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At least 1,351 records · Page 75Linked to original sources
PubMed1992

Map of cis-acting sequences that determine alternative pre-mRNA processing in the E3 complex transcription unit of adenovirus.

The E3 complex transcription unit of adenovirus encodes four major mRNAs (a, c, f, and h) and two minor (d and e) mRNAs with overlapping exons, alternative splice sites, and two polyadenylation sites, termed E3A (upstream) and E3B (downstream). mRNAs a and d use the E3A polyadenylation site, and mRNAs c, e, f, and h use the E3B site. We have analyzed virus mutants with deletions throughout the E3 region in order to identify cis-acting sequences that function in E3 pre-mRNA processing. The results presented in this report as well as previous results are summarized as follows. (i) Deletions in the first (5') intron at nucleotides (nt) 372 to 768 in E3 had no effect unless they removed the consensus sequence for the nt 372 5' splice site; however, the overall pattern of E3 mRNAs did not change significantly. (ii) Deletions in region I (nt 1441 to 2044) eliminated mRNAs a and c and resulted in corresponding increases in mRNAs f and h; we propose that region I contains sequences that suppress splicing. (iii) Mutations in region II (nt 2161 to 2243) resulted in nearly exclusive synthesis of mRNA f; this phenotype is understood and is discussed. (iv) Changing the AUUAAA component of the E3A poly(A) addition signal to AAUAAA resulted in increased mRNA a levels, suggesting that the E3A poly(A) addition signal is intrinsically inefficient. (v) Deletions in region III (nt 2488 to 3002) decreased mRNA a levels about two- to threefold and specifically increased mRNA f levels; we suggest that region III facilitates use of the E3A polyadenylation site. (vi) Deletions in region IV (nt 2904 to 3251) increased mRNA a levels about two- to threefold; we suggest that region IV may contain sequences that facilitate use of the E3B polyadenylation site. A map of sequences that determine alternative pre-mRNA processing in region E3 is now nearly complete.

Adenoviridae↗
PubMed2004

The human visual cortex.

The discovery and analysis of cortical visual areas is a major accomplishment of visual neuroscience. In the past decade the use of noninvasive functional imaging, particularly functional magnetic resonance imaging (fMRI), has dramatically increased our detailed knowledge of the functional organization of the human visual cortex and its relation to visual perception. The fMRI method offers a major advantage over other techniques applied in neuroscience by providing a large-scale neuroanatomical perspective that stems from its ability to image the entire brain essentially at once. This bird's eye view has the potential to reveal large-scale principles within the very complex plethora of visual areas. Thus, it could arrange the entire constellation of human visual areas in a unified functional organizational framework. Here we review recent findings and methods employed to uncover the functional properties of the human visual cortex focusing on two themes: functional specialization and hierarchical processing.

Animals↗
PubMed1996

Normalization and subtraction: two approaches to facilitate gene discovery.

Large-scale sequencing of cDNAs randomly picked from libraries has proven to be a very powerful approach to discover (putatively) expressed sequences that, in turn, once mapped, may greatly expedite the process involved in the identification and cloning of human disease genes. However, the integrity of the data and the pace at which novel sequences can be identified depends to a great extent on the cDNA libraries that are used. Because altogether, in a typical cell, the mRNAs of the prevalent and intermediate frequency classes comprise as much as 50-65% of the total mRNA mass, but represent no more than 1000-2000 different mRNAs, redundant identification of mRNAs of these two frequency classes is destined to become overwhelming relatively early in any such random gene discovery programs, thus seriously compromising their cost-effectiveness. With the goal of facilitating such efforts, previously we developed a method to construct directionally cloned normalized cDNA libraries and applied it to generate infant brain (INIB) and fetal liver/spleen (INFLS) libraries, from which a total of 45,192 and 86,088 expressed sequence tags, respectively, have been derived. While improving the representation of the longest cDNAs in our libraries, we developed three additional methods to normalize cDNA libraries and generated over 35 libraries, most of which have been contributed to our integrated Molecular Analysis of Genomes and Their Expression (IMAGE) Consortium and thus distributed widely and used for sequencing and mapping. In an attempt to facilitate the process of gene discovery further, we have also developed a subtractive hybridization approach designed specifically to eliminate (or reduce significantly the representation of) large pools of arrayed and (mostly) sequenced clones from normalized libraries yet to be (or just partly) surveyed. Here we present a detailed description and a comparative analysis of four methods that we developed and used to generate normalize cDNA libraries from human (15), mouse (3), rat (2), as well as the parasite Schistosoma mansoni (1). In addition, we describe the construction and preliminary characterization of a subtracted liver/spleen library (INFLS-SI) that resulted from the elimination (or reduction of representation) of -5000 INFLS-IMAGE clones from the INFLS library.

