bluuebunny/crossref_metadata_2025 huggingface dataset:
The somatodendritic endosomal regulator NEEP21 facilitates axonal targeting of L1/NgCAM
Authors: Yap Chan Choo , Wisco Dolora , Kujala Pekka , Lasiecka Zofia M. , Cannon Johanna T. , Chang Michael C. , Hirling Harald , Klumperman Judith , Winckler Bettina
Published: February 2008

Correct targeting of proteins to axons and dendrites is crucial for neuronal function. We showed previously that axonal accumulation of the cell adhesion molecule L1/neuron-glia cell adhesion molecule (NgCAM) depends on endocytosis (Wisco, D., E.D. Anderson, M.C. Chang, C. Norden, T. Boiko, H. Folsch, and B. Winckler. 2003. J. Cell Biol. 162:1317–1328). Two endocytosis-dependent pathways to the axon have been proposed: transcytosis and selective retrieval/retention. We show here that axonal accumulation of L1/NgCAM occurs via nondegradative somatodendritic endosomes and subsequent anterograde axonal transport, which is consistent with transcytosis. Additionally, we identify the neuronal-specific endosomal protein NEEP21 (neuron-enriched endosomal protein of 21 kD) as a regulator of L1/NgCAM sorting in somatodendritic endosomes. Down-regulation of NEEP21 leads to missorting of L1/NgCAM to the somatodendritic surface as well as to lysosomes. Importantly, the axonal accumulation of endogenous L1 in young neurons is also sensitive to NEEP21 depletion. We propose that small endosomal carriers derived from somatodendritic recycling endosomes can serve to redistribute a distinct set of membrane proteins from dendrites to axons.
IKK/NF-κB regulates skeletal myogenesis via a signaling switch to inhibit differentiation and promote mitochondrial biogenesis
Authors: Bakkar Nadine , Wang Jingxin , Ladner Katherine J. , Wang Huating , Dahlman Jason M. , Carathers Micheal , Acharyya Swarnali , Rudnicki Michael A. , Hollenbach Andrew D. , Guttridge Denis C.
Published: February 2008

Nuclear factor κB (NF-κB) is involved in multiple skeletal muscle disorders, but how it functions in differentiation remains elusive given that both anti- and promyogenic activities have been described. In this study, we resolve this by showing that myogenesis is controlled by opposing NF-κB signaling pathways. We find that myogenesis is enhanced in MyoD-expressing fibroblasts deficient in classical pathway components RelA/p65, inhibitor of κB kinase β (IKKβ), or IKKγ. Similar increases occur in myoblasts lacking RelA/p65 or IKKβ, and muscles from RelA/p65 or IKKβ mutant mice also contain higher fiber numbers. Moreover, we show that during differentiation, classical NF-κB signaling decreases, whereas the induction of alternative members IKKα, RelB, and p52 occurs late in myogenesis. Myotube formation does not require alternative signaling, but it is important for myotube maintenance in response to metabolic stress. Furthermore, overexpression or knockdown of IKKα regulates mitochondrial content and function, suggesting that alternative signaling stimulates mitochondrial biogenesis. Together, these data reveal a unique IKK/NF-κB signaling switch that functions to both inhibit differentiation and promote myotube homeostasis.
Antagonism of FOG-1 and GATA factors in fate choice for the mast cell lineage
Authors: Cantor Alan B. , Iwasaki Hiromi , Arinobu Yojiro , Moran Tyler B. , Shigematsu Hirokazu , Sullivan Matthew R. , Akashi Koichi , Orkin Stuart H.
Published: February 2008

The zinc finger transcription factor GATA-1 requires direct physical interaction with the cofactor friend of GATA-1 (FOG-1) for its essential role in erythroid and megakaryocytic development. We show that in the mast cell lineage, GATA-1 functions completely independent of FOG proteins. Moreover, we demonstrate that FOG-1 antagonizes the fate choice of multipotential progenitor cells for the mast cell lineage, and that its down-regulation is a prerequisite for mast cell development. Remarkably, ectopic expression of FOG-1 in committed mast cell progenitors redirects them into the erythroid, megakaryocytic, and granulocytic lineages. These lineage switches correlate with transcriptional down-regulation of GATA-2, an essential mast cell GATA factor, via switching of GATA-1 for GATA-2 at a key enhancer element upstream of the GATA-2 gene. These findings illustrate combinatorial control of cell fate identity by a transcription factor and its cofactor, and highlight the role of transcriptional networks in lineage determination. They also provide evidence for lineage instability during early stages of hematopoietic lineage commitment.
Sustained expression of microRNA-155 in hematopoietic stem cells causes a myeloproliferative disorder
Authors: O'Connell Ryan M. , Rao Dinesh S. , Chaudhuri Aadel A. , Boldin Mark P. , Taganov Konstantin D. , Nicoll John , Paquette Ronald L. , Baltimore David
Published: February 2008

