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PubMed1999

AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes.

The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes was estimated by AFLP analysis. Within seven of the 21 ecotypes, a low but significant level of polymorphism was detected, and for five of these ecotypes two or three distinct subgroups could be distinguished. As these ecotypes represent natural populations, this intraecotypic diversity reflects natural genetic variation and diversification within the ecotypes. The source of this diversity remains unclear but is intriguing in view of the predominantly self-fertilizing nature of Arabidopsis. Interrelationships between the different ecotypes were estimated after AFLP fingerprinting using two enzyme combinations (EcoRI/MseI and SacI/MseI) and a number of selective primer pairs. SacI recognition sites are less evenly distributed in the genome than EcoRI sites, and occur more frequently in coding sequences. In most cases, AFLP data from only one enzyme combination are used for genetic diversity analysis. Our results show that the use of two enzyme combinations can result in significantly different classifications of the ecotypes both in cluster and ordination analysis. This difference most probably reflects differences in the genomic distribution of the AFLP fragments generated, depending on the enzymes and selective primers used. For closely related varieties, as in the case of Arabidopsis ecotypes, this can preclude reliable classification.

Arabidopsis↗

PubMed2002

Omnipotent RNA.

The capability of polyribonucleotide chains to form unique, compactly folded structures is considered the basis for diverse non-genetic functions of RNA, including the function of recognition of various ligands and the catalytic function. Together with well-known genetic functions of RNA - coding and complementary replication - this has led to the concept of the functional omnipotence of RNA and the hypothesis that an ancient RNA world supposedly preceded the contemporary DNA-RNA-protein life. It is proposed that the Woese universal precursor in the ancient RNA world could be a cell-free community of mixed RNA colonies growing and multiplying on solid surfaces.

Catalysis↗

PubMed2001

The rally call recognition in males of two hybridizing partridge species, red-legged (Alectoris rufa) and rock (A. graeca) partridges.

The red-legged (Alectoris rufa) and rock (A. graeca) partridges hybridize and produce fertile offspring along a contact zone in French Southern Alps. The rally call emitted during pair formation, could play an important role in species recognition, acting as a behavioral reproductive isolating mechanism between males and females. In the present study, the coding system of the rally call was investigated from captive males of the two species and from F1 hybrids. By playing-back natural signals, we found that the two species as well as hybrid males responded to Alectoris signals but not to another species belonging to the Phasianidae family (Colinus virginianus). Results also indicate that red-legged and rock partridges responded stronger to conspecific calls than to heterospecific ones. However, they reacted similarly to conspecific and hybrid calls. F1 hybrids responded stronger to hybrids calls than to the two species ones. They did not distinguish the two parental species signals from each other. Although the two species showed the ability to discriminate the conspecific from the heterospecific signal, they clearly responded to the other species. This behaviour may play a role in the hybridization phenomenon.

Journal Article↗

PubMed2002

Identification of potential protective antigens of Ostertagia ostertagi with local antibody probes.

The identification of protective helminth antigens remains the most important challenge in the development of parasitic vaccines. To identify protective antigens of Ostertagia ostertagi, an important abomasal parasite of cattle, parasite-specific local antibodies from the abomasal mucus and from the draining lymph nodes were collected from calves immunized with multiple infections and from 'primary infected' animals. With these probes, Western blots of extracts and excretion/ secretion (E/S) material from L3, L4 and adult life-stages as well as cDNA expression libraries were screened to identify antigens that were exclusively recognized by antibodies from 'immunized' calves. In the adult stage, a protein of 32 kDa was specifically detected on Western blot by mucus antibodies from 'immunized' animals. In the L3 and L4 larval stages, proteins situated in the regions of 28-29 kDa were recognized by mucus antibodies and a 59 kDa antigen was specifically recognized by lymph node antibodies from 'immunized' animals. Screening E/S material revealed no specific difference in recognition pattern between 'immunized' and 'primary infected' animals. Screening of the cDNA libraries revealed 26 relevant clones, coding for 15 proteins, among these several with potential protective capacity, immunodominant properties or functional and physiological importance e.g. metalloproteases, an aspartyl protease inhibitor and collagen.

