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Results for “Pathway informed transformer”

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PubMed1990

Renin is sorted to the regulated secretory pathway in transfected PC12 cells by a mechanism which does not require expression of the pro-peptide.

The rat pheochromocytoma cell line PC12 targets secretory proteins into two distinct pathways. When DNA encoding human prorenin was transfected into PC12 cells, the protein was sorted into the regulated secretory pathway and released with similar kinetics to noradrenaline upon carbachol stimulation. To determine whether information for targeting prorenin lies within the pro-peptide we have transfected PC12 cells with a construct lacking the pro-peptide coding sequence. The transformed line secretes an apparently fully active enzyme and responds to carbachol stimulation with a rapid release of renin activity. We conclude that the pro-peptide of renin is not essential for targeting the protein to the regulated pathway in PC12 cells.

Adrenal Gland Neoplasms↗

PubMed2000

Luminance processing in apparent motion, Vernier offset and stereoscopic depth.

We obtained (apparently) linear responses to luminance from three special displays of apparent motion, Vernier offset and stereoscopic depth. In our motion stimulus a dark and a light bar exchanged luminances repetitively on a grey surround. Motion was attributed to the bar that differed more from the surround, that is, on a dark surround the light bar appeared to jump, and on a light surround the dark bar appeared to jump. The apparent motion disappeared when the luminance of the surround lay halfway between that of the bars--on a linear, not a logarithmic scale. Similar results were obtained for special Vernier offset and stereo stimuli. These results cannot be explained if all luminances are processed within the same luminance pathway and that pathway transforms input luminance using non-linear compression. However, the apparent linearity of our results could arise from opposite and equal non-linearities cancelling out within separate ON- and OFF-spatial luminance pathways. A second set of experiments presented one bar separately into each eye on different surrounds (dichoptic presentation of competing apparent motion signals) or manipulated the display spatially so that different surrounds were associated with different bars (binocular presentation of competing Vernier targets). Results showed that apparent motion and Vernier signals of equal Weber contrast (normalisation of linear difference to surround luminance) evoked equal-motion and equal Vernier offset strengths. Given that motion and Vernier strength followed Weber's law, we infer that the ON- and OFF-pathways transform luminance non-linearly. Our third experiment presents an example of a brightness bisection task in which we were able to influence the bisection steps, to follow either a linear or non-linear series. The benefits of parsing the visual scene so that visual information is processed within two opposite luminance pathways is discussed.

Contrast Sensitivity↗

PubMed1990

Fatty acylated proteins as components of intracellular signaling pathways.

From the studies presented above, it is obvious that fatty acylation is a common modification among proteins involved in cellular regulatory pathways, and in certain cases mutational analyses have demonstrated the importance of covalent fatty acids in the functioning of these proteins. Indeed, certain properties provided by fatty acylation make it an attractive modification for regulatory proteins that might interact with many different substrates, particularly those found at or near the plasma membrane/cytosol interface. In the case of intracellular fatty acylated proteins, the fatty acyl moiety allows tight binding to the plasma membrane without the need for cotranslational insertion through the bilayer. For example, consider the tight, salt-resistant interaction of myristoylated SRC with the membrane, whereas its nonmyristoylated counterpart is completely soluble. Likewise for the RAS proteins, which associate weakly with the membrane in the absence of fatty acylation, while palmitoylation increases their affinity for the plasma membrane and their biological activity. Fatty acylation also permits reversible membrane association in some cases, particularly for several myristoylated proteins, thus conferring plasticity on their interactions with various signaling pathway components. Finally, although this has not been demonstrated, it is conceivable that covalent fatty acid may allow for rapid mobility of proteins within the membrane. Several questions remain to be answered concerning requirements for fatty acylation by regulatory proteins. The identity of the putative SRC "receptor" will provide important clues as to the pathways in which normal SRC functions, as well as into the process of transformation by oncogenic tyrosine kinases. The possibility that other fatty acylated proteins associate with the plasma membrane in an analogous manner also needs to be investigated. An intriguing observation that can be made from the information presented here is that at least three different families of proteins involved in growth factor signaling pathways encode both acylated and nonacylated members, suggesting that selective fatty acylation may provide a means of determining the specificity of their interactions with other regulatory molecules. Further studies of fatty acylated proteins should yield important information concerning the regulation of intracellular signaling pathways utilized during growth and differentiation.

Acetyltransferases↗

PubMed1995

Site-specific isotope fractionation in the characterization of biochemical mechanisms. The glycolytic pathway.

