bluuebunny/crossref_metadata_2025 huggingface dataset:
The cis-regulatory map of Shewanella genomes
Authors: Liu Jiajian , Xu Xing , Stormo Gary D.
Published: August 2008

While hundreds of microbial genomes are sequenced, the challenge remains to define their cis-regulatory maps. Here, we present a comparative genomic analysis of the cis-regulatory map of Shewanella oneidensis, an important model organism for bioremediation because of its extraordinary abilities to use a wide variety of metals and organic molecules as electron acceptors in respiration. First, from the experimentally verified transcriptional regulatory networks of Escherichia coli, we inferred 24 DNA motifs that are conserved in S. oneidensis. We then applied a new comparative approach on five Shewanella genomes that allowed us to systematically identify 194 nonredundant palindromic DNA motifs and corresponding regulons in S. oneidensis. Sixty-four percent of the predicted motifs are conserved in at least three of the seven newly sequenced and distantly related Shewanella genomes. In total, we obtained 209 unique DNA motifs in S. oneidensis that cover 849 unique transcription units. Besides conservation in other genomes, 77 of these motifs are supported by at least one additional type of evidence, including matching to known transcription factor binding motifs and significant functional enrichment or expression coherence of the corresponding target genes. Using the same approach on a more focused gene set, 990 differentially expressed genes derived from published microarray data of S. oneidensis during exposure to metal ions, we identified 31 putative cis-regulatory motifs (16 with at least one type of additional supporting evidence) that are potentially involved in the process of metal reduction. The majority (18/31) of those motifs had been found in our whole-genome comparative approach, further demonstrating that such an approach is capable of uncovering a large fraction of the regulatory map of a genome even in the absence of experimental data. The integrated computational approach developed in this study provides a useful strategy to identify genome-wide cis-regulatory maps and a novel avenue to explore the regulatory pathways for particular biological processes in bacterial systems.
miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes
Authors: Liu Qin , Fu Hanjiang , Sun Fang , Zhang Haoming , Tie Yi , Zhu Jie , Xing Ruiyun , Sun Zhixian , Zheng Xiaofei
Published: August 2008

MicroRNAs (miRNAs) are a class of small regulatory RNAs that are thought to be involved in diverse biological processes by regulating gene expression. Numerous miRNAs have been identified in various species, and many more miRNAs remain to be detected. Generally, hundreds of mRNAs have been predicted to be potential targets of one miRNA, so it is a great challenge to identify the genuine miRNA targets. Here, we generated the cell lines depleted of Drosha protein and screened dozens of transcripts (including Cyclin D1) regulated potentially by miRNA-mediated RNA silencing pathway. On the basis of miRNA expressing library, we established a miRNA targets reverse screening method by using luciferase reporter assay. By this method, we found that the expression of Cyclin D1 (CCND1) was regulated by miR-16 family directly, and miR-16 induced G1 arrest in A549 cells partially by CCND1. Furthermore, several other cell cycle genes were revealed to be regulated by miR-16 family, including Cyclin D3 (CCND3), Cyclin E1 (CCNE1) and CDK6. Taken together, our data suggests that miR-16 family triggers an accumulation of cells in G0/G1 by silencing multiple cell cycle genes simultaneously, rather than the individual target.
Studies on the Control of Cylindrocladium buxicola Using Fungicides and Host Resistance
Authors: Henricot B. , Gorton C. , Denton G. , Denton J.
Published: August 2008

Cylindrocladium buxicola is a fungal pathogen that causes a severe leaf and twig blight on Buxus spp. Laboratory experiments were carried out to study the in vitro effect of 13 fungicides on mycelial growth and conidia germination of the fungus. Based on the values of the effective concentration at which mycelial growth was inhibited by 50%, the fungicide Stroby (kresoxim-methyl) and the combined fungicides Opponent (epoxiconazole + kresoxim-methyl + pyraclostrobin), Opera (epoxiconazole + pyraclostrobin), and Signum (boscalid + pyraclostrobin) were the most effective at inhibiting mycelial growth and conidia germination. Pathogenicity assays showed that the host range of the fungus was not limited to the genus Buxus because Sarcococca sp. also was susceptible. None of the 10 boxwood species and cultivars tested were immune to the disease, although Buxus balearica as well as Sarcococca sp. showed significantly lower levels of infection as measured by the expression of leaf symptoms and the number of conidia produced on host tissue, the latter probably contributing to the apparent resistance of these species in the field. Microscopic observation showed that disease development was very rapid and aggressive on B. sempervirens ‘Suffruticosa’ where it was able to survive at least 5 years on decomposing fallen leaves.
Viral Interactions Lead to Decline of Blackberry Plants
Authors: Susaimuthu James , Tzanetakis Ioannis E. , Gergerich Rose C. , Kim Kyung S. , Martin Robert R.
Published: August 2008

Blackberry yellow vein disease (BYVD) poses a new threat to the blackberry industry in the United States. Blackberry yellow vein associated virus (BYVaV) was originally thought to be the sole cause of this disease. However, BYVaV has been found in several asymptomatic blackberry cultivars. An unusual member of the family Potyviridae was identified recently from symptomatic plants and named Blackberry virus Y (BVY). BVY has been shown to spread in the field and cause BYVD when co-infected with BYVaV. Both viruses are asymptomatic in single infections but are readily detectable in asymptomatic plants by reverse transcription–polymerase chain reaction (RT-PCR). However, in mixed infections, the titer of BYVaV is repressed, sometimes to levels undetectable by RT-PCR, while the concentration of BVY is increased several fold. Electron microscopy revealed a variety of viral inclusions in symptomatic leaf samples, but none could be found in single infections with either BVY or BYVaV. Although BYVaV has been consistently associated with BYVD in different geographical regions, the detection of BVY has thus far been restricted to northwest Arkansas. It has been hypothesized that BYVaV is the synergistic determinant of BYVD that causes symptoms in different cultivars at various locations during co-infection with other viruses.
Propiconazole Inhibits Armillaria tabescens In Vitro and Translocates into Peach Roots Following Trunk Infusion
Authors: Amiri A. , Bussey Karen E. , Riley Melissa B. , Schnabel G.
Published: August 2008

