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PubMed2006

Mutation analysis of five candidate genes in familial breast cancer.

Most of the known breast cancer susceptibility genes (BRCA1, BRCA2, CHEK2 and ATM) are involved in the damage response pathway. Other members of this pathway are therefore good candidates for additional breast cancer susceptibility genes. ATR, along with ATM, plays a central role in DNA damage recognition and Chk1 relays checkpoint signals from both ATR and ATM. PPP2R1B and PPP2R5B code for subunits of protein phosphatase 2A (PP2A), which regulates autophosphorylation of ATM. In addition, EIF2S6/Int-6, which was originally identified as a common integration site for the mouse mammary tumour virus in virally induced mouse mammary tumours, is a candidate breast cancer susceptibility gene because of its putative role in maintaining chromosome stability. To investigate the role of ATR, CHK1, PPP2R1B, PPP2R5B and EIF2S6/Int-6, we carried out mutation analysis of these genes in the index cases from non-BRCA1/BRCA2 breast cancer families. We also screened sporadic breast tumours for somatic mutations in PPP2R1B and PPP2R5B. Although we identified many novel variants, we found no evidence that highly penetrant germline mutations in these five genes contribute to familial breast cancer susceptibility.

Adolescent↗

PubMed1988

Structure and organization of Marchantia polymorpha chloroplast genome. I. Cloning and gene identification.

We have determined the complete nucleotide sequence of chloroplast DNA from a liverwort, Marchantia polymorpha, using a clone bank of chloroplast DNA fragments. The circular genome consists of 121,024 base-pairs and includes two large inverted repeats (IRA and IRB, each 10,058 base-pairs), a large single-copy region (LSC, 81,095 base-pairs), and a small single-copy region (SSC, 19,813 base-pairs). The nucleotide sequence was analysed with a computer to deduce the entire gene organization, assuming the universal genetic code and the presence of introns in the coding sequences. We detected 136 possible genes. 103 gene products of which are related to known stable RNA or protein molecules. Stable RNA genes for four species of ribosomal RNA and 32 species of tRNA were located, although one of the tRNA genes may be defective. Twenty genes encoding polypeptides involved in photosynthesis and electron transport were identified by comparison with known chloroplast genes. Twenty-five open reading frames (ORFs) show structural similarities to Escherichia coli RNA polymerase subunits, 19 ribosomal proteins and two related proteins. Seven ORFs are comparable with human mitochondrial NADH dehydrogenase genes. A computer-aided homology search predicted possible chloroplast homologues of bacterial proteins; two ORFs for bacterial 4Fe-4S-type ferredoxin, two for distinct subunits of a protein-dependent transport system, one ORF for a component of nitrogenase, and one for an antenna protein of a light-harvesting complex. The other 33 ORFs, consisting of 29 to 2136 codons, remain to be identified, but some of them seem to be conserved in evolution. Detailed information on gene identification is presented in the accompanying papers. We postulated that there were 22 introns in 20 genes (8 tRNA genes and 12 ORFs), which may be classified into the groups I and II found in fungal mitochondrial genes. The structural gene for ribosomal protein S12 is trans-split on the opposite DNA strand. The universal genetic code was confirmed by the substitution pattern of simultaneous codons, and by possible codon recognition of the chloroplast-encoded tRNA molecules, assuming no importation of tRNA molecules from the cytoplasm. The nucleotide residue A or T is preferred at the third position of the codons (G+C, 11.9%) and in intergenic spacers (G+C, 19.5%), resulting in an overall G+C content that is low (28.8%) throughout the liverwort chloroplast genome. Possible gene expression signals such as promoters and terminators for transcription, predicted locations of gene products, and DNA replicative origins are discussed.

Base Sequence↗

PubMed1993

IL-2 regulates the expression of the NK-TR gene via an alternate RNA splicing mechanism.

We have recently isolated and characterized human and mouse genes of a putative natural killer (NK) cell tumour-recognition protein (NK-TR) that is specifically expressed in NK cells. This gene codes for a 150 kD protein with a cyclophilin-related amino terminus followed by several positively charged domains. We report here the discovery of two sites of alternate splicing in the 5' region of the NK-TR mRNA. One of these events caused a frameshift in the open reading frame by splicing in a 28 bp exon within the cyclophilin coding region, resulting in the premature termination of the NK-TR protein. The second alternate splice stemmed from the use of an internal splice acceptor within an exon, producing a deletion of 25 amino acids in the NK-TR protein. The activation of NK cells by IL-2 produced a change in the splicing pattern that resulted in increased production of mRNAs capable of producing the complete NK-TR protein.

