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At least 649 records · Page 36Linked to original sources
PubMed2004

Evolving new genetic codes.

Although the genetic code is almost universal, natural variations exist that have caused evolutionary biologists to speculate about codon evolution. There are two predominant hypotheses that specify either a gradual (ambiguous intermediate) or stochastic (codon capture) change in the code. These hypotheses are similar to two biotechnology techniques that have been used to engineer the genetic code: a 'top down' approach, in which the whole organism is evolved for the ability to incorporate unnatural amino acids, and a 'bottom up' approach, in which aminoacyl-tRNA synthetases and their cognate tRNAs are engineered. The biotechnology experiments provide insights into natural codon evolution, and a combination of these approaches should enable the evolution of organisms that can incorporate unnatural amino acids throughout their proteomes.

Journal Article↗
PubMed2003

Adaptation to display rotation and display gain distortions during drawing.

The relationship between movement extent and movement direction coding mechanisms was investigated using a visuomotor adaptation paradigm. To determine if these mechanisms are either modular or interdependent, young healthy college students were tested while they performed a visually guided drawing task that incorporated varying combinations of movement distance and direction distortions. Analysis of participants' standardized movement duration, initial directional error, and movement length over the course of the adaptation process revealed a certain degree of interdependence between direction and extent coding mechanisms. Specifically, changes in final adaptation levels and after-effects depended on the order of introduction of the visual distortions. This interaction can be characterized as unidirectional, where alterations in rotational feedback interfere with subsequent adaptation to gain changes, whereas alterations in "display gain" do not significantly impede the adaptation to "display rotation". Moreover, simultaneous exposure to gain and rotational distortions resulted in better learning. The results argue against an independent coding of movement direction and extent during adaptation by the central nervous system.

Adaptation, Physiological↗
PubMed1986

Nucleotide and derived amino acid sequences of a cDNA coding for pre-uteroglobin from the lung of the hare (Lepus capensis).

An almost full-length cDNA coding for pre-uteroglobin from hare lung was cloned and sequenced. The derived amino acid sequence indicated that hare pre-uteroglobin contained 91 amino acids, including a signal peptide of 21 residues. Comparison of the nucleotide sequence of hare pre-uteroglobin cDNA with that previously reported for the rabbit gene indicated five silent point substitutions and six others leading to amino acid changes in the coding region. The untranslated regions of both pre-uteroglobin mRNAs were very similar. The amino acid changes observed are discussed in relation to the different progesterone-binding abilities of both homologous proteins.

Amino Acid Sequence↗
PubMed1999

Elucidating sequence codes: three codes for evolution.

The sequences are related to evolution in several ways. First, they carry traces of a distant past. Two sequence features point to the earliest sequence organization. The universal hidden GCU-periodical pattern in mRNA suggests the earliest codons: GCU and its nine-point-change derivatives. They code for seven amino acids that by several criteria are also the oldest. Together it makes the earliest form of the triplet code, still recognizable in the extant sequences. Another feature present in the sequences, apparently, since separation of prokaryotes and eukaryotes, is hidden genome segmentation. Both protein-coding and noncoding sequences appear to have been formed by fusion of standard size units, about 360 bp (120 aa) in eukaryotes and 450 bp (150 aa) in prokaryotes. Presumably, the units have been functioning at some stage of evolution as autonomous single-gene size elements. There are sequence designs that promote evolution. One such design suitable for fast adaptation is the tandem repetition of identical sequences, so that their copy numbers in the repeat arrays would modulate (tune) the expression of nearby genes. The tandem repeat expansion diseases illustrate this mechanism in a dramatic way: overtuning of the respective gene expression leads to the disease.

Adaptation, Biological↗
PubMed2002

Temporal pitch in electric hearing.

Both place and temporal codes in the peripheral auditory system contain pitch information, however, their actual use by the brain is unclear. Here pitch data are reported from users of the cochlear implant, which provides the ability to change the temporal code independently from the place code. With fixed electrode stimulation, both frequency discrimination and pitch estimate data show that the cochlear implant users can only discern differences in pitch for frequencies up to about 300 Hz. An integration model can predict pitch estimation from frequency discrimination, reinforcing Fechner's hypothesis relating sensation magnitude to stimulus discriminability. The present results suggest that 300 Hz is the upper boundary of the temporal code and that the absolute place information should be included in the present pitch models. They further suggest that future cochlear implants need to increase the number of independent electrodes to restore normal pitch range and resolution.

Adult↗
PubMed2000

[History of medical ethics in Korea: focused on analysis of medical codes and covenants].

