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PubMed1998

Mapping diplosporous apomixis in tetraploid Tripsacum: one gene or several genes?

Polyploids in Tripsacum, a wild relative of maize, reproduce through the diplosporous type of apomixis, an asexual mode of reproduction through seeds. Diplosporous apomixis involves both the failure of meiosis and the parthenogenetic development of the unreduced gametes, resulting in progenies that are exact genetic copies of the mother plant. Apomixis is believed to be controlled by one single dominant allele, responsible for the whole developmental process. Construction of a linkage map for the chromosome controlling diplosporous apomixis in Tripsacum was carried out in both tetraploid-apomictic and diploid-sexual Tripsacum species using maize restriction fragment length polymorphism (RFLP) probes. A high level of collinearity was observed between the Tripsacum chromosome carrying the control of apomixis and a duplicated segment in the maize genome. In the apomictic tetraploid, there was a strong restriction to recombination, as compared to the corresponding genomic segment in sexual plants and maize. This suggests that apomixis, although inherited as a single Mendelian allele, might really be controlled by a cluster of linked loci. The analysis also revealed the tetrasomic nature of the inheritance of the chromosomal segment controlling apomixis, which contradicts the usually accepted hypothesis of an allopolyploid origin of apomictic species. The implications of these data for the transfer of apomixis into cultivated crops are discussed, and a new approach to studying the genetics of apomixis, based on comparative mapping, is proposed.

Chromosome Mapping↗
PubMed1989

Immunohistochemical localization of microtubule-associated proteins in the nervous system of the small intestine of guinea pig.

Layers containing Auerbach's and Meissner's plexuses were dissected from the small intestine of guinea pig and immunostained with affinity-purified antibodies against brain-specific microtubule-associated proteins (MAPs): MAP1, MAP2 and tau and a MAP with a molecular weight of 190,000 dalton purified from bovine adrenal cortex (190-kDa MAP). MAP1 antibody stained the network of nerve fibers and the cell bodies of enteric neurons in both Auerbach's and Meissner's plexuses. Staining with anti-tau antibody gave the same results. Antibody against MAP2 stained neuronal cell bodies and short thin processes extending from them. Interganglionic strands composed mainly of long processes were unstained. Anti-190-kDa MAP antibody stained both the neuronal cell bodies and bundles of nerve fibers. However, the staining was less intense than that with anti-MAP1 and tau antibodies. Differentiation in the structure of the cytoskeleton probably exists in the neuronal processes of the enteric neurons as is shown in the dendrites and axons in some neurons of the central nervous system. Thus, enteric neurons possess axon-like processes containing MAP1, tau and probably lower amounts of 190-kDa MAP. Cell bodies and dendrite-like structures of these neurons contain MAP2 in addition to MAP1, tau and 190-kDa MAP.

Animals↗
PubMed2006

Mapping and profile of emission sources for airborne volatile organic compounds from process regions at a petrochemical plant in Kaohsiung, Taiwan.

This work surveyed five process regions inside a petrochemical plant in Taiwan to characterize the profiles of airborne volatile organic compounds (VOCs) and locate emission sources. Samples, taken with canisters, were analyzed with gas chromatography-mass spectrometry according to the TO-14 method. Each region was deployed with 24 sampling sites, sampled twice, and 240 samples in total were measured during the survey period. All of the data were consolidated into a database on Excel to facilitate retrieval, statistical analysis, and presentation in the form of a table or graph, and, subsequently, the profile of VOCs was elucidated. Emission sources were located by mapping the concentration distribution of either an individual or a type of species in terms of contour maps on Surfer. Through the cross-analysis of data, the abundant VOCs included alkenes, dienes, alkanes, and aromatics. A total of 19 emission sources were located from these five regions. The sources for alkanes stood inside first, third aromatic, and fourth naphtha cracking regions, whereas the ones for alkenes were inside two naphtha cracking regions. The sources for dienes were found inside the third naphtha cracking region alone; in contrast, the sources for aromatics were universally traced except inside the third naphtha cracking region. The measured intensity for sources mostly ranged from 1000 to 7000 ppb.

Air Pollutants↗
PubMed1999

Identifying and mapping novel retinal-expressed ESTs from humans.