Intravascular trunk infusion of propiconazole has been associated with beneficial effects on Armillaria root rot control in Prunus sp. but its basipetal movement has not been verified. Propiconazole, a sterol demethylation inhibitor fungicide, was more effective in inhibiting mycelial growth of Armillaria tabescens isolates in vitro (average effective concentration to inhibit mycelial growth by 50% [EC50 value] of 0.6 μg/ml) compared with fungicides from five other chemical classes (EC50 values ranging from 4.6 to >1,000 μg/ml). The fungicide was infused into the vascular system of peach trees in the spring, summer, and fall of 2005 and 2006. Propiconazole concentration was determined using gas chromatography mass spectrometry in trunk sections above and below the infusion site and in primary roots. Over two experimental years, spring and fall infusions resulted in consistent propiconazole accumulations in primary peach roots. Spring infusions yielded propiconazole concentrations of 1.7 μg/g in 2005 and 5.6 μg/g in 2006, whereas the highest accumulations were detected following fall infusions with 9.2 μg/g in 2005 and 6.7 μg/g in 2006. Propiconazole was also consistently detected in trunk sections collected from above and below the infusion site. The basipetal movement of propiconazole in peach trees and its inhibitory activity against A. tabescens in vitro suggest that propiconazole infusion could be useful for targeted Armillaria root rot management.
Root and Crown Rot Fungi Associated with Spring, Facultative, and Winter Wheat in Turkey
Authors: Tunali Berna , Nicol Julie M. , Hodson David , Uçkun Zafer , Büyük Orhan , Erdurmuş Durmuş , Hekimhan Hakan , Aktaş Hüseyin , Akbudak M. Aydin , Bağci S. Ahmet
Published: August 2008

The objective of this study was to determine the distribution frequency of the fungi associated with wheat (Triticum aestivum) crowns and roots in cereal producing areas of Turkey through a targeted survey of 518 commercial fields over a 2-year period. More than 26% of the fields had one or more of the fungal species commonly reported as part of the dryland root rot complex, Fusarium culmorum (14%) > Bipolaris sorokiniana (10%) > F. pseudograminearum (2%). The fungi considered to be part of the high rainfall root rot complex were found at very low frequencies: 2% for Gaeumannomyces graminis and 3% for Pythium spp. Species of Rhizoctonia were found in 22% of the fields. Several Fusarium species considered to be less or nonpathogenic to cereals were also found in high frequencies at 11% (F. oxysporum, F. chlamydosporum), 10% (F. sporotrichioides), and 8% (F. avenaceum and F. solani). The mostly random distribution of cereal root-rotting species across the survey area suggests the fungi are not distributed in any distinct agroecological relationship. As a result, the relative economic importance of a given species on wheat will be determined by a number of factors, such as their fungal pathogenicity, host susceptibility/tolerance, and the seasonal conditions. Results from this study suggest that there are a wide range of fungal species associated with root and crown tissues of wheat.
Response of Butternut Selections to Inoculation with Sirococcus clavigignenti-juglandacearum
Authors: Ostry M. E. , Moore M.
Published: August 2008

Butternut trees (Juglans cinerea) clonally propagated via grafting from source trees with putative resistance to butternut canker were inoculated monthly with two isolates of Sirococcus clavigignenti-juglandacearum in a field planting in Minnesota. Significant differences in resulting canker length were found among (i) month of inoculation, (ii) accession, and (iii) isolate. Results support the suggestion that canker-free butternut occasionally found growing among butternut severely affected by butternut canker potentially have disease resistance and may have value for genetic conservation and restoration of the species. Developing an effective resistance screening technique will require additional information on the natural infection process and testing under various climatic conditions across the range of butternut.
Analysis of Fire Blight Shoot Infection Epidemics on Apple
Authors: Biggs Alan R. , Turechek William W. , Gottwald Tim R.
Published: August 2008

Fire blight incidence and spread of the shoot blight phase of the disease was studied in four apple cultivars in replicated blocks over 4 years (1994 to 1997). Cv. York was highly susceptible, followed by ‘Fuji’ and ‘Golden Delicious,’ which were moderately susceptible, and ‘Liberty,’ which was least susceptible. On York, the first appearance of shoot blight was within 48 h of its predicted appearance according to the Maryblyt model in 3 of the 4 years studied. Shoot blight epidemics in York in 1995 and 1996, and Fuji in 1995, were best described with a logistic model that showed apparent infection rates ranging from 0.05 to 0.20, indicating a low to moderately high rate of disease increase. The spatial positions (row and column) of all infected plants in each subplot were recorded on plot maps on each sampling date. The binomial and β-binomial distributions were fit to the data to test for spatial aggregation of disease incidence for each cultivar plot. Maximum likelihood estimation was possible for 92 (43.6%) of the 211 data sets subjected to this analysis. Of these, 35 data sets were better fit by the β-binomial distribution than the binomial distribution. The binary power law was used to characterize the relationship between the variance among quadrats within each plot to the variance expected for that plot given the observed level of disease incidence. The binary power law provided an excellent fit to the full data set and to nearly all of the subsets and, with b > 1, indicated that heterogeneity changed systematically with disease incidence. A covariance analysis was conducted to determine the effect of the factors ‘year,’ ‘cultivar,’ ‘orchard plot,’ and ‘observation date’ on the intercept and slope parameters of the binary power law. In general, plot followed by year had the greatest impact on parameter estimates and is an indication that location and seasonal factors impact heterogeneity of disease, although the specifics could not be ascertained from this study. Ordinary runs analysis was used to analyze the pattern of diseased trees within rows and detected significant nonrandom patterns of disease incidence in 63.5% of the orchard plots over the 4-year study. From these data sets, 68.7% had significantly fewer runs, particularly at disease incidences greater than 0.1. The fewer-than-expected runs at incidences greater than 0.10 provides strong evidence of localized spread.
Comparison of Application Methods of Systemic Fungicides to Suppress Branch Cankers in Clementine Trees Caused byPhytophthora citrophthora
Authors: Alvarez L. A. , Vicent A. , Soler J. M. , De la Roca E. , Bascón J. , García-Jiménez J.
Published: August 2008

