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At least 1,153 records · Page 64Linked to original sources
PubMed1988

Bacteriophage T3 connector: three-dimensional structure and comparison with other viral head-tail connecting regions.

The bacteriophage T3 connector, which consists of 12 copies of protein gp8, has been studied by image processing of electron micrographs from negatively stained ordered aggregates. A three-dimensional reconstruction of T3 connectors was obtained by collection of tilted views and using the direct Fourier method, up to 2.3 nm resolution. The reconstructed unit cell contains two connectors whose main structural features are essentially identical, but facing in opposite directions. The T3 connector has a height of about 10.9 nm, with two clearly defined domains: a wider one 14.4 nm in diameter, with 12 morphological units in the periphery, and a narrower one, 9.7 nm in diameter. There is a channel clearly defined in the narrower domain that almost closes along the wider domain. Comparison of the three-dimensional structure obtained for the connector of phages T3 and phi 29, and that of the neck extracted from phage phi 29 particles, reveals striking similarities and significant differences. A model for a general connector to account for the common functions carried out by these viral assemblies is discussed together with the possible role of the channel for DNA translocation.

Computer Graphics↗
PubMed1996

Juridical and sociocultural problems on the definition of a law concerning property, usage and access to genetic resources in Colombia.

The property, usage, and access to genetic resources, is today one of the primary topics in international business, as a result of the strategic importance of the resources for the biotechnology industry. Internationally, the sovereignty that each country has over its natural patrimony is recognized. However, the new laws of international marketing have obligated countries in the process of development, such as Colombia, to adopt and copy a concept of intellectual property on living resources that does not have anything to do with the country's sociocultural identity, and sometimes even does not take into account its material enjoyment. The new juridical movement that treats genetic resources as private property produces a cultural conflict between indigenous populations, Afro-Americans and peasants, because for them the genetic resources are an element of community life. In these communities, knowledge is freely transmitted; it is an understanding that they have to conserve their agricultural customs and the relationship that they have with the environment. They do not recognize the term "property' according to patenting laws. These elements have to be considered, respected, and guaranteed in the laws that recognize the genetic resources in the country. On the other hand, not even countries that are pioneers in biotechnological development can adopt a concept about patents that is in agreement with the particularities that the living materials possess. This is obviously the reason for the numerous discussions on the legal interpretation, as well as complicated debates in court. Confronting that situation, there are countries rich in biodiversity, such as Colombia, but which do not have a proper concept and are not economically strong in the international context. These countries have to copy inadequate protection policies that do not take into account all their rights. This paper describes some of the technical, juridical, and sociocultural difficulties which Colombia has to confront, in order to set a guideline on patenting living organisms, and on the access and usage of the genetic resources.

Breeding↗
PubMed1991

Sequence variation between alleles reveals two types of copy correction at the 27-kDa zein locus of maize.

In many inbred lines of maize, two 27-kDa storage protein (zein) genes are found within tandem duplications of 12 kb. Both genes of the duplicated allele from the maize inbred line A188 were sequenced and compared to a similar duplicated allele in another inbred line, W22, and to a single-copy allele in the inbred line W64A. The comparisons reveal interesting patterns in the distribution of sequence changes between these alleles. Differences between the two duplicated alleles that are conserved between the two genes of each allele are found exclusively in the 5' region. In contrast, differences between the individual genes of each allele in the 3' region are conserved between the two alleles. The first case is indicative of an intraallelic copy correction mechanism, whereas the second may result from interallelic copy correction. These may be mediated by gene conversion processes, as previously described for other multigene families.

Alleles↗
PubMed1991

Recent advances in the study of electroreception.

Recent studies on electroreception in fish have focused on the structure and function of recurrent descending pathways, efference copy mechanisms, and multiple neuronal maps involved in the processing of sensory information. Studies on a neuronal oscillator have revealed that different neuronal inputs modulate the pattern of oscillations to produce different forms of behavioral output.

Animals↗
PubMed1983

Deletion analysis of a complex promoter for a developmentally regulated gene from Bacillus subtilis.