Animals↗

PubMed2002

Free energy simulations come of age: protein-ligand recognition.

In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide an understanding of the interactions involved that goes beyond, and is an important complement to, experimental studies. Poisson-Boltzmann electrostatic models provide a faster and simpler free energy method in cases where electrostatic interactions are important. We illustrate both molecular dynamics and Poisson-Boltzmann methods with a detailed study of amino acid recognition by aspartyl-tRNA synthetase, whose specificity is important for maintaining the integrity of the genetic code.

Computer Simulation↗

PubMed1996

Functional replacement of hamster lysyl-tRNA synthetase by the yeast enzyme requires cognate amino acid sequences for proper tRNA recognition.

We cloned the cDNA encoding a 597-aa hamster lysyl-tRNA synthetase. This enzyme is a close homologue of the 591-aa Saccharomyces cerevisiae enzyme, with the noticeable exception of their 60-aa N-terminal regions, which differ significantly. Several particular features of this polypeptide fragment from the hamster lysyl-tRNA synthetase suggest that it is implicated in the assembly of that enzyme within the multisynthetase complex. However, we show that this protein domain is dispensable in vivo to sustain growth of CHO cells. The cross-species complementation was investigated in the lysine system. The mammalian enzyme functionally replaces a null-allele of the yeast KRS1 gene. Conversely, the yeast enzyme cannot rescue Lys-101 cells, a CHO cell line with a temperature-sensitive lysyl-tRNA synthetase. The yeast and mammalian enzymes, overexpressed in yeast, were purified to homogeneity. The hamster lysyl-tRNA synthetase efficiently aminoacylates both mammalian and yeast tRNA(Lys), whereas the yeast enzyme aminoacylates mammalian tRNA(Lys) with a catalytic efficiency 20-fold lower, as compared to its cognate tRNA. The 152-aa C-terminus extremity of the hamster enzyme provides the yeast enzyme with the capacity to complement Lys-101 cells. This hybrid protein is fairly stable and aminoacylates both yeast and mammalian tRNA(Lys) with similar catalytic efficiencies. Because this C-terminal polypeptide fragment is likely to make contacts with the acceptor stem of tRNA(Lys), we conclude that it should carry the protein determinants conferring specific recognition of the cognate tRNA acceptor stem and therefore contributes an essential role in the operational RNA code for amino acids.

Alleles↗

PubMed2005

Identification of a splicing enhancer in MLH1 using COMPARE, a new assay for determination of relative RNA splicing efficiencies.

Exonic splicing enhancers (ESEs) are sequences that facilitate recognition of splice sites and prevent exon-skipping. Because ESEs are often embedded within protein-coding sequences, alterations in them can also often be interpreted as nonsense, missense or silent mutations. To correctly interpret exonic mutations and their roles in diseases, it is important to develop strategies that identify ESE mutations. Potential ESEs can be found computationally in many exons but it has proven difficult to predict whether a given mutation will have effects on splicing based on sequence alone. Here, we describe a flexible in vitro method that can be used to functionally compare the effects of multiple sequence variants on ESE activity in a single in vitro splicing reaction. We have applied this method in parallel with conventional splicing assays to test for a splicing enhancer in exon 17 of the human MLH1 gene. Point mutations associated with hereditary non-polyposis colorectal cancer (HNPCC) have previously been found to correlate with exon-skipping in both lymphocytes and tumors from patients. We show that sequences from this exon can replace an ESE from the mouse IgM gene to support RNA splicing in HeLa nuclear extracts. ESE activity was reduced by HNPCC point mutations in codon 659, indicating that their primary effect is on splicing. Surprisingly, the strongest enhancer function mapped to a different region of the exon upstream of this codon. Together, our results indicate that HNPCC point mutations in codon 659 affect an auxillary element that augments the enhancer function to ensure exon inclusion.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Morse code application for wireless environmental control systems for severely disabled individuals.

