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At least 145 records · Page 8Linked to original sources
PubMed1990

A set of tRNAs that lack either the T psi C arm or the dihydrouridine arm: towards a minimal tRNA adaptor.

The mitochondrial DNA (mtDNA) molecules of the nematode worms, Caenorhabditis elegans and Ascaris suum contain 22 putative genes for non-standard forms of tRNAs. The inferred transcripts can be folded into 20 separate structures each resembling a tRNA whose T psi C arm and variable loop are replaced with a simple loop of 6-12 nucleotides. In two further structures [that resemble tRNAs for ser(UCN) and ser(AGN)], the dihydrouridine arm is replaced by a loop of 5-8 nucleotides. By hybridizing mt-tRNA gene-specific oligonucleotide probes to nematode RNAs, we have obtained evidence for transcription of at least nine C.elegans and three A.suum mt-tRNA genes. Each transcript (tRNA) is the exact size predicted from the respective DNA sequence, to which three nucleotides, presumably CCA, have been added following transcription. An exception was C.elegans mt-tRNAasn, most molecules of which had one nucleotide (plus CCA) more than predicted from the gene. The data presented strongly support the conclusion that the functional mt-tRNAs of nematode worms are direct transcripts (with only CCA addition) of the structurally unusual mt-tRNA genes. There is no evidence of trans-splicing or RNA editing to add the sequences missing from these nonstandard tRNAs. We presume, therefore, that the non-standard forms are active in mitochondrial protein synthesis.

Animals↗
PubMed1980

Kinetics of DNA replication in a dicentric X chromosome formed by long arm to long arm fusion.

Utilizing the 5-bromo-deoxyuridine (BrdU) incorporation technique, we have recently studied the DNA replication kinetics in a dicentric X chromosome, formed by long arm-to-long arm fusion at band q23, for a 16-year-old black female with primary amenorrhea. The patient has a karyotype 45,X/46,X,dic(X)(q23). In the buccal smear the presence of X chromatin was found in 33% of the cells examined. The Barr bodies are large and 21% of them are bipartite. DNA replication studies were performed on the patient's lymphocytes by the thymidine pulse (T-pulse) method and confirmed comparatively by the BrdU pulse (B-pulse) method. The results indicate that the dicentric X chromosome is always late-replicating. The replication pattern is symmetric on both sides of the breakpoint and the replication sequence is, in order, p11, p22, q1(1-3), q22, q23, p21, and q21. This finding is comparable to those of other investigators and supports the theory that there exist two inactivation centers in the dicentric X chromosome, located on or near the q21 band.

Amenorrhea↗
PubMed2002

Mapping of DNA markers to arms and sub-arm regions of Nicotiana sylvestris chromosomes using aberrant alien addition lines.

Seven monosomic addition plants, each containing the full complement of Nicotiana plumbaginifolia (2n = 20, genome constitution PP) and an aberrant chromosome of Nicotiana sylvestris (2n = 24, SS), were produced from backcrosses of hyperdiploid derivatives of the sesquidiploid hybrid PPS to N. plumbaginifolia. The N. sylvestris chromosomes in these plants were characterized by karyotype analysis, Southern hybridization with DNA markers previously localized on N. sylvestris chromosomes and a 269-bp fragment from the 3' end of 25S rDNA, and fluorescence in situ hybridization using 25S rDNA, 5S rDNA and telomere repeats (TTTAGGG)(n) as probes. The N. sylvestris chromosomes in these plants were identified to be telocentrics 6S, 7S and 8S, and deletions 7S, 10, 12S and 12L, respectively. The successful identification of aberrant chromosomes in these lines enabled us to assign DNA markers to arms and sub-arm regions of N. sylvestris chromosomes. All aberrant chromosomes in the addition lines could be transmitted through mitosis and meiosis. The potential applications of the addition lines in high-resolution physical mapping, the isolation of N. sylvestris chromosomes by flow cytometry, and an understanding of the chromosomal distribution of 45S rDNA in N. sylvestris are discussed.

Journal Article↗
PubMed1998

Cloning and mapping of bovine ZFX gene to the long arm of the X-chromosome (Xq34) and homologous mapping of ZFY gene to the distal region of the short arm of the bovine (Yp13), ovine (Yp12-p13), and caprine (Yp12-p13) Y chromosome.