SpoVG is a developmentally regulated gene from the spore-forming bacterium Bacillus subtilis. The transcription initiation region for spoVG consists of two overlapping promoters whose startpoints of RNA synthesis are ten base pairs apart (Moran et al., 1981a). These startpoints are separately utilized by two forms of RNA polymerase holoenzyme containing different species of B. subtilis sigma factor. We have constructed a series of deletion mutations that extend into the spoVG promoter region from the downstream and from the upstream directions. Transcription studies with these mutated promoters showed that the functional boundaries of the spoVG promoters extended from the region of the transcription startpoints into an upstream A + T-rich box, which was located 76 to 51 base pairs preceding the downstream startsite. We have unexpectedly discovered that propagation of the spoVG promoter region on a high copy number plasmid in B. subtilis interferes with the process of sporulation by impairing development at an early stage. This was not a general effect of promoter amplification, since the propagation on plasmids of two other strong Bacillus promoters had little or no effect on spore formation. Deletion analysis established that the region of spoVG causing sporulation inhibition closely correlated with DNA sequences required for efficient promoter utilization in vitro. We propose that amplification of spoVG titrates a sporulation-specific regulatory protein that binds at or near the region of transcription initiation.

Bacillus subtilis↗
PubMed2003

Dynamic responses of protein homeostatic regulatory mechanisms to perturbations from steady state.

Nineteen hypothetical protein homeostatic regulatory mechanisms were constructed and analysed in terms of the rate at which they recovered from a perturbation in the steady-state concentration of any component. Systems were constructed to symbolize transcription/translation processes of the average protein from Escherichia coli (1000 copies of protein P along with 1 gene G per cell). In some model systems, G catalysed the synthesis of P directly, while in others G catalysed the synthesis of mRNA (called M), and M catalysed the synthesis of P in a subsequent step. Recovery rates for each regulatory mechanism were obtained by generating the corresponding system of differential equations, linearizing the system about the steady state, and determining eigenvalues of the associated coefficient matrix. The optimal rate of recovery for a given mechanism, R(D), was determined by combining random and gradient search approaches to find rate constants for which the system recovered fastest. Regulatory elements that improved dynamic regulation were identified. These consisted of negative feedback relationships that involved P binding to either G (to shut off the synthesis of P) or M (to stimulate its degradation). Regulation improved as increasing numbers of P's bound to either G or M; however, the binding to M was more effective. In other mechanisms PP dimers bound G. Dimer-binding mechanisms were roughly twice as effective in terms of regulation as those that bound P monomers. The effect of linking two regulatory "modules" was also investigated. Linking had no effect on R(D), but optimal rate constants for the linked system were similar to those of the unlinked modules, suggesting that it may be feasible to construct regulatory networks by linking individual modules of this type.

Animals↗
PubMed1989

Confirmation of HIV infection using gene amplification.

Direct recognition of viral gene sequences can be used to detect human immunodeficiency virus (HIV-1) in clinical specimens. A modification of the polymerase chain reaction (PCR) for amplification of gene sequences was used for detection of HIV-1-specific RNA prepared from peripheral blood mononuclear cells (PBMC). The RNA served as a template for reverse transcriptase using primers derived from both the 3'ORF and the LTR regions of HIV-1, as well as from the control cellular sequences encoding beta-actin and T cell receptor. The resultant DNA was amplified with DNA polymerase. A transcriptional step using the bacteriophage T7 promoter recognition sequences, incorporated into the primers, was used to enhance the efficiency of the amplification process. This assay detects as few as 100 RNA copies of cloned HIV-1 genome. Starting with 1 microgram RNA isolated from PBMC, we were able to detect HIV-1 sequences in patients with symptomatic and asymptomatic HIV-1 infection. The inclusion of T cell-specific primers permitted simultaneous evaluation of an immunologic parameter. The PCR can be applied to RNA samples for detection of viral and cellular sequences and is a rapid and efficient means for detection of HIV-1 sequences as well as potentially informative cellular sequences.

Blotting, Western↗
PubMed2003

Lower respiratory tract infections in adults: non-antibiotic prescriptions by GPs.