This article deals with the emergence of the codes of medical ethics and their change in Korean history. The modernized medical codes or covenants by the group of medical doctors has been made from the mid-twentieth century, although Korea has a long tradition of medical ethics, so called the Confucian medical ethics, Insul or Uido which were taken on very strong paternalistic characters. The history of the codes of medical ethics in contemporary Korea showed several revisions in 1961, 1965, 1979, and 1997 since the first establishment in 1955. Changes of political circumstances, the cultural level of the people, medical care system, and medical power leaded to the revisions. Throughout the revisions the codes or covenants of medical ethics in Korea has changed from simple translations of the codes by the World Medical Association and the American Medical Association to the reflexes of domestic medical situations; from the ones based on paternalistic doctor-patient relationship to more democratic ones; from the ones that only medical ethics were expressed to the ones that bioethics was expressed too.

Ethics, Medical↗
PubMed2004

Alterations of the tumor suppressor gene Parkin in non-small cell lung cancer.

PURPOSE: Parkin, a gene mutated in autosomal recessive juvenile Parkinsonism and mapped to the common fragile site FRA6E on human chromosome 6q25-q27, is associated with a frequent loss of heterozygosity and altered expression in breast and ovarian carcinomas. In addition, homozygous deletions of exon 2 creating deleterious truncations of the Parkin transcript were observed in the lung adenocarcinoma cell lines Calu-3 and H-1573, suggesting that the loss of this locus and the resulting changes in its expression are involved in the development of these tumors. EXPERIMENTAL DESIGN: We examined 20 paired normal and non-small cell lung cancer samples for the presence of Parkin alterations in the coding sequence and changes in gene expression. We also restored gene expression in the Parkin-deficient lung carcinoma cell line H460 by use of a recombinant lentivirus containing the wild-type Parkin cDNA. RESULTS: Loss of heterozygosity analysis identified a common region of loss in the Parkin/FRA6E locus with the highest frequency for the intragenic marker D6S1599 (45%), and semi-quantitative reverse transcription-PCR revealed reduced expression in 3 of 9 (33%) lung tumors. Although we did not observe any in vitro changes in cell proliferation or cell cycle, ectopic Parkin expression had the ability to reduce in vivo tumorigenicity in nude mice. CONCLUSION: These data suggest that Parkin is a tumor suppressor gene whose inactivation may play an important role in non-small cell lung cancer tumorigenesis.

Animals↗
PubMed2000

Representation of waveform periodicity in the auditory midbrain of the bullfrog, Rana catesbeiana.

The period of complex signals is encoded in the bullfrog's eighth nerve by a synchrony code based on phase-locked responding. We examined how these arrays of phase-locked activity are represented in different subnuclei of the auditory midbrain, the torus semicircularis (TS). Recording sites in different areas of the TS differ in their ability to synchronize to the envelope of complex stimuli, and these differences in synchronous activity are related to response latency. Cells in the caudal principal nucleus (cell sparse zone) have longer latencies, and show little or no phase-locked activity, even in response to low modulation rates, while some cells in lateral areas of the TS (magnocellular nucleus, lateral part of principal nucleus) synchronize to rates as high as 90-100 Hz. At midlevels of the TS, there is a lateral-to-medial gradient of synchronization ability: cells located more laterally show better phaselocking than those located more medially. Pooled all-order interval histograms from short latency cells located in the lateral TS represent the waveform periodicity of a biologically relevant complex harmonic signal at different stimulus levels, and in a manner consistent with behavioral data from vocalizing male frogs. Long latency cells in the caudal parts of the TS (cell sparse zone, caudal magnocellular nucleus) code stimulus period by changes in spike rate, rather than by changes in synchronized activity. These data suggest that neural codes based on rate processing and time domain processing are represented in anatomically different areas of the TS. They further show that a populationbased analysis can increase the precision with which temporal features are represented in the central auditory system.

Acoustic Stimulation↗
PubMed2003

The epigenome as a target for cancer chemoprevention.

Epigenetic events, a key driving force in the development of cancer, are alterations in gene expression without changes in the DNA coding sequence that are heritable through cell division. Such changes occur throughout all stages of tumorigenesis, including the early phases, and are increasingly recognized as major mechanisms involved in silencing tumor suppressor genes. Epigenetic changes can be reversed by the use of small molecules and, thus, such changes are promising targets for cancer chemopreventive drug development. This review examines the basis for targeting the epigenome as a prevention strategy, focusing on understanding the epigenetic changes that occur before the development of frank malignancy, when chemopreventive intervention will have the maximal impact.

Animals↗
PubMedDate not supplied

Using facilitators in mock codes: recasting the parts for success.