For a given biochemical transformation, such as the fermentation reaction, the redistribution coefficients, which relate the natural site-specific isotope contents in end products to those of their precursors, are a source of mechanistic information. These coefficients characterize the traceability of specific hydrogens in the products (ethanol and water) to their parent hydrogens in the starting materials (glucose and water). In conditions of complete transformation, they also enable intermolecular exchanges with the water medium to be estimated. Thus it is directly confirmed that hydrogens 1, 2, 6, and 6' of glucose are strongly connected to the methyl site I of ethanol obtained by fermentation by Saccharomyces cerevisiae. However, whereas hydrogens 6 and 6' are transferred to a great extent, transfer is only partial for hydrogen 2, and it is even less for hydrogen 1. Because the two moieties of glucose corresponding to carbons 1-2-3 and 4-5-6 are scrambled by the aldolase and triosephosphate isomerase reactions, additional exchange of hydrogens at positions 1 and 2 must have occurred before these steps. The value of the coefficient that relates site 2 of glucose to site I of ethanol in particular can be used to quantify the contribution of intermolecular exchange occurring in the course of the transfer from site 2 of glucose 6-phosphate to site 1 of fructose 6-phosphate mediated by phosphoglucoisomerase. The average hydrogen isotope effects associated with the transfer of hydrogen from the water pool to the methyl or methylene site of ethanol are estimated. In contrast to conventional experiments carried out in strongly deuterium-enriched media where metabolic switching may occur, the NMR investigation of site-specific natural isotope fractionation, which operates at tracer isotopic abundance, faithfully describes the unperturbed metabolic pathways.

Deuterium↗

PubMed2005

Activity properties and location of neurons in the motor thalamus that project to the cortical motor areas in monkeys.

The activity of neurons in the motor nuclei of the thalamus that project to the cortical motor areas (the primary motor cortex, the ventral and dorsal premotor cortex, and the supplementary motor area) was investigated in monkeys that were performing a task in which wrist extension and flexion movements were instructed by visuospatial cues before the onset of movement. Movement was triggered by a visual, auditory, or somatosensory stimulus. Thalamocortical neurons were identified by a spike collision, and exhibited 2 distinct types of task-related activity: 1) a sustained change in activity during the instructed preparation period in response to the instruction cues (set-related activity); and 2) phasic changes in activity during the reaction and movement time periods (movement-related activity). A number of set- and moment-related neurons exhibited direction selectivity. Most movement-related neurons were similarly active, irrespective of the different sensory modalities of the cue for movement. These properties of neuronal activity were similar, regardless of their target cortical motor areas. There were no significant differences in the antidromic latencies of neurons that projected to the primary and nonprimary motor areas. These results suggest that the thalamocortical neurons play an important role in the preparation for, and initiation and execution of, the movements, but are less important than neurons of the nonprimary cortical motor areas in modality-selective sensorimotor transformation. It is likely that such transformations take place within the nonprimary cortical motor areas, but not through thalamocortical information channels.

Action Potentials↗

PubMedDate not supplied

Polyamines and apoptosis.

The natural polyamines putrescine, spermidine and spermine are in multiple ways involved in cell growth and the maintenance of cell viability. In the course of the last 15 years more and more evidence hinted also at roles in gene regulation. It is therefore not surprising that the polyamines are involved in events inherent to genetically programmed cell death. Following inhibition of ornithine decarboxylase, a key step in polyamine biosynthesis, numerous links have been identified between the polyamines and apoptotic pathways. Examples of activation and prevention of apoptosis due to polyamine depletion are known for several cell lines. Elevation of polyamine concentrations may lead to apoptosis or to malignant transformation. These observations are discussed in the present review, together with possible mechanisms of action of the polyamines. Contradictory results and incomplete information blur the picture and complicate interpretation. Since, however, much interest is focussed at present on all aspects of programmed cell death, a considerable progress in the elucidation of polyamine functions in apoptotic signalling pathways is expected, even though enormous difficulties oppose pinpointing specific interactions of the polyamines with pro- and anti-apoptotic factors. Such situation is quite common in polyamine research.

Animals↗

PubMed1992

A comparison of the interaural time sensitivity of neurons in the inferior colliculus and thalamus of the unanesthetized rabbit.

