plants for each isolate. Plants were grown singly in 18-cm-diameter pots maintained in a greenhouse under shade and were regularly irrigated and fertilized. Mycelium plugs 1 cm2 were excised from a 10-day-old PDA culture of both isolates and placed on the soil surface around the base of each plant. Ten noninoculated plants served as controls. Plants were maintained in a greenhouse under shade at temperatures ranging between 6 and 22°C (average 18°C) and relative humidity at >90%. The inoculation trial was carried out twice. All inoculated plants developed leaf yellowing by 22 days after inoculation. White, cottony mycelium and black sclerotia developed on stems and at the base of all inoculated plants. Eventually, infected plants wilted. Control plants remained symptomless. S. sclerotiorum was reisolated from the stems of inoculated plants. To our knowledge, this is the first report of S. sclerotiorum causing white mold on A. frutescens in Italy as well as worldwide. The economic importance of this disease can be considered limited at the moment. References: (1) S. F. Altschul et al. Nucleic Acids Res. 25:3389, 1997 (2) N. F. Buchwald. Kongl. Veterisk Landb. Aarssk. 75, 1949.