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PubMed2003

Inhibition of transcription at a coding sequence by alkylating polyamide.

Transcription from DNA sequence-specifically alkylated by a hairpin polyamide (ImPyPy-gamma-ImPyLDu86, 1) was investigated. High-resolution polyacrylamide gel electrophoresis demonstrated that conjugate 1 alkylated a 993-bp DNA fragment, in accordance with the Py-Im recognition rule, predominantly at the one match site on the GFP-encoding strand and at four sites (I'-IV') on the noncoding strand. Alkylation of DNA inhibited the formation of full-length mRNA and caused the transcription of truncated mRNA. Polyacrylamide gel electrophoresis demonstrated that the length of the truncated mRNA was consistent with the alkylated site on the coding strand. Complete inhibition of full-length mRNA synthesis was observed in the presence of 50 nM 1. In clear contrast, the hydrolyzed derivative of 1, designated 2, produced no truncated mRNA, nor did it significantly retard transcription: >80% transcription of full-length mRNA was observed at 50 nM. These results clearly indicate that inhibition of transcription can be achieved with alkylating Py-Im polyamide even in the coding regions of genes.

Alkylation↗

PubMed1997

Expression of a streptomycete leaderless mRNA encoding chloramphenicol acetyltransferase in Escherichia coli.

The chloramphenicol acetyltransferase (cat) gene from Streptomyces acrimycini encodes a leaderless mRNA. Expression of the cat coding sequence as a leaderless mRNA from a modified lac promoter resulted in chloramphenicol resistance in Escherichia coli. Transcript mapping with nuclease S1 confirmed that the 5' end of the cat message initiated at the A of the AUG translational start codon. Site-directed mutagenesis of the lac promoter or the cat start codon abolished chloramphenicol resistance, indicating that E. coli initiated translation at the 5' terminal AUG of the cat leaderless mRNA. Addition of 5'-AUGC-3' to the 5' end of the cat mRNA resulted in translation occurring also from the reading frame defined by the added AUG triplet, suggesting that a 5'-terminal start codon is an important recognition feature for initiation and establishing reading frame during translation of leaderless mRNA. Addition of an untranslated leader and Shine-Dalgarno sequence to the cat coding sequence increased cat expression in a cat:lacZ fusion; however, the level of expression was significantly lower than when a fragment of the bacteriophage lambda cI gene, also encoding a leaderless mRNA, was fused to lacZ. These results indicate that in the absence of an untranslated leader and Shine-Dalgarno sequence, the streptomycete cat mRNA is translated by E. coli; however, the cat translation signals, or other features of the cat mRNA, provide for only a low level of expression in E. coli.

Chloramphenicol↗

PubMed2005

Call-based species recognition in black-capped chickadees.

Species recognition is essential for efficient communication between conspecifics. For this to occur, species information must be unambiguously encoded in the repertoire of each species' vocalizations. Until now, the study of species recognition in songbirds has been focused mainly on male songs and male territorial behaviour. Species recognition of other learned vocalizations, such as calls, have not been explored, and could prove useful as calls are used in a wider range of contexts. Here, we present an experimental field study investigating the coding of species information in a learned vocalization, the 'chick-a-dee' call of the black-capped chickadee (Poecile atricapillus). By modifying natural calls in both temporal and spectral domains and by observing the vocal responses of black-capped chickadees following the playback of these modified calls, we demonstrate that species recognition in chickadees relies on several acoustic features including syntax, frequency modulation, amplitude modulation, and to a lesser extent, call rhythmicity and frequency range.

Animal Communication↗

PubMed1992

mRNAs containing extensive secondary structure in their 5' non-coding region translate efficiently in cells overexpressing initiation factor eIF-4E.