Adult↗
PubMed1978

Interpretation of the body surface isopotential maps of patients with right bundle branch block. Determination of the region of the delayed activation within the right ventricle.

Body surface isopotential maps were produced by computer processing of the 85 electrocardiograms obtained from the entire thorax of 28 patients with complete or incomplete right bundle branch block (RBBB). We divided the map patterns into the following 3 groups. Type I map pattern (10 cases): at the early stage of QRS, the maximum was located in the left chest. It shifted to the left from the normal position; at the instant of 44 msec, on the average, after the onset of QRS breakthrough minimum appeared over the left chest. Its appearance was delayed and its site shifted to the left as compared with the normal; at the late stage, the positive zone covered extensively the right chest and the right back; terminally, the maximum was positioned along the right parasternum. Type II map pattern (13 cases): at the early stage of QRS, the maximum was in the left chest as in Type I; breakthrough minimum appeared at 38 msec on the average, later than in the normal, but the site of breakthrough minimum varied from the left chest as in Type I to the midsternal region as in the normal; at the late stage, the positive zone covered the upper part of the right chest and the right back, less extensively than in Type I; the terminal maximum was in the upper sternal region. Type III map pattern (5 cases): the map pattern passed normally until the late stage, but thereafter a small positive zone survived over the upper sternal region. In Type I the delayed activation was presumed to occur all over the right ventricle, in Type II mainly over the smaller area of the right anterior free wall, and in Type III over the localized area of the outflow tract. Patients with complete RBBB showed Type I pattern. Patients with incomplete RBBB showed Type II or Type III pattern, although electrocardiograms failed to differentiate Type II patients from Type III patients. These findings suggest that the electrocardiographic pattern of incomplete RBBB probably arises from the various mechanisms.

Adult↗
PubMed1999

Integrins mediate the inhibitory effect of focal adhesion on angiotensin II-induced p44/42 mitogen-activated protein (MAP) kinase activity in human mesangial cells.

Previously, we reported that the formation of focal adhesion accelerated by accumulation of extracellular matrices may inhibit the angiotensin II-stimulated proliferation of human mesangial cells (HMCs). The process is regulated by p44/42 MAP kinase activity through the mediation of paxillin and GTPase activating proteins. In this report, we investigated the effect of integrin molecules on the angiotensin II-induced p44/42 MAP kinase activation in non-adherent HMCs. The results demonstrated that incubation of cells with both antibody to integrin beta(1) chain (K20) and GRGDS peptide induced integrin clustering, paxillin aggregation, and marked suppression of angiotensin II-induced p44/42 MAP kinase activation. On the other hand, incubation of cells with K20 alone induced integrin clustering without paxillin aggregation and the suppressive effect on angiotensin II-stimulated p44/42 MAP kinase activity. Our results strongly suggest the pivotal role of integrins in the inhibitory effect of focal adhesion on p44/42 MAP kinase activity, the checking system against angiotensin II-induced MAP kinase overactivation.

Angiotensin II↗
PubMed2001

Comparative genomic analysis of genes encoding translation elongation factor 1B(alpha) in human and mouse shows EEF1B1 to be a recent retrotransposition event.