Since 2002, considerable losses of Clementine trees (Citrus clementina) have been observed in Spain due to Phytophthora branch canker of citrus caused by Phytophthora citrophthora. Due to the low efficiency of the available cultural and genetic control measures, application of fungicides is required for economic management of the disease. Fosetyl-Al, metalaxyl, and its enantiomer mefenoxam are the only systemic fungicides registered for control of Phytophthora diseases in Spain. However, their efficacy has not been tested against Phytophthora branch canker. Greenhouse and field experiments were conducted for 3 years in Spain to evaluate the ability of these fungicides and application methods to reduce lesion expansion. Nevertheless, with the inoculation technique used, it was not possible to evaluate the protective activity of fungicides, which can play an important role in their performance under field conditions. None of the fungicide treatments inhibited lesion expansion when applications were made on a curative basis. The residual effect was better on young than on mature trees. Paint treatments were generally more effective in reducing lesion expansion that drip chemigation or foliar sprays. However, this application method is laborious and becomes uneconomical in Spain. Trunk and branch sprays as well as long-term programs of foliar sprays or drip chemigation for control of spring and autumn infections are proposed as targets for future research.
First Report of Wheat streak mosaic virus in Slovakia
Authors: Kúdela O. , Kúdelová M. , Nováková S. , Glasa M.
Published: August 2008

The occurrence of Wheat streak mosaic virus (WSMV; genus Tritimovirus) was monitored by testing 91 wheat and barley samples collected from various localities of Slovakia from March to June 2007. Samples were screened by a commercial double-antibody sandwich-ELISA kit (Loewe Biochemica, Sauerlach, Germany). Positive results were obtained from two wheat (Triticum aestivum L.) samples from the same locality of western Slovakia. Molecular analysis of both samples was performed by reverse transcription-PCR with WSMV-specific primers (WS-8166F 5′ GAGAGCAATACTGCGTGTACG 3′ and WS-8909R 5′ GCATAATGGCTCGAAGTGATG 3′) designed according to available sequences. The expected 750-bp PCR fragment containing the N-terminal and core region of the coat protein gene (from 8166 to 8909 nt based on the Sidney81 isolate, GenBank Accession No AF057533) was obtained from both Slovak isolates. Direct sequencing (GenBank Accession Nos. EU723085 and EU723086) revealed that the two isolates have nucleotide and amino acid sequence identities of 98.3 and 100%, respectively. Except for the highly divergent Mexican isolate (Accession No. AF285170), pairwise comparisons of the Slovak isolates with sequences of other WSMV isolates (1) available in GenBank indicated respective nucleotide and amino acid sequence identities ranging from 87.6 to 98.7% and 95.2 to 100%. The Slovak isolates were most closely related to isolates from Czech Republic, Hungary, and Russia (GenBank Accession Nos. AF454454, AF454456, and AF454459). To our knowledge, this is the first report of the natural occurrence of WSMV in Slovakia.

Reference: (1) D. C. Stenger et al. Virology 302:58. 2002.
First Report of Little cherry virus 2 from Sweet Cherry in Poland
Authors: Komorowska B. , Cieślińska M.
Published: August 2008

Little cherry disease (LChD) is a serious viral disease of sweet (Prunus avium) and sour (P. cerasus) cherry trees. Infection of sensitive cultivars results in small, angular, and pointed fruits with reduced sweetness. In late summer, leaves show a characteristic red coloration or bronzing of the surfaces. One Ampelovirus species, Little cherry virus 2 (LChV-2) (2), and one unassigned species in the Closteroviridae, Little cherry virus 1 (LChV-1) (3), have been associated with LChD. Twenty-seven sour and sweet cherry trees of six varieties from orchards located in several regions of Poland were tested for LChV-1 and LChV-2. Leaf samples were taken either from trees showing fruit symptoms or from asymptomatic trees during the summer of the 2006 growing season. RNA was isolated from the leaves with an RNeasy Kit (Qiagen, Hilden, CA), and reverse transcription (RT)-PCR was performed using primer pairs LCV1U/LCV1L and LCV2UP2/LCV2LO2, which are specific for a 419-bp fragment of the LChV-1 3′ nontranslated region and a 438-bp fragment of the LChV-2 methyltransferase gene, respectively (1). The primer pair L2CPF (5′-GTTCGAAAGTGTTTCTTGAT-3′) and L2CPR (5′-GCAACAGAAAAACATATGACTCA-3′) was designed from existing LChV-2 sequences (GenBank Accession Nos. AF416335 and NC_005065) to amplify the entire LChV-2 coat protein (CP) gene (nucleotides 13,007 to 14,134). The amplified cDNA fragments of LChV-2 genome were ligated to the bacterial vector pCR2.1-TOPO (Invitrogen, Carlsbad, CA), which was used to transform Escherichia coli TOP10 competent cells following the manufacturer's protocol. Both strands of three clones for each amplified LChV-2 genome fragment were sequenced with an automated nucleotide sequencer at the Institute of Biochemistry and Biophysics in Warsaw. RT-PCR results showed that 6 of 27 trees were infected, with LChV-1 detected in five sweet cherry trees and LChV-2 singly infecting one sweet cherry tree cv Elton (isolate C4/14). The nucleotide sequence of the 438-bp methyltransferase gene fragment of isolate C4/14 showed 86, 85, and 84% identity to GenBank Accession Nos. AF333237, AF531505, and AJ430056, respectively, all previously reported LChV-2 sequences from cherry trees. Sequence analysis of the 1,088-bp coat protein gene showed 89 to 91% and 92 to 93% nucleotide and amino acid identity, respectively, with the aforementioned three LChV-2 isolates. The tree infected with LChV-2 was indexed by graft transmission to the woody indicator, Prunus avium cv. Canindex, which showed reddening of the leaves characteristic of LChD 3 months after inoculation. Since cherry production in Poland is 230,000 t per year, the disease may have a significant economic impact because the affected fruits are unsuitable either for consumption or sale. To our knowledge, this is the first report of LChV-2 in Poland.