Cellular eukaryotic mRNAs (except organellar) contain at the 5' terminus the structure m7(5')Gppp(5')N (where N is any nucleotide), termed cap. Cap recognition by eukaryotic initiation factor eIF-4F plays an important role in regulating the overall rate of translation. eIF-4F is believed to mediate the melting of mRNA 5' end secondary structure and facilitate 43S ribosome binding to capped mRNAs. eIF-4E, the cap-binding subunit of eIF-4F, plays an important role in cell growth; its overexpression results in malignant transformation of rodent cells, and its phosphorylation is implicated in signal transduction pathways of mitogens and growth factors. The molecular mechanism by which eIF-4E transforms cells is not known. Here, we report that overexpression of eIF-4E facilitates the translation of mRNAs containing excessive secondary structure in their 5' non-coding region. This effect may represent one mechanism by which eIF-4E regulates cell growth and transforms cells in culture.

3T3 Cells↗

PubMed2005

The humanID gait challenge problem: data sets, performance, and analysis.

Identification of people by analysis of gait patterns extracted from video has recently become a popular research problem. However, the conditions under which the problem is "solvable" are not understood or characterized. To provide a means for measuring progress and characterizing the properties of gait recognition, we introduce the HumanID Gait Challenge Problem. The challenge problem consists of a baseline algorithm, a set of 12 experiments, and a large data set. The baseline algorithm estimates silhouettes by background subtraction and performs recognition by temporal correlation of silhouettes. The 12 experiments are of increasing difficulty, as measured by the baseline algorithm, and examine the effects of five covariates on performance. The covariates are: change in viewing angle, change in shoe type, change in walking surface, carrying or not carrying a briefcase, and elapsed time between sequences being compared. Identification rates for the 12 experiments range from 78 percent on the easiest experiment to 3 percent on the hardest. All five covariates had statistically significant effects on performance, with walking surface and time difference having the greatest impact. The data set consists of 1,870 sequences from 122 subjects spanning five covariates (1.2 Gigabytes of data). The gait data, the source code of the baseline algorithm, and scripts to run, score, and analyze the challenge experiments are available at http://www.GaitChallenge.org. This infrastructure supports further development of gait recognition algorithms and additional experiments to understand the strengths and weaknesses of new algorithms. The more detailed the experimental results presented, the more detailed is the possible meta-analysis and greater is the understanding. It is this potential from the adoption of this challenge problem that represents a radical departure from traditional computer vision research methodology.

Adult↗

PubMed2001

Translocation within the acceptor helix of a major tRNA identity determinant.

The genetic code is defined by the specific aminoacylations of tRNAs by aminoacyl-tRNA synthetases. Although the synthetases are widely conserved through evolution, aminoacylation of a given tRNA is often system specific-a synthetase from one source will not acylate its cognate tRNA from another. This system specificity is due commonly to variations in the sequence of a critical tRNA identity element. In bacteria and the cytoplasm of eukaryotes, an acceptor stem G3:U70 base pair marks a tRNA for aminoacylation with alanine. In contrast, Drosophila melanogaster (Dm) mitochondrial (mt) tRNA(Ala) has a G2:U71 but not a G3:U70 pair. Here we show that this translocated G:U and the adjacent G3:C70 are major determinants for recognition by Dm mt alanyl-tRNA synthetase (AlaRS). Additionally, G:U at the 3:70 position serves as an anti-determinant for Dm mt AlaRS. Consequently, the mitochondrial enzyme cannot charge cytoplasmic tRNA(Ala). All insect mitochondrial AlaRSs appear to have split apart recognition of mitochondrial from cytoplasmic tRNA(Ala) by translocation of G:U. This split may be essential for preventing introduction of ambiguous states into the genetic code.

Alanine-tRNA Ligase↗

PubMed2004

Taste perception and coding in Drosophila.