Mammalian microRNAs are emerging as key regulators of the development and function of the immune system. Here, we report a strong but transient induction of miR-155 in mouse bone marrow after injection of bacterial lipopolysaccharide (LPS) correlated with granulocyte/monocyte (GM) expansion. Demonstrating the sufficiency of miR-155 to drive GM expansion, enforced expression in mouse bone marrow cells caused GM proliferation in a manner reminiscent of LPS treatment. However, the miR-155–induced GM populations displayed pathological features characteristic of myeloid neoplasia. Of possible relevance to human disease, miR-155 was found to be overexpressed in the bone marrow of patients with certain subtypes of acute myeloid leukemia (AML). Furthermore, miR-155 repressed a subset of genes implicated in hematopoietic development and disease. These data implicate miR-155 as a contributor to physiological GM expansion during inflammation and to certain pathological features associated with AML, emphasizing the importance of proper miR-155 regulation in developing myeloid cells during times of inflammatory stress.
Outbreak ofEnterococcus gallinarumInfections After Total Knee Arthroplasty
Authors: Cooper Michael P. , Lessa Fernanda , Brems Bob , Shoulson Rivka , York Steve , Peterson Alicia , Noble-Wang Judith , Duffy Rosemary , McDonald L. Clifford
Published: February 2008

In September 2006, we investigated a cluster of 9 patients who developedEnterococcus gallinaruminfection after total knee arthroplasty. Isolates recovered from these patients were from the same outbreak strain. Although all 9 patients were monitored by the same healthcare personnel, were given spinal anesthesia, and had the same specific type of wound irrigation procedure performed during their hospitalization, the source or sources of these infections were not identified.
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models
Authors: Hirose Osamu , Yoshida Ryo , Imoto Seiya , Yamaguchi Rui , Higuchi Tomoyuki , Charnock-Jones D. Stephen , Print Cristin , Miyano Satoru
Published: February 2008

Motivation: Statistical inference of gene networks by using time-course microarray gene expression profiles is an essential step towards understanding the temporal structure of gene regulatory mechanisms. Unfortunately, most of the current studies have been limited to analysing a small number of genes because the length of time-course gene expression profiles is fairly short. One promising approach to overcome such a limitation is to infer gene networks by exploring the potential transcriptional modules which are sets of genes sharing a common function or involved in the same pathway.

Results: In this article, we present a novel approach based on the state space model to identify the transcriptional modules and module-based gene networks simultaneously. The state space model has the potential to infer large-scale gene networks, e.g. of order 103, from time-course gene expression profiles. Particularly, we succeeded in the identification of a cell cycle system by using the gene expression profiles of Saccharomyces cerevisiae in which the length of the time-course and number of genes were 24 and 4382, respectively. However, when analysing shorter time-course data, e.g. of length 10 or less, the parameter estimations of the state space model often fail due to overfitting. To extend the applicability of the state space model, we provide an approach to use the technical replicates of gene expression profiles, which are often measured in duplicate or triplicate. The use of technical replicates is important for achieving highly-efficient inferences of gene networks with short time-course data. The potential of the proposed method has been demonstrated through the time-course analysis of the gene expression profiles of human umbilical vein endothelial cells (HUVECs) undergoing growth factor deprivation-induced apoptosis.

Availability: Supplementary Information and the software (TRANS-MNET) are available at http://daweb.ism.ac.jp/~yoshidar/software/ssm/

Contact:  yoshidar@ism.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.
PCCA: a program for phylogenetic canonical correlation analysis
Authors: Revell Liam J. , Harrison Alexis S.
Published: February 2008

Summary: PCCA (phylogenetic canonical correlation analysis) is a new program for canonical correlation analysis of multivariate, continuously valued data from biological species. Canonical correlation analysis is a technique in which derived variables are obtained from two sets of original variables whereby the correlations between corresponding derived variables are maximized. It is a very useful multivariate statistical method for the calculation and analysis of correlations between character sets. The program controls for species non-independence due to phylogenetic history and computes canonical coefficients, correlations and scores; and conducts hypothesis tests on the canonical correlations. It can also compute a multivariate version of Pagel's λ, which can then be used in the phylogenetic transformation.

Availability: PCCA is distributed as DOS/Windows, Mac OS X and Linux/Unix executables with a detailed program manual and is freely available on the World Wide Web at:

http://anolis.oeb.harvard.edu/~liam/programs/.

Contact:  lrevell@fas.harvard.edu
MMG: a probabilistic tool to identify submodules of metabolic pathways
Authors: Sanguinetti Guido , Noirel Josselin , Wright Phillip C.
Published: February 2008

Motivation: A fundamental task in systems biology is the identification of groups of genes that are involved in the cellular response to particular signals. At its simplest level, this often reduces to identifying biological quantities (mRNA abundance, enzyme concentrations, etc.) which are differentially expressed in two different conditions. Popular approaches involve using t-test statistics, based on modelling the data as arising from a mixture distribution. A common assumption of these approaches is that the data are independent and identically distributed; however, biological quantities are usually related through a complex (weighted) network of interactions, and often the more pertinent question is which subnetworks are differentially expressed, rather than which genes. Furthermore, in many interesting cases (such as high-throughput proteomics and metabolomics), only very partial observations are available, resulting in the need for efficient imputation techniques.

Results: We introduce Mixture Model on Graphs (MMG), a novel probabilistic model to identify differentially expressed submodules of biological networks and pathways. The method can easily incorporate information about weights in the network, is robust against missing data and can be easily generalized to directed networks. We propose an efficient sampling strategy to infer posterior probabilities of differential expression, as well as posterior probabilities over the model parameters. We assess our method on artificial data demonstrating significant improvements over standard mixture model clustering. Analysis of our model results on quantitative high-throughput proteomic data leads to the identification of biologically significant subnetworks, as well as the prediction of the expression level of a number of enzymes, some of which are then verified experimentally.