A part of mouse Zfy-2 sequence was synthesized and used to screen a genomic library of the spinous country-rat (Tokudaia osimensis spp., 2n = 45). An isolated clone had the C-terminal region of Zfy, which consisted of 1190 bp, encoded 336 amino acid residues, and harbored 11 out of 13 zinc finger motifs. With this as a probe, a bovine testis cDNA library was screened. Two ZFX clones were isolated and their sequences combined. The short sequence, lacking part of the 5' upstream region, was amplified by PCR or RT-PCR, cloned, and sequenced. A full-length ZFX was constructed by combining these three sequences. The bovine ZFX consisted of 5328 bp and encoded 800 amino acid residues, which contained 13 zinc finger motifs. ZFX was used as a probe for fluorescence in situ hybridization and was mapped to Xq34, different from its previously reported site at Xq21-q231. A SINE (short interspersed nuclear element) sequence consisting of 188 bp was found close to the end of the 3'-untranslated region of ZFX. The SINE sequence hybridized to all bovine chromosomes. ZFY is highly homologous with ZFX and, as a result, ZFY could be mapped simultaneously. ZFY was mapped to the distal region of the short arm of the Y Chromosome (Chr) (Yp13), contradicting the previously reported position Yq1. Ovine and caprine ZFY were also mapped with bovine ZFX. Both were mapped to the distal region of the short arm of the Y Chr (Yp12-p13). Ovine ZFX was mapped to a region close to the centromere of the X Chr (Xq13).

Amino Acid Sequence↗
PubMed2005

Best reproducibility of the ankle-arm index was calculated using Doppler and dividing highest ankle pressure by highest arm pressure.

BACKGROUND AND OBJECTIVE: To investigate which method of ankle-arm index (AAI) measurement in terms of selected arteries and blood pressure devices yields the highest reproducibility. STUDY DESIGN AND SETTING: In this cross-sectional study, duplicate AAI measurements were obtained at the right and left side in 320 postmenopausal women. Analyses were done as proposed by Bland and Altman and intraclass correlation coefficients were calculated. RESULTS: The mean and standard deviation (SD) of the first and second systolic blood pressure (SBP) measurement separately did not differ from the mean and SD of the duplicate SBP measurements averaged. Coefficients of repeatability and intraclass correlation coefficients were comparable when the ankle SBP was measured in the posterior tibial artery or dorsalis pedis artery. Coefficients of repeatability as well as the intraclass correlation were better when the SBP in the brachial artery was measured with Doppler than with Dinamap. CONCLUSIONS: To achieve the best reproducibility and smallest systematic difference in the AAI, single SBP measurements should be obtained by Doppler in the brachial artery, posterior tibial artery and dorsalis pedis artery. The AAI should be calculated for each foot separately by dividing the highest ankle SBP by the highest arm SBP.

Aged↗
PubMed2002

The minimal tRNA: unique structure of Ascaris suum mitochondrial tRNA(Ser)(UCU) having a short T arm and lacking the entire D arm.

The tertiary structure of Ascaris suum mitochondrial tRNA(Ser)(UCU) was examined by nuclear magnetic resonance analysis using its transcript, since tRNA(Ser)(UCU), lacking the D arm and possessing a truncated T arm, is the shortest of all the known tRNAs. Most basepairs in the proposed secondary structure of tRNA(Ser)(UCU) were shown to exist, but the connector region comprising the truncated D loop and the extra loop was flexible. This flexibility, would enable adjustment of the mutual distance between the 3'-terminus and the anticodon consistent with that of usual tRNAs. Thus, tRNA(Ser)UCU appears to function in a similar way to that of usual tRNAs in the ribosome.

Animals↗
PubMed1995

Cerebellar and brainstem hypoplasia in a child with a partial monosomy for the short arm of chromosome 5 and partial trisomy for the short arm of chromosome 10.

A child with hypoplasia of the cerebellum and brainstem in association with an unbalanced translocation, resulting in a partial deletion of the short arm of chromosome 5 and a partial trisomy of the short arm of chromosome 10, is described. A balanced translocation was present in his mother and maternal grandmother. A maternal uncle had died at the age of 4 years with the same clinical picture. After reviewing the literature, we conclude that the monosomy 5p is the most likely cause for this malformation. We suggest that the possible existence of chromosomal anomalies should always be considered in the differential diagnosis of hypoplasia of the cerebellum and/or brainstem.

Brain Stem↗
PubMed1975

A patient with congenital anomalies and a deletion of the long arm of the long arm of chromosome 4 [46,XY,del(4)(q31)].

This paper describes the clinical symptoms and cytogenetic findings in a patient previously described in a doctoral thesis (van Kempen, 1969). The patient is a boy with multiple congenital anomalies and a deletion of the long arm of chromosome 4. A recent Giemsa banding study showed absence of the terminal G-band, as was found in the patient described by Golbus et al (1973). The symptoms and other data on the three patients known to have a deletion of the long arm of chromosome 4 are presented to facillitate comparison of these cases. However, the number of cases so far on record is too small to warrant conclusions on the basis of this comparison.

