Underlying ambiguities in genetic privacy legislation

Advances in genetic testing and research are creating increasing concern regarding genetic privacy. Current and proposed federal and state legislation has failed to provide adequate protection due to confusion over the meaning of privacy, inconsistency in the definition of genetic information, and lack of clarity with regard to the role of insurers in a market driven healthcare environment. Drawing on examples of current and proposed legislation, this paper explores these ambiguities with a view toward future health policy alternatives.     

How principles of domain formation in model membranes may explain ambiguities concerning lipid raft formation in cells

Sphingolipid and cholesterol-rich liquid ordered lipid domains (lipid rafts) have been studied in both eukaryotic cells and model membranes. However, while the coexistence of ordered and disordered liquid phases can now be easily demonstrated in model membranes, the situation in cell membranes remains ambiguous. Unlike the usual situation in model membranes, under most conditions, cell membranes rich in sphingolipid and cholesterol may have a "granular" organization in which the size of ordered and/or disordered domains is extremely small and domains may be of borderline stability. This review attempts to explain the origin of the divergence between of our understanding of rafts in model membranes and in cells, and how the physical properties of model membranes can help explain many of the ambiguities concerning raft formation and properties in cells. How physical principles of ordered domain formation relate to limitations of detergent insolubility and cholesterol depletion methods used to infer the presence of rafts in cells is also discussed. Possible modifications of these techniques that may increase their reliability are considered. It will be necessary to study model membrane systems more closely approximating cell membranes in order gain a complete understanding of raft properties in cells. Very high concentrations of membrane cholesterol and proteins may explain key physical characteristics of domains in cellular membranes, and are the two of the most obvious factors requiring additional study.     

Sexual ambiguities: definition, management, classification

The authors define the field of the sexual ambiguities including not only the cases of ambiguousness in the external genitals, but also those cases which present anomalies in the external or internal genitals or in the gonads, with more or less evident characteristics of the other sex, even if there is no doubt as to the sex attribution. On the contrary the cases with only the lack of gonads are excluded. After a brief recall to some aspects of the sexual differentiation, the authors point up the importance of genetic counselling not only to let a precocious sex registration at the General Register Office, but also with the purpose of a genetic prevention and of a quick corrective intervention. At last the authors propose a personal classification of these defects.     

Recognition of genes in DNA sequence with ambiguities

The search for genes in a newly sequenced DNA is a well known problem. Among other factors, the gene-searching process is hampered by a number of ambiguities which may remain unresolved experimentally for a long time. A computer method that is able to predict genes in a DNA sequence containing ambiguities has been developed, based on the non-homogeneous Markov chain technique. The reliability of the method has been tested using a set of sequences generated by a Monte-Carlo procedure and a set of 425 E. coli sequences with ambiguities introduced artificially.     

Classical plant taxonomic ambiguities extend to the molecular level

Summary The molecular evolution of cytochrome c from angiosperms is compared to that from vertebrates. On the basis of a cladistic analysis from 26 plant species, compared to that from 27 vertebrate species, we find that although the vertebrate sequences yield reasonably well-defined minimal trees that are congruent with the biological tree, the plant sequences yield multiple minimal trees that are not only highly incongruent with each other, but none of which is congruent with any reasonably biological tree. That is, the plant sequence set is much more homoplastic than that of the animal. However, as judged by the relative rate test, the extent of divergence, and degree of functional constraint, cytochrome c evolution in plants does not appear to differ from that of vertebrates.     

Sequence data: Magnitude and implications of some ambiguities

Summary Glx and Asx ambiguities introduce errors into evolutionary conclusions drawn from the sequences of incompletely analyzed proteins. These errors are of sufficient magnitude to invalidate some of these conclusions.     

Removing noise and ambiguities from comparative maps in rearrangement analysis

Comparison of genomic maps is hampered by errors and ambiguities introduced by mapping technology, incorrectly resolved paralogy, small samples of markers, and extensive genome rearrangement. We design an analysis to remove or resolve most of these problems and to extract corrected data where markers occur in consecutive strips in both genomes. To do this, we introduce the notion of prestrip, an efficient way of generating these and a compatibility analysis culminating in a maximum weighted clique (MWC) search. The output can be directly analyzed with genome rearrangement algorithms, allowing the restoration of some of the data not incorporated into the clique solution. We investigate the trade-off between criteria for discarding excessive prestrips to make MWC feasible in terms of retaining as many markers as possible in the solution and producing an economical rearrangement analysis. We explore these questions through simulation and through comparison of the rice and sorghum genomes.     