References: (1) M. E. Rott and W. Jelkmann. Phytopathology 91:261, 2001. (2) M. E. Rott and W. Jelkmann. Arch. Virol. 150:107, 2005. (3) M. Vitushkina et al. Eur. J. Plant Pathol. 103:803, 1997.
Occurrence of Hibiscus chlorotic ringspot virus in Hibiscus spp. in New Zealand
Authors: Tang J. , Elliott D. R. , Quinn B. D. , Clover G. R. G. , Alexander B. J. R.
Published: August 2008

Hibiscus spp. are popular ornamental plants in New Zealand. The genus is susceptible to Hibiscus chlorotic ringspot virus (HCRSV), a member of the genus Carmovirus, which has been reported in Australia, El Salvador, Singapore, the South Pacific Islands, Taiwan, Thailand, and the United States (1–4). In May of 2004, chlorotic spotting and ringspots were observed on the leaves of two H. rosa-sinensis plants in a home garden in Auckland, New Zealand. When inoculated with sap from symptomatic leaves, Chenopodium quinoa and C. amaranticolor developed faint chlorotic local lesions 12 to 15 days later. Phaseolus vulgaris exhibited small necrotic local spots 10 days postinoculation. No symptoms were observed on inoculated plants of Cucumis sativus, Gomphrena globosa, Nicotiana Clevelandii, N. tabacum, or N. sylvestris. Plants of H. rosa-sinensis and the three symptomatic indicator species tested positive for HCRSV using polyclonal antiserum (Agdia Inc., Elkhart, IN) in a double antibody sandwich (DAS)-ELISA. Forward (5′-GGAACCCGTCCTGTTACTTC-3′) and reverse (5′-ATCACATCCACATCCCCTTC-3′) primers were designed on the basis of a conserved region in the coat protein gene (nt 2722–3278) of HCRSV isolates in GenBank (Accession Nos. X86448 and DQ392986). A product of the expected size (557 bp) was amplified by reverse transcription (RT)-PCR with total RNA extracted from the four infected species. Comparison of the sequence of the amplicon from H. rosa-sinensis (GenBank Accession No. EU554660) with HCRSV isolates from Singapore and Taiwan (GenBank Accession Nos. X86448 and DQ392986) showed 99 and 94% nucleotide identity, respectively. From 2006 to 2008, samples from a further 25 symptomatic hibiscus plants were collected from different locations in the Auckland region. Nineteen, including plants of H. diversifolius, H. rosa-sinensis, and H. syriacus, tested positive for HCRSV by RT-PCR. To our knowledge, this is the first report of HCRSV in New Zealand and of the virus in H. diversifolius and H. syriacus. HCRSV is considered to be widespread in New Zealand.

References: (1) A. A. Brunt et al. Plant Pathol. 49:798, 2000. (2) S. C. Li et al. Plant Pathol. 51:803, 2002. (3) H. Waterworth. No.227 in: Descriptions of Plant Viruses. CMI/AAB, Surrey, UK, 1980. (4) S. M. Wong et al. Acta Hortic. 432:76, 1996.
First Report of Sclerotinia sclerotiorum on Lantana camara in Italy
Authors: Garibaldi A. , Pensa P. , Minuto A. , Gullino M. L.
Published: August 2008

Lantana camara L. is grown as an ornamental potted plant in Liguria (northern Italy) and is widely used in private and public gardens in central and southern Italy. In some countries, this plant is considered a noxious weed. In the winter of 2007, a sudden wilt was observed on 22-month-old potted plants grown in a commercial greenhouse. Affected plants showed stem necrosis and watery and necrotic leaf tissues. As stem and foliar necrosis progressed, infected plants died. Some plants wilted unilaterally. Infected plants were characterized by the presence of whitish and cottony mycelium. Dark sclerotia were rapidly and abundantly produced on the mycelium. The diseased stem tissue was surface sterilized for 1 min in 1% NaOCl and plated on potato dextrose agar (PDA) amended with 100 mg/l of streptomycin sulfate. Sclerotinia sclerotiorum (Lib.) de Bary (2) was consistently recovered from infected stem pieces. Typical-sized sclerotia were produced on PDA and measured 1.4 to 7.3 × 1.9 to 8.1 (average 3.6 × 4.5) mm. The internal transcribed spacer (ITS) region of rDNA was amplified using the primers ITS4/ITS6 and sequenced. BLAST analysis (1) of the 506-bp segment showed a 100% homology with the sequence of S. sclerotiorum. The nucleotide sequence has been assigned GenBank Accession No. EU 627006. Pathogenicity of two isolates obtained from infected plants was confirmed by inoculating 10 15-month-old plants grown singly in 14-cm-diameter pots. Mycelium plugs, 1 cm2, were excised from a 10-day-old PDA culture of each isolate and were 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 10 and 26°C (average 17°C) and relative humidity >85%. The inoculation trial was carried out twice. All inoculated plants developed leaf yellowing by 10 days after inoculation. White, cottony mycelium and black sclerotia developed on stems and at the base of all inoculated plants. Eventually, the 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 L. camara as a host of S. sclerotiorum in Italy as well as worldwide. The economic importance of this disease is currently limited.

