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Remote Sensing and GIS for Nonpoint Source Pollution Analysis in the City of Dallas' Western Watersheds
This report describes the findings of a study conducted on the watersheds of "Lake Lewisville, Lake Ray Roberts, Lake Grapevine and the Elm Fork of the Trinity River between Lake Lewisville and Frazier Dam," which are all part of the upper Trinity drainage basin (p. 31). The study examines the potential benefit of "remote sensing and geographic information systems (GIS) for watershed management" in and around Dallas, Texas (p. i). digital.library.unt.edu/ark:/67531/metadc29399/
Remote Sensing and GIS for Nonpoint Source Pollution Analysis in the City of Dallas' Eastern Watersheds
This report describes the findings of a study conducted on the Eastern Watersheds of Lake Lavon, Lake Ray Hubbard, Lake Tawakoni, Lake Palestine and Lake Fork, which are located within the Blackland Prairie, Post Oak Savannah and Pineywoods provinces. These watersheds are among nine that provide drinking water to Dallas, Texas. The study examines the potential benefit of "remote sensing and geographic information systems (GIS) for watershed management" in these five watersheds (p. iii). digital.library.unt.edu/ark:/67531/metadc29400/
Design of highly specific cytotoxins by using trans-splicing ribozymes
This article discusses the design of highly specific cytotoxins by using trans-splicing ribozymes. Abstract: We have designed ribozymes based on a self-splicing group I intron that can trans-splice exon sequences into a chosen RNA target to create a functional chimeric mRNA and provide a highly specific trigger for gene expression. We have targeted ribozymes against the coat protein mRNA of a widespread plant pathogen, cucumber mosaic virus. The ribozymes were designed to trans-splice the coding sequence of the diphtheria toxin A chain in frame with the viral initiation codon of the target sequence. Diphtheria toxin A chain catalyzes the ADP ribosylation of elongation factor 2 and can cause the cessation of protein translation. In a Saccharomyces cerevisiae model system, ribozyme expression was shown to specifically inhibit the growth of cells expressing the virus mRNA. A point mutation at the target splice site alleviated this ribozyme-mediated toxicity. Increasing the extent of base pairing between the ribozyme and target dramatically increased specific expression of the cytotoxin and reduced illegitimate toxicity in vivo. Trans-splicing ribozymes may provide a new class of agents for engineering virus resistance and therapeutic cytotoxins. digital.library.unt.edu/ark:/67531/metadc83320/
Identification of Phloem Involved in Assimilate Loading in Leaves by the Activity of the Galactinol Synthase Promoter
This article discusses identification of phloem. Abstract: The definition of "minor" veins in leaves is arbitrary and of uncertain biological significance. Generally, the term refers to the smallest vein classes in the leaf, believed to function in phloem loading. The authors found that a galactinol synthase promoter, cloned from melon (Cucumis melo), directs expression of the gusA gene to the smallest veins of mature Arabidopsis and cultivated tobacco (Nicotiana tabacum) leaves. This expression pattern is consistent with the role of galactinol synthase in sugar synthesis and phloem loading in cucurbits. The expression pattern in tobacco is especially noteworthy since galactinol is not synthesized in the leaves of this plant. Also, the authors unexpectedly found that expression in tobacco is limited to two of three companion cells in class-V veins, which are the most extensive in the leaf. Thus, the "minor" vein system is defined and regulated at the genetic level, and there is heterogeneity of response to this system by different companion cells of the same vein. digital.library.unt.edu/ark:/67531/metadc81381/
Symplastic Continuity between Companion Cells and the Translocation Stream: Long-Distance Transport Is Controlled by Retention and Retrieval Mechanisms in the Phloem
This article discusses symplastic continuity between companion cells and the translocation stream. Substantial symplastic continuity appears to exist between companion cells (CCs) and sieve elements of the phloem, which suggests that small solutes within the CC are subject to indiscriminate long-distance transport via the translocation stream. To test this hypothesis, the distributions of exotic and endogenous solutes synthesized in the CCs of minor veins were studied. Octopine, a charged molecule derived from arginine and pyruvate, was efficiently transported through the phloem but was also transferred in substantial amounts to the apoplast, and presumably other non-phloem compartments. The disaccharide galactinol also accumulated in non-phloem compartments, but long-distance transport was limited. Conversely, sucrose, raffinose, and especially stachyose demonstrated reduced accumulation and efficient transport out of the leaf. The authors conclude that small metabolites in the cytosol of CCs do enter the translocation stream indiscriminately but are also subject to distributive forces, such as nonselective and carrier-mediated membrane transport and symplastic dispersal, that may effectively clear a compound from the phloem or retain it for long-distance transport. A model is proposed in which the transport or oligosaccharides is an adaptive strategy to improve photoassimilate retention, and consequently translocation efficiency, the phloem. digital.library.unt.edu/ark:/67531/metadc81379/
Functional and Phylogenetic Analyses of a Conserved Regulatory Program in the Phloem of Minor Veins
This article discusses functional and phylogenetic analyses of a conserved regulatory program in the phloem of minor veins. Abstract: The minor-vein phloem of mature leaves is developmentally and physiologically distinct from the phloem in the rest of the vascular system. Phloem loading of transport sugars occurs in the minor veins, and consistent with this, galactinol synthase is expressed in the minor veins of melon (Cucumis melo) as part of the symplastic-loading mechanism that operates in this species. A galactinol synthase promoter from melon drives gene expression in the minor-vein companion cells of both transgenic tobacco (Nicotiana tabacum) and Arabidopsis. Neither of these plants use galactinol in the phloem-loading process, implying that the promoter responds to a minor-vein-specific regulatory cascade that is highly conserved across a broad range of eudicotyledons. Detailed analysis of this promoter by truncation and mutagenesis identified three closely coupled sequences that unambiguously modulate tissue specificity. These sequences cooperate in a combinatorial fashion: two promote expression throughout the vascular system of the plant, whereas the third functions to repress expression in the larger bundles. In a complementary approach, phylogenetic footprinting was used to obtain single-nucleotide resolution of conserved sites in orthologous promoters from diverse members of the Cucurbitaceae. This comparative analysis confirmed the importance of the closely coupled sites but also revealed other highly conserved sequences that may modulate promoter strength or contribute to expression patterns outside of the phloem. The conservation of this regulatory design among species that phloem load by different mechanisms supports a model for organismal development in which tissues and cell types are controlled by relatively ancient and conserved paradigms but expression of genes influencing final form and function are relatively plastic. digital.library.unt.edu/ark:/67531/metadc81378/
Genome-wide mutagenesis of Zea mays L. using RescueMu transposons
This article discusses genome-wide mutagenesis of Zea mays L. using RescueMu transposons. Abstract: Derived from the maize Mu I transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertions and screening of RescueMu plasmid libraries identified plants containing probable germinal insertions. Although frequently recovered parental insertions and insertion hotspots reduce the efficiency of gene discovery per plasmid, RescueMu targets a large variety of genes and produces knockout mutants. digital.library.unt.edu/ark:/67531/metadc77168/
Rapid Analysis of Legume Root Nodule Development Using Confocal Microscopy