Alternative Splicing↗

PubMed2005

Response patterns in adult forest trees to chronic ozone stress: identification of variations and consistencies.

The responsiveness of adult beech and spruce trees to chronic O(3) stress was studied at a free-air O(3) exposure experiment in Freising/Germany. Over three growing seasons, gas exchange characteristics, biochemical parameters, macroscopic O(3) injury and the phenology of leaf organs were investigated, along with assessments of branch and stem growth as indications of tree performance. To assess response pattern to chronic O(3) stress in adult forest trees, we introduce a new evaluation approach, which provides a comprehensive, readily accomplishable overview across several tree-internal scaling levels, different canopy regions and growing seasons. This new approach, based on a three-grade colour coding, combines statistical analysis and the proficient ability of the "human eye" in pattern recognition.

Air Pollutants↗

PubMed2006

Discovery, cloning and heterologous expression of secreted potato proteins reveal erroneous pre-mRNA splicing in Aspergillus oryzae.

A novel transposon assisted signal trapping (TAST) technology, developed to specifically select only the secreted proteins, was used to discover novel extracellular plant proteins from Solarium tuberosum infected with Phytophthora infestans. Analysis of 384 hits provided 191 P. infestans and S. tuberosum sequences of secreted proteins, with an approx. 2/3 of these originating from potato. Subsequent screening for interesting genes was carried out using bioinformatics. A selected variety of the discovered sequences are presented, including a novel S. tuberosum xyloglucan endotransglucosylase (StXTH), which was cloned and subjected to detailed heterologous expression studies in Aspergillus oryzae. RT-PCR analysis of mRNA from A. oryzae StXTH1 transformants revealed that parts of the mRNA pool had been incorrectly processed, and only weak and inconsistent indications of active protein could be detected. A high AT content of StXTH1 and the occurrence of A. oryzae intron donor, acceptor, and branch point recognition sites resulted in erroneous intron interpretation (cryptic introns) of parts of the mRNA coding sequence. This may explain the difficulties generally experienced in expressing plant genes in filamentous fungi.

Aspergillus oryzae↗

PubMed2004

View-independent coding of face identity in frontal and temporal cortices is modulated by familiarity: an event-related fMRI study.

Face recognition is a unique visual skill enabling us to recognize a large number of person identities, despite many differences in the visual image from one exposure to another due to changes in viewpoint, illumination, or simply passage of time. Previous familiarity with a face may facilitate recognition when visual changes are important. Using event-related fMRI in 13 healthy observers, we studied the brain systems involved in extracting face identity independent of modifications in visual appearance during a repetition priming paradigm in which two different photographs of the same face (either famous or unfamiliar) were repeated at varying delays. We found that functionally defined face-selective areas in the lateral fusiform cortex showed no repetition effects for faces across changes in image views, irrespective of pre-existing familiarity, suggesting that face representations formed in this region do not generalize across different visual images, even for well-known faces. Repetition of different but easily recognizable views of an unfamiliar face produced selective repetition decreases in a medial portion of the right fusiform gyrus, whereas distinct views of a famous face produced repetition decreases in left middle temporal and left inferior frontal cortex selectively, but no decreases in fusiform cortex. These findings reveal that different views of the same familiar face may not be integrated within a single representation at initial perceptual stages subserved by the fusiform face areas, but rather involve later processing stages where more abstract identity information is accessed.

Adult↗

PubMed2001

Episodic retrieval is reflected by a process specific increase in human electroencephalographic theta activity.

Is an increase in theta during retrieval due (primarily) to the access of a stored code or to more general processes? The electroencephalogram was recorded while subjects performed a recognition task with pictures. According to the event-related desynchronization/synchronization method, the percentage of band power changes was calculated during encoding and retrieval for a theta and three alpha bands. Significant results were obtained (with minor exceptions) only in the theta band. The increase in theta was significantly larger during retrieval than during encoding but did not differ significantly between new and successfully retrieved old pictures. Because a memory trace is lacking for new pictures, the increase in theta during retrieval reflects primarily general processing demands of a complex episodic memory system.

