bluuebunny/crossref_metadata_2025_split huggingface dataset:
Statistical methods to infer cooperative binding among transcription factors inSaccharomyces cerevisiae
Authors: Datta Debayan , Zhao Hongyu 
Published: November 2007

AbstractMotivation: Transcription factors regulate transcription in prokaryotes and eukaryotes by binding to specific DNA sequences in the regulatory regions of the genes. This regulation usually occurs in a coordinated manner involving multiple transcription factors. Genome-wide location data, also called ChIP-chip data, have enabled researchers to infer the binding sites for individual regulatory proteins. However, current methods to infer binding sites, such as simple thresholding based on p-values, are not optimal for a number of study objectives like combinatorial regulation, leading to potential loss of information. Hence, there is a need to develop more efficient statistical methods for analyzing such data.Results: We propose to use log-linear models to study cooperative binding among transcription factors and have developed an Expectation-Maximization algorithm for statistical inferences. Our method is advantageous over simple thresholding methods both based on simulation and real data studies. We apply our method to infer the cooperative network of 204 regulators in Rich Medium and a subset of them in four different environmental conditions. Our results indicate that the cooperative network is condition specific; for a set of regulators, the network structure changes under different environmental conditions.Availability: Our program is available at http://bioinformatics.med.yale.edu/TFcooperativityContact: hongyu.zhao@yale.eduSupplementary information: Supplementary information is available at Bioinformatics online.
Hierarchical tree snipping: clustering guided by prior knowledge
Authors: Dotan-Cohen Dikla , Melkman Avraham A. , Kasif Simon 
Published: November 2007

AbstractMotivation: Hierarchical clustering is widely used to cluster genes into groups based on their expression similarity. This method first constructs a tree. Next this tree is partitioned into subtrees by cutting all edges at some level, thereby inducing a clustering. Unfortunately, the resulting clusters often do not exhibit significant functional coherence.Results: To improve the biological significance of the clustering, we develop a new framework of partitioning by snipping—cutting selected edges at variable levels. The snipped edges are selected to induce clusters that are maximally consistent with partially available background knowledge such as functional classifications. Algorithms for two key applications are presented: functional prediction of genes, and discovery of functionally enriched clusters of co-expressed genes. Simulation results and cross-validation tests indicate that the algorithms perform well even when the actual number of clusters differs considerably from the requested number. Performance is improved compared with a previously proposed algorithm.Availability: A java package is available at http://www.cs.bgu.ac.il/~dotna/ TreeSnippingContact: dotna@cs.bgu.ac.ilSupplementary information: Supplementary data are available at Bioinformatics online.
Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs
Authors: Shamim Mohammad Tabrez Anwar , Anwaruddin Mohammad , Nagarajaram H.A. 
Published: November 2007

AbstractMotivation: Fold recognition is a key step in the protein structure discovery process, especially when traditional sequence comparison methods fail to yield convincing structural homologies. Although many methods have been developed for protein fold recognition, their accuracies remain low. This can be attributed to insufficient exploitation of fold discriminatory features.Results: We have developed a new method for protein fold recognition using structural information of amino acid residues and amino acid residue pairs. Since protein fold recognition can be treated as a protein fold classification problem, we have developed a Support Vector Machine (SVM) based classifier approach that uses secondary structural state and solvent accessibility state frequencies of amino acids and amino acid pairs as feature vectors. Among the individual properties examined secondary structural state frequencies of amino acids gave an overall accuracy of 65.2% for fold discrimination, which is better than the accuracy by any method reported so far in the literature. Combination of secondary structural state frequencies with solvent accessibility state frequencies of amino acids and amino acid pairs further improved the fold discrimination accuracy to more than 70%, which is ∼8% higher than the best available method. In this study we have also tested, for the first time, an all-together multi-class method known as Crammer and Singer method for protein fold classification. Our studies reveal that the three multi-class classification methods, namely one versus all, one versus one and Crammer and Singer method, yield similar predictions.Availability: Dataset and stand-alone program are available upon request.Contact: han@cdfd.org.inSupplementary information: Supplementary data are available at Bioinformatics online.
Unsupervised feature selection under perturbations: meeting the challenges of biological data
Authors: Varshavsky Roy , Gottlieb Assaf , Horn David , Linial Michal 
Published: November 2007