Availability: MATLAB code is available from http://www.dcs.shef.ac.uk/~guido/software.html

Contact:  guido@dcs.shef.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
GOTreePlus: an interactive gene ontology browser
Authors: Lee Bongshin , Brown Kristy , Hathout Yetrib , Seo Jinwook
Published: February 2008

Summary: We developed an interactive gene ontology (GO) browser named GOTreePlus that superimposes annotation information over GO structures. It can facilitate the identification of important GO terms through interactive visualization of them in the GO structure. The interactive pie chart summarizing an annotation distribution for a selected GO term provides users with a succinct context-sensitive overview of their experimental results. We tested our GOTreePlus using a proteome profiling dataset obtained on differentiation of retinal pigment epithelial cells where 399 proteins were quantified.

Availability:  http://bioinformatics.cnmcresearch.org/GOTreePlus/

Contact:  jseo@cnmcresearch.org
Potential Risk of Commercial Geranium to Infection by Puccinia pelargonii-zonalis
Authors: Buck J. W.
Published: February 2008

Outbreaks of rust caused by the fungus Puccinia pelargonii-zonalis on geraniums can result in large losses due to the plants' reduced aesthetic value and eradication efforts. To assess the potential risk of a rust outbreak in geranium production facilities, 77 commercial varieties of geranium were inoculated with a mixture of two isolates of P. pelargonii-zonalis. All but one variety (98.7%) developed at least one sporulating lesion and 72.7% developed rust lesions on more than 20% of the leaves. Six varieties had lesions on fewer than 10% of the leaves and one variety did not develop visible lesions. These data indicate that the potential for geranium rust to spread throughout commercial greenhouses is very high if an accidental introduction should occur. While fungicides are available to manage the disease, including products with curative properties, minimizing risk by using disease-free cuttings, maintaining clean stock plants, and avoiding leaf wetness is essential to limit losses to geranium rust.

Accepted for publication 16 July 2007. Published 31 October 2007.
Effects of Insecticides on Asian Citrus Psyllid (Hemiptera: Psyllidae) Populations in a Florida Citrus Grove
Authors: Powell Charles A. , Burton Michael S. , Pelosi Robert A. , Ritenour Mark A. , Bullock Robert C.
Published: February 2008

Asian citrus psyllid, Diaphorina citri Kuwayama, populations were monitored in a ‘Valencia’ sweet orange on sour orange rootstock plot planted in 1997. The plot was scouted weekly and the number of psyllids, percent trees infested, and the percentage of flush infested per tree were recorded over a 3-year period. The plot was treated with 7 insect control treatments: Admire (imidacloprid) applied at 12-, 6-, 3-, or 2-month intervals; Temik applied annually; Meta-Systox R applied annually; or no insecticide control using a randomized complete block design. Psyllid infestations persisted throughout the year. The lowest populations occurred during the winter (November-January) with peaks in the spring and fall. Annual applications of Temik, Meta-Systox R, or Admire did not reduce psyllid populations. Biannual or more frequent applications of Admire significantly reduced psyllid numbers, percentage of trees with psyllid infestations, and the percentage of flushes infested with psyllids.

Accepted for publication 29 August 2007. Published 1 November 2007.
Brown Stripe Downy Mildew (Sclerophthora rayssiae var. zeae) of Maize
Authors: Putnam Melodie L.
Published: February 2008

Because of its potential impact on maize, rapid detection and diagnosis of brown stripe downy mildew is essential. The National Plant Diagnostic Network (NPDN) has established protocols for recognition of Select Agents for participating laboratories. Due to the potential impact of an introduction of brown stripe downy mildew, this information is being widely disseminated so that suspect samples can be quickly and correctly identified.

Accepted for publication 10 July 2007. Published 8 November 2007.
First Report of Powdery Mildew of Fringed Willowherb (Epilobium ciliatum) Caused by Podosphaera epilobii in North America
Authors: Koike Steven T. , Glawe Dean A.
Published: February 2008

Description and first report of powdery mildew caused by Podosphaera epilobii on E. ciliatum in North America are presented in this brief. The weed is commonly found in California's Salinas Valley (Monterey Co.). Confirmation of the powdery mildew disease indicates that this weed will not be a source of the powdery mildew diseases that affect nearby vegetable and ornamental crops.

Accepted for publication 4 September 2007. Published 12 November 2007.
Resistance to Myclobutanil in Populations of Venturia inaequalis in Winchester, Virginia
Authors: Marine Sasha C. , Schmale David G. , Yoder Keith S.
Published: February 2008

Sterol-inhibiting (SI) fungicides are widely used to manage apple scab, caused by Venturia inaequalis. However, recent observations indicate that populations of V. inaequalis in orchards in Virginia have developed resistance to myclobutanil and other SI fungicides. Little is known about the frequency and distribution of fungicide resistance in apple scab populations in Virginia. Isolates of V. inaequalis were collected from three different apple orchards in Winchester, VA in 2006. Orchards were treated with myclobutanil on 12 April, 19 April, 1 May, 30 May, and 7 July. The sensitivity of 87 single-spored isolates of V. inaequalis to myclobutanil was determined by monitoring their growth on agar dishes amended with 0, 0.1, 0.5, or 1.0 μg/ml myclobutanil. A relative continuum of fungicide resistance was observed: 16 isolates were resistant, 40 isolates were moderately resistant, and 31 isolates were sensitive to myclobutanil. After 28 days, the mean growth of isolates collected from trees treated with myclobutanil was significantly greater than that of isolates collected from non-treated trees at all concentrations of myclobutanil tested in vitro. High levels of fungicide resistance found in populations of V. inaequalis suggest that replacement programs may need to be developed to manage apple scab in Virginia.