This article discusses the rapid analysis of legume root nodule development using confocal microscopy. A rapid method for detailed analysis of nodule formation has been developed. Inoculated root tissues were stained with SYTO 13, a cell-permeant fluorescent nucleic acid-binding dye, and visualized using confocal laser scanning microscopy (CLSM). Structures with high concentrations of DNA and RNA, such as plant cell nuclei and bacteria, labeled strongly. The autofluorescent properties of cell walls made it possible to use CLSM to visualize both plant and rhizobial structures and generate a three-dimensional reconstruction of the root and invading bacteria. This method allowed clear observation of stages and structures important in nodule formation, such as rhizobial attachment to root hairs, hair deformation, infection thread ramification, nodule primordium development and nodule cell invasion. Bacteroid structures were easily were easily assessed without the need for fixation that might alter cellular integrity. Plant nodulation mutants with phenotypic differences in thread growth, cellular invasion and plant defense response were also documented. Multiple samples can be assessed using detailed microscopy without the need for extensive preparative work, labor-intensive analysis, or the generation of genetically modified samples. digital.library.unt.edu/ark:/67531/metadc40415/
Graft Transmission of a Floral Stimulant Derived from CONSTANS
This article discusses graft transmission of a floral stimulant derived from CONSTANS. Abstract: Photoperiod in plants is perceived by leaves and in many species influences the transition to reproductive growth through long-distance signaling. CONSTANS (CO) is implicated as a mediator between photoperiod perception and the transition to flowering in Arabidopsis. To test the role of CO in long-distance signaling, CO was expressed from a promoter specific to the companion cells of the smallest veins of mature leaves. This expression in tissues at the inception of the phloem translocation stream was sufficient to accelerate flowering at the apical meristem under noninductive (short-day) conditions. Grafts that conjoined the vegetative stems of plants with different flower-timing phenotypes demonstrated that minor-vein expression of CO is able to substitute for photoperiod in generating a mobile flowering signal. The authors' results suggest that a CO-derived signal(s), or possibly CO itself, fits the definition of the hypothetical flowering stimulant, florigen. digital.library.unt.edu/ark:/67531/metadc81380/
LIN, a Medicago truncatula Gene Required for Nodule Differentiation and Persistence of Rhizobial Infections
This article discusses LIN, a Medicago truncatula gene. Abstract: Ethyl methanesulfonate mutagenesis of the model legume Medicago truncatula has previously identified several genes required for early steps in nodulation. Here, the authors describe a new mutant that is defective in intermediate steps of nodule differentiation. The lin (lumpy infections) mutant is characterized by a 4-fold reduction in the number of infections, all of which arrest in the root epidermis, and by nodule primordia that initiate normally but fail to mature. Genetic analyses indicate that the symbiotic phenotype is conferred by a single gene that maps to the lower arm of linkage group 1. Transcriptional markers for early Nod factor responses (RIP1 and ENOD40) are induced in lin, as is another early nodulin, ENOD20, a gene expressed during the differentiation of nodule primordia. By contrast, other markers correlated with primordium differentiation (CCS52A), infection progression (MtN6), or nodule morphogenesis (ENOD2 and ENOD8) show reduced or no induction in homozygous lin individuals. Taken together, these results suggest that LIN functions in maintenance of rhizobial infections and differentiation of nodules from nodule primordia. digital.library.unt.edu/ark:/67531/metadc40388/
Comparative Plant Genomics Resources at Plant GDB
This article discusses comparative plant genomics resources at PlantGDB. Abstract: PlantGDB is a database of plant molecular sequences. Expressed sequence tag (EST) sequences are assembled into contigs that represent tentative unique genes. EST contigs are functionally annotated with information derived from known protein sequences that are highly similar to the putative translation products. Tentative Gene Ontology terms are assigned to match those of the similar sequences identified. Genome survey sequences are assembled similarly. The resulting genome survey sequence contigs are matched to ESTs and conserved protein homologs to identify putative full-length open reading frame-containing genes, which are subsequently provisionally classified according to established gene family designations. For Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), the exon-intron boundaries for gene structures are annotated by spliced alignment of ESTs and full-length cDNAs to their respective complete genome sequences. Unique genome browsers have been developed to present all available EST and cDNA evidence for current transcript models. In addition, a number of bioinformatic tools have been integrated at PlantGDB that enable researchers to carry out sequence analyses on-site using both their own data and data residing within the database. digital.library.unt.edu/ark:/67531/metadc78294/
Characterization of sub-nuclear changes in Caenorhabditis elegans embryos exposed to brief, intermediate and long-term anoxia to analyze anoxia-induced cell cycle arrest
This article discusses the characterization of sub-nuclear changes in Caenorhabditis elegans embryos exposed to brief, intermediate and long-term anoxia to analyze anoxia-induced cell cycle arrest. Abstract: Background: The soil nematode C. elegans survives oxygen-deprived conditions (anoxia; <.001 kPa O₂) by entering into a state of suspended animation in which cell cycle progression reversibly arrests. The majority of blastomeres of embryos exposed to anoxia arrest at interphase, prophase and metaphase. The spindle checkpoint proteins SAN-1 and MDF-2 are required for embryos to survive 24 hours of anoxia. To further investigate the mechanism of cell-cycle arrest, the authors examined and compared sub-nuclear changes such as chromatin localization pattern, post-translational modification of histone H3, spindle microtubules, and localization of the spindle checkpoint protein SAN-1 with respect to various anoxia exposure time points. To ensure analysis of embryos exposed to anoxia and not post-anoxic recovery the authors fixed all embryos in an anoxia glove box chamber. Results: Embryos exposed to brief periods to anoxia (30 minutes) contain prophase blastomeres with chromosomes in close proximity to the nuclear membrane, condensation of interphase chromatin and metaphase blastomeres with reduced spindle microtubules density. Embryos exposed to longer periods of anoxia (1-3 days) display several characteristics including interphase chromatin that is further condensed and in close proximity to the nuclear membrane, reduction in spindle structure perimeter and reduced localization of SAN-1 at the kinetochore. Additionally, the authors show that the spindle checkpoint protein SAN-1 is required for brief periods of anoxia-induced cell cycle arrest, thus demonstrating that this gene product is vital for early anoxia responses. In this report the authors suggest that the events that occur as an immediate response to brief periods of anoxia directs cell cycle arrest. Conclusion: From their results the authors conclude that the sub-nuclear characteristics of embryos exposed to anoxia depends upon exposure time as assayed using brief (30 minutes), intermediate (6 or 12 hours) or long-term (24 or 72 hours) exposures. Analyzing these changes will lead to an understanding of the mechanisms required for initiation for maintenance of cell cycle arrest in respect to anoxia exposure time as well as order the events that occur to bring about anoxia-induced cell cycle arrest. digital.library.unt.edu/ark:/67531/metadc122142/
xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features
This article discusses xGDB. The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, but the software supports inclusion of any property that can be associated with a genomic location. The xGDB distribution and user support utilities are available online at the xGDB project website, http://xgdb.sourceforge.net/. digital.library.unt.edu/ark:/67531/metadc77169/
The AGC Kinase MtIRE: A Link to Phospholipid Signaling During Nodulation?
