bluuebunny/crossref_metadata_2025_split huggingface dataset:
Holocene beach deposits for assessing coastal uplift of the northeastern Boso Peninsula, Pacific coast of Japan
Authors: Tamura Toru , Murakami Fumitoshi , Watanabe Kazuaki 
Published: August 2010

AbstractThis paper presents a case study that assessed spatial variations in the tectonic uplift rates of beach deposits in the relict Kujukuri strand plain, situated on the northeastern coast of the Boso Peninsula, eastern Japan. The southern Boso Peninsula is tilted downward to the northeast due to plate subduction along the Sagami Trough. However, the cause of the northeastern coast uplift creating the relict strand plain is unclear, due to the absence of a Holocene raised marine terrace sequence. Elevations and ages of beach deposits were collected from drilled cores and ground-penetrating radar profiles along three shore-normal sections in the southern Kujukuri strand plain. From this, alongshore variations in the relative sea level since the mid-Holocene could be seen. These corresponded to north-to-northeast downward tilting at a rate of 0.4 m/ka for an interval 10 km and are concordant with the longer term tilting of the last interglacial marine terrace surrounding the plain. Although it is difficult to assess shore-normal variations of uplift based on the present dataset, the recognized tilting apparently continues to the tilting of the southern Boso Peninsula, implying the Sagami Trough probably affects the uplift of the Kujukuri coast.
An information perspective on path dependence
Authors: HEIKKILA ERIC J. 
Published: August 2010

Abstract:This paper proposes an information perspective on path dependence. From this perspective, historical paths are important insofar as knowledge about them shapes current decisions, for better or worse. A key consideration is the extent to which relevant information is fully inscribed in the existing configuration of state variables, including organizational structures and institutional norms. Using a chess analogy, path dependency arises whenever a decision maker's ‘move’ depends not only upon existing state variables, but also knowledge of the path by which this configuration came about. This chess analogy is then extended to various institutional contexts such as legal expungement of criminal records, patient privacy rights, and corporate executive succession strategies. A formal notation is introduced to specify this definition more precisely, and to compare it with other perspectives on path dependency, such as lock-in effects, increasing returns to scale, ergodic equilibria, and generalized notions that ‘history matters’.
Structure and function of the polymerase core of TRAMP, a RNA surveillance complex
Authors: Hamill Stephanie , Wolin Sandra L. , Reinisch Karin M. 
Published: August 2010

The Trf4p/Air2p/Mtr4p polyadenylation (TRAMP) complex recognizes aberrant RNAs in
Saccharomyces cerevisiae
and targets them for degradation. A TRAMP subcomplex consisting of a noncanonical poly(A) RNA polymerase in the Pol ß superfamily of nucleotidyl transferases, Trf4p, and a zinc knuckle protein, Air2p, mediates initial substrate recognition. Trf4p and related eukaryotic poly(A) and poly(U) polymerases differ from other characterized enzymes in the Pol ß superfamily both in sequence and in the lack of recognizable nucleic acid binding motifs. Here we report, at 2.7-Å resolution, the structure of Trf4p in complex with a fragment of Air2p comprising two zinc knuckle motifs. Trf4p consists of a catalytic and central domain similar in fold to those of other noncanonical Pol β RNA polymerases, and the two zinc knuckle motifs of Air2p interact with the Trf4p central domain. The interaction surface on Trf4p is highly conserved across eukaryotes, providing evidence that the Trf4p/Air2p complex is conserved in higher eukaryotes as well as in yeast and that the TRAMP complex may also function in RNA surveillance in higher eukaryotes. We show that Air2p, and in particular sequences encompassing a zinc knuckle motif near its N terminus, modulate Trf4p activity, and we present data supporting a role for this zinc knuckle in RNA binding. Finally, we show that the RNA 3′ end plays a role in substrate recognition.
Anisotropy of wave propagation in the heart can be modeled by a Riemannian electrophysiological metric
Authors: Young Robert J. , Panfilov Alexander V. 
Published: August 2010