Adult↗

PubMed2003

mRNA 5' region sequence incompleteness: a potential source of systematic errors in translation initiation codon assignment in human mRNAs.

The amino acid sequence of gene products is routinely deduced from the nucleotide sequence of the relative cloned cDNA, according to the rules for recognition of start codon (first-AUG rule, optimal sequence context) and the genetic code. From this prediction stem most subsequent types of product analysis, although all standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. Revision by bioinformatics and cloning methods of 109 known genes located on human chromosome 21 (HC 21) shows that 60 mRNAs lack any in-frame stop upstream of the first-AUG, and that in five cases (DSCR1, KIAA0184, KIAA0539, SON, and TFF3) the coding region at the 5' end was incompletely characterized in the original descriptions. We describe the respective consequences for genomic annotation, domain and ortholog identification, and functional experiments design. We have also analyzed the sequences of 13,124 human mRNAs (RefSeq databank), discovering that in 6448 cases (49%), an in-frame stop codon is present upstream of the initiation codon, while in the other 6676 mRNAs (51%), identification of additional bases at the mRNA 5' region could well reveal some new upstream in-frame AUG codons in the optimal context. Proportionally to the HC 21 data, about 550 known human genes might thus be affected by this 5' end mRNA artifact.

5' Untranslated Regions↗

PubMed2004

Sequence-specific gene silencing in mammalian cells by alkylating pyrrole-imidazole polyamides.

Gene silencing was examined by sequence-specific alkylation of DNA by N-methylpyrrole (Py)-N-methylimidazole (Im) hairpin polyamides. Polyamides ImImPyPygammaImImPyLDu86 (A) and ImImPyPygammaImPyPyLDu86 (B) selectively alkylated the coding regions of the renilla and firefly luciferases, respectively, according to the base pair recognition rule of Py-Im polyamides. Two different plasmids, encoding renilla luciferase and firefly luciferase, were used as vectors to examine the effect of alkylation on gene silencing. Transfection of the alkylated luciferase vectors-by polyamide A or B-into HeLa, 293, and NIH3T3 cells demonstrated that these sequence-specific DNA alkylations lead to selective silencing of gene expression. Next, the vectors were cotransfected into HeLa cells and the cells were treated with polyamide A or B. Selective reduction of luciferase activities was caused by both polyamides. On the basis of this sequence-specific alkylation and gene silencing activity, these alkylating Py-Im polyamides thus have potential as antitumor drugs to target specific gene expression in human cells.

Alkylation↗

PubMed1999

The impact of attitudes on memory: an affair to remember.

Many theories of the effects of attitudes on memory for attitude-relevant information would predict that attitudinally congenial information should be more memorable than uncongenial information. Yet, this meta-analysis showed that this congeniality effect is inconsistent across the experiments in this research literature and small when these effects are aggregated. The tendency of the congeniality effect to decrease over the years spanned by this literature appeared to reflect the weaker methods used in the earlier studies. The effect was stronger in 2 kinds of earlier experiments that may be tinged with artifact: those in which the coding of recall measures was not known to be blind and those that used recognition measures that were not corrected for bias. Nonetheless, several additional characteristics of the studies moderated the congeniality effect and suggested that both attitude structure and motivation to process attitude-relevant information are relevant to understanding the conditions under which people have superior memory for attitudinally congenial or uncongenial information.

Attitude↗

PubMed1980

In vitro suppression of UGA codons in a mitochondrial mRNA.