AbstractMotivation: Feature selection methods aim to reduce the complexity of data and to uncover the most relevant biological variables. In reality, information in biological datasets is often incomplete as a result of untrustworthy samples and missing values. The reliability of selection methods may therefore be questioned.Method: Information loss is incorporated into a perturbation scheme, testing which features are stable under it. This method is applied to data analysis by unsupervised feature filtering (UFF). The latter has been shown to be a very successful method in analysis of gene-expression data.Results: We find that the UFF quality degrades smoothly with information loss. It remains successful even under substantial damage. Our method allows for selection of a best imputation method on a dataset treated by UFF. More importantly, scoring features according to their stability under information loss is shown to be correlated with biological importance in cancer studies. This scoring may lead to novel biological insights.Contact: royke@cs.huji.ac.ilSupplementary information and code availability: Supplementary data are available at Bioinformatics online.
Novel cell segmentation and online SVM for cell cycle phase identification in automated microscopy
Authors: Wang Meng , Zhou Xiaobo , Li Fuhai , Huckins Jeremy , King Randall W. , Wong Stephen T.C. 
Published: November 2007

Abstract
Motivation: Automated identification of cell cycle phases captured via fluorescent microscopy is very important for understanding cell cycle and for drug discovery. In this article, we propose a novel cell detection method that utilizes both the intensity and shape information of the cell for better segmentation quality. In contrast to conventional off-line learning algorithms, an Online Support Vector Classifier (OSVC) is thus proposed, which removes support vectors from the old model and assigns new training examples weighted according to their importance to accommodate the ever-changing experimental conditions.
Results: We image three cell lines using fluorescent microscopy under different experiment conditions, including one treated with taxol. Then, we segment and classify the cell types into interphase, prophase, metaphase and anaphase. Experimental results show the effectiveness of the proposed system in image segmentation and cell phase identification.
Availability: The software and test datasets are available from the authors.
Contact: zhou@crystal.harvard.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
First Report of Bois Noir Phytoplasma in Grapevine in Canada
Authors: Rott M. , Johnson R. , Masters C. , Green M. 
Published: November 2007

During the summer and fall of 2006, a survey was done to detect European phytoplasmas of quarantine significance in Canadian vineyards. This survey was developed as one of the 2006 import requirements for grapevine nursery stock from Europe. This addresses the increased concerns regarding inadvertent phytoplasma introductions. Grapevines imported in 2006 and established grapevines were observed for symptoms typical of those associated with diseases caused by phytoplasmas on grapevine. Samples were tested from 155 grapevines. One plant, located in the lower Okanagan Valley, British Columbia, tested positive by a modified real-time PCR assay and TaqMan probe targeting the 16S region of the ribosomal RNA gene (1), which detects a wide variety of known phytoplasmas. The sample was further analyzed and found to be positive by conventional PCR with the phytoplasma-specific primers, P1/P7 (3), and Stolbur specific primers, STOL11f2/r1 (2). Additional PCR tests with primers specific to flavescence doree (FD9f/r) (2) and western X disease (P1/W INT) (3) were negative. These phytoplasmas are also known to infect grapevine. The approximate 1,800-bp fragment obtained with P1/P7 was sequenced (GenBank Accession No. EU086529) and found to have 99.7% nucleotide sequence identity to the Stolbur STOL #11 isolate (GenBank Accession No. AF248959) originally isolated from eastern Europe. This was the highest match to any available phytoplasma sequence obtained and indicates that the phytoplasma in the British Columbian sample is an isolate of bois noir, a pest of quarantine significance to Canada. Additional phylogenetic analysis using CLUSTAL W (Lasergene; DNASTAR, Madison, WI) confirmed this result. The presence and identity of the phytoplasma was confirmed from a second tissue sample that was analyzed by PCR and sequenced using the same test procedures as for the first sample, with identical results. The bois noir phytoplasma belongs to the stolbur group (16SrVII) with the principal vector being a cixiid planthopper. Stolbur phytoplasmas cause diseases in other crops, but bois noir disease is caused by a specific member of that group and is the only stolbur phytoplasma known to infect grapevines in Europe. The infected grapevine was from a lot of 1,965 plants of Grenache clone 70 on rootstock 3309 clone 143 that was imported from Europe in 2006. All plants in this importation have been destroyed. This phytoplasma has not been detected in any other grapevines in Canada. Additional import conditions requiring hot water treatment of European vines have been implemented for 2007. Further survey work for phytoplasma in grapevine will continue. References: (1) N. M. Christensen et al. Mol. Plant-Microbe Interact. 17:1175, 2004. (2) X. D. Daire et al. Eur. J. Plant Pathol. 103:507, 1997. (3) C. D. Smart et al. Appl. Environ. Microbiol. 62:2988, 1996.
Detection of Tomato spotted wilt virus in Tomato in the Baja California Peninsula of Mexico
Authors: Holguín-Peña R. J. , Rueda-Puente E. O. 
Published: November 2007