BACKGROUND: Members of the CHRISTUS Santa Rosa Children's Hospital staff development committee identified a need for a mock code program which would address a range of learning needs for nurses and other caregivers with varying levels of knowledge, skills, and experience. METHOD: We implemented a mock code program using experienced caregivers, usually emergency room and pediatric intensive care RNs and respiratory therapists to serve as facilitators to code participants during the mock code drills. Facilitators have dual roles of teaching and guiding the code participant as well as evaluating performance. RESULTS: Code participants and facilitators benefit from the design of this program. Debriefing session input and written program evaluations show that code participants value the opportunity to practice their skills in a nonthreatening situation in which they receive immediate feedback as needed. Facilitators learn to teach and coach and strengthen their own code knowledge and skills at the same time. CONCLUSION: This mock code program serves as a unique way to include novice and experienced nurses in mock codes together. The knowledge, skills, and confidence of the code participants and the facilitators have matured. The design of the program allows for immediate teaching/learning where needed, as well as appropriate evaluation. This program develops stronger, calmer, more efficient, and more confident nurses during codes. Practice and equipment changes can be based on findings from the mock codes. The program is invaluable to patients, staff, and hospital.

Cardiopulmonary Resuscitation↗
PubMed1981

[Cell membrane characteristics and biological behavior of virus transformed cells (author's transl)].

The transformation of a normal into a tumor cell is not caused by a single molecular event, but is the consequence of several simultaneous or consecutive molecular processes, which lead to a variety of changes in the structure and the metabolism of the cell. Investigations with the Rous sarcoma virus show that a single gene is primarily responsible for these changes that is coding for a phosphoprotein which, however, is multifunctional. The biochemical and biologic events which initiate and maintain the transformed status of the cell involve mainly the cytoplasma membrane. At both the outer and the inner surface of the cell membrane dramatic changes occur which influence the cell structure, permeability of the cytoplasma membrane, and the intracellular metabolic pathways. Most probably, these transformation-associated events are also involved in cell proliferation under physiologic conditions. In the tumor cell, however, they are not further regulated physiologically, with the consequence of an uncontrolled and incessant cell division.

Animals↗
PubMedDate not supplied

Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

OBJECTIVE: To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). METHODS: The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for "parent" and "child" codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. RESULTS: SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p < .00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56, UMLS 3.17; READ 2.14, *p < .005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p < .00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p < .004) associated with a loss of clarity. CONCLUSION: No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. Is suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record.

Abstracting and Indexing↗
PubMed1989

Mapping of attenuating sequences of an avirulent poliovirus type 2 strain.

A mouse model for poliomyelitis was used to identify genomic sequences that attenuate neurovirulence of poliovirus strain P2/P712. This type 2 strain is avirulent in primates and mice yet grows as well as virulent strains in cell culture. The approach used was to exchange portions of the genome of the mouse-virulent P2/Lansing strain with the corresponding region from P2/P712 to identify sequences that could attenuate Lansing neurovirulence in mice. A full-length infectious cDNA of P2/P712 was assembled and used to construct recombinants between P2/P712 and P2/Lansing. The results of neurovirulence testing of 11 recombinants indicated that strong attenuating determinants are located in the 5' noncoding region of P2/P712 and a region encoding capsid protein VP1 and 2Apro, 2B, and part of 2C. An attenuating determinant was further localized to between nucleotides 456 and 628 of P2/P712. A third sequence from P2/P712, nucleotides 752 to 2268, encoding VP4, VP2, and part of VP3, was weakly attenuating. The sequence from nucleotide 4454, approximately halfway through the 2C-coding region, to the end of the P2/P712 genome did not contain attenuating determinants. Nucleotide sequence analysis revealed that P2/P712 differs from the type 2 Sabin vaccine strain by only 22 nucleotides. Six differences lead to amino acid changes in the coding region, and four differences are in the 5' noncoding region. These studies show that, like the type 1 and type 3 Sabin vaccine strains, the attenuated type 2 strain P712 contains multiple attenuating sequences, including strongly attenuating sequences in the 5' noncoding region of the genome.

Animals↗
PubMedDate not supplied

And still more new codes.

Before reporting the new Category III CPT codes, contact payors to determine both acceptance of these temporary codes and reimbursement allowances. Documentation must clearly support all services performed, and the requirements for an online medical evaluation should be followed, with the encounter recorded in the individual patient medical record. Hospitals should also review the quarterly changes to OPPS codes and descriptors and ensure that Charge Description Masters are updated as new codes become effective.

Ambulatory Care↗
PubMed2002

Stabilization of ablative Rayleigh-Taylor instability due to change of the Atwood number.