This article discusses the AGC Kinase gene MtIRE. Abstract: The development of nitrogen fixing root nodules is complex and involves an interplay of signaling processes. During maturation of plant host cells and their endocytosed rhizobia in symbiosomes, host cells and symbiosomes expand. This expansion is accompanied by a large quantity of membrane biogenesis. The authors recently characterized an AGC kinase gene, MtIRE, that could play a role in this expansion. MtIRE's expression coincides with host cell and symbiosome expansion in the proximal side of the invasion zone in developing Medicago truncatula nodules. MtIRE's closest homolog is the Arabidopsis AGC kinase family IRE gene, which regulates root hair elongation. AGC kinases are regulated by phospholipid signaling in animals and fungi as well as in the several instances where they have been studied in plants. Here we suggest that a phospholipid signaling pathway may also activate MtIRE activity and propose possible upstream activators of MtIRE protein's presumed AGC kinase activity. digital.library.unt.edu/ark:/67531/metadc40414/
Role of Hypoxia in the Evolution and Development of the Cardiovascular System
This article discusses the role of hypoxia in the evolution and development of the cardiovascular system. How multicellular organisms obtain and use oxygen and other substrates has evolved over hundreds of millions of years in parallel with the evolution of oxygen-delivery systems. A steady supply of oxygen is critical to the existence of organisms that depend on oxygen as a primary source of fuel (i.e., those that live by aerobic metabolism). Not surprisingly, a number of mechanisms have evolved to defend against oxygen deprivation. This review highlights evolutionary and developmental aspects of O(2) delivery to allow understanding of adaptive responses to O(2) deprivation (hypoxia). First, the authors consider how the drive for more efficient oxygen delivery from the heart to the periphery may have shaped the evolution of the cardiovascular system, with particular attention to the routing of oxygenated and deoxygenated blood in the cardiac outlet. Then the authors consider the role of O(2) in the morphogenesis and the cardiovascular system of animals of increasing size and complexity. The authors conclude by suggesting areas for future research regarding the role of oxygen deprivation and oxidative stress in the normal development of the heart and vascular or in the pathogenesis of congenital heart defects. digital.library.unt.edu/ark:/67531/metadc115191/
Tracembler - software for in-silico chromosome walking in unassembled genomes
This article discusses Tracembler. Background: Whole genome shotgun produces increasingly higher coverage of a genome with random sequence reads. Progressive whole genome assembly and eventual finishing sequencing is a process that typically takes several years for large eukaryotic genomes. In the interim, all sequence reads of public sequencing projects are made available in repositories such as the NCBI Trace Archive. For a particular locus, sequencing coverage may be high enough early on to produce a reliable local genome assembly. The authors have developed software, Tracembler, that facilitates in silico chromosome walking by recursively assembling reads of a selected species from the NCBI Trace Archive starting with reads that significantly match sequence seeds supplied by the user. Results: Tracembler takes one or multiple DNA or protein sequence(s) as input to the NCBI Trace Archive BLAST engine to identify matching sequence reads from a species of interest. The BLAST searches are carried out recursively such that BLAST matching sequences identified in previous rounds of searches are used as new queries in subsequent rounds of BLAST searches. The recursive BLAST search stops when either no more new matching sequences are found, a given maximal number of queries is exhausted, or a specified maximum number of rounds of recursion is reached. All the BLAST matching sequences are then assembled into contigs based on significant sequence overlaps using the CAP3 program. The authors demonstrate the validity of the concept and software implementation with an example of successfully recovering a full-length Chrm2 gene as well as its upstream and downstream genomic regions from Rattus norvegicus reads. In a second example, a query with two adjacent Medicago truncatula genes as seeds resulted in a contig that likely identifies the microsyntenic homologous soybean locus. Conclusion: Tracembler streamlines the process of recursive database searches, sequence assembly, and gene identification in resulting contigs in attempts to identify homologous loci of genes of interest in species with emerging whole genome shotgun reads. A web server hosting Tracembler is provided at http://www.plantgdb.org/tool/tracembler/, and the software is also freely available from the authors for local installations. digital.library.unt.edu/ark:/67531/metadc77112/
An IRE-Like AGC Kinase Gene, MtIRE, Has Unique Expression in the Invasion Zone of Developing Root Nodules in Medicago truncatula
This article discusses AGC kinase genes. Abstract: The AGC protein kinase family (cAMP-dependent protein kinases A, cGMP-dependent protein kinases G, and phospholipid-dependent protein kinases C) have important roles regulating growth and development in animals and fungi. They are activated via lipid second messengers by 3-phosphoinositide-dependent protein kinase coupling lipid signals to phosphorylation of the AGC kinases. These phosphorylate downstream signal transduction protein targets. AGC kiinases are becoming better studied in plants, especially in Arabidopsis (Arabidopsis thaliana), where specific AGC kinases have been shown to have key roles in regulating growth signal pathways. The authors report here the isolation and characterization of the first AGC kinase gene identified in Medicago truncatula, MtIRE. It was cloned by homology with the Arabidopsis INCOMPLETE ROOT HAIR ELONGATION (IRE) gene. Semiquantitative reverse transcription-polymerase chain reaction analysis shows that, unlike its Arabidopsis counterpart, MtIRE is not expressed in uninoculated roots, but is expressed in root systems that have been inoculated with Sinorhizobium meliloti and are developing root nodules. MtIRE expression is also found in flowers. Expression analysis of a time course of nodule development and of nodulating root systems of many Medicago nodulation mutants shows MtIRE expression correlates with infected cell maturation during nodule development. During the course of these experiments, nine Medicago nodulation mutants, including sli and dnf1 to 7 mutants, were evaluated for the first time for their microscopic nodule phenotype using S. meliloti constitutively expressing lacZ. Spatial localization of a pMtIRE-gusA transgene in transformed roots of composite plants showed that MtIRE expression is confined to the proximal part of the invasion zone, zone II, found in indeterminate nodules. This suggests MtIRE is useful as an expression marker for this region of the invasion zone. digital.library.unt.edu/ark:/67531/metadc40389/
A self-adaptive burst-detection algorithm