Accepted for publication 4 September 2007. Published 13 November 2007.
Characterization of a Severe Virus-like Disease in Chardonnay Grapevines in Missouri
Authors: Qiu Wenping , Avery John D. , Lunden Shaista
Published: February 2008

A severe virus-like disease emerged on Chardonnay vines in a Missouri vineyard that resulted in significant reduction of vine vigor and yield. The pathogens can be transmitted via cutting and grafting. Chardonnay, Cabernet franc and Baco franc vines that were grafted with the buds of the original diseased Chardonnay vines exhibited distinct vein-clearing symptom. The result of reverse transcription polymerase chain reaction indicated the association of Grapevine fanleaf virus with this disease.

Accepted for publication 26 September 2007. Published 19 November 2007.
First Report of Monarda didyma Infection with Impatiens necrotic spot virus in Washington State
Authors: Naidu Rayapati A. , Alabi Olufemi J. , Karthikeyan Gandhi , Nelson Mark , Morrell Anne
Published: February 2008

Monarda didyma is an herbaceous perennial widely used as a garden ornamental plant throughout USA. Infection of M. didyma by Impatiens necrotic spot virus (INSV) in commercial greenhouse settings has been reported only in Pennsylvania in 1992. Therefore, this is the first report of INSV infecting a M. didyma in the field.

Accepted for publication 25 September 2007. Published 19 November 2007.
Occurrence of Viroids in Commercial Hop (Humulus lupulus L.) Production Areas of Washington State
Authors: Eastwell Kenneth C. , Nelson Mark E.
Published: February 2008

Viroid status was investigated in commercial hop (Humulus lupulus) plantings in three regions of intensive hop production in Washington State. Hop stunt viroid (HSVd), the causal agent of hop stunt disease, was detected for the first time in hop plants in North America. HSVd was detected in samples from 10 of the 33 hop gardens sampled and in 19 of 126 plant samples. Infection with HSVd was associated with chlorosis and reduced plant vigor. Reverse transcription-polymerase chain reaction amplification, sequence identity, and pathogenicity of hop extracts on cucumber seedlings confirmed the presence of HSVd. Apple fruit crinkle viroid (AFCVd), recently reported in hops in Japan, was not detected by RT-PCR in any samples. Hop latent viroid (HLVd), which is frequently associated with hop germplasm world-wide, was detected with high frequency (98 of 126 hop plants surveyed).

Accepted for publication 23 September 2007. Published 27 November 2007.
First Report of Capsicum chlorosis virus in Tomato in India
Authors: Kunkalikar Suresh , Poojari Sudarsana , Rajagopalan Prem , Zehr Usha B. , Naidu Rayapati A. , Kankanallu Ravi S.
Published: February 2008

CaCV is as an economically important virus infecting tomato and pepper in Australia and Thailand and recently peanut in China. To our knowledge, this is the first report of CaCV in tomato in India. Both PBNV and CaCV can produce similar symptoms in tomato warranting further studies on crop improvement strategies against these two tospoviruses in vegetable and legume crops in India. This report highlights the need for continuous monitoring on the prevalence of CaCV in India and other countries in the Asia-Pacific region.

Accepted for publication 10 October 2007. Published 4 December 2007.
First Report of Powdery Mildew of Stachys byzantina (Lamb's Ear) Caused by Neoerysiphe galeopsidis in North America
Authors: Glawe Dean A. , Koike Steven T.
Published: February 2008

During the summer of 2007 the authors encountered a previously unrecorded powdery mildew disease on several plants of the perennial ornamental plant Stachys byzantina K. Koch ex Scheele (common names: woolly hedgenettle, woolly betony, and lamb's ear) growing in a plant bed near a commercial building in Salinas (Monterey Co.), California. This report documents the occurrence of Neoerysiphe galeopsidis on this host in North America.

Accepted for publication 11 October 2007. Published 17 December 2007.
Isolation, Storage, Pathotype Characterization, and Evaluation of Resistance for Phytophthora sojae in Soybean
Authors: Dorrance Anne E. , Berry Sue Ann , Anderson Terry R. , Meharg Chuck
Published: February 2008

Phytophthora sojae is effectively managed through soybean cultivars with single resistance genes (Rps) and partial resistance inherited quantitatively. There are over 50 described races of Phytophthora sojae, but many more pathotypes have been reported. Many of the isolates recently collected are more complex, causing disease on plants with 3 or more Rps genes. This diagnostic guide provides some standard assays to assist in the identification of virulence types of P. sojae and genetic resistance in soybean.