References: (1) S. F. Altschul et al. Nucleic Acids Res. 25:3389, 1997. (2) N. F. Buchwald. Kongl. Veterisk Landb. Aarssk. 75, 1949.
Occurrence of Telia of Phakopsora pachyrhizi on Kudzu in Texas
Authors: Isakeit T. , Jo Y.
Published: August 2008

The first discovery of Asian soybean rust (ASR) caused by Phakopsora pachyrhizi H. Sydow & Sydow in the continental United States was in Louisiana in 2004 (3). In Texas, the uredial stage of this fungus was first found on kudzu (Pueraria lobata) in November 2005 and 3 months later on soybean (Glycine max) (2). The telial stage of P. pachyrhizi was first reported in the continental United States on kudzu in central Florida (1). On January 5, 2008, telia of P. pachyrhizi along with uredia were found on living kudzu leaves at two locations in Polk and Liberty counties of East Texas, where only the uredial stage had been found in September of 2007. The kudzu in both locations had died back more than 99% in January. A single telium or a cluster of telia were found along with uredinia on the abaxial leaf surface. Telia and uredinia (n = 20) were similar in size, 136.3 ± 26.3 and 133.1 ± 16.4 μm in diameter, respectively. Telia were dark brown to black compared with tan colored uredinia. Elongated, oval-shaped teliospores (n = 15) were 18.1 ± 1.7 μm long and 10.6 ± 1.0 μm wide. A reexamination of herbarium specimens from previous ASR collections indicated that telia had been present on kudzu leaves from Liberty County collected in December of 2005 and 2006. In contrast, telia were not found on soybean leaves collected in February of 2006 and 2007 and January of 2008 from Hidalgo County in the Lower Rio Grande Valley (LRGV), an area with a subtropical climate where ASR hosts could survive year round. Kudzu does not occur in the LRGV. Infected kudzu in East Texas can support production of telia over the winter months. However, the hosts that can be infected by basidiospores have not been identified, and so the significance of telia as a source of genetic variation is not known. To our knowledge, this is the first report of the telial stage of P. pachyrhizi in Texas.

References: (1) C. L. Harmon et al. Plant Dis. 90:380, 2006. (2) T. Isakeit et al. Plant Dis. 90:971, 2006. (3) R. W. Schneider et al. Plant Dis. 89:774, 2005.
First Report of Root-Knot Nematode Meloidogyne enterolobii on Tomato and Cucumber in Switzerland
Authors: Kiewnick S. , Karssen G. , Brito J. A. , Oggenfuss M. , Frey J.-E.
Published: August 2008

Severe stunting and extensive root galling were observed on tomato rootstock (Solanum lycopersicum L. cv. Maxifort) resistant to Meloidogyne incognita (Kofoid & White, 1919) Chitwood, 1949, M. javanica (Treub, 1885), and M. arenaria (Neal, 1889) Chitwood, 1949 and cucumber (Cucumis sativus L. cv. Loustik) from two commercial greenhouses in the cantons Aargau and Lucerne in northern Switzerland. Examination of the roots of infected plants revealed the presence of root-knot nematodes in large numbers. Juveniles, males, and females were isolated, and the species was determined on the basis of morphological characteristics, including the female perineal pattern. Identification was confirmed by female esterase (Est) and malate dehydrogenase (MdH) electrophoresis (20 each for Est and MdH). All methods of identification were consistent with M. enterolobii Yang & Eisenback, 1983 (4). For further confirmation, type material of M. enterolobii (from the original host Enterolobium contortisiliquum (Vell.) Morong) from China (4) was used. Furthermore, comparison of the sequence data from 12 individuals of each of the two Swiss populations and the type material of a 310-bp fragment of cytochrome oxidase I (COI), a 723-bp fragment covering the internal transcribed spacer (ITS) region 1, 5.8s, ITS2, and part of the 26s, the mtDNA 63-bp repeat region, and a 780-bp fragment of the intergenic spacer region (1–3) showed 100% homology and confirmed the identification as M. enterolobii. The species M. enterolobii is of great importance because it is able to reproduce on resistant tobacco, pepper, watermelon, and tomato (4). To our knowledge, this is the first report of M. enterolobii in Switzerland.

References: (1) M. A. M. Adam et al. Plant Pathol. 56:190, 2007. (2) V. C. Blok et al. Nematology 4:773, 2002. (3) T. C. Vrain et al. Fundam. Appl. Nematol. 15:565, 1992. (4) B. Yang and J. D. Eisenback. J. Nematol. 15:381, 1983.
A Phytoplasma Closely Related to the Pigeon Pea Witches'-Broom Phytoplasma (16Sr IX) Is Associated with Citrus Huanglongbing Symptoms in the State of São Paulo, Brazil
Authors: Teixeira D. C. , Wulff N. A. , Martins E. C. , Kitajima E. W. , Bassanezi R. , Ayres A. J. , Eveillard S. , Saillard C. , Bové J. M.
Published: August 2008