BACKGROUND: Discrimination between edible and contaminated foods is crucial for the survival of animals. In Drosophila, a family of gustatory receptors (GRs) expressed in taste neurons is thought to mediate the recognition of sugars and bitter compounds, thereby controlling feeding behavior. RESULTS: We have characterized in detail the expression of eight Gr genes in the labial palps, the fly's main taste organ. These genes fall into two distinct groups: seven of them, including Gr66a, are expressed in 22 or fewer taste neurons in each labial palp. Additional experiments show that many of these genes are coexpressed in partially overlapping sets of neurons. In contrast, Gr5a, which encodes a receptor for trehalose, is expressed in a distinct and larger set of taste neurons associated with most chemosensory sensilla, including taste pegs. Mapping the axonal targets of cells expressing Gr66a and Gr5a reveals distinct projection patterns for these two groups of neurons in the brain. Moreover, tetanus toxin-mediated inactivation of Gr66a- or Gr5a-expressing cells shows that these two sets of neurons mediate distinct taste modalities-the perception of bitter (caffeine) and sweet (trehalose) taste, respectively. CONCLUSION: Discrimination between two taste modalities-sweet and bitter-requires specific sets of gustatory receptor neurons that express different Gr genes. Unlike the Drosophila olfactory system, where each neuron expresses a single olfactory receptor gene, taste neurons can express multiple receptors and do so in a complex Gr gene code that is unique for small sets of neurons.

Animals↗

PubMed1991

Origin of genetically encoded protein synthesis: a model based on selection for RNA peptidation.

The difficulty in explaining the origin of genetic coding centres on the need to identify selective advantages that could account for the synthesis of peptidyl-tRNA, the essential intermediate in genetically programmed translation. It is resolved by a recognition of the functional advantages derivable from the post-transcriptional addition of peptide cofactors to RNA apo-catalysts. This enables the formulation of a theory for the origin of the genetic encoding of protein synthesis by RNA.

Amino Acid Sequence↗

PubMed1997

Supervised adaptive Hamming net for classification of multiple-valued patterns.

A Supervised Adaptive Hamming Net (SAHN) is introduced for incremental learning of recognition categories in response to arbitrary sequences of multiple-valued or binary-valued input patterns. The binary-valued SAHN derived from the Adaptive Hamming Net (AHN) is functionally equivalent to a simplified ARTMAP, which is specifically designed to establish many-to-one mappings. The generalization to learning multiple-valued input patterns is achieved by incorporating multiple-valued logic into the AHN. In this paper, we examine some useful properties of learning in a P-valued SAHN. In particular, an upper bound is derived on the number of epochs required by the P-valued SAHN to learn a list of input-output pairs that is repeatedly presented to the architecture. Furthermore, we connect the P-valued SAHN with the binary-valued SAHN via the thermometer code.

Artificial Intelligence↗

PubMed2001

[Impaired recognition of faces: implicit recognition, feeling of familiarity, role of each hemisphere].

We report three observations of patients who suffered from impaired face recognition following cerebral lesions. Two had classical prosopagnosia, resulting from bilateral in one case and right unilateral occipito-temporal in the other. They could not differentiate famous face from unknown ones, and did not feel any familiarity. The third patient has a normal feeling of knowing, could distinguish between familiar and unfamiliar faces, but was unable to evoke any biographical information about the personalities. Prosopagnosic patients demonstrated, in an experimental condition of learning face-name pairs, implicit knowledge. We assume that these capacities were dependent of the activation of networks coding familiar faces in memory. Mental imagery of faces were normal in theses two cases. In addition, stimulation of mental imagery in the first patient improved implicit knowledge in forced choice tasks. These cases throws a light on the respective role of each hemisphere in face recognition. The right hemisphere is advantaged in perceptual analysis, and activates, from the perceived faces, mnestic systems which codes for previously encountered faces. It generates feeling of familiarity, probably by the way of specific systems which differs from, and completes, those allowing identification. The left hemisphere enable access to semantic-biographic knowledge in a conscious, verbal and explicit way.

Aged↗

PubMed2005

Nutritional assessment and management in hospitalised patients: implication for DRG-based reimbursement and health care quality.