Accepted for publication 4 October 2007. Published 18 January 2008.
Shift in Virulence of Soybean Cyst Nematode is Associated with Use of Resistance from PI 88788
Authors: Niblack T. L. , Colgrove A. L. , Colgrove K. , Bond J. P.
Published: February 2008

The soybean cyst nematode (SCN) is the most economically important pathogen of soybean in the United States. Most of the SCN-resistant cultivars being grown in this region have resistance derived from a single source, Plant Introduction (PI) 88788. A survey conducted in 2005 showed that 83% of the soybean hectarage in Illinois is infested with SCN, with average population densities high enough to cause significant yield suppression (2,700 eggs/100 cm3 soil). Further characterization of these populations showed that 70% have adapted to PI 88788 at some level, reducing the effectiveness of using SCN-resistant cultivars as a crop management tool. Rotation with alternative sources of resistance is recommended as a means to slow the adaptation to PI 88788.

Accepted for publication 11 October 2007. Published 18 January 2008.
Phytophthora ramorum Infects Hazelnut, Vine Maple, Blue Blossom, and Manzanita Species in California
Authors: DiLeo Matthew V. , Bienapfl John C. , Rizzo David M.
Published: February 2008

Phytophthora ramorum was isolated from symptomatic tissue of California hazelnut, vine maple, blue blossom, and two species of manzanita. This is the first report of these plant species as natural hosts of P. ramorum. The native ranges of these new host species overlap considerably with regions that are highly favorable to P. ramorum epidemics. It is unknown how these newly-identified hosts affect the epidemiology of sudden oak death in California ecosystems or the spread of P. ramorum into un-infested areas.

Accepted for publication 15 November 2007. Published 18 January 2008.
Evaluation of Fungicides for the Control of Phytophthora ramorum Infecting Rhododendron, Camellia, Pieris, and Viburnum
Authors: Tjosvold S. A. , Koike S. T. , Chambers D. L.
Published: February 2008

Fungicides were evaluated for pre- and post-infection control of ramorum blight, caused by Phytophthora ramorum, on Rhododendron cvs. Cunningham's White and Irish Lace, Camellia japonica, Pieris japonica, and Viburnum tinus. Cyazofamid, dimethomorph, mefenoxam, pyraclostrobin, and fenamidone applied as foliar sprays consistently provided preventative control as indicated by reduced lesion size compared to water controls. These fungicides provided preventative activity for at least 28 days in the tested species except in Rhododendron where fungicides were active for at least 14 days following application. With preventative fungicide applications, the pathogen was recovered from most fungicide-treated leaves by isolation onto selective media. Dimethomorph consistently reduced the percent recovery from diseased Rhododendron leaves. With post-infection treatments, the fungicides did not significantly reduce lesion growth and percent recovery of the pathogen. The pathogen was recovered from lesions consistently at least 6 weeks after fungicide application in Rhododendron regardless of treatment on intact and fallen diseased leaves. However, the cultures resulting from isolations of diseased tissue treated with cyazofamid and dimethomorph were significantly slower growing than those cultures from other fungicide treatments. P. ramorum management issues relating to fungicide use in commercial nurseries are discussed

Accepted for publication 12 October 2007. Published 8 February 2008.
Evaluation of Chemical Agents for the Control of Phytophthora ramorum and Other Species of Phytophthora on Nursery Crops
Authors: Linderman Robert G. , Davis E. Anne
Published: February 2008

Phytophthora diseases occur frequently in nurseries, and the recent incidence of ramorum blight, caused by P. ramorum, on nursery crops has underscored the need for improved management strategies against all Phytophthora diseases. We evaluated several chemicals that target Oomycete pathogens, inoculating detached rhododendron or lilac leaves removed from plants previously treated with various chemicals, or chemically-treated leaves on intact plants. Results indicated that Subdue MAXX (drench or foliar application) was the most effective chemical in suppressing infections caused by all species of Phytophthora tested (P. ramorum, P. citricola, P. citrophthora, and P. nicotianae) except P. citrophthora; with P. ramorum, it was active for at least 6 weeks after spray application. More chemicals were effective when sporangial rather than mycelial plug inoculum of P. ramorum was used, including Aliette, Ranman, Stature DM, and Fenamidone. All chemicals tested were fungistatic, not fungicidal. These tests indicate that several materials inhibit infection by Phytophthora species, and that the detached leaf test is effective in evaluating efficacy of chemical agents for the suppression of Phytophthora pathogens from nurseries.

Accepted for publication 10 November 2007. Published 11 February 2008.
QoI Resistance of Plasmopara viticola and Erysiphe necator in the Mid-Atlantic United States
Authors: Baudoin Anton , Olaya Gilberto , Delmotte François , Colcol Jeneylyne F. , Sierotzki Helge
Published: February 2008

Of 20 Plasmopara viticola isolates collected in four locations in Virginia and northwest North Carolina in 2005, 16 were resistant to QoI fungicides. The resistance factor was over 100, and label rates of formulated azoxystrobin and pyraclostrobin provided little or no control of these isolates. Additional sampling in 2006 revealed at least 15 additional vineyards with QoI-resistant P. viticola in Virginia, Maryland, and Pennsylvania. Of 22 isolates of Erysiphe (Uncinula) necator collected in 2005 from five Virginia locations, 20 isolates from 4 locations showed resistance to QoI fungicides. The G143A mutation for resistance was detected in several isolates of both pathogens. This is the first detection of this type of resistance in P. viticola in North America, and the second North American report of QoI resistance in E. necator.