Recent experiment [S.G. Glendinning et al., Phys. Rev. Lett. 78, 3318 (1997)] showed that the measured growth rate of laser ablative Rayleigh-Taylor (RT) instability with preheating is about 50% of the classic value and is reduced by about 18% compared with the simulated value obtained with the computer code LASNEX. By changing the temperature variation of the electron thermal conductivity at low temperatures, the density profile from the Bhatnagar-Gross-Krook approximation is recovered in the simulation, and the simulated RT growth rate is in good agreement with the experimental value from Glendinning et al. The preheated density profile on ablative RT stablization is studied numerically. A change of the Atwood number in the preheating case also leads to RT stabilization. The RT growth formula gamma=square root of [Akg/(1+AkL)] - 2kV(a) agrees well with experiment and simulation, and is appropriate for the preheating case.

Journal Article↗
PubMed1997

Delimitation of a critical tumour suppressor region at distal 1p in neuroblastoma tumours.

We analysed DNA from 68 neuroblastoma tumours for loss of heterozygosity (LOH) on the distal chromosome 1p (1p-LOH) using PCR-based DNA polymorphisms. Fifteen tumours (22%) displayed 1p-LOH. The shortest region of overlap (SRO) for the deletions was defined proximally by marker D1S244 and distally by marker D1S80. The CDC2L1 locus, located on chromosome 1p36, has been put forward as a neuroblastoma tumour suppressor. We analysed coding regions of the CDC2L1 gene in a subset of aggressive neuroblastoma tumours with known allelic loss for different 1p-markers. Single-stranded conformation polymorphism, heteroduplex and sequencing analysis of tumour DNA did not reveal any significant changes in the coding region. Using a DNA sequence polymorphism, we showed, in a primary tumour with an interstitial allelic deletion, that this tumour had both alleles of the CDC2L1 locus retained in the tumour. Thus, we showed that the neuroblastoma tumour suppressor critical region on 1p in our material is defined by loci D1S244 and D1S80 and that the CDC2L1 locus is distal to the critical region.

Child↗
PubMed2006

CHST6 mutations in North American subjects with macular corneal dystrophy: a comprehensive molecular genetic review.

PURPOSE: To evaluate mutations in the carbohydrate sulfotransferase-6 (CHST6) gene in American subjects with macular corneal dystrophy (MCD). METHODS: We analyzed CHST6 in 57 patients from 31 families with MCD from the United States, 57 carriers (parents or children), and 27 unaffected blood relatives of affected subjects. We compared the observed nucleotide sequences with those found by numerous investigators in other populations with MCD and in controls. RESULTS: In 24 families, the corneal disorder could be explained by mutations in the coding region of CHST6 or in the region upstream of this gene in both the maternal and paternal chromosome. In most instances of MCD a homozygous or heterozygous missense mutation in exon 3 of CHST6 was found. Six cases resulted from a deletion upstream of CHST6. CONCLUSIONS: Nucleotide changes within the coding region of CHST6 are predicted to alter the encoded protein significantly within evolutionary conserved parts of the encoded sulfotransferase. Our findings support the hypothesis that CHST6 mutations are cardinal to the pathogenesis of MCD. Moreover, the observation that some cases of MCD cannot be explained by mutations in CHST6 suggests that MCD may result from other subtle changes in CHST6 or from genetic heterogeneity.

5' Untranslated Regions↗
PubMed1988

cDNA cloning and sequence of a new type of actin in mouse B16 melanoma.

Parent B16 melanoma and B16-F1 cell lines express a third actin (Ax) in addition to beta- and gamma-actin. It has the same molecular mass (43,000 daltons) and a more acidic isoelectric point (pI = 5.2) than the latter two actins (pI = 5.3) (Taniguchi, S., Kawano, T., Kakunaga, T., and Baba, T. (1986) J. Biol. Chem. 261, 6100-6106). We constructed a cDNA library from poly(A)+ RNA of B16-F1 and then isolated Ax actin candidate clones. According to the nucleotide sequencing analysis for one of the candidate clones, pMA 30, the predicted amino acid sequence was composed of 375 amino acids and was similar to that of beta-actin, but differed at the 28th amino acid in that leucine replaced the arginine of beta-actin. When RNA synthesized from the clone pMA 30 with the SP6 transcription system was translated in vitro using reticulocyte lysate, we identified a polypeptide which had the same isoelectric point and molecular weight as Ax actin; the polypeptide had binding activity to DNase I, a common characteristic of native actin. These observations provide evidence that the clone pMA 30 encodes the mRNA for Ax actin. In the nucleotide sequence of the Ax cDNA, there are: 1) one base change in the coding region which causes a loss of the SmaI site and an amino acid exchange, as mentioned above; 2) four deletion sites in the 3'-noncoding region; 3) one insertion site in the 3'-noncoding region; and 4) one base change in the 5'-noncoding region, as compared with hitherto known mouse beta-actin cDNA. These differences between Ax and beta-actin cDNA indicate that the Ax actin is encoded by an unique gene set, independent of beta-actin.

Actins↗