The localization of low-frequency sounds (less than 3 kHz) along the azimuth involves comparing the ongoing difference in the time of arrival of a sound at the two ears. Information about interaural time differences (ITDs) is derived from an initial comparison performed in the superior olivary complex. However, little is known about which aspects of this information are transformed as it ascends the brainstem. To address this issue, we compared the ITD sensitivity of neurons in the inferior colliculus (IC) and auditory thalamus, successive stations in the auditory pathway. We found ITD sensitivity in the IC and thalamus to be similar in several respects. At both levels, the large majority of neurons responded maximally to ITDs within the range that a rabbit would normally encounter (+/- 300 microseconds) and preferred ipsilateral delays, delays that would be created by sounds in the contralateral sound field. The range of frequencies over which ITD sensitivity was expressed was also similar in the midbrain and thalamus. Several differences were also apparent. In comparison to IC neurons, neurons in the thalamus responded over more restricted ranges of ITD, responded at lower rates, and, in response to monaural stimulation, showed an increased influence of inhibition. Finally, a greater proportion of thalamic units had characteristic delays corresponding to intermediate discharge rates. The preservation of a bias for ipsilateral delays from IC to thalamus suggests that a representation of contralateral azimuths is present at both levels. Similarities between the two levels suggest that information about ITDs is faithfully transmitted from midbrain to thalamus. Differences in ITD sensitivity, such as the sharper tuning for ITDs, suggest that the thalamus is not a simple relay. Enhanced sensitivity to ITDs should translate to better-defined azimuthal receptive fields, and therefore may be a step toward achieving an optimal representation of azimuth within the auditory pathway.

Acoustic Stimulation↗

PubMed1993

A computational model of echo processing and acoustic imaging in frequency-modulated echolocating bats: the spectrogram correlation and transformation receiver.

The spectrogram correlation and transformation (SCAT) model of the sonar receiver in the big brown bat (Eptesicus fuscus) consists of a cochlear component for encoding the bat's frequency modulated (FM) sonar transmissions and multiple FM echoes in a spectrogram format, followed by two parallel pathways for processing temporal and spectral information in sonar echoes to reconstruct the absolute range and fine range structure of multiple targets from echo spectrograms. The outputs of computations taking place along these parallel pathways converge to be displayed along a computed image dimension of echo delay or target range. The resulting image depicts the location of various reflecting sources in different targets along the range axis. This series of transforms is equivalent to simultaneous, parallel forward and inverse transforms on sonar echoes, yielding the impulse responses of targets by deconvolution of the spectrograms. The performance of the model accurately reproduces the images perceived by Eptesicus in a variety of behavioral experiments on two-glint resolution in range, echo phase sensitivity, amplitude-latency trading of range estimates, dissociation of time- and frequency-domain image components, and ranging accuracy in noise.

Animals↗

PubMed1997

Spatially selective auditory responses in the superior colliculus of the echolocating bat.

When a bat approaches a target, it continuously modifies its echolocation sounds and relies on incoming echo information to shape the characteristics of its subsequent sonar cries. In addition, acoustic information about the azimuth and elevation of a sonar target elicits orienting movements of the head and pinnae toward the sound source. This requires a common sensorimotor interface, where echo information is used to guide motor behaviors. Using single-unit neurophysiological methods and free-field auditory stimulation, we present data on biologically relevant specializations in the superior colliculus (SC) of the bat for orientation by sonar. In the bat's SC, two classes of spatially tuned neurons are distinguished by their sensitivity to echoes. One population shows facilitated, delay-tuned responses to pairs of sounds, simulating sonar emissions and echoes. Delay tuning, related to encoding target range, may play a role in guiding motor responses in echolocation, because the bat adjusts its emissions with changes in target distance. The delay-facilitated response depends on the direction of stimulation and on the temporal relationship between the simulated emission and echo in the sound pair, suggesting that this class of neurons represents the location of a target in three dimensions. A second population encodes the target in two dimensions, azimuth and elevation, and does not show a facilitated response to echoes delivered from any locus. Encoding of azimuth and elevation may be important for directing head aim, and this class may function in transforming auditory spatial information into signals used to guide acoustic orientation.

Acoustic Stimulation↗

PubMedDate not supplied

The pathway from GTP to tetrahydrobiopterin: three-dimensional structures of GTP cyclohydrolase I and 6-pyruvoyl tetrahydropterin synthase.

The complex organic chemistry involved in the transformation of GTP to tetrahydrobiopterin is catalysed by only three enzymes: GTP cyclohydrolase I, 6-pyruvoyltetrahydropterin synthase and sepiapterin reductase. The committing reaction step from GTP to dihydroneopterin triphosphate is catalysed by GTP cyclohydrolase I and requires no cofactor. 6-Pyruvoyl tetrahydropterin synthase, a Zn-dependent metalloprotein, transforms dihydroneopterin triphosphate into 6-pyruvoyltetrahydropterin in the presence of Mg(II). Sepiapterin reductase is a NADPH-dependent short-chain dehydrogenase which reduces 6-pyruvoyltetrahydropterin to BH4. Here we review the structural and mechanistic information on the biosynthetic pathway from GTP to BH4 on the basis of the recently determined crystal structures of CYH and PTPS.

