Cracking the code of neuronal apoptosis and survival.
Ontology highlight
ABSTRACT:
SUBMITTER: Cavallaro S
PROVIDER: S-EPMC4670922 | biostudies-other | 2015
REPOSITORIES: biostudies-other
Similar Datasets
Project description:Transcriptional regulation is fundamental to most biological processes and reverse-engineering programs can be used to decipher the underlying programs. In this review, we describe how genomics is offering a systems biology-based perspective of the intricate and temporally coordinated transcriptional programs that control neuronal apoptosis and survival. In addition to providing a new standpoint in human pathology focused on the regulatory program, cracking the code of neuronal cell fate may offer innovative therapeutic approaches focused on downstream targets and regulatory networks. Similar to computers, where faults often arise from a software bug, neuronal fate may critically depend on its transcription program. Thus, cracking the code of neuronal life or death may help finding a patch for neurodegeneration and cancer.
| S-EPMC10093029 | biostudies-literature
Project description:Neural oscillations are ubiquitous measurements of cognitive processes and dynamic routing and gating of information. The fundamental and so far unresolved problem for neuroscience remains to understand how oscillatory activity in the brain codes information for human cognition. In a biologically relevant cognitive task, we instructed six human observers to categorize facial expressions of emotion while we measured the observers' EEG. We combined state-of-the-art stimulus control with statistical information theory analysis to quantify how the three parameters of oscillations (i.e., power, phase, and frequency) code the visual information relevant for behavior in a cognitive task. We make three points: First, we demonstrate that phase codes considerably more information (2.4 times) relating to the cognitive task than power. Second, we show that the conjunction of power and phase coding reflects detailed visual features relevant for behavioral response--that is, features of facial expressions predicted by behavior. Third, we demonstrate, in analogy to communication technology, that oscillatory frequencies in the brain multiplex the coding of visual features, increasing coding capacity. Together, our findings about the fundamental coding properties of neural oscillations will redirect the research agenda in neuroscience by establishing the differential role of frequency, phase, and amplitude in coding behaviorally relevant information in the brain.
| S-EPMC3096604 | biostudies-literature
Project description:The genetic code is textbook scientific knowledge that was soundly established without resorting to Artificial Intelligence (AI). The goal of our study was to check whether a neural network could re-discover, on its own, the mapping links between codons and amino acids and build the complete deciphering dictionary upon presentation of transcripts proteins data training pairs. We compared different Deep Learning neural network architectures and estimated quantitatively the size of the required human transcriptomic training set to achieve the best possible accuracy in the codon-to-amino-acid mapping. We also investigated the effect of a codon embedding layer assessing the semantic similarity between codons on the rate of increase of the training accuracy. We further investigated the benefit of quantifying and using the unbalanced representations of amino acids within real human proteins for a faster deciphering of rare amino acids codons. Deep neural networks require huge amount of data to train them. Deciphering the genetic code by a neural network is no exception. A test accuracy of 100% and the unequivocal deciphering of rare codons such as the tryptophan codon or the stop codons require a training dataset of the order of 4-22 millions cumulated pairs of codons with their associated amino acids presented to the neural network over around 7-40 training epochs, depending on the architecture and settings. We confirm that the wide generic capacities and modularity of deep neural networks allow them to be customized easily to learn the deciphering task of the genetic code efficiently.
| S-EPMC10117997 | biostudies-literature
Project description:Word segmentation, detecting word boundaries in continuous speech, is a critical aspect of language learning. Previous research in infants and adults demonstrated that a stream of speech can be readily segmented based solely on the statistical and speech cues afforded by the input. Using functional magnetic resonance imaging (fMRI), the neural substrate of word segmentation was examined on-line as participants listened to three streams of concatenated syllables, containing either statistical regularities alone, statistical regularities and speech cues, or no cues. Despite the participants' inability to explicitly detect differences between the speech streams, neural activity differed significantly across conditions, with left-lateralized signal increases in temporal cortices observed only when participants listened to streams containing statistical regularities, particularly the stream containing speech cues. In a second fMRI study, designed to verify that word segmentation had implicitly taken place, participants listened to trisyllabic combinations that occurred with different frequencies in the streams of speech they just heard ("words," 45 times; "partwords," 15 times; "nonwords," once). Reliably greater activity in left inferior and middle frontal gyri was observed when comparing words with partwords and, to a lesser extent, when comparing partwords with nonwords. Activity in these regions, taken to index the implicit detection of word boundaries, was positively correlated with participants' rapid auditory processing skills. These findings provide a neural signature of on-line word segmentation in the mature brain and an initial model with which to study developmental changes in the neural architecture involved in processing speech cues during language learning.
| S-EPMC3713232 | biostudies-literature
Project description:To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking.
| S-EPMC5987255 | biostudies-literature
Project description:Heat shock protein 70 (Hsp70) is a molecular chaperone required for protein folding, cell viability, and cancer cell proliferation. Recent studies suggest that Hsp70 phosphorylation regulates important cellular processes, such as cell cycle progression, apoptosis, protein degradation, and resistance to anticancer therapeutics.