This article accompanies a poster presentation on a self-adaptive burst-detection algorithm. A self-adaptive, time-scale invariant single-unit spike train analysis technique is introduced to detect burst firings in neurons. This burst-detection method is an adaptive algorithm that uses the characteristic firing patterns statistics within and between bursts to identify the inter-burst period, intra-burst period and burst duration. digital.library.unt.edu/ark:/67531/metadc122157/
Genetic analysis of the spindle checkpoint genes san-I, mdf-2, bub-3 and the CENP-F homologues hcp-1 and hcp-2 in Caenorhabditis elegans
This article discusses genetic analysis of the spindle checkpoint genes san-1, mdf-2, bub-3 and the CENP-F homologues hcp-1 and hcp-2 in Caenorhabditis elegans. Abstract: Background: The spindle checkpoint delays the onset of anaphase until all sister chromatids are aligned properly at the metaphase plate. To investigate the role san-1, the MAD3 homologue, has in Caenorhabditis elegans embryos, the authors used RNA interference (RNAi) to identify genes synthetic lethal with the viable san-1 (ok1580) deletion mutant. Results: The san-1 (ok1580) animal has low penetrating phenotypes including an increased incidence of males, larvae arrest, slow growth, protruding vulva, and defects in vulva morphogenesis. The authors found that the viability of san-1 (ok1580) embryos is significantly reduced when HCP-1 (CENP-F homologue) are reduced by RNAi. Interestingly, the viability of san-1 (ok1580) embryos is not significantly reduced when the paralog of HCP-1, HCP-2, is reduced. The phenotype of san-1 (ok1580); hcp-1 (RNAi) embryos includes embryonic and larval lethality, abnormal organ development, and an increase in abnormal chromosome segregation (abberrant mitotic nuclei, anaphase bridging). Several of the san-1 (ok1580); hcp-1(RNAi) animals displayed abnormal kinetochore (detected by MPM-2) and microtubule structure. The survival of mdf-2 (RNAi); hcp-1 (RNAi) embryos but not bub-3 (RNAi); hcp-1 (RNAi) embryos was also compromised. Finally, the authors found that san-1 (ok1580) and bub-3 (RNAi), but not hcp-1 (RNAi) embryos, were sensitive to anoxia, suggesting that like SAN-1, BUB-3 has a functional role as a spindle checkpoint protein. Conclusion: Together, these data suggest that in the C. elegans embryo, HCP-1 interacts with a subset of the spindle checkpoint pathway. Furthermore, the fact that san-1 (ok1580); hcp-1 (RNAi) animals had a severe viability defect whereas in the san-1 (ok1580); hcp-2 (RNAi) and san-1 (ok1580); hcp-2 (ok1757) animals the viability defect was not as severe suggesting that hcp-1 and hcp-2 are not completely redundant. digital.library.unt.edu/ark:/67531/metadc122165/
TableMaker: An ad hoc Query Tool for Relational Databases
This paper discusses an ad hoc query tool for relational databases. Most Web servers hosting biological data limit users to a defined set of search options and output formats that are short of the whole range of options available to users with direct database access. However, to make full use of the wealth of data in the database resource, it is desirable to have an intermediate solution that provides a broad range of flexible query and output options through a Web portal. digital.library.unt.edu/ark:/67531/metadc78297/
Theoretical derivation of EMOTION-I model for emotional feel of sensation
This article accompanies a poster presentation on the theoretical derivation of EMOTION-I model for emotional feel of sensation. The first of a series of emotional models called "Emotional Model of The Theoretical Interpretation Of Neuro-processing" (EMOTION-I) is derived theoretically to address the origin of emotions in evolutionary process. It is based on first principles without any 'a priori' assumptions about what emotions are and what they are used for. The model is derived based on the necessary principles essential for the survival of an autonomous system (either an organism or an autonomous robot) when interacting with the real-world environment. digital.library.unt.edu/ark:/67531/metadc122158/
Theoretical derivation of EMOTION-II model for happy and unhappy emotions
This article accompanies a poster presentation on theoretical derivation of EMOTION-II model for happy and unhappy emotions. The second of a series of emotional models called "Emotional Model of Theoretical Interpretation Of Neuroprocessing" (EMOTION-II) is derived theoretically to address the emergency of happy and unhappy emotions based on the first principles without any 'a priori' assumptions about what these emotions are and what they are used for. digital.library.unt.edu/ark:/67531/metadc122159/
Functional Characterization of the Arabidopsis AtSUC2 Sucrose/H+ Symporter by Tissue-Specific Complementation Reveals an Essential Role in Phloem Loading But Not in Long-Distance Transport
This article discusses functional characterization of the Arabidopsis AtSUC2 Sucrose/H+ Symporter. Abstract: AtSUC2 (At1g22710) encodes a phloem-localized sucrose (Suc)/H+ symporter necessary for efficient Suc transport from source tissues to sink tissues in Arabidopsis (Arabidopsis thaliana). AtSUC2, however, is also expressed strongly in the transport phloem, where its role is more ambiguous, and it has been implicated in mediating both efflux and retrieval to and from flanking tissues via the apoplast. To characterize the role of AtSUC2 in controlling carbon partitioning along the phloem path, AtSUC2 cDNA was expressed from tissue-specific promoters in an Atsuc2 mutant background. Suc transport in this mutant is highly compromised, as indicated by stunted growth and the accumulation of large quantities of sugar and starch in vegetative tissues. Expression of AtSUC2 cDNA from the 2-kb AtSUC2 promoter was sufficient to restore growth and carbon partitioning to nearly wild-type levels. The GALACTINOL SYNTHASE promoter of Cucumis melo (CmGAS1p) confers expression only in the minor veins of mature leaves, not in the transport phloem of larger leaf veins and stems. Mutant plants expressing AtSUC2 cDNA from CmGAS1p had intermediate growth and accumulated sugar and starch, but otherwise they had normal morphology. These characteristics support a role for AtSUC2 in retrieval but not efflux along the transport phloem and show that the only vital function of AtSUC2 in photoassimilate distribution is phloem loading. In addition, AtSUC2 mutant plants, although debilitated, do grow, and AtSUC2-independent modes of phloem transport are discussed, including an entirely symplastic pathway from mesophyll cells to sink tissues. digital.library.unt.edu/ark:/67531/metadc78290/
BOV - a web-based BLAST output visualization tool
This article discusses BOV, a web-based BLAST output visualization tool. Abstract: Background: The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. The authors have developed a web-based program, BLAST Output Visualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns. Results: Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV. Conclusion: BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations. digital.library.unt.edu/ark:/67531/metadc77114/
Effective carbon partitioning driven by exotic phloem-specific regulatory elements fused to the Arabidopsis thaliana AtSUC2 sucrose-proton symporter gene