PURPOSE: The goal of this study was to develop efficient methods to identify tissue-specific expressed sequence tags (ESTs) and to map their locations in the human genome. Through a combination of database analysis and laboratory investigation, unique retina-specific ESTs were identified and mapped as candidate genes for inherited retinal diseases. METHODS: DNA sequences from retina-specific EST clusters were obtained from the TIGR Human Gene Index Database. Further processing of the EST sequence data was necessary to ensure that each EST cluster represented a novel, non-redundant mapping candidate. Processing involved screening for homologies to known genes and proteins using BLAST, excluding known human gene sequences and repeat sequences, and developing primers for PCR amplification of the gene encoding each cDNA cluster from genomic DNA. The EST clusters were mapped using the GeneBridge 4.0 Radiation Hybrid Mapping Panel with standard PCR conditions. RESULTS: A total of 83 retinal-expressed EST clusters were examined as potential novel, non-redundant mapping candidates. Fifty-five clusters were mapped successfully and their locations compared to the locations of known retinal disease genes. Fourteen EST clusters localize to candidate regions for inherited retinal diseases. CONCLUSIONS: This pilot study developed methodology for mapping uniquely expressed retinal ESTs and for identifying potential candidate genes for inherited retinal disorders. Despite the overall success, several complicating factors contributed to the high failure rate (33%) for mapping EST-clustered sequences. These include redundancy in the sequence data, widely dispersed sequences, ambiguous nucleotides within the sequences, the possibility of amplifying through introns and the presence of repetitive elements within the sequence. However, the combination of database analysis and laboratory mapping is a powerful method for identification of candidate genes for inherited diseases.

Chromosome Mapping↗
PubMed2002

The SNOMED clinical terms development process: refinement and analysis of content.

SNOMED Clinical Terms is a comprehensive concept-based health care terminology that was created by merging SNOMED RT and Clinical Terms Version 3. Following the mapping of concepts and descriptions into a merged database, the terminology was further refined by adding new content, modeling the relationships of individual concepts, and reviewing the hierarchical structure. A quality control process was performed to ensure integrity of the data. Additional features such as subsets, qualifiers, and mappings to other coding systems were added or updated to facilitate usability. We then analyzed the content of the completed work. This paper describes the refinement processes and compares the actual content of SNOMED CT with the early data obtained from analysis of the description mapping process. As predicted, the majority of concepts in SNOMED CT originated from SNOMED RT or CTV3, but not both.

Subject Headings↗
PubMed2005

Comprehensive interaction map of the Arabidopsis MADS Box transcription factors.

Interactions between proteins are essential for their functioning and the biological processes they control. The elucidation of interaction maps based on yeast studies is a first step toward the understanding of molecular networks and provides a framework of proteins that possess the capacity and specificity to interact. Here, we present a comprehensive plant protein-protein interactome map of nearly all members of the Arabidopsis thaliana MADS box transcription factor family. A matrix-based yeast two-hybrid screen of >100 members of this family revealed a collection of specific heterodimers and a few homodimers. Clustering of proteins with similar interaction patterns pinpoints proteins involved in the same developmental program and provides valuable information about the participation of uncharacterized proteins in these programs. Furthermore, a model is proposed that integrates the floral induction and floral organ formation networks based on the interactions between the proteins involved. Heterodimers between flower induction and floral organ identity proteins were observed, which point to (auto)regulatory mechanisms that prevent the activity of flower induction proteins in the flower.

Arabidopsis↗
PubMed2006

The functional neuroanatomy of autobiographical memory: a meta-analysis.

Autobiographical memory (AM) entails a complex set of operations, including episodic memory, self-reflection, emotion, visual imagery, attention, executive functions, and semantic processes. The heterogeneous nature of AM poses significant challenges in capturing its behavioral and neuroanatomical correlates. Investigators have recently turned their attention to the functional neuroanatomy of AM. We used the effect-location method of meta-analysis to analyze data from 24 functional imaging studies of AM. The results indicated a core neural network of left-lateralized regions, including the medial and ventrolateral prefrontal, medial and lateral temporal and retrosplenial/posterior cingulate cortices, the temporoparietal junction and the cerebellum. Secondary and tertiary regions, less frequently reported in imaging studies of AM, are also identified. We examined the neural correlates of putative component processes in AM, including, executive functions, self-reflection, episodic remembering and visuospatial processing. We also separately analyzed the effect of select variables on the AM network across individual studies, including memory age, qualitative factors (personal significance, level of detail and vividness), semantic and emotional content, and the effect of reference conditions. We found that memory age effects on medial temporal lobe structures may be modulated by qualitative aspects of memory. Studies using rest as a control task masked process-specific components of the AM neural network. Our findings support a neural distinction between episodic and semantic memory in AM. Finally, emotional events produced a shift in lateralization of the AM network with activation observed in emotion-centered regions and deactivation (or lack of activation) observed in regions associated with cognitive processes.