| S-EPMC5701876 | biostudies-literature
Project description:Human listeners excel at forming high-level social representations about each other, even from the briefest of utterances. In particular, pitch is widely recognized as the auditory dimension that conveys most of the information about a speaker's traits, emotional states, and attitudes. While past research has primarily looked at the influence of mean pitch, almost nothing is known about how intonation patterns, i.e., finely tuned pitch trajectories around the mean, may determine social judgments in speech. Here, we introduce an experimental paradigm that combines state-of-the-art voice transformation algorithms with psychophysical reverse correlation and show that two of the most important dimensions of social judgments, a speaker's perceived dominance and trustworthiness, are driven by robust and distinguishing pitch trajectories in short utterances like the word "Hello," which remained remarkably stable whether male or female listeners judged male or female speakers. These findings reveal a unique communicative adaptation that enables listeners to infer social traits regardless of speakers' physical characteristics, such as sex and mean pitch. By characterizing how any given individual's mental representations may differ from this generic code, the method introduced here opens avenues to explore dysprosody and social-cognitive deficits in disorders like autism spectrum and schizophrenia. In addition, once derived experimentally, these prototypes can be applied to novel utterances, thus providing a principled way to modulate personality impressions in arbitrary speech signals.
| S-EPMC5899438 | biostudies-literature
Project description:Patterns of resting potential in non-excitable cells of living tissue are now known to be instructive signals for pattern formation during embryogenesis, regeneration and cancer suppression. The development of molecular-level techniques for tracking ion flows and functionally manipulating the activity of ion channels and pumps has begun to reveal the mechanisms by which voltage gradients regulate cell behaviors and the assembly of complex large-scale structures. A recent paper demonstrated that a specific voltage range is necessary for demarcation of eye fields in the frog embryo. Remarkably, artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm. These data challenge the existing models of eye fate restriction and tissue competence maps, and suggest the presence of a bioelectric code-a mapping of physiological properties to anatomical outcomes. This Addendum summarizes the current state of knowledge in developmental bioelectricity, proposes three possible interpretations of the bioelectric code that functionally maps physiological states to anatomical outcomes, and highlights the biggest open questions in this field. We also suggest a speculative hypothesis at the intersection of cognitive science and developmental biology: that bioelectrical signaling among non-excitable cells coupled by gap junctions simulates neural network-like dynamics, and underlies the information processing functions required by complex pattern formation in vivo. Understanding and learning to control the information stored in physiological networks will have transformative implications for developmental biology, regenerative medicine and synthetic bioengineering.
| S-EPMC3689572 | biostudies-literature
Project description:The two basic processes underlying perceptual decisions-how neural responses encode stimuli, and how they inform behavioral choices-have mainly been studied separately. Thus, although many spatiotemporal features of neural population activity, or "neural codes," have been shown to carry sensory information, it is often unknown whether the brain uses these features for perception. To address this issue, we propose a new framework centered on redefining the neural code as the neural features that carry sensory information used by the animal to drive appropriate behavior; that is, the features that have an intersection between sensory and choice information. We show how this framework leads to a new statistical analysis of neural activity recorded during behavior that can identify such neural codes, and we discuss how to combine intersection-based analysis of neural recordings with intervention on neural activity to determine definitively whether specific neural activity features are involved in a task.
| S-EPMC5308795 | biostudies-literature
Project description:Background and Aims:The leaf axis of members of the order Cycadales ('cycads') has long been recognized by its configuration of independent vascular bundles that, in transverse section, resemble the Greek letter omega (hence the 'omega pattern'). This provides a useful diagnostic character for the order, especially when applied to paleobotany. The function of this pattern has never been elucidated. Here we provide a three-dimensional analysis and explain the pattern in terms of the hydraulic architecture of the pinnately compound cycad leaf. Methods:The genus Cycas was used as a simple model, because each leaflet is supplied by a single vascular bundle. Sequential sectioning was conducted throughout the leaf axis and photographed with a digital camera. Photographs were registered and converted to a cinematic format, which provided an objective method of analysis. Key Results:The omega pattern in the petiole can be sub-divided into three vascular components, an abaxial 'circle', a central 'column' and two adaxial 'wings', the last being the only direct source of vascular supply to the leaflets. Each leaflet is supplied by a vascular bundle that has divided or migrated directly from the closest wing bundle. There is neither multiplication nor anastomoses of vascular bundles in the other two components. Thus, as one proceeds from base to apex along the leaf axis, the number of vascular bundles in circle and column components is reduced distally by their uniform migration throughout all components. Consequently, the distal leaflets are irrigated by the more abaxial bundles, guaranteeing uniform water supply along the length of the axis. Conclusions:The omega pattern exemplifies one of the many solutions plants have achieved in supplying distal appendages of an axis with a uniform water supply. Our method presents a model that can be applied to other genera of cycads with more complex vascular organization.
| S-EPMC5838846 | biostudies-other