Some physically-disabled people with neuromuscular diseases such as amyotrophic lateral sclerosis, multiple sclerosis, muscular dystrophy, or other conditions that hinder their ability to write, type, and speak, require an assistive tool for purposes of augmentative and alternative communication in their daily lives. In this paper, we designed and implemented a wireless environmental control system using Morse code as an adapted access communication tool. The proposed system includes four parts: input-control module; recognition module; wireless-control module; and electronic-equipment-control module. The signals are transmitted using adopted radio frequencies, which permits long distance transmission without space limitation. Experimental results revealed that three participants with physical handicaps were able to gain access to electronic facilities after two months' practice with the new system.

Activities of Daily Living↗

PubMed1986

Cloning and characterization of the dcm locus of Escherichia coli K-12.

The dcm locus of Escherichia coli K-12 has been shown to code for a methylase that methylates the second cytosine within the sequence 5'-CC(A/T)GG-3'. This sequence is also recognized by the EcoRII restriction-modification system coded by the E. coli plasmid N3. The methylase within the EcoRII system methylates the same cytosine as the dcm protein. We have isolated, from a library of E. coli K-12 DNA, two overlapping clones that carry the dcm locus. We show that the two clones carry overlapping sequences that are present in a dcm+ strain, but are absent in a delta dcm strain. We also show that the cloned gene codes for a methylase, that it complements mutations in the EcoRII methylase, and that it protects EcoRII recognition sites from cleavage by the EcoRII endonuclease. We found no phage restriction activity associated with the dcm clones.

Base Sequence↗

PubMed1989

Irradiation and food processing.

After more than four decades of research and development, food irradiation has been demonstrated to be safe, effective and versatile as a process of food preservation, decontamination or disinfection. Its various applications cover: inhibition of sprouting of root crops; insect disinfestation of stored products, fresh and dried food; shelf-life extension of fresh fruits, vegetables, meat and fish; destruction of parasites and pathogenic micro-organisms in food of animal origin; decontamination of spices and food ingredients, etc. Such applications provide consumers with the increase in variety, volume and value of food. Although regulations on food irradiation in different countries are largely unharmonized, national authorities have shown increasing recognition and acceptance of this technology based on the Codex Standard for Irradiated Foods and its associated Code of Practice. Harmonization of national legislations represents an important prerequisite to international trade in irradiated food. Consumers at large are still not aware of the safety and benefits that food irradiation has to offer. Thus, national and international organizations, food industry, trade associations and consumer unions have important roles to play in introducing this technology based on its scientific values. Public acceptance of food irradiation may be slow at the beginning, but should increase at a faster rate in the foreseeable future when consumers are well informed of the safety and benefits of this technology in comparison with existing ones. Commercial applications of food irradiation has already started in 18 countries at present. The volume of food or ingredients treated on a commercial scale varies from country to country ranging from several tons of spices to hundreds of thousands of tons of grains per annum. With the increasing interest of national authorities and the food industry in applying the process, it is anticipated that some 25 countries will use some 55 commercial facilities to treat different foods on an industrial scale by 1990.

Food Irradiation↗

PubMed1995

Demodulation, predictive coding, and spatial vision.

We argue that some aspects of human spatial vision, particularly for textured patterns and scenes, can be described in terms of demodulation and predictive coding. Such nonlinear processes encode a pattern into local phasors that represent it completely as a modulation, in phase and amplitude, of a prediction associated with the image structure in some region by its predominant undulation(s). The demodulation representation of a pattern is an anisotropic, second-order form of predictive coding, and it offers a particularly efficient way to analyze and encode textures, as it identifies and exploits their underlying redundancies. In addition, self-consistent domains of redundancy in image structure provide a basis for image segmentation. We first provide an algorithm for computing the three elements of a complete demodulation transform of any image, and we illustrate such decompositions for both natural and synthetic images. We then present psychophysical evidence from spatial masking experiments, as well as illustrations of perceptual organization, that suggest a possible role for such underlying representations in human vision. In psychophysical experiments employing masks with more than two oriented Fourier components, we find that peaks of threshold elevation occur at locations in the Fourier plane remote from the orientations and frequencies of the actual mask components. Rather, as would occur from demodulation, these peaks in the frequency plane are related to the vector difference frequencies between the actual masking components and their spectral centers of mass. We offer a neural interpretation of demodulation coding, and finally we demonstrate a practical application of this process in a system for automatic visual recognition of personal identity by demodulation of a facial feature.