Autobiographies as Topic↗
PubMed2006

Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

The genome-wide mapping of gene-regulatory motifs remains a major goal that will facilitate the modelling of gene-regulatory networks and their evolution. The repressor element 1 is a long, conserved transcription factor-binding site which recruits the transcriptional repressor REST to numerous neuron-specific target genes. REST plays important roles in multiple biological processes and disease states. To map RE1 sites and target genes, we created a position specific scoring matrix representing the RE1 and used it to search the human and mouse genomes. We identified 1301 and 997 RE1s inhuman and mouse genomes, respectively, of which >40% are novel. By employing an ontological analysis we show that REST target genes are significantly enriched in a number of functional classes. Taking the novel REST target gene CACNA1A as an experimental model, we show that it can be regulated by multiple RE1s of different binding affinities, which are only partially conserved between human and mouse. A novel BLAST methodology indicated that many RE1s belong to closely related families. Most of these sequences are associated with transposable elements, leading us to propose that transposon-mediated duplication and insertion of RE1s has led to the acquisition of novel target genes by REST during evolution.

Animals↗
PubMed2006

The functional value of Caribbean coral reef, seagrass and mangrove habitats to ecosystem processes.

Caribbean coral reef habitats, seagrass beds and mangroves provide important goods and services both individually and through functional linkages. A range of anthropogenic factors are threatening the ecological and economic importance of these habitats and it is vital to understand how ecosystem processes vary across seascapes. A greater understanding of processes will facilitate further insight into the effects of disturbances and assist with assessing management options. Despite the need to study processes across whole seascapes, few spatially explicit ecosystem-scale assessments exist. We review the empirical literature to examine the role of different habitat types for a range of processes. The importance of each of 10 generic habitats to each process is defined as its "functional value" (none, low, medium or high), quantitatively derived from published data wherever possible and summarised in a single figure. This summary represents the first time the importance of habitats across an entire Caribbean seascape has been assessed for a range of processes. Furthermore, we review the susceptibility of each habitat to disturbances to investigate spatial patterns that might affect functional values. Habitat types are considered at the scale discriminated by remotely-sensed imagery and we envisage that functional values can be combined with habitat maps to provide spatially explicit information on processes across ecosystems. We provide examples of mapping the functional values of habitats for populations of three commercially important species. The resulting data layers were then used to generate seascape-scale assessments of "hot spots" of functional value that might be considered priorities for conservation. We also provide an example of how the literature reviewed here can be used to parameterise a habitat-specific model investigating reef resilience under different scenarios of herbivory. Finally, we use multidimensional scaling to provide a basic analysis of the overall functional roles of different habitats. The resulting ordination suggests that each habitat has a unique suite of functional values and, potentially, a distinct role within the ecosystem. This review shows that further data are required for many habitat types and processes, particularly forereef and escarpment habitats on reefs and for seagrass beds and mangroves. Furthermore, many data were collected prior to the regional mass mortality of Diadema and Acropora, and subsequent changes to benthic communities have, in many cases, altered a habitat's functional value, hindering the use of these data for parameterising maps and models. Similarly, few data exist on how functional values change when environmental parameters, such as water clarity, are altered by natural or anthropogenic influences or the effects of a habitat's spatial context within the seascape. Despite these limitations, sufficient data are available to construct maps and models to better understand tropical marine ecosystem processes and assist more effective mitigation of threats that alter habitats and their functional values.

Algorithms↗
PubMed1989

[Computerized precordial mapping--the Mapcard system].

A computerized Data Acquisition System conceived and built by LNETI/DEE in cooperation with Department of Cardiology of Hospital Santa Cruz, and its application to processing and representation of cardiac precordial maps (MAPCARD SYSTEM), was described. A description was made about the evolution on cardiac maps, their main areas of interest, pointing to future ways. With this economic and easy to use system, important perspectives of hospital utilization are opened, in the fields of non invasive diagnostic and clinical research technics.

Cardiology↗
PubMed1980

Epstein-Barr virus RNA. V. Viral RNA in a restringently infected, growth-transformed cell line.