BACKGROUND: The AIR II study is a prospective multicentre assessing management of lower respiratory tract infections (LRTIs) in adults by general practitioners (GPs). Epidemiological studies generally address the prescriptions of antibiotics. To our knowledge, little is known about the real impact of non-antibiotic therapeutic prescriptions (defined here as co-prescriptions) in LRTI. Therefore, the aim of the study was to evaluate non-antibiotic prescriptions in LRTIs. METHODS: Two thousand general practitioners (GPs) were randomly selected and asked to participate in each of 30 predefined areas covering mainland France. The patient's sociomedical record was completed by the GP during the consultation and sent to the data processing centre at the same time as an anonymous copy of his prescription. The GP also had to report the inclusion by telephone and agree to a telephone appointment with an interviewer. RESULTS: GPs (n = 3144) reported 5469 evaluable cases. Pneumonia accounted for 9.6% of diagnoses, acute exacerbations of chronic bronchitis 14.9% and acute bronchitis 72.5%. Antibiotics were prescribed to 96.5% of patients. In addition to the 5270 prescriptions of antibiotics, co-prescriptions proved to be twice as numerous as prescriptions of antibiotics (10,027 prescriptions for 5115 patients). Mucomodifiers, steroidal anti-inflammatory drugs and bronchodilators were significantly more prescribed in AECB than others. Non-steroidal anti-inflammatory drugs and antitussives were significantly more prescribed in acute bronchitis than AECB or CAP. CONCLUSIONS: Our results suggest that recommendations of management in LRTIs need to take into account co-prescriptions.

Adolescent↗
PubMed1976

Rolling hairpin model for replication of parvovirus and linear chromosomal DNA.

A novel, quasicircular scheme is proposed for the replication of parvovirus DNA. Daughter strands are initiated after the copying and rearrangement of a terminal palindromic sequence, a process termed 'hairpin transfer'. Such a process may be involved in the replication of other viruses and host cell DNA.

Base Sequence↗
PubMedDate not supplied

Evidence of chromosomal instability in prostate cancer determined by spectral karyotyping (SKY) and interphase fish analysis.

The way in which cytogenetic aberrations develop in prostate cancer (CaP) is poorly understood. Spectral karyotype (SKY) analysis of CaP cell lines has shown that they have unstable karyotypes and also have features associated with chromosomal instability (CIN). To accurately determine the incidence of de novo structural and numerical aberrations in vitro in CaP, we performed SKY analysis of three independent clones derived from one representative cell line, DU145. The frequent generation of new chromosomal rearrangements and a wide variation in the number of structural aberrations within two to five passages suggested that this cell line exhibited some of the features associated with a CIN phenotype. To study numerical cell-to-cell variation, chromosome 8 aneusomy was assessed in the LNCaP, DU145, and PC-3 cell lines and a patient cohort of 15 CaP primary tumors by interphase fluorescence in situ hybridization (FISH). This analysis showed that a high frequency of numerical alteration affecting chromosome 8 was present in both in vitro and in CaP tissues. In comparison to normal controls, the patient cohort had a statistically significant (P<.05), greater frequency of cells with one and three centromere 8 copies. These data suggest that a CIN-like process may be contributing towards the generation of de novo numerical and structural chromosome abnormalities in CaP.

Chromosome Aberrations↗
PubMed1991

Development of an integrated filing system for endoscopic images.

A new integrated filing system for endoscopic images has been developed, comprising a main image filing system and subsystems located at different stations. A hybrid filing system made up of both digital and analog filing devices was introduced to construct this system that combines the merits of the two filing methods. Each subsystem provided with a video processor, is equipped with a digital filing device, and routine images were recorded in the analog image filing device of the main system. The use of a multi-input adapter enabled simultaneous input of analog images from up to 8 video processors. Recorded magneto-optical disks make it possible to recall the digital images at any station in the hospital; the disks are copied without image degradation and also utilised for image processing. This system promises reliable storage and integrated, efficient management of endoscopic information. It also costs less to install than the so-called PACS (picture archiving and communication system), which connects all the stations of the hospital using optical fiber cables.

Analog-Digital Conversion↗
PubMed2001

Comparative mapping of RPL3, a gene overexpressed in multiple obesity models.