Algorithms↗

PubMedDate not supplied

Necrotizing enterocolitis in an infant with Omenn syndrome.

Omenn syndrome (OS) is a rare disorder within the combined immunodeficiency family that is characterized by a diffuse exudative, erythematous rash, lymphadenopathy, hepatosplenomegaly, alopecia, and failure to thrive. Specific lab findings unique to OS include hypereosinophilia, elevated IgE, excess production of oligoclonal T-cells and near-to-absent B-cells. Much remains elucidated about the underlying genetic cause of OS. Until recently, it was felt that the disease was primarily caused by mutations of the RAG1 or RAG2 genes. The type of mutation of the RAG1 and RAG2 genes in patients with OS affects the degree of functioning variable (diversity) joining [V(D)J] recombination activity, which is critical to the development of lymphoid cell receptor diversity. New work has also shown that thymic tissue in OS patients demonstrates a severe defect in the expression of the autoimmune regulator element. This may contribute to the development of autoreactive T-cells that are felt to be the causative agent of a number of the clinical hallmarks unique to OS. The genetic spectrum of OS was further expanded when a patient with clinical and immunologic features consistent with OS, without RAG mutation, was found to have mutations in both alleles coding for ARTEMIS, a key V(D)J recombination/DNA repair factor. Regardless of the underlying cause, early recognition is critical because patients die at a very young age without bone marrow transplantation. We describe an infant diagnosed with OS post-mortem in which death was directly related to the development of necrotizing enterocolitis.

Enterocolitis, Necrotizing↗

PubMed1999

Ethical considerations and training recommendations for philosophical counseling.

Philosophical counseling is a diverse and burgeoning type of mental health service delivery. Despite competing approaches to theory and practice, the field has largely strayed from an ethical critique of its methodology and counselor training requirements. This article outlines several ethical considerations and training recommendations that are proposed to bolster the quality and effectiveness of philosophical practice. As philosophical counseling gains increasing recognition in North America, recently established national organizations in philosophical practice may profit from revisiting their interim codes for professional conduct. Proposed training suggestions for counselor preparation my further assist institutions and board-regulated agencies in establishing competent and acceptable standards of client care.

Codes of Ethics↗

PubMedDate not supplied

[Recognition of the depth of tumor extent in the cerebral hemispheres by electroencephalographic signs using a computer].

To obtain electroencephalographic criteria for in-depth occurrence of supratentorial tumours the mathematical theory of image recognition has been used. A map of electroencephalographic signs has been drawn up and 182 patients were coded electroencephalographically. Six signs were obtained with the help of the linear minimax algorhythm and in constructing diagnostic combinations of sign gradations--20 syndromes were fixed with whose help it becomes possible to recognize the depth of the tumour occurrence. Both rules were applied in an examination sequence of 51 EEG. The reliability of the results is as high as 0.95.

Adult↗

PubMed1989

[The structure of eukaryotic genes].

The structure of eukaryotic transcription units and already known DNA elements which influence gene expression and eukaryotic gene regulation are described. In recent years molecular genetics approaches have been used to identify and characterize the molecular anatomy of protein-coding eukaryotic genes. Within these genes there are modular sequences, consisting of arrays of short, highly conserved recognition elements that are essential for the initiation of transcription, translation, and tissue-specificity of gene expression. The skillful combination of promoters, enhancers and other regulatory sequences allows the expression of every gene in every organ or tissue of a transgenic animal.

Animals↗

PubMed1996

[Considerations on the rehabilitation of the hearing in cochlear implant patients].