It is well established that wave propagation in the heart is anisotropic and that the ratio of velocities in the three principal directions may be as large as
v

f

∶
v

s

∶
v

n

≈ 4(fibers)∶2(sheets)∶1(normal). We develop an alternative view of the heart based on this fact by considering it as a non-Euclidean manifold with an electrophysiological(
el
-) metric based on wave velocity. This metric is more natural than the Euclidean metric for some applications, because
el
-distances directly encode wave propagation. We develop a model of wave propagation based on this metric; this model ignores higher-order effects like the curvature of wavefronts and the effect of the boundary, but still gives good predictions of local activation times and replicates many of the observed features of isochrones. We characterize this model for the important case of the rotational orthotropic anisotropy seen in cardiac tissue and perform numerical simulations for a slab of cardiac tissue with rotational orthotropic anisotropy and for a model of the ventricles based on diffusion tensor MRI scans of the canine heart. Even though the metric has many slow directions, we show that the rotation of the fibers leads to fast global activation. In the diffusion tensor MRI-based model, with principal velocities 0.25∶05∶1 m/s, we find examples of wavefronts that eventually reach speeds up to 0.9 m/s and average velocities of 0.7 m/s. We believe that development of this non-Euclidean approach to cardiac anatomy and electrophysiology could become an important tool for the characterization of the normal and abnormal electrophysiological activity of the heart.
Conformational dynamics of bacteriophage T7 DNA polymerase and its processivity factor,
Escherichia coli
thioredoxin
Authors: Akabayov Barak , Akabayov Sabine R. , Lee Seung-Joo , Tabor Stanley , Kulczyk Arkadiusz W. , Richardson Charles C. 
Published: August 2010

Gene 5 of bacteriophage T7 encodes a DNA polymerase (gp5) responsible for the replication of the phage DNA. Gp5 polymerizes nucleotides with low processivity, dissociating after the incorporation of 1 to 50 nucleotides. Thioredoxin (trx) of
Escherichia coli
binds tightly (Kd = 5 nM) to a unique segment in the thumb subdomain of gp5 and increases processivity. We have probed the molecular basis for the increase in processivity. A single-molecule experiment reveals differences in rates of enzymatic activity and processivity between gp5 and gp5/trx. Small angle X-ray scattering studies combined with nuclease footprinting reveal two conformations of gp5, one in the free state and one upon binding to trx. Comparative analysis of the DNA binding clefts of DNA polymerases and DNA binding proteins show that the binding surface contains more hydrophobic residues than other DNA binding proteins. The balanced composition between hydrophobic and charged residues of the binding site allows for efficient sliding of gp5/trx on the DNA. We propose a model for trx-induced conformational changes in gp5 that enhance the processivity by increasing the interaction of gp5 with DNA.
Epidemiology of Helicobacter pylori infection.
Authors: Malaty H. M. 
Published: August 2010

Abstract

This chapter discusses the relationship between Helicobacter pylori infection and associated diseases (chronic gastritis, peptic ulcer disease and gastric adenocarcinoma) and describes the route of H. pylori transmission. The geographical distribution and changing trends of the prevalence of H. pylori infection, the changes in the environment and human behaviour that influence the prevalence of H. pylori infection, and the decreasing prevalence of infection-induced ulcers in western countries are reviewed.
Innate immune initiators and effectors in Helicobacter pylori infection.
Authors: Kaparakis M. , Allison C. C. , Hutton M. L. , Ferrero R. L. 
Published: August 2010

Abstract

This chapter discusses the innate immune responses generated by the host in an attempt to control Helicobacter pylori infection. The roles of host pathogen-recognition molecules in the identification of H. pylori within the gastric mucosa and the downstream signalling events that these molecules trigger are described. Some of the key H. pylori products that facilitate the initiation of inflammation are identified. How these processes result in the production of proinflammatory cytokines, ultimately leading to the development of gastritis within the host, are discussed.
MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences
Authors: Darzentas N. , Bousios A. , Apostolidou V. , Tsaftaris A. S. 
Published: August 2010