In 2005, serological screening by ELISA of 24 tomato (Solanum lycopersicon Mill.) plants with virus-like foliar symptoms (locally known as “marchitez manchada” [spotted wilt] disease) was done for a variety of RNA viruses: Tomato spotted wilt virus (TSWV; family Bunyaviridae, genus Tospovirus) was specifically detected. The symptomatic plants testing positive were from the most important tomato areas in San Quintin, in the north of Baja California. Symptoms characteristic of TSWV (4), including chlorosis, malformation of apical leaves, stunting, and ringspot lesions, were observed in this region and throughout the peninsula. In 2006, 42 symptomatic tomato plants from La Paz, in the south of Baja California, were analyzed for TSWV by double-antibody sandwich (DAS)-ELISA with a commercially available kit (TSWV ImmunoStrip Kit; Agdia Inc., Elkhart, IN). Total nucleic acids of the TSWV ELISA-positive samples (16 of 42 = 38%) were extracted and preserved on FTA cards (Whatman, Brentford, U.K.) and processed according to the manufacturer's protocol. The positive TSWV samples were verified by reverse transcription (RT)-PCR with primers specific to the TSWV nucleocapsid protein gene, 5′-ATGTCTAAGGTTAAGCTC-3′ and 5′-TTAAGCAAGTTCTGTGAG-3′ (2). Amplicons of the expected size (approximately 800 bp) were obtained from all 16 positive samples but not in the ELISA-negative samples. The spotted wilt disease was mechanically transmitted to tomato (cv. Rutgers) and Nicotiana glauca seedlings. Symptoms on leaves consisting of chlorotic ring patterns and necrotic lesions were observed in tomato, and slightly concentric chlorotic lesions were observed in N. glauca. All symptomatic plants from San Quintin and La Paz were positive for TSWV in the DAS-ELISA and RT-PCR tests and none were positive for the tobamoviruses, Tomato mosaic virus (ToMV) and Tobacco mosaic virus (TMV). TSWV was not detected in symptomless tomato plants used as negative controls. TSWV was detected in Mexico in tomatillo (Physalis ixocarpa), tobacco (Nicotiana tabacum), jimsonweed (Datura stramonium) (3), and recently, in tomato and pepper in the Central Plateau of Mexico (1). Although spotted wilt disease has been previously observed in San Quintin tomato-producing areas, to our knowledge, this is the first confirmation of TSWV in the Baja Peninsula. The role of weed hosts as a natural reservoir and the role of species of thrips in the epidemiology of the disease are currently unknown, although the incidence of the virus in these regions has risen to destructive levels in tomato. References: (1) R. De La Torre-Almaráz et al. Agrociencia 36:211, 2002. (2). R. K. Jain et al. Plant Dis. 82:900, 1998. (3) M. E. Llamas-Llamas et al. Plant Pathol. 47:341, 1998. (4) G. Marchoux et al. Plant Pathol. 40:347, 1991.
First Report of Apium virus Y in Celery in New Zealand
Authors: Tang J. , Clover G. R. G. , Alexander B. J. R. 
Published: November 2007