In this study, the Cochlear Implant Programme of the ENT Department of Ospedale Civile di Venezia, is presented. Between 1989 and 1994, after a rigorous selection process, 36 patients were selected to be implanted with a cochlear prostheses: 28 with the multichannel Nucleus 22 device, 5 with the Clarion implant and 3 with the single channel Med-E1 BTE device. The distribution of the patients according to age, etiology, duration of auditory deprivation, age at onset of deafness, is presented. The different speech-coding strategies of the Nucleus system (Wearable Speech Processing, Multipeak speech processing and Spectral Maximum Sound processor) and the stimulation mode (common ground, bipolar, bipolar + 1) as well as the Clarion speech coding strategy (Continuous Interleaved Samples and Compressed Analog) are briefly discussed. The rehabilitation programme, the specific speech recognition assessment test batteries-Consonant Confusion Test, Vocal Confusion Test, Speech Tracking, MAC battery-as they are employed in our department, are presented. As we have analyzed our results, certain factors appear as predicting a favourable outcome: - age of onset of deafness; postlingual patients, who have developed communication skills compare favourably to the perilingual group. - durations of auditory deprivation, as it is related to surviving cells in the cochlea: the shorter the period of deafness, the better the results. - length of electrode insertion, as it is determined by ossification of the cochlea. - high dynamic range of the MAP. - percent of activated electrodes: a number of 10 active electrodes or less predicts a poor outcome. - for simplification reasons, a new variable is introduced-Auditory Deprivation Index- and its positive correlation to the performance presented. - the time period of experience with the device, length and quality of rehabilitation and family support have to be mentioned.

Adolescent↗

PubMed1985

DNA packaging initiation of Salmonella bacteriophage P22: determination of cut sites within the DNA sequence coding for gene 3.

DNA packaging of Salmonella phage P22 starts at a defined site on a concatemer of P22 genomes. The molecular ends formed at the packaging initiation site (pac) map within a region of ca. 120 base pairs and may contain any of the four nucleotides at their 5' end. The determination of the positions of the cuts within the sequence demonstrates a characteristic distribution of cut sites which apparently cannot be attributed to the sequence organization of the involved regions. Symmetric elements of the sequence might serve as signals for a recognition event(s) at pac in a separate process preceding the cutting reaction. The region of packaging initiation is located within the sequence coding for gene 3. The 3 protein is responsible for the site specificity of this process. We find no significant homology to Nu1 protein, which appears to have an analogous or similar function in the DNA maturation of Escherichia coli phage lambda.

Base Sequence↗

PubMed2006

Modulation of neonatal microbial recognition: TLR-mediated innate immune responses are specifically and differentially modulated by human milk.

The mechanisms controlling innate microbial recognition in the neonatal gut are still to be fully understood. We have sought specific regulatory mechanisms operating in human breast milk relating to TLR-mediated microbial recognition. In this study, we report a specific and differential modulatory effect of early samples (days 1-5) of breast milk on ligand-induced cell stimulation via TLRs. Although a negative modulation was exerted on TLR2 and TLR3-mediated responses, those via TLR4 and TLR5 were enhanced. This effect was observed in human adult and fetal intestinal epithelial cell lines, monocytes, dendritic cells, and PBMC as well as neonatal blood. In the latter case, milk compensated for the low capacity of neonatal plasma to support responses to LPS. Cell stimulation via the IL-1R or TNFR was not modulated by milk. This, together with the differential effect on TLR activation, suggested that the primary effect of milk is exerted upstream of signaling proximal to TLR ligand recognition. The analysis of TLR4-mediated gene expression, used as a model system, showed that milk modulated TLR-related genes differently, including those coding for signal intermediates and regulators. A proteinaceous milk component of > or =80 kDa was found to be responsible for the effect on TLR4. Notably, infant milk formulations did not reproduce the modulatory activity of breast milk. Together, these findings reveal an unrecognized function of human milk, namely, its capacity to influence neonatal microbial recognition by modulating TLR-mediated responses specifically and differentially. This in turn suggests the existence of novel mechanisms regulating TLR activation.

Cell Line↗