Abstract
Summary: We present MASiVE, an expertly built tool for the large-scale, yet sensitive and highly accurate, discovery, preliminary analysis and insertion age estimation of intact Sirevirus LTR-retrotransposons in plant genomic sequences. Validation was based on the recently available and annotated large maize chromosome one. Results show a considerable improvement in the annotation of Sireviruses, and support our approach as an important addition to the bioinformatics toolbox of plant biologists.
Availability: PERL source code and essential files are available online at http://bat.ina.certh.gr/tools/masive/. The freely available Vmatch, LTRharvest, Wise2, and MAFFT algorithms are required.
Contact: ndarz@certh.gr
Supplementary information: Supplementary data are available at Bioinformatics online.
Stem Rot of Branched Broomrape (Orobanche ramosa) Caused by Sclerotium rolfsii in Chile
Authors: Galdames R. , Diaz J. 
Published: August 2010

Branched broomrape is a holoparasitic weed present in some areas of central and southern Chile (33°S to 38°S), which is often found parasitizing tomato and tobacco crops. During an extensive survey conducted in different tomato-growing areas during the summer of 2010, branched broomrape plants with stem rot symptoms were detected in a commercial tomato crop located in the central zone (34°14′S, 71°1′W). Rotten stems were observed with white mycelia and approximately 1-mm-diameter spherical sclerotia on affected tissue below the soil surface. Parasitized tomato plants showed no symptoms. Sclerotia were taken directly from affected stems with a dissecting needle under a stereoscopic microscope in a flow chamber and placed on potato dextrose agar (PDA) medium. Germinating sclerotia consistently produced colonies similar to Sclerotium rolfsii with new sclerotia formed within 6 to 7 days. Mycelia produced hyphal clamp connections under the light microscope (2). DNA was extracted from one fungal culture. The ITS1 region, 5.8S rRNA gene, and the ITS2 region of the nuclear-encoded ribosomal RNA gene were amplified with primers ITS1 and ITS4 (4). The sequence was deposited in GenBank (Accession No. HM222638) and showed ≥99% identity values with sequences of similar regions from Athelia rolfsii (anamorph S. rolfsii; Accession Nos. AB075304, DQ0595578, AF499018, and AB075305). Different pathogenicity tests were performed. Inoculum was prepared by placing mycelia plugs from a PDA-grown, 6-day-old colony in a flask with sterilized wheat seeds and incubated for 2 weeks. Three Orobanche plants, each one with 10 to 15 shoots at different aerial stages (starting emergence, flowering, and formed capsules) were gently planted separately in 35-cm pots. Inoculum (10 g per pot) was placed in the soil surrounding the plants. One pot was used as a control. Forty-five-day-old tomato and tobacco plants were additionally inoculated by a similar procedure. After 12 days, inoculated Orobanche plants showed reduced vigor and stem decay. After 9 days, tomato and tobacco plants showed wilt. In all cases, the fungus was reisolated on PDA from all inoculated plants. To our knowledge, this is the first report of S. rolfsii on O. ramosa (1). A previous report of S. rolfsii parasitizing O. cernua has also been made (3). The high susceptibility of tomato and tobacco plants to this isolate of S. rolfsii precludes the use of this pathogen as a biological control agent against broomrape. References: (1) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved May 14, 2010, from http://nt.ars-grin.gov/fungaldatabases . (2) Z. K. Punja and A. Damiani. Mycologia 88:694, 1996. (3) C. A. Raju et al. Phytoparasitica 23:235, 1995. (4) T. J. White et al. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, New York, 1990.
First Report of Southern Blight of Okra (Abelmoschus esculentus) Caused by Sclerotium rolfsii in Côte d'Ivoire
Authors: Koné D. , Mohamed D. , Soro S. , Bolou Bi B. A. , Kouadio Y. J. , Ji P. 
Published: August 2010