Abnormalities, Multiple↗
PubMed2005

Dissociation of cohesin from chromosome arms and loss of arm cohesion during early mitosis depends on phosphorylation of SA2.

Cohesin is a protein complex that is required to hold sister chromatids together. Cleavage of the Scc1 subunit of cohesin by the protease separase releases the complex from chromosomes and thereby enables the separation of sister chromatids in anaphase. In vertebrate cells, the bulk of cohesin dissociates from chromosome arms already during prophase and prometaphase without cleavage of Scc1. Polo-like kinase 1 (Plk1) and Aurora-B are required for this dissociation process, and Plk1 can phosphorylate the cohesin subunits Scc1 and SA2 in vitro, consistent with the possibility that cohesin phosphorylation by Plk1 triggers the dissociation of cohesin from chromosome arms. However, this hypothesis has not been tested yet, and in budding yeast it has been found that phosphorylation of Scc1 by the Polo-like kinase Cdc5 enhances the cleavability of cohesin, but does not lead to separase-independent dissociation of cohesin from chromosomes. To address the functional significance of cohesin phosphorylation in human cells, we have searched for phosphorylation sites on all four subunits of cohesin by mass spectrometry. We have identified numerous mitosis-specific sites on Scc1 and SA2, mutated them, and expressed nonphosphorylatable forms of both proteins stably at physiological levels in human cells. The analysis of these cells lines, in conjunction with biochemical experiments in vitro, indicate that Scc1 phosphorylation is dispensable for cohesin dissociation from chromosomes in early mitosis but enhances the cleavability of Scc1 by separase. In contrast, our data reveal that phosphorylation of SA2 is essential for cohesin dissociation during prophase and prometaphase, but is not required for cohesin cleavage by separase. The similarity of the phenotype obtained after expression of nonphosphorylatable SA2 in human cells to that seen after the depletion of Plk1 suggests that SA2 is the critical target of Plk1 in the cohesin dissociation pathway.

Amino Acid Substitution↗
PubMed2005

Genome sequence comparative analysis of long arm and short arm of human X chromosome.

30% of the genes tested on Xp escaped inactivation, whereas less than 3% of the genes on Xq escaped inactivation. To investigate the molecular mechanism involved in the propagation and maintenance of X chromosome inactivation and escape, the long arm and short arm of the X chromosome were compared for RNA binding density. Nucleotide sequences on the X chromosome were divided into 50 kb per segment that was recorded as a set of frequency values of 7-nucleotide (7 nt) strings using all possible 7 nt strings (4(7) = 16 384). 120 genes highly expressed in the tonsil germinal center B cells were selected for calculating the 7 nt string frequency values of all introns (intron 7nt). Intron 7nt was considered RNAs (RNA population) that simulated the total of small RNA fragments in cells. Knowing the 7 nt frequency values of DNA segments and the intron 7nt, we can calculate the binding density of DNA segments to the intron 7nt that was termed as RNA binding density. The RNA binding density was determined by the amount of complement sequences. The more amount of complement sequences, the more density of RNA binding. The RNA binding density simulated the total of small RNA fragments bound to the DNA segment. Several principal characteristics were observed for the first time: (1) The mean value of RNA binding density of DNA segments on Xp was significantly higher than that on Xq ( P < 0.001); (2) The numbers of DNA segments highly binding RNAs were more on Xp than on Xq (P < 0.001); (3) The clusters of RNA highly binding DNA segments were associated with regions in which genes escape inactivation. It has been suggested that RNAs activate genes and the interaction of RNA-DNA in cells are extensive, for example, RNAs increase DNase I sensitivity of DNA, there is plenty of nonprotein-coding RNAs in cells, the binding specificity of DNA-RNA is far higher than that of DNA-protein and the affinity of DNA with RNA is increased, as compared with DNA. The nonrandom properties of distribution of RNA highly binding segments between Xp and Xq, combined with the finding of RNA activating genes, provide a strong evidence that RNA highly binding segments may serve as DNA signals to propagate activation along a chromosome and vice versa, the DNA segments that less bind RNAs may silence the genes.

B-Lymphocytes↗
PubMed1978

Complex arming in antibody-dependent cell-mediated cytotoxicity: ultrastructural studies of the interaction between human effector cells armed with aggregated anti-DNP antibody and DNP-coated erythrocytes.

We have examined, by transmission electron microscopy, mixtures of DNP-coated chicken red blood cells and normal human peripheral blood leucocytes 'armed' with alkali-aggregated anti-dinitrophenyl (DNP) antibody. The combination of these observations with chromium release assays enabled us to identify four types of effector cell interacting with the target erythrocytes, viz. phagocytic and non-phagocytic monocytes, neutrophils and lymphocytes. Comparison of these findings with previous work, using antibody-coated targets, allowed us to conclude that the mechanisms and cell types involved are similar. We also demonstrated the short-lived cytotoxic potential of cells armed in this manner.