INTRODUCTION: Malnutrition is associated with a higher morbidity resulting in an increased need for medical resources and economic expenses. In order to ensure sufficient nutritional care it is mandatory to identify the effect of malnutrition and nutritional care on direct cost and reimbursement. The primary aim of this study was to evaluate the economic effect of a nutritional screening procedure on the identification and coding of malnutrition in the G-DRG system. METHODS: All G-DRG relevant parameters of 541 consecutive patients at a gastroenterology ward were documented. Moreover, all patients were screened for malnutrition by a dietician according to the subjective global assessment (SGA). Patients were then grouped into the appropriate G-DRG and the effective cost weight (CW) was calculated. RESULTS: Ninety-two of 541 patients (19%) were classified malnourished (SGA B or C). Recognition of malnutrition increase from 4% to 19%. Malnourished patients exhibited a significantly increased length of hospital stay (7.7+/-7 to 11+/-9, P<0.0001). In 26/98 (27%) patients, the coding of malnutrition was considered relevant by grouping and resulted in a rise of DRG benefit. Mean case mix value and patients' complexity and comorbidity level (PCCL) increased after including malnutrition in the codification (CV 1.53+/-2.9 to 1.65+/-2.9, P=0.001 and PCCL 2.69+/-1.4 to 3.47+/-0.82, P<0.0001). The reimbursement increase by 360/malnourished patient or an additional reimbursement of 35280 (8.3% of the total reimbursement for all patients of 423186). Nutritional support in a subgroup of 50 randomly selected patients resulted in additional costs of 10268 . Forty-four of these patients (86%) were classified malnourished (32 SGA B and 12 SGA C). However, the subsequent reimbursement covered only approximately 75% of the expenses (7869), but did not include the potential financial benefits resulting from clinical interventions. CONCLUSION: Malnourished patients can be detected with a structured assessment and documentation of nutritional status and this is partly reflected in the G-DRG/ICD 10 system. In addition to increasing direct health care reimbursement, nutritional screening and intervention has the potential to improve health care quality.

Comorbidity↗

PubMed1998

Interpreting neuronal population activity by reconstruction: unified framework with application to hippocampal place cells.

Physical variables such as the orientation of a line in the visual field or the location of the body in space are coded as activity levels in populations of neurons. Reconstruction or decoding is an inverse problem in which the physical variables are estimated from observed neural activity. Reconstruction is useful first in quantifying how much information about the physical variables is present in the population and, second, in providing insight into how the brain might use distributed representations in solving related computational problems such as visual object recognition and spatial navigation. Two classes of reconstruction methods, namely, probabilistic or Bayesian methods and basis function methods, are discussed. They include important existing methods as special cases, such as population vector coding, optimal linear estimation, and template matching. As a representative example for the reconstruction problem, different methods were applied to multi-electrode spike train data from hippocampal place cells in freely moving rats. The reconstruction accuracy of the trajectories of the rats was compared for the different methods. Bayesian methods were especially accurate when a continuity constraint was enforced, and the best errors were within a factor of two of the information-theoretic limit on how accurate any reconstruction can be and were comparable with the intrinsic experimental errors in position tracking. In addition, the reconstruction analysis uncovered some interesting aspects of place cell activity, such as the tendency for erratic jumps of the reconstructed trajectory when the animal stopped running. In general, the theoretical values of the minimal achievable reconstruction errors quantify how accurately a physical variable is encoded in the neuronal population in the sense of mean square error, regardless of the method used for reading out the information. One related result is that the theoretical accuracy is independent of the width of the Gaussian tuning function only in two dimensions. Finally, all the reconstruction methods considered in this paper can be implemented by a unified neural network architecture, which the brain feasibly could use to solve related problems.

Action Potentials↗

PubMed2005

Taste recognition: food for thought.

The ability to identify food that is nutrient-rich and avoid toxic substances is essential for an animal's survival. Although olfaction and vision contribute to food detection, the gustatory system acts as a final checkpoint control for food acceptance or rejection behavior. Recent studies with model organisms such as mice and Drosophila have identified candidate taste receptors and examined the logic of taste coding in the periphery. Despite differences in terms of gustatory anatomy and taste-receptor families, these gustatory systems share a basic organization that is different from other sensory systems. This review will summarize our current understanding of taste recognition in mammals and Drosophila, highlighting similarities and raising several as yet unanswered questions.

Animals↗

PubMed1978