A continuous lymphoblastoid cell line, IB-4, was established by infection and growth transformation of normal neonatal B lymphocytes with the B95-8 isolate of Epstein-Barr virus (EBV). The IB-4 cells contained the intranuclear antigen, EBNA, but not early antigen, EA. The fragments produced by the digestion of intracellular episomal viral DNA (density, 1.700 to 1.720 g/cm3) with EcoRI restriction endonuclease were identical in size to the A, B, C, E, F, G, and H fragments of virion DNA. As expected from the previous observation that episomal intracellular DNA is circular, the fragment containing the rightward terminal sequences of EBV DNA in IB-4 cells was larger than the corresponding fragment of linear viral DNA, probably as a consequence of covalent linkage to the leftward terminal fragment. Also, two fragments, EcoRI-I and -J, which were adjacent to each other in the virion DNA, were absent from the intracellular DNA. The labeled EcoRI-J of viral DNA hybridized instead to a new fragment equal in size to EcoRI-I and -J combined. Analysis of viral RNA in IB-4 cells showed that RNAs encoded by more than 30% of the viral DNA comprised approximately 0.06% of the nuclear RNA, whereas RNAs encoded by 20% and 10% of the viral DNA comprised approximately 0.06% and 0.003% of the polyadenylated and polyribosomal RNAs, respectively. Viral mRNA (polyribosomal RNA) was encoded by DNA which mapped at 0.05 x 10(8) to 0.36 x 10(8) daltons and to a lesser extent by DNAs which mapped at 0.62 x 10(8) to 0.67 x 10(8), 0.70 x 10(8) to 0.73 x 10(8), and 1.13 x 10(8) to 1.15 x 10(8) daltons in the B95-8 genome. The most agundant nuclear viral RNAs were encoded primarily by DNA which mapped at the same loci; but RNAs encoded by many other fragments of viral DNA could also be detected among nuclear RNAs. Viral mRNA(s) (polyribosomal) was encoded by about 40% of the internal reiteration and by 25% of the BamHI-H fragments which mapped from 0.32 x 10(8) to 0.36 x 10(8) daltons, nuclear RNAs were encoded by at least 57% of the internal reiteration and 40% of BamHI-H. These data indicate that there is selective accumulation of some viral RNAs within the nucleus of IB-4 cells and that there is selective post-transcriptional processing of these RNAs. Finer mapping of the DNA which encodes mRNA (polyribosomal) in IB-4 cells indicated that some of this DNA is deleted in the DNA of the P3 HR-1 virus, the only isolate of EBV which cannot initiate growth transformation. These data, therefore, support the hypothesis that expression of this region of EBV genome is important for growth transformation or for the maintenance of restrigent infection.

B-Lymphocytes↗
PubMed2003

Automated data interpretation based on the concept of "negative signature mass" for mass-mapping disulfide structures of cystinyl proteins.

An efficient method for data processing and interpretation is needed to support and extend disulfide mass-mapping methodology based on partial reduction and cyanylation-induced cleavage to proteins containing more than four cystines. Here, the concept of "negative signature mass" is introduced as the novel feature of an algorithm designed to identify the disulfide structure of a cystinyl protein given an input of mass spectral data and an amino acid sequence. The "negative signature mass" process is different from the conventional approach in that it does not directly rule-in disulfide linkages, but rather eliminates linkages from a list of all possible theoretical linkages, with the goal of ruling out enough linkages so that only one disulfide structure can be constructed. The operating principles and the effectiveness of the algorithm are described in the context of analyzing ribonuclease A, a 124-residue protein containing eight cysteines in the form of four cystines (disulfides).

Amino Acid Sequence↗
PubMed1985

Human metallothionein-II processed gene is located in region p11----q21 of chromosome 4.

Metallothionein (MT) genes comprise a multigene family encoding low-molecular-weight, heavy-metal-binding proteins. We have mapped a human MT-II processed gene to chromosome 4, using Southern blotting in combination with a human X mouse hybrid clone panel containing defined subsets of human chromosomes. We have further localized this gene to region p11----q21, using in situ hybridization.

Animals↗
PubMed1999

Measurement of Automotive Catalyst Washcoat Loading Parameters by Microscopy Techniques.

: Washcoat loading on automotive exhaust catalysts is normally determined, in production, by a weight gain procedure, which gives an accurate measure of washcoat weight present on an individual catalyst but does not address such parameters as uniformity of washcoat loading and geometric surface area within the monolith. Both issues are important factors that affect the catalytic activity (especially during catalyst lightoff) and catalyst cost (due to a thick, less functional washcoat) in an automotive exhaust system. Washcoat loading also plays a role in post-use analysis to determine possible reasons for changes (i.e., loss) in catalytic activity. For the post-use examinations weighing techniques are not useful since the washcoat cannot be preferentially removed and part of the weight gain is due to contamination from the combustion process. In the present work a combination of scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS) X-ray mapping, light microscopy, and digital image processing was used. Two methods have been demonstrated for the determination of the density of calcined alumina washcoats. Additionally, a method has been developed to determine catalyst washcoat loading, either on a sampling basis after manufacture or in studies of catalysts after use. Methods also have been developed to determine other important parameters such as monolith wall thickness, percent open area in a catalyst monolith, geometric surface area, and hydraulic diameter. A linear correlation has been shown between hydrocarbon conversion efficiency and measured geometric surface area, with a coefficient of determination (r(2)) of 0.84.