Although both prokaryotic and eukaryotic messenger RNAs can be easily translated in heterologous protein-synthesizing systems, attempts to achieve correct synthesis of mitochondrial proteins by translation of mitochondrial mRNAs in such systems have failed. In general, the products of synthesis are of low molecular weight and presumably represent fragments of mitochondrial proteins. These fragments display a strong tendency to aggregate. Explanations have included the use by mitochondria of codons requiring a specialized tRNA population and the fortuitous occurrence within genes of purine-rich sequences resembling bacterial ribosome binding sites. In addition, the long 5'-leader sequences present in many mitochondrial (mt) RNAs may also contribute to difficulties in mRNA recognition by heterologous ribosomes. Recent sequence analysis of human mtDNA suggests that the genetic code used by mammalian mitochondria deviates in a number of respects from the 'universal' code, the most striking of these being the use of the UGA termination codon to specify tryptophan. That this may also apply in yeast mitochondria has been shown by Fox and Macino et al., thus providing an obvious and easily testable explanation for the inability of heterologous systems to synthesize full-length mitochondrial proteins. We confirm this explanation and describe here the in vitro synthesis of a full-length subunit II of yeast cytochrome c oxidase in a wheat-germ extract supplemented with a partially purified mitochondrial mRNA for this protein and a UGA-suppressor tRNA from Schizosaccharomyces pombe.

Codon↗

PubMed1979

HLA-linked genetic control of the specicity of human cytotoxic T-cell responses to influenza virus.

We have investigated elements of the genetic control of human in vitro cytotoxic T-cell responses to influenza virus-infected autologous cells by studies of a large family. The pattern of virus-immune cytotoxicity among siblings demonstrated T-cell recognition of influenza virus predominantly (greater than 90%) in association with determinants which are coded by genes linked to HLA (P less than 0.0002). Many family members consistently generated cytotoxic activity against influenza predominantly in association with antigens coded by genes of only one of their HLA haplotypes. Such haplotype preferences were consistent among HLA-identical siblings, indicating that the specificity of the T-cell response to influenza virus in association with HLA-A and -B antigens is controlled by genes linked to HLA.

Cytotoxicity, Immunologic↗

PubMed1982

A flexible new computer program for handling DNA sequence data.

A compact new computer program for handling nucleic acid sequence data is presented. It consists of a number of different subsets, which may be used according to a given code system. The program is designed for the determination of restriction enzyme and other recognition sites in correlation with translation patterns, and allows tabulation of codon frequencies and protein molecular weights within specified gene boundaries. The program is especially designed for detection of overlapping genes. The language, is FORTRAN and thus the program may be used on small computers; it may also be used without any prior computer experience. Copies are available on request.

Amino Acid Sequence↗

PubMed1999

Human hepatic glyceraldehyde-3-phosphate dehydrogenase binds to the poly(U) tract of the 3' non-coding region of hepatitis C virus genomic RNA.

The unique poly(U/UC) tract, the middle part of the tripartite 3' non-coding region (3'NCR) of hepatitis C virus (HCV) genomic RNA, may represent a recognition signal for the HCV replicase complex. In this study, several proteins binding specifically to immobilized ribooligonucleotide r(U)(25) mimicking this structure were identified using cytosolic extracts from HCV-negative or -positive liver explants, and a prominent 36 kDa protein was studied further. Competition experiments including homoribopolymers revealed binding affinities in the order: oligo/poly(U)>(A)>(C)>(G). The protein was identified as glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a multifunctional protein known to bind RNA. GAPDH bound efficiently to the full-length HCV RNA and binding to various 3'NCR constructs revealed critical dependence upon the presence of the middle part of the 3'NCR. Polypyrimidine tract-binding protein, described previously to bind the 3'NCR, did not bind efficiently to the middle part of 3'NCR and was captured from liver extracts in considerably smaller quantities.

3' Untranslated Regions↗

PubMed2006

EEG evidence for the presence of an action observation-execution matching system in children.

In the adult human brain, passive observation of actions performed by others activates some of the same cortical areas that are involved in the execution of actions, thereby contributing to action recognition. This mechanism appears to occur through activation of a population of action-coding cells known as mirror neurons (MN). In the adult motor cortex, performing actions and observing human movement reduces the magnitude of the mu (8-13 Hz) rhythm, possibly reflecting MN system activity. Despite the wealth of information available regarding the adult MN system, little is known about its existence in children. Here, we used EEG to probe mu rhythm modulation in 15 children during observation and execution of hand actions. Our data show that mu rhythm attenuation occurs in children under 11 years old during observation of hand movements. Similarly to what has been reported in adults, observation of goal/object-orientated movement produces greater modulation of the mu rhythm than intransitive movement. These data confirm the existence of an observation-execution matching system in the immature human brain and may be of clinical value in the understanding of neurodevelopmental disorders associated with a faulty MN system, such as autism spectrum disorder.