This article discusses effective carbon partitioning. Abstract: Background: AtSUC2 (At1g22710) from Arabidopsis thaliana encodes a phloem-localized sucrose/proton symporter required for efficient photoassimilate transport from source tissues to sink tissues. AtSUC2 plays a key role in coordinating the demands of sink tissues with the output capacity of source leaves, and in maintaining phloem hydrostatic pressure during changes in plant-water balance. Expression and activity are regulated, both positively and negatively, by developmental (sink or source transition) and environmental cues, including light, diurnal changes, photoassimilate levels, turgor pressure, drought and osmotic stress, and hormones. Results: To assess the importance of this regulation to whole-plant growth and carbon partitioning, AtSUC2 cDNA was expressed from two exotic, phloem-specific promoters in a mutant background debilitated for AtSUC2 function. The first was a promoter element from Commelina Yellow Mottle Virus (CoYMV), and the second was the rolc promoter from Agrobacterium rhizogenes. CoYMVp::AtSUC2 cDNA restored growth and carbon partitioning to near wild-type levels, whereas plants harboring rolCp::AtSUC2 cDNA showed only partial complementation. Conclusion: Expressing AtSUC2 cDNA from exotic, phloem-specific promoters argues that strong, phloem-localized expression is sufficient for efficient transport. Expressing AtSUC2 from promoters that foster efficient phloem transport but are subject to regulatory cascades different from the endogenous sucrose/proton symporter genes has implications for biotechnology. digital.library.unt.edu/ark:/67531/metadc78288/
Expression of genes associated with carbohydrate metabolism in cotton stems and roots
This article discusses the expression of genes associated with carbohydrate metabolism in cotton stems and roots. Abstract: Background: Cotton (Gossypium hirsutum L) is an important crop worldwide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. Domesticated cotton makes these reserves available to developing seeds which impacts seed yield. The goals of these analyses were to identify genes and physiology pathways that establish cotton stems and roots as physiological sinks and investigate the role these pathways play in cotton development during seed set. Results: Analysis of field-grown cotton plants indicated that starch levels peaked about the time of first anthesis and then declined similar to reports in greenhouse-grown cotton plants. Starch accumulated along the length of the stem and the shape and size of the starch grains from stems were easily distinguished from transient starch. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with starch synthesis, starch degradation, hexose metabolism, raffinose synthesis and trehalose synthesis. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in selected tissues. Conclusion: In domesticated cotton starch stored prior to flowering was available to support seed production. Starch accumulation observed in young field-grown plants was not observed in greenhouse grown plants. A suite of genes associated with starch biosynthesis was identified. The pathway for starch utilization after flowering was associated with an increase in expression of a glucan water dikinase gene as has been implicated in utilization of transient starch. Changes in raffinose levels and levels of expression of genes controlling trehalose and raffinose biosynthesis were also observed in vegetative cotton tissues as plants age. digital.library.unt.edu/ark:/67531/metadc78286/
RICHEST - a web server for richness estimation in biological data
This article discusses RICHEST, a web server for richness estimation in biological data. Richness is defined as the number of distinct species or classes in a sample or population. Although richness estimation is an important practice, it requires mathematical and computational methods that are challenging to understand and implement. The authors have developed a web server, RICHness ESTimator (RICHEST), which implements three non-parametric statistical methods for richness estimation. Its user-friendly web interface allows users to analyze and compare their data conveniently over the web. digital.library.unt.edu/ark:/67531/metadc77159/
ESTPiper - a web-based analysis pipeline for expressed sequence tags
This article discusses ESTPiper, a web-based analysis pipeline for expressed sequence tags. Abstract: Background: EST sequencing projects are increasing in scale and scope as the genome sequencing technologies migrate from core sequencing centers to individual research laboratories. Effectively, generating EST data is no longer a bottleneck for investigators. However, processing large amounts of EST data remains a non-trivial challenge for many. Web-based EST analysis tools are proving to be the most convenient option for biologists when performing their analysis, so these tools must continuously improve on their utility to keep in step with the growing needs of research communities. The authors have developed a web-based EST analysis pipeline called ESTPiper, which streamlines typical large-scale EST analysis components. Results: The intuitive web interface guides users through each step of base calling, data cleaning, assembly, genome alignment, annotation, analysis of gene ontology (GO), and microarray oligonucleotide probe design. Each step is modularized. Therefore, a user can execute them separately or together in batch mode. In addition, the user has control over the parameters used by the underlying programs. Extensive documentation of ESTPiper's functionality is embedded throughout the web site to facilitate understanding of the required input and interpretation of the computational results. The user can also download intermediate results and port files to separate programs for further analysis. In addition, the authors' server provides a time-stamped description of the run history for reproducability. The pipeline can also be installed locally, allowing researchers to modify ESTPiper to suit their own needs. Conclusion: ESTPiper streamlines the typical process of EST analysis. The pipeline was initially designed in part to support the Daphnia pulex cDNA sequencing project. A web server hosting ESTPiper is provided at http://estpiper.cgb.indiana.edu/ to now support projects of all size. The software is also freely available from the authors for local institutions. digital.library.unt.edu/ark:/67531/metadc77113/
A theoretical analysis of an alternative CUSUM statistic called CUSUM-slope for detecting signals from background noise in a low signal-to-noise environment
This article accompanies a poster presentation on a theoretical analysis of an alternative CUSUM statistic called CUSUM-slope for detecting signals from background noise in a low signal-to-noise environment. Signal detection in a low signal-to-noise environment, such as signals recorded from fMRI or EEG, is often a daunting task. In this paper, the authors limit the definition of noise to events that are generated from a random process whereas signal is defined as events that are generated from a non-random process. This paper introduces an alternate method, called CUSUM-slope, in which the "slope" of the CUSUM-curve is used as an approximation of the discrete-time-derivative of the CUSUM curve to provide time-independence and origin-independence of the analysis. digital.library.unt.edu/ark:/67531/metadc122148/