Alcohol Oxidoreductases↗

PubMed2005

Prostaglandin-dependent activation of ERK mediates cell proliferation induced by transforming growth factor beta in mouse osteoblastic cells.

Transforming growth factor beta (TGF(beta)) is a major coupling factor for bone turnover and is known to stimulate osteoblastic proliferation. Recent information indicates that, in addition to the Smad pathway, TGF(beta) also activates MAP kinases in osteoblastic cells. The role of these signaling cascades in cell proliferation induced by TGF(beta) as well as the cellular and molecular mechanisms of their activation by TGF(beta) has been investigated in this study. In MC3T3-E1 cells, TGF(beta) enhanced cell proliferation by about 2-fold and induced activation of the three MAP kinases, extracellular regulated kinase (ERK), p38, and c-Jun N-terminal kinase (JNK). Surprisingly, however, whereas activation of Smad2 was rapid and maximal after 15-min incubation, activation of MAP kinases was delayed with p38 stimulation detected after 1-h exposure and activation of ERK and JNK after 3 h, suggesting indirect activation of MAP kinases by TGF(beta). Among factors known to be released in response to TGF(beta) in osteoblastic cells and influence their growth, prostaglandins (PGs) were good candidates that were further investigated for mediating TGF(beta)-induced activation of MAP kinases and cell proliferation. Indomethacin, a selective inhibitor of PG synthesis, completely blunted cell proliferation induced by TGF(beta) and markedly reduced activation of MAP kinases without influencing Smad2 phosphorylation. EP4A, a specific PGE2 receptor antagonist, also blunted TGF(beta)-induced osteoblastic proliferation. In addition to these effects, PGE2 rapidly activated MAP kinases in MC3T3-E1 cells and increased cell proliferation by about 2-fold. The role of each MAP kinases in mediating TGF(beta)- and PGE2-induced cell proliferation was investigated using selective inhibitors. U0126, a specific inhibitor of the ERK pathway, completely blocked both TGF(beta)- and PGE2-induced cell proliferation whereas SB203580 and SP600125, which are selective inhibitors of, respectively, p38 and JNK pathways, had no effect. Finally, the effect of PGE2 on activation of ERK was mimicked by phorbol esters and not by forskolin, and was associated with activation of protein kinase C. This latter effect and the stimulation of ERK induced by PGE2 were completely blocked by a specific inhibitor of PKC. In conclusion, data presented in this study strongly suggest that the local release of PGE2 is involved in cell proliferation induced by TGF(beta) in osteoblastic cells. This effect is mediated by the ERK pathway activated by a PKC-dependent mechanism.

3T3 Cells↗

PubMed2005

A transition path for the pressure-induced wurtzite- to NaCl-type transformation described in Pna2(1).

Quite recently, two further mechanisms for the pressure-induced transition from the wurtzite to the NaCl type were proposed [Shimojo et al. (2004). Phys. Rev. B, 70, 184111-1-6] but no symmetry information was given. It will be shown that a slight modification of one of the assumed transition pathways allows a crystallographic description on the basis of a deformation of a heterogeneous 4-connected sphere packing in Pna2(1). All investigations were done with the help of the corresponding homogeneous packing in Pnma where the transition may be described as a deformation of a lonsdaleite configuration into a cubic primitive lattice cP. During the transformation, all sphere contacts are maintained. The new transition model is compared with the well known Cmc2(1) mechanism. Further related mechanisms can also be derived.

Journal Article↗

PubMed2000

Inactivation of p53 and retinoblastoma family pathways in canine osteosarcoma cell lines.

Canine osteosarcoma (OS) has been used as a model system for the study of cancer biology and treatment despite the lack of information regarding its pathogenesis. Expression of tumor suppressor genes known to participate in malignant transformation were studied in five different OS cell lines. Each of the cell lines exhibited properties of transformed cells, and those that were tested grew in soft agarose and formed osteoid-containing tumors when injected subcutaneously into nude mice. p53 function was determined to be defective in each cell line as indicated by the lack of induction of p53-responsive genes, p21 and mdm2, following treatment with 5-fluorouracil. p53 mRNA and protein levels were elevated in three cell lines and were extremely low in two cell lines. p53 protein overexpression correlated with the presence of mutations within the DNA binding domain. Four cell lines appeared to contain normal retinoblastoma (Rb) mRNA and Rb protein and no detectable p16 mRNA or protein. In contrast, the remaining cell line contained high levels of p16 mRNA and protein and significantly reduced levels of Rb, p107, and p130 proteins. These results underscore the importance of inactivating p53 and Rb family pathways in canine OS and suggest that unlike human OS, cells derived from canine OS contain mutations that simultaneously inactivate all three Rb family members.