Southern blight caused by Sclerotium rolfsii Sacc. was observed on okra (Abelmoschus esculentus) cv. Clemson Spineless in January 2010 during a survey of vegetable fields in Rubbino, Côte d'Ivoire, which is one of the most important areas for vegetable production. Plants exhibited symptoms of a dark brown lesion on the stems near the soil line. Upper roots became light to dark brown, the lower leaves wilted, turned yellow, and a white mat of fungal mycelium developed on the stem lesion. Numerous, white, spherical sclerotia formed on the infected stem and on soil surfaces around the infected plants. Sclerotia (0.5 to 1.2 mm in diameter) later turned tan to dark brown and the entire plant wilted. Eleven fields, with a total of approximately 26 ha surveyed, were affected and disease incidence reached approximately 15% in the fields. Sclerotia were collected and the fungus cultured on acidified potato dextrose agar (PDA) plates. The fungus grew rapidly on PDA and the hyphae at the edge of the colonies were large straight cells with one or more clamp connections at each septum. Secondary and tertiary hyphae were slender and lacked clamp connections. Whitish sclerotia were observed on the mycelial mats 5 to 7 days after incubation, which later turned tan to brown when mature. The fungus was identified as S. rolfsii based on the characteristics of mycelia and sclerotia (1). Sclerotia produced on PDA were used to inoculate okra seedlings under greenhouse conditions at rates of 10, 20, and 30 sclerotia per plant. Sclerotia were placed just under the soil surface around the root of 4-week-old seedlings of okra cv. Clemson Spineless. Symptoms identical to those on field samples developed on all inoculated plants. S. rolfsii was reisolated from diseased plants and the identity was confirmed. S. rolfsii has previously been reported as causing disease in Côte d'Ivoire (2). To our knowledge, this is the first report of southern blight caused by S. rolfsii on okra in this country. Okra is an important vegetable crop in Côte d'Ivoire and therefore the occurrence of southern blight and susceptibility of okra cultivars to this disease needs to be taken into account in okra production. References: (1) Z. K. Punja and A. Damiani. Mycologia 88:694, 1996. (2) R. Resplandy et al. Ann. Epiphyt. 1:1, 1954.
First Report of Root and Basal Rot of Angelica acutiloba Caused by Fusarium solani in Taiwan
Authors: Chern L. L. , Feng C. T. , Yu C. H. , Ho W. C. 
Published: August 2010

Angelica (Angelica acutiloba (Siebold. & Zucc.) Kitag.) is one of the most important traditional Chinese medicines in Taiwan. The medicinal herb has been mainly imported from China, but cultivation at a commercial scale has also been established in recent years in Hualien County, Taiwan. In September 2008, angelica plants in a field at Liou-shih-dan Mountain displayed symptoms of yellowing, stunting, rotting of roots and basal stem, and wilting. A severe brown discoloration of vascular tissue along the stems of infected plants was observed. One or more Fusarium spp. was consistently isolated from the roots and stems of diseased plants. Isolates R3, R4, and R5 were incubated for 14 days on celery tissues to produce chlamydospores, and 33 g of celery tissue with chlamydospores were mixed with 500 ml of soil per pot as inoculum. One 4-month-old angelica seedling was planted per pot. Three angelica plants were inoculated with each isolate in the first test and nine plants were inoculated with each isolate in the second test. Other seedlings were inoculated with water as checks. Pathogenicity tests were conducted twice. Incidence of diseased plants was 66, 100, and 33% in the first test, and 66, 100, and 44% in the second test for the R3, R4, and R5 isolates, respectively. Symptoms similar to those on the diseased plants in the field were produced, with leaves turning yellow starting 7 days after inoculation and wilt and discoloration of roots 14 days after inoculation. Fusarium spp. also were reisolated from the diseased plants. Genomic DNA was extracted from mycelium with a fungal genomic DNA purification kit, and the internal transcribed spacer (ITS) rDNA region was amplified and sequenced with primers ITS-4 and ITS-5. The sequence of the resulting ~550-bp amplicon was compared with those in GenBank. The ITS sequences of the R3, R4, and R5 isolates shared 98.7, 98.7, and 97.9% similarity with F. solani isolate AF129104 (3), respectively. Phylogenetic analysis also showed that the three isolates were closer to F. solani than to other Fusarium species. Both macroconidia and microconidia of the R4 isolate were produced on potato dextrose agar. Macroconidia were three to five septate and 27.2 to 37.8 × 4.4 to 6.2 μm; microconidia were zero to one septate and 9.3 to 14.7 × 2.9 to 4.8 μm. Chlamydospores produced on celery juice agar were terminal or intercalary, solitary, in pairs or in chains, and 9.3 to 12.1 μm. Morphological characteristics identified the three isolates as F. solani (Martius) Snyder & Hansen according to Fu and Chang (2) and Chung et al. (1), which agrees with the ITS comparison. To our knowledge, this is the first report of root and basal rot caused by F. solani on angelica in Taiwan. References: (1) W. C. Chung et al. Plant Prot. Bull. 40:177, 1998. (2) C. H. Fu and T. T. Chang. Taiwan J. For. Sci. 14:223, 1999. (3) H. Suga et al. Mycol. Res. 104:1175, 2000.
First Report of the Telial Stage of Japanese Apple Rust on Juniperus chinensis in North America and the Aecial Stage on Malus domestica
Authors: Gregory N. F. , Bischoff J. F. , Dixon L. J. , Ciurlino R. 
Published: August 2010