A theoretical model of emotion processing for optimizing the cost function of discrepancy errors between wants and gets
This article accompanies a poster presentation on a theoretical model of emotion processing for optimizing the cost function of discrepancy errors between wants and gets. A number of theoretical model of emotional processing were derived previously called EMOTION-I and EMOTION-II from the basic evolutionary principles of survival function in a real-world model of the interaction between an autonomous agent (organism or autonomous robot) and its environment. An associative reinforcement learning model was used to establish the innate and acquired behaviors for evaluating the survivability of the agent with respect to the environment. digital.library.unt.edu/ark:/67531/metadc122147/
Enabling Large Scale Scientific Computations for Expressed Sequence Tag Sequencing over Grid and Cloud Computing Clusters
This paper discusses expressed sequence tag sequencing over grid and cloud computing clusters. Abstract: Computer-intensive biological applications are heavily reliant on the availability of computing resources. Grid based HPC clusters and emerging Cloud computing clusters provide a large scale computing environment for scientific users. However, large scale biological application often involves various types of computational tasks which can benefit from different types of computing clusters. Therefore, a high level job scheduling environment which integrates the Grid style HPC clusters and the Cloud computing clusters and manages jobs accordingly based on the characteristics of the jobs is required. In this paper, the authors propose a Web service framework for high-level job scheduling - Swarm. Swarm is developed for scientific applications that must submit massive number of high-throughput jobs or workflows to highly distributed computing clusters. Swarm allows the users to submit jobs to both Grid HPC and Cloud computing clusters. The Swarm service itself is designed to be extensible, lightweight, and easily installable on a desktop or a small server. As a Web service, derivative services based on Swarm can be straightforwardly integrated with Web portals and science gateways. This paper provides the motivation for this research, the architecture of the Swarm framework, and a performance evaluation of the system prototype. digital.library.unt.edu/ark:/67531/metadc78330/
The neuroprotective properties of palmitoylethanolamine against oxidative stress in a neuronal cell line
This article discusses the neuroprotective properties of palmitoylethanolamine against oxidative stress in a neuronal cell line. Background: N-acylethanolamines (NAEs) are lipids upregulated in response to cell and tissue injury and are involved in cytoprotection. Arachidonylethanolamide (AEA) is a well characterized NAE that is an endogenous ligand at cannabinoid and vanilloid receptors, but it exists in small quantities relative to other NAE types. The abundance of other NAE species, such as palmitoylethanolamine (PEA), together with their largely unknown function and receptors, has prompted us to examine the neuroprotective properties and mechanism of action of PEA. The authors hypothesized that PEA protects HT22 cells from oxidative stress and activates neuroprotective kinase signaling pathways. Results: Indeed PEA protected HT22 cells from oxidative stress in part by mediating an increase in phosphorylated Akt (pAkt) and ERK 1/2 immunoreactivity as well as pAkt nuclear translocation. These changes take place within a time frame consistent with neuroprotection. Furthermore, the authors determined that changes in pAkt immunoreactivity elicited by PEA were not mediated by activation of cannabinoid receptor type 2 (CB2), thus indicating a novel mechanism of action. These results establish a role for PEA as a neuroprotectant against oxidative stress, which occurs in a variety of neurodegenerative diseases. Conclusions: The results from this study reveal that PEA protects HT22 cells from oxidative stress and alters the localization and expression levels of kinases known to be involved in neuroprotection by a novel mechanism. Overall, these results identify PEA as a neuroprotectant with potential as a possible therapeutic agent in neurodegenerative diseases involving oxidative stress. digital.library.unt.edu/ark:/67531/metadc122166/
A Putative Transporter is Essential for Integrating Nutrient and Hormone Signaling with Lateral Root Growth and Nodule Development in Medicago truncatula
This article discusses a putative transporter for integrating nutrient and hormone signaling with lateral root growth and nodule development in Medicago truncatula. Legume root architecture involves not only elaboration of the root system by the formation of lateral roots but also the formation of symbiotic root nodules in association with nitrogen-fixing soil rhizobia. The Medicago truncatula LATD/NIP gene plays an essential role in the development of both primary and lateral roots as well as nodule development. We have cloned the LATD/NIP gene and show that it encodes a member of the NRT1(PTR) transporter family. LATD/NIP is expressed throughout the plant. pLATD/NIP-GFP promoter-reporter fusions in transgenic roots establish the spatial expression of LATD/NIP in primary root, lateral root and nodule meristems and the surrounding cells. Expression of LATD/NIP is regulated by hormones, in particular by abscisic acid which has been previously shown to rescue the primary and lateral root meristem arrest of latd mutants. latd mutants respond normally to ammonium but have defects in responses of the root architecture to nitrate. Taken together, these results suggest that LATD/NIP may encode a nitrate transporter or transporter of another compound. digital.library.unt.edu/ark:/67531/metadc40412/
Using WebGBrowse to Visualize Genome Annotation on GBrowse
This article discusses using WebGBrowse to visualize genome annotation on GBrowse. Although GBrowse is popular for visualizing genomic features along a reference sequence, its installation and configuration are difficult for many biologists. WebGBrowse is a web server that takes a user-supplied annotation file, guides users to configure the display of each genomic feature, and allows users to visualize the genome annotation with integrated GBrowse software. This protocol guides the user through each step of using WebGBrowse. digital.library.unt.edu/ark:/67531/metadc78332/
Temporal associative memory (TAM) by spike-timing dependent plasticity
This article accompanies a poster presentation on temporal associative memory (TAM). Spike-timing synaptic plasticity (STDP) describes the increase and decrease in synaptic strength depending on the relative arrival time of the pre- and post-synaptic spikes. The relative timing that determines whether the synapse is strengthened by long-term potentiation (LTP), or weakened by long-term depression (LTD) was first reported experimentally and computationally. Because of the asymmetry in timing, it is also called "temporally asymmetric Hebbian plasticity" theoretically. Numerous studies on STDP had explored the biological mechanisms for induction of LTP and LTD. This paper will focus on the computational function of STDP in the formation of temporal associative memory (TAM). digital.library.unt.edu/ark:/67531/metadc122149/
