A DNA-based pattern classifier with in vitro learning and associative recall for genomic characterization and biosensing without explicit sequence knowledge

BACKGROUND: Genetic material extracted from in situ microbial communities has high promise as an indicator of biological system status. However, the challenge is to access genomic information from all organisms at the population or community scale to monitor the biosystem’s state. Hence, there is a need for a better diagnostic tool that provides a holistic view of a biosystem’s genomic status. Here, we introduce an in vitro methodology for genomic pattern classification of biological samples that taps large amounts of genetic information from all genes present and uses that information to detect changes in genomic patterns and classify them. RESULTS: We developed a biosensing protocol, termed Biological Memory, that has in vitro computational capabilities to “learn” and “store” genomic sequence information directly from genomic samples without knowledge of their explicit sequences, and that discovers differences in vitro between previously unknown inputs and learned memory molecules. The Memory protocol was designed and optimized based upon (1) common in vitro recombinant DNA operations using 20-base random probes, including polymerization, nuclease digestion, and magnetic bead separation, to capture a snapshot of the genomic state of a biological sample as a DNA memory and (2) the thermal stability of DNA duplexes between new input and the memory to detect similarities and differences. For efficient read out, a microarray was used as an output method. When the microarray-based Memory protocol was implemented to test its capability and sensitivity using genomic DNA from two model bacterial strains, i.e., Escherichia coli K12 and Bacillus subtilis, results indicate that the Memory protocol can “learn” input DNA, “recall” similar DNA, differentiate between dissimilar DNA, and detect relatively small concentration differences in samples. CONCLUSIONS: This study demonstrated not only the in vitro information processing capabilities of DNA, but also its promise as a genomic pattern classifier that could access information from all organisms in a biological system without explicit genomic information. The Memory protocol has high potential for many applications, including in situ biomonitoring of ecosystems, screening for diseases, biosensing of pathological features in water and food supplies, and non-biological information processing of memory devices, among many. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1754-1611-8-25) contains supplementary material, which is available to authorized users

Pharmacological And Genetic Reversal Of Age-Dependent Cognitive Deficits Attributable To Decreased Presenilin Function

Alzheimer\u27s disease (AD) is the leading cause of cognitive loss and neurodegeneration in the developed world. Although its genetic and environmental causes are not generally known, familial forms of the disease (FAD) are attributable to mutations in a single copy of the Presenilin (PS) and amyloid precursor protein genes. The dominant inheritance pattern of FAD indicates that it may be attributable to gain or change of function mutations. Studies of FAD-linked forms of presenilin (psn) in model organisms, however, indicate that they are loss of function, leading to the possibility that a reduction in PS activity might contribute to FAD and that proper psn levels are important for maintaining normal cognition throughout life. To explore this issue further, we have tested the effect of reducing psn activity during aging in Drosophila melanogaster males. We have found that flies in which the dosage of psn function is reduced by 50% display age-onset impairments in learning and memory. Treatment with metabotropic glutamate receptor (mGluR) antagonists or lithium during the aging process prevented the onset of these deficits, and treatment of aged flies reversed the age-dependent deficits. Genetic reduction of Drosophila metabotropic glutamate receptor (DmGluRA), the inositol trisphosphate receptor (InsP(3)R), or inositol polyphosphate 1-phosphatase also prevented these age-onset cognitive deficits. These findings suggest that reduced psn activity may contribute to the age-onset cognitive loss observed with FAD. They also indicate that enhanced mGluR signaling and calcium release regulated by InsP(3)R as underlying causes of the age-dependent cognitive phenotypes observed when psn activity is reduced

Interaction of nutrition and genetics via DNMT3L-mediated DNA methylation determines cognitive decline