Following a report in April 2009 of the presence of Gymnosporangium yamadae Miyabae ex G. Yamada on crabapple (Malus toringo Siebold) in Wilmington, DE (2), University of Delaware, State of Delaware, and USDA/APHIS PPQ personnel collaborated to confirm and document the pathogen. G. yamadae is the causal agent of Japanese apple rust. The fungus is known from Asia with an aecial state on economically important Malus species and telial state on Juniperus chinensis. During the April 2009 site visit, ornamental J. chinensis were observed near the original crabapples. On May 7, 2009, telial galls were collected from the ornamental J. chinensis at the Wilmington site. The telia were confirmed to be G. yamadae by morphometric analysis and molecular data. The rDNA large subunit (LSU) sequence derived from the collected telial galls (GenBank Accession No. GU058012) was identical to the eight G. yamadae LSU sequences (GenBank Accession Nos. FJ848760–FJ848765, FJ559373, and FJ559375) reported from Korea by Yun et al. (3). Teliospores were 45 to 54 μm long with pedicels that were wide (7.0 to 8.4 μm) along the full length. The G. yamadae telial gall collected from Wilmington, DE was deposited into the U.S. National Fungus Collection (BPI 879273). Leaves of M. domestica on the University of Delaware farm in Newark were confirmed to have Japanese apple rust on Aug 4, 2009. Identification was made on the morphological presence of unique roestelioid aecia with long cornulated peridia that lacerate along the sides. The aecia differ from those of G. juniperi-virginianae, the causal agent of cedar apple rust, which has aecial peridia that fimbriate to the base and are strongly recurved (1). Following release of a USDA Pest Alert, subsequent samples submitted to USDA/APHIS PPQ indicated widespread incidence of the G. yamadae aecial state in the northeast, including Maryland, Maine, New Hampshire, New Jersey, New York, Pennsylvania, and Rhode Island. Japanese apple rust likely went undetected for several years because of similar symptomatology to cedar apple rust. To our knowledge, this is the first report of the telial stage of G. yamadae in North America and the first report of this pathogen on Malus domestica in the United States. Knowledge of the geographic distribution of G. yamadae is of significance because of the actionable regulatory status of the pathogen and its potential impact on ornamental and fruit growers of Malus spp. in the United States. References: (1) F. D. Kern. A Revised Taxonomic Account of Gymnosporangium. Pennsylvania State University Press, University Park, PA, 1973. (2) H. Y. Yun et al. Plant Dis. 93:430, 2009. (3) H. Y. Yun et al. Mycologia 101:790, 2009.