Variables governing emotion and decision-making: human objectivity underlying its subjective perception
This article accompanies a poster presentation on the variables governing emotion and decision-making. Although decision-making is a logical reasoning process, it is often influenced by the underlying emotions at the moment of decision. The ability to recognize one's emotion and assess one's judgement in order to make a prudent decision is called "emotional intelligence." Yet, the definition and role of emotion played in these cognitive processes are often controversial in the psychological field. The authors have derived an objective model of emotion based on biological evolutionary principles and engineering principles that uses a computational approach to address the role of emotions played in animals. digital.library.unt.edu/ark:/67531/metadc122151/
Computational criteria for establishing reflex from plasticity to hardwiring
This article accompanies a poster presentation on computational criteria for establishing reflex from plasticity to hardwiring. The role of synaptic plasticity in associative learning has been explored extensively computationally. Yet, the computational mechanism for hardwiring of the neural circuit has only been addressed recently using a systems approach of whole-animal behavior based on an evolutionary process for survival. In this paper, the authors will explore the computational criteria needed to establish the hardwiring of reflex. digital.library.unt.edu/ark:/67531/metadc122150/
Characteristic Male Urine Microbiomes Associate with Asymptomatic Sexually Transmitted Infection
This article discusses characteristic male urine microbiomes. Abstract: Background: The microbiome of the male urogenital tract is poorly described but it has been suggested that bacterial colonization of the male urethra might impact risk of sexually transmitted infection (STI). Previous cultivation-dependent studies showed that a variety of non-pathogenic bacteria colonize the urethra but did not thoroughly characterize these microbiomes or establish links between the compositions of urethral microbiomes and STI. Methodology/Findings: Here, the authors used 165 rRNA PCR and sequencing to identify bacteria in urine specimens collected from men who lacked symptoms of urethral inflammation but who differed in status for STI. All of the urine samples contained multiple bacteria genera and many contained taxa that colonize the human vagina. Uncultivated bacteria associated with female genital tract pathology were abundant in specimens from men who had STI. Conclusions: Urine microbiomes from men with STI were dominated by fastidious, anaerobic and uncultivated bacteria. The same taxa were rare in STI negative individuals. The authors' findings suggest that the composition of male urine microbiomes is related to STI. digital.library.unt.edu/ark:/67531/metadc78333/
Control of Root Architecture and Nodulation by the LATD/NIP Transporter
This article discusses root architecture and nodulation. Abstract: The Medicago truncatula LATD/NIP gene is essential for the development of lateral and primary root and nitrogen-fixing nodule meristems as well as for rhizobial invasion of nodules. LATD/NIP encodes a member of the NRT1(PTR1) nitrate and di-and tri-peptide transporter family, suggesting that its function is to transport one of these or another compound(s). Because latd/nip mutants can have their lateral and primary root defects rescued by ABA, ABA is a potential substrate for transport. LATD/NIP expression in the root meristem was demonstrated to be regulated by auxin, cytokinin and abscisic acid, but not by nitrate. LATD/NIP's potential function and its role in coordinating root architecture and nodule formation are discussed. digital.library.unt.edu/ark:/67531/metadc40391/
GSV: a web-based genome synteny viewer for customized data
This article discusses GSV, a web-based genome synteny viewer for customized data. Abstract: Background: The analysis of genome synteny is a common practice in comparative genomics. With the advent of DNA sequencing technologies, individual biologists can rapidly produce their genomic sequences of interest. Although web-based synteny visualization tools are convenient for biologists to use, none of the existing ones allow biologists to upload their own data for analysis. Results: The authors have developed the web-based Genome Synteny Viewer (GSV) that allows users to upload two data files for synteny visualization, the mandatory synteny file for specifying genomic positions of conserved regions and the optional genome annotation file. GSV presents two selected genomes in a single integrated view while still retaining the browsing flexibility necessary for exploring individual genomes. Users can browse and filter for genomic regions of interest, change the color or shape of each annotation track as well as re-order, hide or show the tracks dynamically. Additional features include downloadable images, immediate email notification and tracking of usage history. The entire GSV package is also light-weighted which enables easy local installation. Conclusions: GSV provides a unique option for biologists to analyze genome synteny by uploading their own data set to a web-based comparative genome browser. A web server hosting GSV is provided at http://cas.bioinfo.cas.unt.edu/gsv, and the software is also freely available for local installations. digital.library.unt.edu/ark:/67531/metadc77111/
The Ecoresponsive Genome of Daphnia pulex
This article discusses the ecoresponsive genome of Daphnia pulex. Abstract: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges. digital.library.unt.edu/ark:/67531/metadc78299/
WebGBrowse 2.1 - A Web Server Supporting Multiple Versions of the Generic Genome Browser for Customizable Genome Annotation Display
In this book, the authors discuss WebGBrowse 2.1. Genome browsers are critical bioinformatics tools for biologists to visualize genome annotations and the other sequence features along a reference sequence. GBrowse is one of the most popular genome browsers used by the research community. However, its installation and configuration prove to be difficult for many biologists. The authors have developed a web server, WebGBrowse, which takes a user-supplied annotation file in GFF3 format, guides users through the configuration of the display of each genomic feature, and allows them to visualize the genome annotation information via the GBrowse software. This book describes an upgraded WebGBrowse server, WebGBrowse 2.0, which provides users with a choice to display their genome annotation with different versions of the GBrowse software. digital.library.unt.edu/ark:/67531/metadc81382/
A cytochrome P450 monooxygenase commonly used for negative selection in transgenic plants causes growth anomalies by disrupting brassinosteroid signaling