Accepted for publication 26 November 2007. Published 11 February 2008.
First Report of Stem Rot of Dracaena Caused by Aspergillus niger in Iran
Authors: Abbasi Mehrdad , Aliabadi Faezeh
Published: February 2008

Specimen plants of Dracaena sanderiana showing stem rot symptoms were collected from a local market in Tehran. Aspergillus niger was isolated from all diseased plants. Healthy greenhouse plants were inoculated and developed disease symptoms. The authors were able to isolate A. niger from all inoculated plants. This is believed to be the first report of A. nigercausing stem rot of D. sanderiana in Iran.

Accepted for publication 26 November 2007. Published 12 February 2008.
Should hunting mortality mimic the patterns of natural mortality?
Authors: Bischof Richard , Mysterud Atle , Swenson Jon E
Published: February 2008

With growing concerns about the impact of selective harvesting on natural populations, researchers encourage managers to implement harvest regimes that avoid or minimize the potential for demographic and evolutionary side effects. A seemingly intuitive recommendation is to implement harvest regimes that mimic natural mortality patterns. Using stochastic simulations based on a model of risk as a logistic function of a normally distributed biological trait variable, we evaluate the validity of this recommendation when the objective is to minimize the altering effect of harvest on the immediate post-mortality distribution of the trait. We show that, in the absence of compensatory mortality, harvest mimicking natural mortality leads to amplification of the biasing effect expected after natural mortality, whereas an unbiased harvest does not alter the post-mortality trait distribution that would be expected in the absence of harvest. Although our approach focuses only on a subset of many possible objectives for harvest management, it illustrates that a single strategy, such as hunting mimicking natural mortality, may be insufficient to address the complexities of different management objectives with potentially conflicting solutions.
Optimal foraging: Lévy pattern or process?
Authors: Plank M.J , James A
Published: February 2008

Many different species have been suggested to forage according to a Lévy walk in which the distribution of step lengths is heavy-tailed. Theoretical research has shown that a Lévy exponent of approximately 2 can provide a higher foraging efficiency than other exponents. In this paper, a composite search model is presented for non-destructive foraging behaviour based on Brownian (i.e. non-heavy-tailed) motion. The model consists of an intensive search phase, followed by an extensive phase, if no food is found in the intensive phase. Quantities commonly observed in the field, such as the distance travelled before finding food and the net displacement in a fixed time interval, are examined and compared with the results of a Lévy walk model. It is shown that it may be very difficult, in practice, to distinguish between the Brownian and the Lévy models on the basis of observed data. A mathematical expression for the optimal time to switch from intensive to extensive search mode is derived, and it is shown that the composite search model provides higher foraging efficiency than the Lévy model.
CD4
+
T cells do not mediate within-host competition between genetically diverse malaria parasites
Authors: Barclay Victoria C , Råberg Lars , Chan Brian H.K , Brown Sheila , Gray David , Read Andrew F
Published: February 2008

Ecological interactions between microparasite populations in the same host are an important source of selection on pathogen traits such as virulence and drug resistance. In the rodent malaria model
Plasmodium chabaudi
in laboratory mice, parasites that are more virulent can competitively suppress less virulent parasites in mixed infections. There is evidence that some of this suppression is due to immune-mediated apparent competition, where an immune response elicited by one parasite population suppress the population density of another. This raises the question whether enhanced immunity following vaccination would intensify competitive interactions, thus strengthening selection for virulence in
Plasmodium
populations. Using the
P. chabaudi
model, we studied mixed infections of virulent and avirulent genotypes in CD4
+
T cell-depleted mice. Enhanced efficacy of CD4
+
T cell-dependent responses is the aim of several candidate malaria vaccines. We hypothesized that if immune-mediated interactions were involved in competition, removal of the CD4
+
T cells would alleviate competitive suppression of the avirulent parasite. Instead, we found no alleviation of competition in the acute phase, and significant enhancement of competitive suppression after parasite densities had peaked. Thus, the host immune response may actually be alleviating other forms of competition, such as that over red blood cells. Our results suggest that the CD4
+
-dependent immune response, and mechanisms that act to enhance it such as vaccination, may not have the undesirable affect of exacerbating within-host competition and hence the strength of this source of selection for virulence.
Neural correlates of Early Stone Age toolmaking: technology, language and cognition in human evolution
Authors: Stout Dietrich , Toth Nicholas , Schick Kathy , Chaminade Thierry
Published: February 2008

Archaeological and palaeontological evidence from the Early Stone Age (ESA) documents parallel trends of brain expansion and technological elaboration in human evolution over a period of more than 2 Myr. However, the relationship between these defining trends remains controversial and poorly understood. Here, we present results from a positron emission tomography study of functional brain activation during experimental ESA (Oldowan and Acheulean) toolmaking by expert subjects. Together with a previous study of Oldowan toolmaking by novices, these results document increased demands for effective visuomotor coordination and hierarchical action organization in more advanced toolmaking. This includes an increased activation of ventral premotor and inferior parietal elements of the parietofrontal praxis circuits in both the hemispheres and of the right hemisphere homologue of Broca's area. The observed patterns of activation and of overlap with language circuits suggest that toolmaking and language share a basis in more general human capacities for complex, goal-directed action. The results are consistent with coevolutionary hypotheses linking the emergence of language, toolmaking, population-level functional lateralization and association cortex expansion in human evolution.
The role of cultural practices in the emergence of modern human intelligence
Authors: Hutchins Edwin
Published: February 2008