The ribosomal protein 3 gene is differentially expressed in hypothalamus and brown adipose tissue between mouse lines divergently selected for heat loss, and in skeletal muscle of the ob/ob mouse model. Unfortunately, multiple Rpl3-processed pseudogenes have hampered mapping of the functional gene copy in mammalian species. Using PCR amplification with intronic primer binding, we have mapped Rpl3 to MMU15, and have also localized RPL3 to BTA5 in cattle. Comparative mapping implicates a previously mapped copy of RPL3 on HSA22 as the functional copy of human RPL3, while predictive mapping places the porcine homologue on SSC5.

Animals↗
PubMed1988

DNA sequence (H) curves of the human immunodeficiency virus 1 and some related viral genomes.

The complete nucleotide sequences of several human immunodeficiency virus 1 (HIV-1) genomes were converted by computer to respective H curves. These three-dimensional space curves embody all the information contained in the sequence due to their abstract vectorial structure. For one sequence (HIV-1 isolate BRU) special efforts were made to maximize the available resolution (the number of nucleotides visually discernible within a unit length of the curve) when making a hard, master copy of the H curve. Using a computergraphic/photographic hybrid process the 9191 nucleotides of this HIV-1 sequence were condensed into an H curve of only 37.1 cm vertical length. Although each 1-mm segment of this curve represented 25 nucleotide residues, each of the individual nucleotides of the entire sequence was still distinguishable upon direct inspection using a simple magnifying lens. Several functionally important loci of the HIV-1 sequence could be recognized on the H curve owing to characteristic line forms at corresponding locations. Utilizing H curves of lower resolution, the total nucleotide sequences of several different HIV-1 isolates and related viral sequences [Visna, equine infectious anemia (EIAV), Moloney murine leukemia (Mo-MLV), bovine leukemia (BLV), and human T-cell leukemia, type I (HTLV-I)] were visually compared side by side. An interesting similarity was noted between the location of the S3 fragment of the EIAV sequence and that of a relatively G-C rich region on the env portion of the HIV-1 sequences.

Base Sequence↗
PubMed1994

Gene and allelic genealogies at a gametophytic self-incompatibility locus.

The properties of gene and allelic genealogies at a gametophytic self-incompatibility locus in plants have been investigated analytically and checked against extensive numerical simulations. It is found that, as with overdominant loci, there are two genealogical processes with markedly different time scales. First, functionally distinct allelic lines diverge on an extremely long time scale which is inversely related to the mutation rate to new alleles. These alleles show a genealogical structure which is similar, after an appropriate rescaling of time, to that described by the coalescent process for genes at a neutral locus. Second, gene copies sampled within the same functional allelic line show genealogical relationships similar to neutral gene genealogies but on a much shorter time scale, which is on the same order of magnitude as the harmonic mean of the number of gene copies within an allelic line. These results are discussed in relation to data showing trans-specific polymorphisms for alleles at the gametophytic self-incompatibility locus in the Solanaceae. It is shown that population sizes on the order of 4 x 10(5) and a mutation rate per locus per generation as high as 10(-6) could account for estimated allelic divergence times in this family.

Alleles↗
PubMed2001

Network analysis provides insights into evolution of 5S rDNA arrays in Triticum and Aegilops.

We have used network analysis to study gene sequences of the Triticum and Aegilops 5S rDNA arrays, as well as the spacers of the 5S-DNA-A1 and 5S-DNA-2 loci. Network analysis describes relationships between 5S rDNA sequences in a more realistic fashion than conventional tree building because it makes fewer assumptions about the direction of evolution, the extent of sexual isolation, and the pattern of ancestry and descent. The networks show that the 5S rDNA sequences of Triticum and Aegilops species are related in a reticulate manner around principal nodal sequences. The spacer networks have multiple principal nodes of considerable antiquity but the gene network has just one principal node, corresponding to the correct gene sequence. The networks enable orthologous groups of spacer sequences to be identified. When orthologs are compared it is seen that the patterns of intra- and interspecific diversity are similar for both genes and spacers. We propose that 5S rDNA arrays combine sequence conservation with a large store of mutant variations, the number of correct gene copies within an array being the result of neutral processes that act on gene and spacer regions together.

Algorithms↗
PubMed2006

Pervasive purifying selection characterizes the evolution of I2 homologs.