Apium virus Y (ApVY) has been detected for the first time in New Zealand. In January 2006, leaf mosaic and vein-banding symptoms were observed on cultivated celery (Apium graveolens cv. Tongo) in Wanganui, New Zealand. Symptoms were widespread and seen in several paddocks. Similar symptoms were also observed in poison hemlock (Conium maculatum), a weed commonly found growing along the edges of the crop. Chenopodium amaranticolor and C. quinoa plants inoculated with leaf sap from a single, symptomatic celery or hemlock plant developed necrotic local spots after 9 and 12 days, respectively. Six Nicotiana spp. did not develop symptoms and were not tested further. Electron microscopy of sap from the celery, hemlock, and C. quinoa plants revealed the presence of elongated flexuous virus particles, 650 to 850 nm long. Symptomatic plants of these three species were tested for ApVY by reverse transcription (RT)-PCR using novel forward (5′-ATGATGCGTGGTTTGAAGG-3′) and reverse (5′-CTTGGTGCGTGAGTTCTTG-3′) primers specific to the coat protein gene (GenBank Accession No. AF203529). Amplicons of the expected size (approximately 425 bp) were obtained from all samples, and an amplicon from celery was sequenced (GenBank Accession No. EU127499). Comparison with ApVY sequences in GenBank confirmed the identity of the product, which had 97 to 99% nucleotide identity with GenBank Accession Nos. AF 203529, AF207594, and AY049716. The effect of ApVY on celery is unknown. ApVY has recently been described and infects three species of Apiaceae in Australia (2). In this study, diseased celery, but not the hemlock plants, were found to be coinfected with Celery mosaic virus (CeMV) by enzyme-linked immunsorbent assays with CeMV-specific antibodies (Loewe Biochemica GmbH, Sauerlach, Germany). Therefore, the symptoms observed in celery may be induced by ApVY or CeMV. CeMV is a serious disease of celery in New Zealand (1) and CeMV symptoms may mask the presence of ApVY. References: (1) P. R. Fry and C. H. Procter. N. Z. Commer. Grower 24:23, 1968. (2) J. Moran et al. Arch. Virol. 147:1855, 2002.
First Report of the Nematode, Tylenchulus palustris, Parasitizing Peach in Virginia
Authors: Eisenback J. D. , Reaver D. , Ashley J. E. 
Published: November 2007

In the fall of 2005 during routine sampling for plant-parasitic nematodes in a nematicide evaluation trial, juveniles of Tylenchulus palustris Inserra, Vovlas, O'Bannon & Esser, 1988 (1) were recovered by semi-automatic elutriation and centrifugation. Mature, sedentary females were hand picked from infected root tissues. The nematodes were parasitizing peach (Prunus persica (L.) Batsch.) at Crown Orchards Purvis Farm (37°51.638′N 78°43.062′W, elevation 230 m.) on U.S. Highway 29S near Faber, VA. Twelve of eighty samples contained the nematode with a density that varied from 10 to 70 nematodes per 500 ml3 of soil. Such low numbers may have been due to the severe state of decline of the 30+-year-old peach orchard; the stunted and nearly dead trees were being removed at the time of sampling. Ironically, this nematode was discovered by the first author more than 20 years ago in this same location before it was described as a new species; however, additional research is necessary to determine the role that this nematode played in the decline of this orchard. Identification was based on morphology of the female including the postvulval body terminus and morphometrics of 15 second-stage juveniles. Voucher specimens were placed in the Virginia Tech Nematode Collection and voucher cultures are maintained in the Virginia Tech Nematode Culture Collection. T. palustris was originally found in Florida parasitizing Carolina ash (Fraxinus caroliniana Mill.) and saltbush (Baccharis halimifolia L.) (1). This nematode has been reported previously on peach in Alabama, Arkansas, and Georgia (2). References: (1) R. N. Inserra et al. J. Nematol. 20:266, 1988. (2) R. N. Inserra et al. J. Nematol. 22:45, 1990.
Identification of New Alternative Weed Hosts for Iris yellow spot virus in the Pacific Northwest
Authors: Sampangi R. K. , Mohan S. K. , Pappu H. R. 
Published: November 2007