In February 2007, sweet orange trees with characteristic symptoms of huanglongbing (HLB) were encountered in a region of São Paulo state (SPs) hitherto free of HLB. These trees tested negative for the three liberibacter species associated with HLB. A polymerase chain reaction (PCR) product from symptomatic fruit columella DNA amplifications with universal primers fD1/rP1 was cloned and sequenced. The corresponding agent was found to have highest 16S rDNA sequence identity (99%) with the pigeon pea witches'-broom phytoplasma of group 16Sr IX. Sequences of PCR products obtained with phytoplasma 16S rDNA primer pairs fU5/rU3, fU5/P7 confirm these results. With two primers D7f2/D7r2 designed based on the 16S rDNA sequence of the cloned DNA fragment, positive amplifications were obtained from more than one hundred samples including symptomatic fruits and blotchy mottle leaves. Samples positive for phytoplasmas were negative for liberibacters, except for four samples, which were positive for both the phytoplasma and ‘Candidatus Liberibacter asiaticus’. The phytoplasma was detected by electron microscopy in the sieve tubes of midribs from symptomatic leaves. These results show that a phytoplasma of group IX is associated with citrus HLB symptoms in northern, central, and southern SPs. This phytoplasma has very probably been transmitted to citrus from an external source of inoculum, but the putative insect vector is not yet known.
The Role of Silicon in Preventing Appressorial Penetration by the Rice Blast Fungus
Authors: Hayasaka T. , Fujii H. , Ishiguro K.
Published: August 2008

To test the hypothesis that silicon (Si) confers resistance against appressorial penetration of the rice blast fungus, the proportion of appressorial penetration into the leaf epidermis to total appressoria formed was compared among rice plants amended with various rates of silica gel to those plants nonamended. The amounts of Si in the youngest leaves were consistent with the amounts of silica gel applied to the rice plants. Relative Si levels on the adaxial surface of leaves as detected by energy dispersive X-ray analysis also increased with the amounts of silica gel applied. Based on light microscopic observation of the adaxial surface of rice leaves, the proportion of appressorial penetration was reduced by increasing amounts of silica gel applied and increased with the length of period after spray inoculation. Consequently, these results strongly support the hypothesis and suggest that Si in the leaf epidermis may confer resistance against appressorial penetration. Meanwhile, the number of lesions per leaf also decreased with the amount of Si applied, while only a certain part of penetrated appressoria could become sporulating susceptible lesions. This suggests that Si also confers physiological resistance against blast infection after the penetration.
Detection of Ralstonia solanacearum by Loop-Mediated Isothermal Amplification
Authors: Kubota R. , Vine B. G. , Alvarez A. M. , Jenkins D. M.
Published: August 2008

Ralstonia solanacearum is a pathogenic bacterium that causes wilt in over 200 plant species. Here we report a rapid and sensitive detection of R. solanacearum using an isothermal method for copying DNA known as loop-mediated amplification (LAMP). A set of four primers was designed to replicate the gene coding for the flagellar subunit, fliC, and conditions for detection were optimized to complete in 60 min at 65°C. Magnesium pyrophosphate resulting from the amplification reaction could be detected optically as an increase in the solution turbidity, and the DNA products spread in a reproducible ladder-like banding pattern after electrophoresis in an agarose gel. Replication of the fliC gene was detected only from R. solanacearum. The detection limit of this LAMP assay was between 104 to 106 colony forming units/ml, and the technique may be useful for developing rapid and sensitive detection methods for the R. solanacearum pathogen in soil and water.
Rice ROOT ARCHITECTURE ASSOCIATED1 Binds the Proteasome Subunit RPT4 and Is Degraded in a D-Box and Proteasome-Dependent Manner
Authors: Han Ye , Cao Hong , Jiang Jiafu , Xu Yunyuan , Du Jizhou , Wang Xin , Yuan Ming , Wang Zhiyong , Xu Zhihong , Chong Kang
Published: August 2008

Root growth is mainly determined by cell division and subsequent elongation in the root apical area. Components regulating cell division in root meristematic cells are largely unknown. Previous studies have identified rice (Oryza sativa) ROOT ARCHITECTURE ASSOCIATED1 (OsRAA1) as a regulator in root development. Yet, the function of OsRAA1 at the cellular and molecular levels is unclear. Here, we show that OsRAA1-overexpressed transgenic rice showed reduced primary root growth, increased numbers of cells in metaphase, and reduced numbers of cells in anaphase, which suggests that OsRAA1 is responsible for limiting root growth by inhibiting the onset of anaphase. The expression of OsRAA1 in fission yeast also induced metaphase arrest, which is consistent with the fact that OsRAA1 functions through a conserved mechanism of cell cycle regulation. Moreover, a colocalization assay has shown that OsRAA1 is expressed predominantly at spindles during cell division. Yeast two-hybrid and pull-down assays, as well as a bimolecular fluorescence complementation assay, all have revealed that OsRAA1 interacts with a rice homolog of REGULATORY PARTICLE TRIPLE-A ATPASE4, a component that is involved in the ubiquitin pathway. Treating transgenic rice with specific inhibitors of the 26S proteasome blocked the degradation of OsRAA1 and increased the number of cells in metaphase. Mutation of a putative ubiquitination-targeting D-box (RGSLDLISL) in OsRAA1 interrupted the destruction of OsRAA1 in transgenic yeast. These results suggest that ubiquitination and proteasomic proteolysis are involved in OsRAA1 degradation, which is essential for the onset of anaphase, and that OsRAA1 may modulate root development mediated by the ubiquitin-proteasome pathway as a novel regulatory factor of the cell cycle.
Reg IV is an independent prognostic factor for relapse in patients with clinically localized prostate cancer
Authors: Ohara Shinya , Oue Naohide , Matsubara Akio , Mita Koji , Hasegawa Yasuhisa , Hayashi Tetsutaro , Usui Tsuguru , Amatya Vishwa Jeet , Takeshima Yukio , Kuniyasu Hiroki , Yasui Wataru
Published: August 2008