Innate cognitive capacities are orchestrated by cultural practices to produce high-level cognitive processes. In human activities, examples of this phenomenon range from everyday inferences about space and time to the most sophisticated reasoning in scientific laboratories. A case is examined in which chimpanzees enter into cultural practices with humans (in experiments) in ways that appear to enable them to engage in symbol-mediated thought. Combining the cultural practices perspective with the theories of embodied cognition and enactment suggests that the chimpanzees' behaviour is actually mediated by non-symbolic representations. The possibility that non-human primates can engage in cultural practices that give them the appearance of symbol-mediated thought opens new avenues for thinking about the coevolution of human culture and human brains.
Why religion is nothing special but is central
Authors: Bloch Maurice
Published: February 2008

It is proposed that explaining religion in evolutionary terms is a misleading enterprise because religion is an indissoluble part of a unique aspect of human social organization. Theoretical and empirical research should focus on what differentiates human sociality from that of other primates, i.e. the fact that members of society often act towards each other in terms of essentialized roles and groups. These have a phenomenological existence that is not based on everyday empirical monitoring but on imagined statuses and communities, such as clans or nations. The neurological basis for this type of social, which includes religion, will therefore depend on the development of imagination. It is suggested that such a development of imagination occurred at about the time of the Upper Palaeolithic ‘revolution’.
Neuroscience, evolution and the sapient paradox: the factuality of value and of the sacred
Authors: Renfrew Colin
Published: February 2008

The human genome, and hence the human brain at birth, may not have changed greatly over the past 60 000 years. Yet many of the major behavioural changes that we associate with most human societies are very much more recent, some appearing with the sedentary revolution of some 10 000 years ago. Among these are activities implying the emergence of powerful concepts of value and of the sacred. What then are the neuronal mechanisms that may underlie these consistent, significant (and emergent) patterns of behaviour?
Between brains, bodies and things:tectonoeticawareness and the extended self
Authors: Malafouris Lambros
Published: February 2008

This paper presents the possible outline of a framework that will enable the incorporation of material culture into the study of the human self. To this end, I introduce the notions ofextended selfandtectonoetic awareness. Focusing on the complex interactions between brains, bodies and things and drawing a number of different and usually unconnected threads of evidence from archaeology, philosophy and neuroscience together, I present a view of selfhood as an extended and distributed phenomenon that is enacted across the skin barrier and which thus comprises both neural and extra-neural resources. Finally, I use the example of a gold Mycenaean signet ring to explore how a piece of inanimate matter can be seen (sometimes) as a constitutive and efficaciouspartof the human self-system.
Scanning the human genome at kilobase resolution
Authors: Chen Jun , Kim Yeong C. , Jung Yong-Chul , Xuan Zhenyu , Dworkin Geoff , Zhang Yanming , Zhang Michael Q. , Wang San Ming
Published: February 2008

Normal genome variation and pathogenic genome alteration frequently affect small regions in the genome. Identifying those genomic changes remains a technical challenge. We report here the development of the DGS (Ditag Genome Scanning) technique for high-resolution analysis of genome structure. The basic features of DGS include (1) use of high-frequent restriction enzymes to fractionate the genome into small fragments; (2) collection of two tags from two ends of a given DNA fragment to form a ditag to represent the fragment; (3) application of the 454 sequencing system to reach a comprehensive ditag sequence collection; (4) determination of the genome origin of ditags by mapping to reference ditags from known genome sequences; (5) use of ditag sequences directly as the sense and antisense PCR primers to amplify the original DNA fragment. To study the relationship between ditags and genome structure, we performed a computational study by using the human genome reference sequences as a model, and analyzed the ditags experimentally collected from the well-characterized normal human DNA GM15510 and the leukemic human DNA of Kasumi-1 cells. Our studies show that DGS provides a kilobase resolution for studying genome structure with high specificity and high genome coverage. DGS can be applied to validate genome assembly, to compare genome similarity and variation in normal populations, and to identify genomic abnormality including insertion, inversion, deletion, translocation, and amplification in pathological genomes such as cancer genomes.
Copy number variation at the 7q11.23 segmental duplications is a susceptibility factor for the Williams-Beuren syndrome deletion
Authors: Cuscó Ivon , Corominas Roser , Bayés Mònica , Flores Raquel , Rivera-Brugués Núria , Campuzano Victoria , Pérez-Jurado Luis A.
Published: February 2008