Antibodies↗
PubMed1999

Simulation of the primate motor cortex and free arm movements in three-dimensional space: a robot arm system controlled by an artificial neural network.

It has been recently discovered that neuronal activity in the primate motor cortex varies in an orderly fashion with the direction of movement of behaving monkeys in three-dimensional (3-D) space. Furthermore, cell activity is highest in a certain direction, the cell's preferred direction, and decreases progressively in other directions. For a particular movement direction, each cell makes a contribution in the direction of its preferred direction to yield a neuronal population vector that points in the direction of movement well before the movement begins. Simulation of motor cortical activity is useful with a randomly selected Poisson distribution. Poisson spike trains are used as input to an artificial neural network (ANN) that produces motor actions in the form of a Cartesian coordinate to a PUMA robotic arm system. The ANN consists of a three-layered feed-forward system that uses a specific cosine algorithm as synaptic weights between the interconnected units described in the angle between the preferred direction vector of the neuron and the movement vector. The robot responds to commands, generating actual trajectories in close agreement with desired trajectories. It is shown that the time-varying motor output is controlled by the impulse activity with a good estimate of the direction of movement with 100-150 cells.

Animals↗
PubMed1996

Sequence analysis of a 40.7 kb segment from the left arm of yeast chromosome X reveals 14 known genes and 13 new open reading frames including homologues of genes clustered on the right arm of chromosome XI.

The complete nucleotide sequence of a 40.7 kb segment about 130 kb from the left end of chromosome X of Saccharomyces cerevisiae was determined from two overlapping cosmids. Computer analysis of that sequence revealed the presence of the previously known genes VPS35, INO1, SnR128, SnR190, MP12, YAK1, RPB4, YUR1, TIF2, MRS3 and URA2, three previously sequenced open reading frames (ORFs) of unknown function 5' of the INO1, 5' of the MP12 and 3' of the URA2 genes and 13 newly identified ORFs. One of the new ORFs is homologous to mammalian glycogenin glycosyltransferases and another has similarities to the human phospholipase D. Some others contain potential transmembrane regions or leucine zipper motifs. The existence of yeast expressed sequence tags for some of the newly identified ORFs indicates that they are transcribed. A cluster of six genes within 10 kb (YUR1, TIF2, two new ORFs, an RSP25 homologue and MRS3) have homologues arranged similarly within 28.5 kb on the right arm of chromosome XI.

Amino Acid Sequence↗
PubMed2004

Detailed comparison between the wheat chromosome group 7 short arms and the rice chromosome arms 6S and 8L with special reference to genes involved in starch biosynthesis.

Rice bacterial artificial chromosome (BAC) clones have been identified that contain sequences orthologous to each EST localized to wheat chromosome 7AS deletion stocks by Southern blot hybridization. This information has been used to relate the DNA sequence included in each wheat deletion stock to a complement of rice BACs. A virtual contig was used that covered 90 cM (21 Mb) of DNA sequence (with a gap for the 6S/8L junction). Comparison of the positions of orthologous genes on the rice virtual contig and on wheat chromosome 7AS showed that there was an unexpectedly low level of synteny (31.4%) and a high level of chromosome rearrangements (68.6%). The non-syntenous loci were of two classes: wheat and rice genes found at different locations in the genome (32.6%), and ESTs in wheat not present in rice (36.0%). Four starch synthetic genes, GBSSI, SSI, SSIIa and DBEI, were located at similar positions on wheat chromosome 7AS and the virtual rice contig covering wheat chromosome 7AS. A preliminary comparison between the short arms of chromosome 7A and 7D in wheat showed that both chromosomes had a similar level of sequence synteny with rice. Therefore, there appears to be considerable variation in gene order between wheat chromosome 7S and rice chromosome 6S and 8L.

Chromosomes, Artificial, Bacterial↗
PubMed2002

Armed therapeutic viruses: strategies and challenges to arming oncolytic viruses with therapeutic genes.

Oncolytic viruses are attractive therapeutics for cancer because they selectively amplify, through replication and spread, the input dose of virus in the target tumor. To date, clinical trials have demonstrated marked safety but have not realized their theoretical efficacy potential. In this review, we consider the potential of armed therapeutic viruses, whose lytic potential is enhanced by genetically engineered therapeutic transgene expression from the virus, as potential vehicles to increase the potency of these agents. Several classes of therapeutic genes are outlined, and potential synergies and hurdles to their delivery from replicating viruses are discussed.

Animals↗