Regenerating islet‐derived family, member 4 (REG4, which encodes Reg IV) is a candidate marker for cancer and inflammatory bowel disease. We investigated the potential prognostic role of Reg IV immunostaining in clinically localized prostate cancer (PCa) after radical prostatectomy. Immunohistochemical staining of Reg IV was performed in 98 clinically localized PCa tumors obtained during curative radical prostatectomy. Intestinal and neuroendocrine differentiation was investigated by MUC2 and chromogranin A immunostaining, respectively. The prognostic significance of immunohistochemical staining for these factors on prostate‐specific antigen (PSA)‐associated recurrence was assessed by Kaplan–Meier analysis and a Cox regression model. Phosphorylation of the epidermal growth factor receptor (EGFR) by Reg IV was analyzed by Western blot. In total, 14 (14%) of the 98 PCa cases were positive for Reg IV staining. Reg IV positivity was observed frequently in association with MUC2 (P = 0.0182) and chromogranin A positivity (P = 0.0012). Univariate analysis revealed that Reg IV staining (P = 0.0004), chromogranin A staining (P = 0.0494), Gleason score (P < 0.0001) and preoperative PSA concentration (P = 0.0167) were significant prognostic factors for relapse‐free survival. Multivariate analysis indicated that Reg IV staining (P = 0.0312), Gleason score (P = 0.0014) and preoperative PSA concentration (P = 0.0357) were independent predictors of relapse‐free survival. In the LNCaP cell line, EGFR phosphorylation was induced by the addition of Reg IV‐conditioned medium. These results suggest that Reg IV expression is an independent prognostic indicator of relapse after radical prostatectomy. (Cancer Sci 2008; 99: 1570–1577)
N‐Glycan fucosylation of epidermal growth factor receptor modulates receptor activity and sensitivity to epidermal growth factor receptor tyrosine kinase inhibitor
Authors: Matsumoto Kazuko , Yokote Hideyuki , Arao Tokuzo , Maegawa Mari , Tanaka Kaoru , Fujita Yoshihiko , Shimizu Chikako , Hanafusa Toshiaki , Fujiwara Yasuhiro , Nishio Kazuto
Published: August 2008

The glycosylation of cell surface proteins is important for cancer biology processes such as cellular proliferation or metastasis. α1,6‐Fucosyltransferase (FUT8) transfers a fucose residue to n‐linked oligosaccharides on glycoproteins. Herein, we study the effect of fucosylation on epidermal growth factor receptor (EGFR) activity and sensitivity to an EGFR‐specific tyrosine kinase inhibitor (EGFR‐TKI). The increased fucosylation of EGFR significantly promoted EGF‐mediated cellular growth, and the decreased fucosylation by stable FUT8 knockdown weakened the growth response in HEK293 cells. The overexpression of FUT8 cells were more sensitive than the control cells to the EGFR‐TKI gefitinib, and FUT8 knockdown decreased the sensitivity to gefitinib. Finally, to examine the effects in a human cancer cell line, we constructed stable FUT8 knockdown A549 cells, and found that these cells also decreased EGF‐mediated cellular growth and were less sensitive than the control cells to gefitinib. In conclusion, we demonstrated that the modification of EGFR fucosylation affected EGF‐mediated cellular growth and sensitivity to gefitinib. Our results provide a novel insight into how the glycosylation status of a receptor may affect the sensitivity of the cell to molecular target agents. (Cancer Sci 2008; 99: 1611–1617)
Epstein–Barr virus nuclear antigen 1‐specific CD4+ T cells directly kill Epstein–Barr virus‐carrying natural killer and T cells
Authors: Demachi‐Okamura Ayako , Ito Yoshinori , Akatsuka Yoshiki , Tsujimura Kunio , Morishima Yasuo , Takahashi Toshitada , Kuzushima Kiyotaka
Published: August 2008

Epstein–Barr virus (EBV) nuclear antigen (EBNA)1 is expressed in every EBV‐infected cell, regardless of the state of EBV infection. Although EBNA1 is thought to be a promising antigen for immunotherapy of all EBV‐associated malignancies, it is less clear whether EBNA1‐specific CD4+ T cells can act as direct effectors. Herein, we investigated the ability of CD4+ T‐cell clones induced with overlapping peptides covering the C‐terminal region of EBNA1, and identified minimal epitopes and their restricted major histocompatibility complex class II molecules. Of these, a novel epitope, EYHQEGGPD, was found to be presented by DRB1*0401, 0403 and 0406. Five CD4+ T‐cell clones recognized endogenously processed and presented antigens on EBV‐transformed lymphoblastoid cell lines (LCL) and one example proved capable of killing EBV‐carrying natural killer (NK) and T‐cell lines derived from patients with chronic active EBV infection (CAEBV). Identification of minimal epitopes facilitates design of peptide‐based vaccines and our data suggest that EBNA1‐specific CD4+ T cells may play roles as direct effectors for immunotherapy targeting EBV‐carrying NK and T‐cell malignancies. (Cancer Sci 2008; 99: 1633–1642)
Intracellular zinc homeostasis and zinc signaling
Authors: Murakami Masaaki , Hirano Toshio
Published: August 2008

Zinc (Zn) is an essential heavy metal that is incorporated into a number of human Zn metalloproteins. Zn plays important roles in nucleic acid metabolism, cell replication, and tissue repair and growth. Zn deficiency is associated with a range of pathological conditions, including impaired immunity, retarded growth, brain development disorders and delayed wound healing. Moreover, many reports have suggested that Zn is involved in cancer development and levels of Zn in serum and malignant tissues of patients with various types of cancer are abnormal. Zn may directly affect tumor cells by regulating gene expression profiles and/or cell viability, both of which are mediated in part by tumor‐induced changes in Zn transporter expression. On the other hand, Zn may indirectly influence tumor cells by affecting processes within the cancer microenvironment, including immune responses; the functions and/or activity levels of immune cells that attack tumor cells are influenced by the intracellular Zn concentrations within those cells. In both cases, Zn contributes to intracellular metal homeostasis and/or signal transduction in tumor and immune cells. In this review article, we will summarize the current understanding of the roles of Zn homeostasis and signaling primarily in immune cells, with a discussion of the contributions of these processes to oncogenesis. (Cancer Sci 2008; 99: 1515–1522)
Divalent cations modulate the integrin‐mediated malignant phenotype in pancreatic cancer cells
Authors: Grzesiak John J. , Bouvet Michael
Published: August 2008