This article discusses a cytochrome P450 monooxygenase. Abstract: Background: Cytochrome P450 monooxygenases form a large superfamily of enzymes that catalyze diverse reactions. The P450su1 gene from the soil bacteria Streptomyces griseolus encodes CYP105A1 which acts on various substrates including sulfonylurea herbicides, vitamin D, coumarins, and based on the work presented here, brassinosteroids. P450su1 is used as a negative-selection marker in plants because CYP105A1 converts the relatively benign sulfonyl urea pro-herbicide R7402 into a highly phytotoxic product. Consistent with its use for negative selection, transgenic Arabidopsis plants were generated with P450su1 situated between recognition sequences for FLP recombinase from yeast to select for recombinase-mediated excision. However, unexpected and prominent developmental aberrations resembling those described for mutants defective in brassinosteroid signaling were observed in many of the lines. Results: The phenotypes of the most affected lines included severe stunting, leaf curling, darkened leaves characteristic of anthocyanin accumulation, delayed transition to flowering, low pollen and seed yields, and delayed senescence. Phenotype severity correlated with P450su1 transcript abundance, but not with transcript abundance of other experimental genes, strongly implicating CYP105A1 as responsible for the defects. Germination and seedling growth of transgenic and control lines in the presence and absence of 24-epibrassinolide indicated that CYP105A1 disrupts brassinosteroid signaling, most likely by inactivating brassinosteroids. Conclusions: Despite prior use of this gene as a genetic tool, deleterious growth in the absence of R7402 has not been elaborated. The authors show that this gene can cause aberrant growth by disrupting brassinosteroid signaling and affecting homeostasis. digital.library.unt.edu/ark:/67531/metadc81383/
The Microbial Communities in Male First Catch Urine Are Highly Similar to Those in Paired Urethral Swab Specimens
This article discusses microbial communities. Urine is the CDC-recommended specimen for STI testing. It was unknown if the bacterial communities (microbiomes) in urine reflected those in the distal male urethra. The authors compared microbiomes of 32 paired urine and urethral swab specimens obtained from adult men attending an STD clinic, by 16S rRNA PCR and deep pyrosequencing. Microbiomes of urine and swabs were remarkably similar, regardless of STI status of the subjects. Thus, urine can be used to characterize urethral microbiomes when swabs are undesirable, such as in population-based studies of the urethral microbiome or where multiple sampling of participants is required. digital.library.unt.edu/ark:/67531/metadc78335/
Use of prior odds for missing persons identifications
This article discusses the use of prior odds for missing persons identifications. Identification of missing persons from mass disasters is based on evaluation of a number of variables and observations regarding the combination of features derived from these variables. DNA typing now is playing a more prominent role in the identification of human remains, and particularly so for highly decomposed and fragmented remains. The strength of genetic associations, by either direct or kinship analyses, is often quantified by calculating a likelihood ratio. The likelihood ratio can be multiplied by prior odds based on nongenetic evidence to calculate the posterior odds, that is, by applying Bayes' Theorem, to arrive at a probability of identity. For the identification of human remains, the path creating the set and intersection of variables that contribute to the prior odds needs to be appreciated and well defined. Other than considering the total number of missing persons, the forensic DNA community has been silent on specifying the elements of prior odds computations. The variables include the number of missing individuals, eyewitness accounts, anthropological features, demographics and other identifying characteristics. The assumptions, supporting data and reasoning that are used to establish a prior probability that will be combined with the genetic data need to be considered and justified. Otherwise, data may be unintentionally or intentionally manipulated to achieve a probability of identity that cannot be supported and can thus misrepresent the uncertainty with associations. The forensics DNA community needs to develop guidelines for objectively computing prior odds. digital.library.unt.edu/ark:/67531/metadc122168/
Contributing factors in judgement of fairness by monetary value
This article accompanies a poster presentation on contributing factors in judgement of fairness by monetary value. Given that the authors have developed for emotional response (Emotional-Gain Model) and a model for fairness (Fairness-Equity Model) that quantified emotional bias and fairness bias, the authors will use these models to reveal the hidden factors contributing to the emotional bias and fairness bias. Using the Ultimatum Game (UG) with human subjects to split a sum of money, the authors compare the responses between sharing $10 vs. $10 million. digital.library.unt.edu/ark:/67531/metadc122155/
Gender difference of emotional bias in sharing love
This article accompanies a poster presentation on the gender difference of emotional bias in sharing love. Having developed a computational model for emotional response (Emotional-Gain Model) and a model for fairness (Fairness-Equity Model) that quantified emotional bias and fairness bias, the authors will address the gender difference between the perception of love. The authors employed the experimental paradigm called "ultimatum game" to elicit emotional responses to the sharing of love and money. digital.library.unt.edu/ark:/67531/metadc122154/
Quantification of emotional bias by an Emotional-Gain Model
This article accompanies a poster presentation on the quantification of emotional bias by an Emotional-Gain model. The authors have developed a computational model that quantifies emotion objectively based on neurobiological mechanisms that increases the chance of survival in the real world. This model is based on the EMOTION-I and EMOTION-II models with the extension of proportionality hypothesis added to the desirable gain signal to these models. digital.library.unt.edu/ark:/67531/metadc122152/
Quantification of fairness bias by a Fairness-Equity Model
This paper accompanies a poster presentation on the quantification of fairness bias by a Fairness-Equity Model. The authors have developed a computational model that quantifies fairness objectively based on equity/disparity between the shares by two individuals. The Fairness-Equity Model represents the relationship between fairness perception intensity and the disparity (or equity) between two individuals graphically. digital.library.unt.edu/ark:/67531/metadc122153/
Response to: Use of prior odds for missing persons identifications - author's reply
This article is in response to an authors' reply to 'Use of prior odds for missing persons identifications.' This response is to the reply by Alex Biedermann, Franco Taroni, and Pierre Margot. digital.library.unt.edu/ark:/67531/metadc122169/
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