Large copy number variants (CNVs) have been recently found as structural polymorphisms of the human genome of still unknown biological significance. CNVs are significantly enriched in regions with segmental duplications or low-copy repeats (LCRs). Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder caused by a heterozygous deletion of contiguous genes at 7q11.23 mediated by nonallelic homologous recombination (NAHR) between large flanking LCRs and facilitated by a structural variant of the region, a ∼2-Mb paracentric inversion present in 20%–25% of WBS-transmitting progenitors. We now report that eight out of 180 (4.44%) WBS-transmitting progenitors are carriers of a CNV, displaying a chromosome with large deletion of LCRs. The prevalence of this CNV among control individuals and non-transmitting progenitors is much lower (1%, n = 600), thus indicating that it is a predisposing factor for the WBS deletion (odds ratio 4.6-fold, P = 0.002). LCR duplications were found in 2.22% of WBS-transmitting progenitors but also in 1.16% of controls, which implies a non–statistically significant increase in WBS-transmitting progenitors. We have characterized the organization and breakpoints of these CNVs, encompassing ∼100–300 kb of genomic DNA and containing several pseudogenes but no functional genes. Additional structural variants of the region have also been defined, all generated by NAHR between different blocks of segmental duplications. Our data further illustrate the highly dynamic structure of regions rich in segmental duplications, such as the WBS locus, and indicate that large CNVs can act as susceptibility alleles for disease-associated genomic rearrangements in the progeny.
Distinct neural mechanisms mediate olfactory memory formation at different timescales
Authors: McNamara Ann Marie , Magidson Phillip D. , Linster Christiane , Wilson Donald A. , Cleland Thomas A.
Published: February 2008

Habituation is one of the oldest forms of learning, broadly expressed across sensory systems and taxa. Here, we demonstrate that olfactory habituation induced at different timescales (comprising different odor exposure and intertrial interval durations) is mediated by different neural mechanisms. First, the persistence of habituation memory is greater when mice are habituated on longer timescales. Second, the specificity of the memory (degree of cross-habituation to similar stimuli) also depends on induction timescale. Third, we demonstrate a pharmacological double dissociation between the glutamatergic mechanisms underlying short- and long-timescale odor habituation. LY341495, a class II/III metabotropic glutamate receptor antagonist, blocked habituation only when the induction timescale was short. Conversely, MK-801, an N-methyl-D-aspartate (NMDA) receptor antagonist, prevented habituation only when the timescale was long. Finally, whereas short-timescale odor habituation is mediated within the anterior piriform cortex, infusion of MK-801 into the olfactory bulbs prevented odor habituation only at longer timescales. Thus, we demonstrate two neural mechanisms underlying simple olfactory learning, distinguished by their persistence and specificity, mediated by different olfactory structures and pharmacological effectors, and differentially utilized based solely on the timescale of odor presentation.
Perseverative interference with object-in-place scene learning in rhesus monkeys with bilateral ablation of ventrolateral prefrontal cortex
Authors: Baxter Mark G. , Browning Philip G.F. , Mitchell Anna S.
Published: February 2008

Surgical disconnection of the frontal cortex and inferotemporal cortex severely impairs many aspects of visual learning and memory, including learning of new object-in-place scene memory problems, a monkey model of episodic memory. As part of a study of specialization within prefrontal cortex in visual learning and memory, we tested monkeys with bilateral ablations of ventrolateral prefrontal cortex in object-in-place scene learning. These monkeys were mildly impaired in scene learning relative to their own preoperative performance, similar in severity to that of monkeys with bilateral ablation of orbital prefrontal cortex. An analysis of response types showed that the monkeys with lesions were specifically impaired in responding to negative feedback during learning: The post-operative increase in errors was limited to trials in which the first response to each new problem, made on the basis of trial and error, was incorrect. This perseverative pattern of deficit was not observed in the same analysis of response types in monkeys with bilateral ablations of the orbital prefrontal cortex, who were equally impaired on trials with correct and incorrect first responses. This may represent a specific signature of ventrolateral prefrontal involvement in episodic learning and memory.
Association of the variable number of tandem repeats polymorphism in the promoter region of the SMYD3 gene with risk of esophageal squamous cell carcinoma in relation to tobacco smoking
Authors: Wang Haijian , Liu Yang , Tan Wen , Zhang Yang , Zhao Naiqing , Jiang Yan , Lin Chengzhao , Hao Bingtao , Zhao Dan , Qian Ji , Lu Daru , Jin Li , Wei Qingyi , Lin Dongxin , He Fuchu
Published: February 2008

The etiology of esophageal squamous cell carcinoma (ESCC) has been shown to be multifactorial, including genetic, epigenetic, and environmental factors, such as tobacco smoking. A variable number of tandem repeats (VNTR) polymorphism in the promoter region of SMYD3, a recently characterized histone lysine methyltransferase gene that is implicated in cell proliferation and carcinogenesis, has been shown to be functional, but its association with cancer risk has not been well established because of apparently discrepant results in different populations. In this case‐control study, we genotyped 567 patients with newly diagnosed ESCC and 567 healthy controls and found an increased ESCC risk (odds ratio [OR] = 1.42, 95% confidence interval [CI] = 1.05–1.91) associated with the common SMYD3 VNTR genotype. Stratification analysis revealed that the increased risk was limited to smokers (OR = 1.99; 95% CI = 1.27–3.12). Furthermore, compared with the reference group of non‐smokers carrying the homozygous or heterozygous genotype, ORs (95% CI) of the wild genotype for non‐smokers, smokers who smoked <25, and ≥25 pack‐years were 1.03 (0.70–1.53), 2.80 (1.66–4.70), and 4.76 (2.67–8.46), respectively (P < 0.001 for trend test), suggesting an interaction between this genetic polymorphism and smoking status. These findings provide additional evidence that the common VNTR polymorphism in the promoter region of SMYD3 gene may be a susceptibility factor for human cancers such as ESCC by interacting with tobacco carcinogens. (Cancer Sci 2008; 99: 787–791)