Animals↗

PubMed2002

Malignant worms: what cancer research can learn from C. elegans.

Developmental processes in the nematode C. elegans are controlled by pathways of gene functions that are analogous to those used in mammals. Hence, genetic studies in C. elegans have helped build the frameworks for these regulatory pathways. Many homologs of human genes that are targets for mutation in cancer have been found to function at distinct steps within such genetic pathways. This way, studies in C. elegans have provided important clues about the functions of human oncogenes and tumor suppressors. Understanding how human cancer genes function and act in signaling cascades is of great importance. This information reveals what kind of molecular changes contribute to the process of cell transformation. Moreover, additional candidate oncogenes and tumor suppressors may be revealed by identifying the functional partners of genes with an established role in cancer. Furthermore, identifying a cascade of gene functions increases the number of potential targets for therapeutic intervention, as blocking either one of multiple genes may interfere with signal transduction through the pathway. Simultaneous approaches in a number of different model systems act synergistically in solving pathways of gene functions. By using multiple models, the field takes advantage of the strengths of each system and circumvents its limitations. As one of the most powerful genetic animal systems, C. elegans will continue to reveal new mammalian signaling components. In addition, now that the C. elegans genome sequence has been completed, an increasing number of researchers are likely to discover homologs of human disease genes in the nematode and to analyze gene function in the worm model. Combined with the great potential of this animal in drug screens, it is simple to predict that C. elegans will worm its way deeper and deeper into cancer research.

Animals↗

PubMed1991

A kinetic model of the odor response in single olfactory receptor neurons.

The detection of odor molecules by olfactory receptors is a biochemical process, but the neural signal is electrical. The transformation of chemical information into a change in membrane potential, i.e. the process of signal transduction, is accomplished in olfactory receptor neurons by a multi-step second messenger pathway resulting finally in the activation of ion channels by cAMP. Many of the biochemical and physiological details of this process are beginning to be appreciated, giving rise to a comprehensive model of the basic mechanisms of olfactory transduction that has much in common with those of other signal transduction systems. One interesting result of these new insights is that the olfactory neuron may act more as a molecule counter than a concentration detector, as had been believed previously.

Action Potentials↗

PubMed2006

The generation of receptive-field structure in cat primary visual cortex.

Cells in primary visual cortex show a remarkable variety of receptive-field structures. In spite of the extensive experimental and theoretical effort over the past 50 years, it has been difficult to establish how this diversity of functional-response properties emerges in the cortex. One of the reasons is that while functional studies in the early visual pathway have been usually carried out in vivo with extracellular recording techniques, investigations about the precise structure of the cortical network have mainly been conducted in vitro. Thus, the link between structure and function has rarely been explicitly established, remaining a well-known controversial issue. In this chapter, I review recent data that simultaneously combines anatomy with physiology at the intracellular level; trying to understand how the primary visual cortex transforms the information it receives from the thalamus to generate receptive-field structure, contrast-invariant orientation tuning and other functional-response properties.

Animals↗

PubMed2005

Making light work of enzyme catalysis: protochlorophyllide oxidoreductase.

In the chlorophyll biosynthetic pathway, the enzyme protochlorophyllide oxidoreductase (POR) catalyses a key light-driven reaction that triggers a profound transformation in plant development. Because POR is activated by light, it can provide information on the way in which light energy can be harnessed to power enzyme reactions and it presents us with a unique opportunity to study catalysis at low temperatures and on ultrafast timescales that are not accessible for most analyses of enzyme function. Recent advances in our understanding of the catalytic mechanism of POR illustrate why it is an important generic model for studying enzyme catalysis and reaction dynamics.

Catalysis↗

PubMed1998

Mechanisms of central color vision.

In monkey cerebral cortex, color information is processed along the ventral visual pathway. This pathway starts in the primary visual cortex and ends in area TE of the inferior temporal cortex. Recent studies indicate that the transformation of cone signals occurs early in the pathway to form neurons selective to a narrow range of hues. In addition, it has become apparent that area TE plays a vital role in color discrimination.

Animals↗