Journal Article↗
PubMed2005

Analysis of training-induced changes in ethyl acetate odor maps using a new computational tool to map the glomerular layer of the olfactory bulb.

Odor quality is thought to be encoded by the activation of partially overlapping subsets of glomeruli in the olfactory bulb (odor maps). Mouse genetic studies have demonstrated that olfactory sensory neurons (OSNs) expressing a particular olfactory receptor target their axons to a few individual glomeruli in the bulb. While the specific targeting of OSN axons provides a molecular underpinning for the odor maps, much remains to be understood about the relationship between the functional and molecular maps. In this article, we ask the question whether intensive training of mice in a go/no-go operant conditioning odor discrimination task affects odor maps measured by determining c-fos up-regulation in periglomerular cells. Data analysis is performed using a newly developed suite of computational tools designed to systematically map functional and molecular features of glomeruli in the adult mouse olfactory bulb. This suite provides the necessary tools to process high-resolution digital images, map labeled glomeruli, visualize odor maps, and facilitate statistical analysis of patterns of identified glomeruli in the olfactory bulb. The software generates odor maps (density plots) based on glomerular activity, density, or area. We find that training up-regulates the number of glomeruli that become c-fos positive after stimulation with ethyl acetate.

Acetates↗
PubMed2005

KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps.

The application of DNA array technology and chromatographic separation techniques coupled with mass spectrometry to transcriptomic and metabolomic analyses in plants has resulted in the generation of considerable quantitative data related to transcription and metabolism. The integration of "omic" data is one of the major concerns associated with research into identifying gene function. Thus, we developed a Web-based tool, KaPPA-View, for representing quantitative data for individual transcripts and/or metabolites on plant metabolic pathway maps. We prepared a set of comprehensive metabolic pathway maps for Arabidopsis (Arabidopsis thaliana) and depicted these graphically in Scalable Vector Graphics format. Individual transcripts assigned to a reaction are represented symbolically together with the symbols of the reaction and metabolites on metabolic pathway maps. Using quantitative values for transcripts and/or metabolites submitted by the user as Comma Separated Value-formatted text through the Internet, the KaPPA-View server inserts colored symbols corresponding to a defined metabolic process at that site on the maps and returns them to the user's browser. The server also provides information on transcripts and metabolites in pop-up windows. To demonstrate the process, we describe the dataset obtained for transgenic plants that overexpress the PAP1 gene encoding a MYB transcription factor on metabolic pathway maps. The presentation of data in this manner is useful for viewing metabolic data in a way that facilitates the discussion of gene function.

Computational Biology↗
PubMed2005

The future of mapping sensory cortex in primates: three of many remaining issues.

After 100 years of progress in understanding the organization of cerebral cortex, three issues have persisted over the last 35 years, which are revisited in this paper. First, is V3 an established or questionable area of visual cortex? Second, does taste cortex include part of area 3b (S1 proper) and other somatosensory areas? Third, is primary auditory cortex, A1, of primates the homologue of A1 in cats? The existence of such questions about even the early stages of cortical processing reflects the difficulties in mapping cerebral cortex, and reminds us that the era of basic discovery is far from over.

Animals↗
PubMed2002

Restraint of proinflammatory cytokine biosynthesis by mitogen-activated protein kinase phosphatase-1 in lipopolysaccharide-stimulated macrophages.

Exposure of macrophages to LPS elicits the production of proinflammatory cytokines, such as TNF-alpha, through complex signaling mechanisms. Mitogen-activated protein (MAP) kinases play a critical role in this process. In the present study, we have addressed the role of MAP kinase phosphatase-1 (MKP-1) in regulating proinflammatory cytokine production using RAW264.7 macrophages. Analysis of MAP kinase activity revealed a transient activation of c-Jun N-terminal kinase (JNK) and p38 after LPS stimulation. Interestingly, MKP-1 was induced concurrently with the inactivation of JNK and p38, whereas blocking MKP-1 induction by triptolide prevented this inactivation. Ectopic expression of MKP-1 accelerated JNK and p38 inactivation and substantially inhibited the production of TNF-alpha and IL-6. Induction of MKP-1 by LPS was found to be extracellular signal-regulated kinase dependent and involved enhanced gene expression and increased protein stability. Finally, MKP-1 expression was also induced by glucocorticoids as well as cholera toxin B subunit, an agent capable of preventing autoimmune diseases in animal models. These findings highlight MKP-1 as a critical negative regulator of the macrophage inflammatory response, underscoring its premise as a potential target for developing novel anti-inflammatory drugs.

Animals↗