Iris yellow spot virus (IYSV; family Bunyaviridae, genus Tospovirus) is an economically important viral pathogen of onion bulb and seed crops in several parts of the United States and the world (1). IYSV is primarily transmitted by onion thrips (Thrips tabaci) and there is no evidence of seed transmission (1). However, susceptible cultivated and weed species could serve as reservoirs of inoculum from which thrips could acquire the virus to introduce and spread it in onion fields. Samples from asymptomatic and symptomatic volunteer onion plants in some of the commonly cultivated crops in the region (corn, wheat, grapes, mint, carrot, alfalfa, and sugar beets) and several common weeds in and around onion bulb and seed fields with a history of IYSV in Idaho and Washington were collected during the months of July, August, September and October of 2006. More than 175 samples from 35 plant species were analyzed for IYSV by a commercially available ELISA kit (Agdia Inc., Elkhart, IN). With the exception of a few volunteer onions, none of the other plant species had any symptoms of virus infection. Symptoms on volunteer onions included characteristic diamond-shaped lesions. To confirm the presence of IYSV in the ELISA-positive samples, total nucleic acids were extracted (2) and used in a reverse transcription (RT)-PCR assay (3). The primer pair consisted of 5′-TAA AAC AAA CAT TCA AAC AA-3′ and 5′-CTC TTA AAC ACA TTT AAC AAG CAC-3′. This primer pair flanks the nucleocapsid (N) gene of IYSV and generates an approximate 1.2-kb amplicon (3) that includes the complete N gene. An amplicon of expected size was obtained from each IYSV-positive sample. The amplicons were cloned and sequenced. There was a 95% sequence identity with known IYSV sequences. While several weed species gave ELISA values that suggested the presence of IYSV, results of RT-PCR assays failed to confirm the presence of the virus. This discrepancy between ELISA and RT-PCR results could be due to nonspecific reaction in ELISA (4) or difficulty associated with obtaining RT-PCR-quality templates for amplification. Only volunteer onions and the following weeds tested positive for IYSV by ELISA and RT-PCR: redroot pigweed (Amaranthus retroflexus), puncturevine (Tribulus terrestris), kochia (Kochia scoparia), prickly lettuce (Lactuca serriola), and common lambsquarters (Chenopodium album). Of these, redroot pigweed was recently reported to be ELISA-positive for IYSV (1). This information on the wider natural host range of IYSV, including potential alternative hosts that could serve as virus reservoirs, is useful for a better understanding of the disease epidemiology and in developing an integrated management strategy for reducing the impact of this disease. References: (1) D. Gent et al. Plant Dis. 90:1468, 2006. (2) H. R. Pappu et al. HortScience 40:697, 2005. (3) H. R. Pappu et al. Arch. Virol. 151:1015, 2006. (4) T. N. Smith et al. Plant Dis. 90:729, 2006.
First Report of Powdery Mildew on Greenhouse Tomatoes Caused by Oidium neolycopersici in Michoacan, Mexico
Authors: Rodríguez-Alvarado G. , García-López J. , Rodríguez-Fernández R. , Fernández-Pavía S. P. , Garay-Serrano E. 
Published: November 2007

During June and July of 2007, powdery mildew-infected tomato (Lycopersicum esculentum Mill. cv. Reserve) plants were observed in a commercial greenhouse with an open hydroponic system in Morelia County. Disease incidence increased from 0.5% to more than 90% in 1 month. Infected plants showed leaves with irregular areas of dense, white mycelium covering most of the upper surface. Microscopic analysis showed hyaline, septate hyphae with lobed appressoria. Conidia were ellipsoid to ovoid and 30 to 45 (38) μm × 15 to 20 (16) μm. Conidiophores were erect, 80 to 120 (103) μm, consisted of a foot cell 42 to 67 (56) μm, and two to three short cells. Conidia were produced singly. On the basis of the observed morphological characteristics, the fungus was identified as Oidium neolycopersici L. Kiss (1). Pathogenicity tests were conducted on fourth true-leaf tomato seedlings cv. Reserve under greenhouse conditions (22 ± 5°C). Inoculation was performed by transferring conidia from infected leaves to the leaves of uninfected tomato seedlings with a single-edged razor blade. Powdery mildew symptoms began to develop 7 days after inoculation. Symptoms and morphological characteristics were similar to those observed in the commercial greenhouse. Noninoculated plants remained healthy throughout the experiments. To our knowledge, this is the first report of O. neolycopersici causing powdery mildew on tomato in Michoacan, Mexico. This disease has been reported from Canada, Europe, Japan, the United States (2), and Venezuela (3) on greenhouse and field tomato crops. The observed high incidence and severe infection indicates that this disease may become an important problem in greenhouse tomatoes in Mexico. References: (1) L. Kiss et al. Mycol. Res. 105:684, 2001. (2) L. Kiss et al. Plant Dis. 89:491, 2005. (3) J. O. Montilla et al. Plant Dis. 91:910, 2007.