We have previously demonstrated that pathophysiological shifts in the concentrations of extracellular Mg2+ and Ca2+ activate the α2β1 integrin‐mediated malignant phenotype on type I collagen in pancreatic cancer cells, as evidenced by increased adhesion, migration and proliferation. In the present study, we examined the integrin and divalent cation specificity of pancreatic cancer cell interactions with other physiologically relevant extracellular matrix proteins, including fibronectin, type IV collagen, laminin and vitronectin. Our results indicate that, like α2β1 integrin‐mediated interactions with type I collagen, β1 integrin‐mediated adhesion to fibronectin, type IV collagen and laminin are promoted by Mg2+ but not by Ca2+. On vitronectin, cells attach via αvβ5 and β1 integrins, and in the presence of either divalent cation. We also demonstrate that, like type I collagen, pancreatic cancer cell migration and proliferation on fibronectin, laminin and type IV collagen is maximal when Mg2+ is present at concentrations that promote optimal adhesion and Ca2+ is present at concentrations less than Mg2+. On vitronectin, Panc‐1 cell migration is maximal with decreased Mg2+ and increased Ca2+, but the reverse is true for BxPC‐3 cells. Both cell lines exhibited maximal proliferation with increased Mg2+ and decreased Ca2+, however. Together with evidence indicating that the in vivo local tumor microenvironment contains increased Mg2+ and decreased Ca2+, our studies demonstrate that such divalent cation shifts could activate the integrin‐mediated malignant phenotype in pancreatic cancer. (Cancer Sci 2008; 99: 1553–1563)
Dendritic cells stimulated with cytidine‐phosphate‐guanosine oligodeoxynucleotides and interferon‐α‐expressing tumor cells effectively reduce outgrowth of established tumors in vivo
Authors: Hiraide Ayako , Hiroishi Kazumasa , Eguchi Junichi , Ishii Shigeaki , Doi Hiroyoshi , Imawari Michio
Published: August 2008

Dendritic cells (DC) are potent antigen‐presenting cells that elicit immune responses to foreign antigens. We have previously demonstrated the synergistic effects of cytidine‐phosphate‐guanosine (CpG) oligodeoxynucleotides (ODN) and interferon (IFN)‐α on DC maturation in vitro. In the present study, the antitumor effects of DC preincubated with IFN‐α gene‐overexpressing murine colorectal cancer MC38 cells (MC38‐IFN‐α) and CpG ODN were evaluated in a poorly immunogenic murine cancer system. When we injected DC preincubated with MC38‐IFNα and CpG ODN subcutaneously to mice bearing MC38 wild‐type tumors, the outgrowth of the established parental tumors was suppressed significantly compared with that following administration of DC with MC38‐IFN‐α (P = 0.008). All mice injected with DC preincubated with MC38‐IFN‐α and CpG ODN rejected a subsequent parental tumor challenge. Immunohistochemical and flow cytometric analyses showed that CD4+, CD8+, and NK1.1+ cells markedly infiltrated the established tumors of mice treated with DC preincubated with MC38‐IFN‐α and CpG ODN. From the results in immune cell‐depleted mice, CD4+ and asialo‐GM‐1+ cells seemed to contribute to the antitumor effects induced by the combination DC therapy. Furthermore, non‐specific cytolysis was detected when splenocytes of mice inoculated with DC preincubated with MC38‐IFNα and CpG ODN were used as effector cells. Using an interleukin (IL)‐12‐neutralizing antibody it was suggested that IL‐12 stimulates natural killer cells and contributes in part to the antitumor effects induced by DC incubated with CpG ODN and IFN‐α. As DC‐based immunotherapy with CpG ODN and IFN‐α‐expressing tumor cells induces a potent antitumor immune response, it should be considered for clinical application. (Cancer Sci 2008; 99: 1663–1669)
Cotylenin A, a new differentiation inducer, and rapamycin cooperatively inhibit growth of cancer cells through induction of cyclin G2
Authors: Kasukabe Takashi , Okabe‐Kado Junko , Honma Yoshio
Published: August 2008

Cotylenin A, a plant growth regulator, and rapamycin, an inhibitor of mammalian target of rapamycin (mTOR), are potent inducers of differentiation of myeloid leukemia cells. Recently, we found that cotylenin A and rapamycin effectively inhibited the proliferation of several human breast cancer cell lines including MCF‐7. Herein, we demonstrate that cotylenin A and rapamycin rapidly and markedly induced the cyclin G2 gene expression in several cancer cells including MCF‐7 cells. The growth arrest of the MCF‐7 cells at the G1 phase, induced by the treatment with cotylenin A and rapamycin or the culture in low serum medium, markedly induced the cyclin G2 gene expression. Anticancer drugs including doxorubicin, etoposide and 5‐fluorouracil also induced cyclin G2 expression during induction of growth arrest of the MCF‐7 cell at the G1 phase or G2/M phase. Ectopically inducible cyclin G2 expression potently inhibited the proliferation of MCF‐7 cells. Furthermore, cyclin G2 knockdown induced by cyclin G2 small interfering RNA markedly reduced the potency of cotylenin A plus rapamycin to induce growth inhibition. Taken together, our results suggest that cotylenin A and rapamycin induce inhibition of cancer cell growth through the induction of cyclin G2. (Cancer Sci 2008; 99: 1693–1698)