We have characterized genomic loci encoding translation elongation factor 1B(alpha) (eEF1B(alpha)) in mice and humans. Mice have a single structural locus (named Eef1b2) spanning six exons, which is ubiquitously expressed and maps close to Casp8 on mouse chromosome 1, and a processed pseudogene. Humans have a single intron-containing locus, EEF1B2, which maps to 2q33, and an intronless paralogue expressed only in brain and muscle (EEF1B3). Another locus described previously, EEF1B1, is actually a processed pseudogene on chromosome 15 corresponding to an alternative splice form of EEF1B2. Our study illustrates the value of comparative mapping in distinguishing between processed pseudogenes and intronless paralogues.

Alternative Splicing↗
PubMed1999

An algorithmic approach to multiple complete digest mapping.

Multiple Complete Digest (MCD) mapping is a method of determining the locations of restriction sites along a target DNA molecule. The resulting restriction map has many potential applications in DNA sequencing and genetics. In this work, we present a heuristic algorithm for fragment identification, a key step in the process of constructing an MCD map. Given measurements of the restriction fragment sizes from one or more complete digestions of each clone in a clone library covering the molecule to be mapped, the algorithm identifies groups of restriction fragments on different clones that correspond to the same region of the target DNA. Once these groups are correctly determined the desired map can be constructed by solving a system of simple linear inequalities. We demonstrate the effectiveness of our algorithm on real data provided by the Genome Center at the University of Washington.

Algorithms↗
PubMed1998

Visually guided movements: learning with modular neural maps in robotics.

Robotics involves complex processing and requires modular controllers. For the connectionist approach, the adaptation of each module within the global system remains a major problem to be solved. This paper proposes the idea that biological learning can take advantage of the structures of the modules and the nature of modular decomposition. Therefore, we address this problem starting with the architecture of the system. We illustrate this approach using a robotic application: the visual servoing of the arm's end-effector. The on-line adaptation of a simple controller permits excellent results. To process several variables, and to limit the size of the memory required, this controller is decomposed into modules, in the image of sensorial or motor processing centers. The learning of the modules is realized on-line, a bi-directional architecture permits the adaptation of each module using a simple algorithm. The results obtained with various modular arrangements, both during intensive computer simulations and on our robotic platform, confirm the practical interest of this approach.

Journal Article↗
PubMed1991

Auditory cortex: comparative aspects of maps and plasticity.

Much recent work in the field of auditory cortex analysis consists of an intensified search for complex sound representation and sound localization mechanisms using tonotopic maps as a frame of reference. Mammalian species rely on parallel processing in multiple tonotopic and non-tonotopic maps but show different degrees of unit complexity, and orderly representation of acoustic dimensions in such maps depending on the predictability of sounds in their environment. Birds appear to rely chiefly on one tonotopic map which harbours multidimensional complex representations. During development and after partial hearing loss, tonotopic organization changes in a predictable manner. Learning also modifies the spatial representation of sounds and even modifies tonotopic organization, but the spatial rules involved in this process have not yet emerged.

Animals↗
PubMed2004

[Relationship between phosphorus and bacterial regrowth in drinking water].

Limitation of phosphorus on bacterial regrowth was studied in source water, water treatment process and a main distribution pipe of J waterwork in T city, by modified assimilable organic carbon (AOC) method and microbially available phosphorus (MAP) analysis. Based on the study, the result showed that: (1) Concentration of MAP was higher in source water and water treatment process, which was 5-38 microg/L (PO4(3-)-P). However in water distribution system, concentration of MAP was lower, which was less than 5 microg/L (PO4(3-)-P). It changed very little in distribution system. (2) Traditional treatment process can remove MAP efficiently 34.0%-83.7% of MAP can be removed in the process. (3) Generally in source water and water treatment process, there was no evident difference between AOC(potential), AOC(P) and AOC(native). So AOC was the most important factor of bacterial growth. In the main distribution pipe, the concentration of AOC(potential) and AOC(P) were 2-8.7 times of the concentration of AOC(native). So phosphorus limited bacterial regrowth.

Bacteria↗
PubMed2006

Cortical reorganization in the aging brain.