A model for thermograms

Thermograms are curves resulting from thermal analysis and are of great interest in the study of various food and biological products physical properties. A method to separate underlying peaks is proposed, and statistical properties of estimates for some characteristic parameters are derived. The total number of peaks can be estimated with a sequential analysis of the residual plots. For each new peak, a statistical criterion is proposed to check whether it is significantly different from the noise of the recording. As an example, the method is applied to a summer milk fat fusion thermogram.     

A model for differentiation

A model is proposed, in which differentiation is attributed to colinearity between polymerase states and promotors. The promotors are considered the equal of ordinal numbers, and the state of a polymerase molecule is changed by the activity of the products of the gene it has transcribed. Introns are assumed to be involved in this possibility. Repeated sequences function as labels of chromosomes and chromosome regions, and interact with the diffusing RNA polymerase molecules aimed at a given class of promotors, increasing the speed of specific interactions. The possibility that a quantitative code, with a form of scansion, exists to order promotors as well as repeated sequences, is discussed. A correlation between the base sequence of repeats and promotors is predicted.     

Eye movement parameters in reading sentences with syntactic ambiguities in Russian

We studied eye movement parameters in reading syntactically ambiguous sentences with the feminine variant of relative clause in Russian. A priori difficulty in analyzing the structure of the sentence leads to the increased time of its reading, compared with the time of reading control (unambiguous) sentences. The time of reading increases due to higher frequencies of regressive saccades made by the subjects for rereading the ambiguous fragments of the sentence. This fact, in turn, leads to an increased number of fixations and their longer duration. The total reading time for the particular words that make up the ambiguous fragment depended on disambiguation result (the type of closure). When the subjects attached the subordinate clause to the first noun of the noun group (early closure), the time of reading this noun increased, compared to the reading time required for the second noun. When the subjects chose the second noun (late closure), the time of reading either of the two did not differ. Our results indicate that the increased time of reading the first noun of the noun group attached to the subordinate clause depends on the prevalence of early closure in the Russian language.     

Resolving current disagreements and ambiguities in the terminology of animal communication

Communication is central to most interactions between organisms. There is currently considerable controversy about the evolution, function and even about the most basic definition of communication. The controversy is linked to definitional ambiguities and disagreements. Here we discuss how some recent disagreements can be resolved and offer a clear set of definitions. Central to our approach is a definition of communication as being a trade between one organism (the informer) and another (the perceiver). The informer exerts influence on the perceiver through the communication process, and the perceiver experiences a change in its informational state (that is, gains information) as a consequence of detecting the communication. We define both influence and information explicitly and delineate between signalling, deceptive communication, and situations where perceivers respond to cues rather than signals. We demonstrate how our definitions allow resolution of conflicts arising in recent publications on the definitions on communication and related terms.     

X-ray sequence ambiguities of Sclerotium rolfsii lectin resolved by mass spectrometry

X-ray crystallography, although a powerful technique for determining the three-dimensional structure of proteins, poses inherent problems in assigning the primary structure in residues Asp/Asn and Glu/Gln since these cannot be distinguished decisively in the electron density maps. In our recently published X-ray crystal structure of the Sclerotium rolfsii lectin (SRL) at 1.1 A resolution, amino acid sequence was initially deduced from the electron density map and residues Asp/Asn and Glu/Gln were assigned by considering their hydrogen bonding potential within their structural neighborhood. Attempts to verify the sequence by Edman sequencing were not successful as the N terminus of the protein was blocked. Mass spectrometry was applied to verify and resolve the ambiguities in the SRL X-ray crystal structure deduced sequence. From the Matrix assisted laser desorption/ionization time-of-flight-mass spectrometry (MALDI TOF-MS) and liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysis of tryptic and chymotryptic peptides of SRL, we could confirm and correct the sequence at five locations with respect to Asp/Asn and Glu/Gln. Analysis data also confirmed the positions of Leu/Ile, Gln/Lys residues and the sequence covering 118 of the total 141 residues accounting to 83.68% of the earlier deduced sequence of SRL.     

A model for planning rhinoplasty

A rhinoplasty model is detailed in which nasal shape is conceived as a dynamic system, the result of powerful expansive and contractile forces, of a skin sleeve in equilibrium with a dynamic skeleton, in which the alar cartilages are external to the remaining skeleton and support a large area of lower nasal skin. In this system, changes in one region have "global" effects. Consequently, one powerful way to control nasal shape is to maintain skin sleeve size and thus maintain the preoperative nasal equilibrium. The surgeon who controls the postoperative equilibrium controls the postoperative result.