Allan A. Sioson
Virginia Tech
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Featured researches published by Allan A. Sioson.
Plant Physiology | 2003
Jonathan I. Watkinson; Allan A. Sioson; Cecilia Vasquez-Robinet; Maulik Shukla; Deept Kumar; Margaret Ellis; Lenwood S. Heath; Naren Ramakrishnan; Boris I. Chevone; Layne T. Watson; Leonel van Zyl; Ulrika Egertsdotter; Ronald R. Sederoff; Ruth Grene
Because the product of a single gene can influence many aspects of plant growth and development, it is necessary to understand how gene products act in concert and upon each other to effect adaptive changes to stressful conditions. We conducted experiments to improve our understanding of the responses of loblolly pine (Pinus taeda) to drought stress. Water was withheld from rooted plantlets of to a measured water potential of -1 MPa for mild stress and -1.5 MPa for severe stress. Net photosynthesis was measured for each level of stress. RNA was isolated from needles and used in hybridizations against a microarray consisting of 2,173 cDNA clones from five pine expressed sequence tag libraries. Gene expression was estimated using a two-stage mixed linear model. Subsequently, data mining via inductive logic programming identified rules (relationships) among gene expression, treatments, and functional categories. Changes in RNA transcript profiles of loblolly pine due to drought stress were correlated with physiological data reflecting photosynthetic acclimation to mild stress or photosynthetic failure during severe stress. Analysis of transcript profiles indicated that there are distinct patterns of expression related to the two levels of stress. Genes encoding heat shock proteins, late embryogenic-abundant proteins, enzymes from the aromatic acid and flavonoid biosynthetic pathways, and from carbon metabolism showed distinctive responses associated with acclimation. Five genes shown to have different transcript levels in response to either mild or severe stress were chosen for further analysis using real-time polymerase chain reaction. The real-time polymerase chain reaction results were in good agreement with those obtained on microarrays.
Plant Physiology and Biochemistry | 2010
Cecilia Vasquez-Robinet; Jonathan I. Watkinson; Allan A. Sioson; Naren Ramakrishnan; Lenwood S. Heath; Ruth Grene
Heat shock proteins (HSPs) are induced not only under heat stress conditions but also under other environmental stresses such as water stress. In plants, HSPs families are larger than those of other eukaryotes. In order to elucidate a possible connection between HSP expression and photosynthetic acclimation or conditioning, we conducted a water stress experiment in loblolly pine (Pinus taeda L.) seedlings involving progressive treatment consisting of one cycle of mild stress (-1 MPa) followed by two cycles of severe stress (-1.7 MPa). Net photosynthesis was measured at each stress level. Photosynthetic acclimation occurred in the progressive treatment after the first cycle, but not in the severe treatment, suggesting that a cycle of mild stress conditioned the trees to adapt to a more severe stress. Real time results indicated specific patterns in needles in the expression of HSP70, HSP90 and sHSP genes for each treatment, both at maximum stress and at recovery. We identified a pine homolog to GRP94 (ER resident HSP90) that was induced after rehydration coincident with acclimation. Further analysis of the promoter region of the pine GRP94 showed putative cis-elements associated with water stress and rehydration, corresponding to the expression pattern observed in our experiment.
IEEE/ACM Transactions on Computational Biology and Bioinformatics | 2009
Lenwood S. Heath; Allan A. Sioson
A multimodal network (MMN) is a novel graph-theoretic formalism designed to capture the structure of biological networks and to represent relationships derived from multiple biological databases. MMNs generalize the standard notions of graphs and hypergraphs, which are the bases of current diagrammatic representations of biological phenomena and incorporate the concept of mode. Each vertex of an MMN is a biological entity, a biot, while each modal hyperedge is a typed relationship, where the type is given by the mode of the hyperedge. The current paper defines MMNs and concentrates on the structural aspects of MMNs. A companion paper develops MMNs as a representation of the semantics of biological networks and discusses applications of the MMNs in managing complex biological data. The MMN model has been implemented in a database system containing multiple kinds of biological networks.