Aging exerts major reorganization and remodeling at all levels of brain structure and function. Studies in aged animals and in human elderly individuals demonstrate that sensorimotor cortical representational maps undergo significant alterations. Because cortical reorganization is paralleled by a decline in perceptual and behavioral performance, this type of cortical remodeling differs from the plastic reorganization observed during learning processes in young individuals where map changes are associated with a gain in performance. It is now clear that brain plasticity is operational into old age; therefore, protocols for interventions such as training, exercising, practicing, and stimulation, which make use of neuroplasticity principles, are effective to ameliorate some forms of cortical and behavioral age-related changes, indicating that aging effects are not irreversible but treatable. However, old individuals cannot be rejuvenated, but restoration of function is possible through the emergence of new processing strategies. This implies that cortical reorganization in the aging brain occurs twice: during aging, and during treatment of age-related changes.

Aging↗
PubMed2000

Map kinases in fungal pathogens.

MAP kinases in eukaryotic cells are well known for transducing a variety of extracellular signals to regulate cell growth and differentiation. Recently, MAP kinases homologous to the yeast Fus3/Kss1 MAP kinases have been identified in several fungal pathogens and found to be important for appressorium formation, invasive hyphal growth, and fungal pathogenesis. This MAP kinase pathway also controls diverse growth or differentiation processes, including conidiation, conidial germination, and female fertility. MAP kinases homologous to yeast Slt2 and Hog1 have also been characterized in Candida albicans and Magnaporthe grisea. Mutants disrupted of the Slt2 homologues have weak cell walls, altered hyphal growth, and reduced virulence. The Hog1 homologues are dispensable for growth but are essential for regulating responses to hyperosmotic stress in C. albicans and M. grisea. Overall, recent studies have indicated that MAP kinase pathways may play important roles in regulating growth, differentiation, survival, and pathogenesis in fungal pathogens.

Bacterial Proteins↗
PubMedDate not supplied

A polynomial-time algorithm for the matching of crossing contact-map patterns.

Contact maps are a model to capture the core information in the structure of biological molecules, e.g., proteins. A contact map consists of an ordered set S of elements (representing a protein's sequence of amino acids), and a set A of element pairs of S, called arcs (representing amino acids which are closely neighbored in the structure). Given two contact maps (S, A) and (Sp, Ap) with /A/ > or = /Ap/, the CONTACT MAP PATTERN MATCHING (CMPM) problem asks whether the "pattern" (Sp, A,) "occurs" in (S, A), i.e., informally stated, whether there is a subset of /Ap/ arcs in A whose arc structure coincides with Ap. CMPM captures the biological question of finding structural motifs in protein structures. In general, CMPM is NP-hard. In this paper, we show that CMPM is solvable in O(/A/6/Ap/2) time when the pattern is {precedes, crosses}-structured, i.e., when each two arcs in the pattern are disjoint or crossing. Our algorithm extends to other closely related models. In particular, it answers an open question raised by Vialette that, rephrased in terms of contact maps, asked whether CMPM for {precedes, crosses}-structured patterns is NP-hard or solvable in polynomial time. Our result stands in sharp contrast to the NP-hardness of closely related problems. We provide experimental results which show that contact maps derived from real protein structures can be processed efficiently.

Algorithms↗
PubMed2002

Gas-phase ion unimolecular dissociation for rapid phosphopeptide mapping by IRMPD in a Penning ion trap: an energetically favored process.

This communication discusses the efficient detection of the most important and common protein modification, phosphorylation, using ESI-FTICR-MS and IRMPD. Preliminary studies have demonstrated that within a complex protein digest, all phosphopeptides can be identified by a single IR laser irradiation event due to preferential dissociation of the modified peptides. This research demonstrates that the energy of activation for dissociation of the phosphopeptides is lower than that of the unmodified analogues providing the basis for the success of this technique. However, the P-O stretch (9.6-11 mum or 1042-909 cm-1) of this posttranslational modification is in direct resonance with the CO2 IR laser (10.6 mum or 943 cm-1) used for IRMPD. Therefore, the vibrational frequency of the phosphate moiety may be an additional factor in the rapid first-order decay of phosphopeptides. Based upon the energetics of dissociation discussed in this manuscript, IRMPD of ions in a Penning ion trap is an ideal platform for rapid phosphopeptide mapping.