We sampled 384 sequences related to the Solanum pimpinellifolium (=Lycopersicon pimpinellifolium) disease resistance (R) gene 12 from six species, potato, S. demissum, tomato, eggplant, pepper, and tobacco. These species represent increasing phylogenetic distance from potato to tobacco, within the family Solanaceae. Using sequence data from the nucleotide binding site (NBS) region of this gene, we tested models of gene family evolution and inferred patterns of selection acting on the NBS gene region and I2 gene family. We find that the I2 family has diversified within the family Solanaceae for at least 14 million years and evolves through a slow birth-and-death process requiring approximately 12 million years to homogenize gene copies within a species. Analyses of selection resolved a general pattern of strong purifying selection acting on individual codon positions within the NBS and on NBS lineages through time. Surprisingly, we find nine codon positions strongly affected by positive selection and six pairs of codon positions demonstrating correlated amino acid substitutions. Evolutionary analyses serve as bioinformatic tools with which to sort through the vast R gene diversity in plants and find candidates for new resistance specificities or to identify specific amino acid positions important for biochemical function. The slow birth-and-death evolution of I2 genes suggests that some NBS-leucine rich repeat-mediated resistances may not be overcome rapidly by virulence evolution and that the natural diversity of R genes is a potentially valuable source for durable resistance.

DNA-Binding Proteins↗
PubMed2004

Polymorphisms in the prion precursor functional gene but not the pseudogene are associated with susceptibility to chronic wasting disease in white-tailed deer.

Chronic wasting disease (CWD) status and PrP genotypes were determined for a group of 133 wild white-tailed deer in a 780 acre enclosure in western Nebraska, USA. Approximately half of the deer tested showed evidence of PrPd in the brainstem or lymphoid tissues. Four PRNP alleles encoding amino acid substitutions were identified, with substitutions at residues 95 (Q-->H), 96 (G-->S) or 116 (A-->G), each with serine (S) at residue 138. In addition, a processed pseudogene with two alleles encoding five or six copies of the octapeptide repeat was identified in 26 % of the deer. Both alleles encoded asparagine (N) at residue 138. The functional gene alleles sorted into five major diploid genotypes and four rare genotypes. Although all five major diploid genotypes were found in deer with CWD, unaffected deer were less likely to have the allele QGAS and more likely to have QSAS compared with CWD-affected deer. Late-stage disease (PrPd in brainstem) was noted in deer less than 1 year of age, although no single genotype was associated with this rapid neuroinvasion. Early-stage disease (PrPd distribution limited to the lymphoid system) was observed in deer estimated to be more than 5 years old, suggesting that they were infected as adults or that the incubation time might be extremely long in some individuals. The pseudogene was found in deer of all major PRNP genotypes and was not correlated with CWD status. The large number of susceptible genotypes and the possibility of adult-to-adult transmission suggest that much of the white-tailed deer population may be at risk for disease following exposure to CWD, despite the association of specific genotypes with CWD noted here.

Age Factors↗
PubMed2004

Recolonization and radiation in Larix (Pinaceae): evidence from nuclear ribosomal DNA paralogues.

Gene paralogy frequently causes the conflict between gene tree and species tree, but sometimes the coexistence of a few paralogous copies could provide more markers for tracing the phylogeographical process of some organisms. In the present study, nrDNA ITS paralogues were cloned from all but one species of Larix, an Eocene genus having two sections, Larix and Multiserialis, with a huge circumboreal distribution and an Eastern Asia-Western North America disjunction, respectively. A total of 96 distinct clones, excluding five putative pseudogenes or recombinants, were obtained and used in the gene genealogy analysis. The clones from all Eurasian species of section Larix are mixed together, suggesting that recolonization and recent morphological differentiation could have played important roles in the evolution of this section. In contrast, the species diversification of the Eurasian section Multiserialis may result from radiation in the east Himalayas and its vicinity, considering extensive nrDNA founder effects in this group. Our study also suggests that the distribution pattern analysis of members of multiple gene family would be very useful in tracking the evolutionary history of some taxa with recent origin or rapid radiation that cannot be resolved by other molecular markers.

Base Sequence↗