Brain Mapping↗

PubMed2006

Haematopoietic stem cells and mesenchymal stem cells as tools for present and future cellular therapies.

Postnatal stem cells are present in many adult tissues, and are thought to ensure homoeostasis by replacing functionally declining cells by newly differentiated ones. Postnatal stem cells used as such or after in vitro manipulation hold out strong hopes for reconstructive therapies. For instance, the grafting of native haematopoietic stem cells (HSC) restores haematopoiesis in genetically deficient individuals or in lethally conditioned leukaemic patients, and systemic injection of in vitro amplified mesenchymal stem cells (MSC) induces recovery of bone growth in patients with osteogenesis imperfecta. Moreover, cells differentiated in vitro from postnatal stem cells exhibiting a specific function can also be used for cell therapy. Myeloid dendritic cells (DC) derived from cultures of HSC may induce tumour-specific cytotoxic T lymphocytes to eradicate the tumour via antigen recognition. In addition, long-lived MSC has been engineered to secrete specific proteins coded by a transgene and used as a source of therapeutic molecules in vivo. All these approaches require large quantities of cells that cannot be obtained (with the exception of HSC) directly from the donor. In vitro procedures allowing the production of therapeutic cells from postnatal stem cells are needed and are at present under development. Below we discuss the rationale and methods currently available for generation of therapeutic cells derived from haematopoietic and mesenchymal stem cells.

Animals↗

PubMed1975

Young children's coding and storage of visual and verbal material.

36 preschool children (mean age 4.2 years) were each tested on 3 recognition memory lists differing in test mode (visual only, verbal only, combined visual-verbal). For one-third of the children, original list presentation was visual only, for another third, presentation was verbal only, and the final third received combined visual-verbal presentation. The subjects generally performed at a high level of correct responding. Verbal-only presentation resulted in less correct recognition than did either visual-only or combined visual-verbal presentation. However, because performances under both visual-only and combined visual-verbal presentation were statistically comparable, and a high level of spontaneous labeling was observed when items were presented only visually, a dual-processing conceptualization of memory in 4-year-olds was suggested.

Acoustic Stimulation↗

PubMed1992

Cytotoxic T lymphocytes do not appear to select for mutations in an immunodominant epitope of simian immunodeficiency virus gag.

Studies to date assessing HIV escape from CTL in vivo have yielded conflicting results. Previous studies have demonstrated that simian immunodeficiency virus of macaques (SIVmac)-infected rhesus monkeys expressing the MHC class I allele Mamu-A*01 reproducibly develop a gag-specific CTL response limited to a 9-amino acid epitope of the SIVmac gag protein (residues 182-190 within peptide 11C). To determine whether CTL have a role in selecting for AIDS virus mutants, we examined mutations in SIVmac proviral DNA encoding this gag CTL epitope in PBL of infected rhesus monkeys. Three Mamu-A*01+ rhesus monkeys were infected with SIVmac and assessed for gag- and peptide 11C-specific CTL responses. This specific CTL response was maintained in two monkeys, but lost in the third animal 2 yr after infection. The generation of proviral gag mutations was then determined by sequencing 500-bp proviral fragments amplified from fresh PBL obtained from the monkeys more than 2.5 yr after infection. Although numerous point mutations were characterized in 131 polymerase chain reaction-generated clones of SIVmac gag, only four mutations within the gag CTL epitope-coding region of the genome were identified. Comparison of synonymous and nonsynonymous nucleotide substitutions in the regions encoding peptide 11C (p11C) and the flanking gag protein indicated a lack of selective pressure for viral mutations in the CTL epitope coding region. Interestingly, a predominant gag mutant encoding a single amino acid change in p11C was found in a monkey which lost its CTL activity. However, even in this setting there was no evidence for selection of mutations in the CTL epitope coding region when compared with the flanking region. Furthermore, synthetic peptides corresponding to all naturally occurring variants in the gag epitope-coding region were recognized by cloned and bulk cultured effector cells of the infected monkeys with persistent CTL. These results indicate that SIVmac gag- and p11C-specific CTL do not select for mutations in the immunodominant epitope-coding region and that the naturally occurring mutants do not appear to escape CTL recognition.

Amino Acid Sequence↗