Amino Acid Sequence↗
PubMed1987

Precise identification of cleavage sites involved in the unusual processing of trypanosome ribosomal RNA.

The large subunit ribosomal RNA (LSRNA) of Trypanosoma brucei is unusual in being cleaved at multiple sites to yield six stable fragments of RNA. We report here the complete nucleotide sequence of two regions of the ribosomal DNA repeat unit. The first sequence includes all of the processing sites involved in the generation of one of the small LSRNA fragments. The second region encodes the trypanosome 5.8 S RNA. By RNA sequencing and S1 nuclease mapping, we have identified the processing sites involved in the generation of both of these small RNAs. On the basis of predicted secondary structure models, we infer that all the cleavages apparently occur near the junction of single- and double-stranded regions. The sites involved in the novel LSRNA processing show a clear symmetry with respect to a conserved region of ten base-pairs. No such signals are evident for the processing sites that generate the 5.8 S RNA.

Animals↗
PubMed2004

A brief visual primer for the mapping of mortality trend data.

Maps are increasingly used to visualize and analyze data, yet the spatial ramifications of data structure are rarely considered. Data are subject to transformations made throughout the research process and then used to map, visualize and conduct spatial analysis. We used mortality data to answer three research questions: Are there spatial patterns to mortality, are these patterns statistically significant, and are they persistent across time? This paper provides differential spatial patterns by implementing six data transformations: standardization, cut-points, class size, color scheme, spatial significance and temporal mapping. We use numerous maps and graphics to illustrate the iterative nature of mortality mapping, and exploit the visual nature of the International Journal of Health Geographics journal on the World Wide Web to present researchers with a series of maps.

Journal Article↗
PubMed1997

Visualizing the secondary structure of tubulin: three-dimensional map at 4 A.

We are in the process of determining the structure of tubulin using electron crystallography of zinc-induced, crystalline sheets. We have now extended the resolution to 4 A, and there are many features in the map that appear to show details of the secondary structure. X-ray crystallographers are well aware of the problems of interpreting maps with such limited resolution, and the additional problem of the missing cone of data inherent in electron crystallography may make interpretation even more difficult. To investigate how reliably these maps can be interpreted, we have calculated density maps of a known structure, actin, under conditions similar to those of the tubulin map. Results of these simulations support the limited interpretations we made previously in the 6.5-A maps and the more extensive interpretations we make here in the 4-A map. Most of the secondary structure of the tubulin dimer can now be identified.

Actins↗
PubMed1997

A 1.1-Mb transcript map of the hereditary hemochromatosis locus.

In the process of positionally cloning a candidate gene responsible for hereditary hemochromatosis (HH), we constructed a 1.1-Mb transcript map of the region of human chromosome 6p that lies 4.5 Mb telomeric to HLA-A. A combination of three gene-finding techniques, direct cDNA selection, exon trapping, and sample sequencing, were used initially for a saturation screening of the 1.1-Mb region for expressed sequence fragments. As genetic analysis further narrowed the HH candidate locus, we sequenced completely 0.25 Mb of genomic DNA as a final measure to identify all genes. Besides the novel MHC class 1-like HH candidate gene HLA-H, we identified a family of five butyrophilin-related sequences, two genes with structural similarity to a type 1 sodium phosphate transporter, 12 novel histone genes, and a gene we named RoRet based on its strong similarity to the 52-kD Ro/SSA lupus and Sjogren's syndrome auto-antigen and the RET finger protein. Several members of the butyrophilin family and the RoRet gene share an exon of common evolutionary origin called B30-2. The B30-2 exon was originally isolated from the HLA class 1 region, yet has apparently "shuffled" into several genes along the chromosome telomeric to the MHC. The conservation of the B30-2 exon in several novel genes and the previously described amino acid homology of HLA-H to MHC class 1 molecules provide further support that this gene-rich region of 6p21.3 is related to the MHC. Finally, we performed an analysis of the four approaches for gene finding and conclude that direct selection provides the most effective probes for cDNA screening, and that as much as 30% of ESTs in this 1.1-Mb region may be derived from noncoding genomic DNA.

Amino Acid Sequence↗