BMC Bioinformatics | 2006
Allan A. Sioson; Shrinivasrao P. Mane; Pinghua Li; Wei Sha; Lenwood S. Heath; Hans J. Bohnert; Ruth Grene
BackgroundAnalysis of DNA microarray data takes as input spot intensity measurements from scanner software and returns differential expression of genes between two conditions, together with a statistical significance assessment. This process typically consists of two steps: data normalization and identification of differentially expressed genes through statistical analysis. The Expresso microarray experiment management system implements these steps with a two-stage, log-linear ANOVA mixed model technique, tailored to individual experimental designs. The complement of tools in TM4, on the other hand, is based on a number of preset design choices that limit its flexibility. In the TM4 microarray analysis suite, normalization, filter, and analysis methods form an analysis pipeline. TM4 computes integrated intensity values (IIV) from the average intensities and spot pixel counts returned by the scanner software as input to its normalization steps. By contrast, Expresso can use either IIV data or median intensity values (MIV). Here, we compare Expresso and TM4 analysis of two experiments and assess the results against qRT-PCR data.ResultsThe Expresso analysis using MIV data consistently identifies more genes as differentially expressed, when compared to Expresso analysis with IIV data. The typical TM4 normalization and filtering pipeline corrects systematic intensity-specific bias on a per microarray basis. Subsequent statistical analysis with Expresso or a TM4 t-test can effectively identify differentially expressed genes. The best agreement with qRT-PCR data is obtained through the use of Expresso analysis and MIV data.ConclusionThe results of this research are of practical value to biologists who analyze microarray data sets. The TM4 normalization and filtering pipeline corrects microarray-specific systematic bias and complements the normalization stage in Expresso analysis. The results of Expresso using MIV data have the best agreement with qRT-PCR results. In one experiment, MIV is a better choice than IIV as input to data normalization and statistical analysis methods, as it yields as greater number of statistically significant differentially expressed genes; TM4 does not support the choice of MIV input data. Overall, the more flexible and extensive statistical models of Expresso achieve more accurate analytical results, when judged by the yardstick of qRT-PCR data, in the context of an experimental design of modest complexity.
IEEE/ACM Transactions on Computational Biology and Bioinformatics | 2009
Lenwood S. Heath; Allan A. Sioson
A multimodal network (MMN) is a novel graph-theoretic formalism designed to capture the structure of biological networks and to represent relationships derived from multiple biological databases. MMNs generalize the standard notions of graphs and hypergraphs, which are the bases of current diagrammatic representations of biological phenomena, and incorporate the concept of mode. Each vertex of an MMN is a biological entity, a biot, while each modal hyperedge is a typed relationship, where the type is given by the mode of the hyperedge. The semantics of each modal hyperedge e is given through denotational semantics, where a valuation function f_{e} defines the relationship among the values of the vertices incident on e. The meaning of an MMN is denoted in terms of the semantics of a hyperedge sequence. A companion paper defines MMNs and concentrates on the structural aspects of MMNs. This paper develops MMN denotational semantics when used as a representation of the semantics of biological networks and discusses applications of MMNs in managing complex biological data.
international conference on information intelligence systems and applications | 2013
Allan A. Sioson
The codeCurator is an automatic C++ solution grader used in teaching programming to first year College students in Ateneo de Naga University. It provides programming exercises and challenge problems based on a prescribed sequence of programming topics. The exercises and challenge problems are designed to help students get a grip on formulation of functions, class methods, complete class implementation, or complete stand-alone programs in C++. Solutions are typically short and are checked using automatic testing techniques similar to online judge of ACM ICPC problems. In this paper, we present an analysis of the frequency of submissions, similarity of submitted solutions, categories of problems, and prospects on how to achieve an effective delivery of instruction.
Plant Cell and Environment | 2006
Pinghua Li; Shrinivasrao P. Mane; Allan A. Sioson; Cecilia Vasquez Robinet; Lenwood S. Heath; Hans J. Bohnert; Ruth Grene
Journal of Experimental Botany | 2007
Shrinivasrao P. Mane; Cecilia Vasquez-Robinet; Allan A. Sioson; Lenwood S. Heath; Ruth Grene
Plant Molecular Biology | 2006
Pinghua Li; Allan A. Sioson; Shrinivasrao P. Mane; Alexander V. Ulanov; Gregory Grothaus; Lenwood S. Heath; T. M. Murali; Hans J. Bohnert; Ruth Grene
Plant Physiology and Biochemistry | 2008
Jonathan I. Watkinson; Lori Hendricks; Allan A. Sioson; Lenwood S. Heath; Hans J. Bohnert; Ruth Grene