Low homocysteine levels and B vitamin treatment are reported to protect against declining cognitive health. Both B vitamins and homocysteine are involved in the production of S-adenosylmethionine, a universal methyl donor essential for the process of DNA methylation. We investigated the effect of a damaging coding variant within the DNA methyltransferase gene, DNMT3L (R278G, A/G) by examining B vitamin intake, homocysteine levels, cognitive performance, and brain atrophy in individuals in the VITACOG study of Mild Cognitive Impairment and the TwinsUK cohort. In the VITACOG study, individuals who received a two- year treatment of B vitamins and carried the G allele, showed better ‘visuospatial associative memory’ and slower rates of brain atrophy. In the TwinsUK study, improved ‘visuospatial associative memory’ was evident in individuals who reported regular vitamin intake and were A/A homozygotes. In silico modelling indicated that R278G disrupts protein interaction between DNMT3L and DNMT3A, affecting the DNMT3A-3L-H3 complex required for DNA methylation. These findings show that vitamin intake and genetic variation within DNMT3L interact to influence cognitive decline

Déclenchement de la LTP hippocampique et de l'apprentissage par la dopamine : un signal d'apprentissage

L'hippocampe est la principale structure cérébrale impliquée dans la formation de la mémoire épisodique. Les mécanismes sous-jacents la mémoire hippocampique ont été étudié en détail chez les rongeurs, en particulier grâce à l'utilisation de tests de mémoire contextuelle. La potentialisation à long terme (PLT) est une augmentation de la transmission synaptique des afférences glutamatergiques ; elle sous-tend la formation des mémoires hippocampiques. Elle peut être déclenchée par une stimulation à haute fréquence (SHF). Ce mécanisme a permis de déchiffrer les mécanismes de la mémoire, montrant que la PLT, tout comme la mémoire, repose dans sa phase précoce sur des mécanismes de phosphorylation, ensuite, elle nécessite la formation de protéines de novo. Le lien entre la mémoire et la PLT est démontré par le fait que le blocage des différentes étapes de la PLT empêche la formation de la mémoire contextuelle et que celle-ci déclenche la PLT dans le CA1 de l'hippocampe. Étant donné que la PLT, tout comme la mémoire, est saturable, le système nerveux ne peut pas enregistrer tous les évènements vécus par l'animal. De plus, la SHF n'est pas compatible avec l'activité neuronale. Cela implique l'existence d'un signal d'apprentissage qui choisirait les entrées pertinentes à sauvegarder, et qui serait le déclencheur moléculaire de la PLT lors de l'apprentissage. La dopamine est un neuro-modulateur longtemps considéré comme indiquant la récompense. Cependant, la dopamine est libérée en réponse à tous les événements saillants, y compris aversifs. Les récepteurs dopaminergiques peuvent déclencher la phosphorylation et la formation de novo des protéines, et les récepteurs dopaminergiques D1/5 sont nécessaires pour la PLT tardive et la mémoire à long terme. De plus, la stimulation dopaminergique in vitro peut moduler la transmission synaptique du CA1. Dans ce travail, nous avons utilisé le comportement et l'électrophysiologie couplés aux manipulations optogénétiques des afférences dopaminergiques du mésencéphale et à l'inhibition pharmacologique des récepteurs dopaminergiques D1/5 pour étudier le rôle de la dopamine en tant que signal d'apprentissage déclenchant la PLT et l'apprentissage. En utilisant l'électrophysiologie, nous montrons que le couplage de stimulations optogénétiques des afférences dopaminergiques du mésencéphalique avec des entrées glutamatergiques du CA1 induit une PLT progressive de ces dernières, qui atteint un plateau 90 minutes après la dernière stimulation dopaminergique. Cette PLT dure au moins 5 heures, dépend des récepteurs D1/5 et occlue partiellement la PLT déclenchée par SHF. Ensuite, en utilisant le conditionnement de peur contextuel, nous montrons que l'infusion intra-hippocampique de de l'inhibiteur des récepteurs D1/5, SCH23390, bloque l'apprentissage du conditionnement de peur au contextuel mais pas à un indice auditif. Nous concluons que les récepteurs D1/5 hippocampiques sont nécessaires pour la mémoire de peur contextuelle. Enfin, nous avons utilisé une variante du conditionnement de peur au contexte appelée effet de facilitation par la préexposition contextuelle. Dans ce test, le conditionnement de peur a lieu le lendemain de l'apprentissage contextuel. Il permet ainsi d'étudier indépendamment chacune de ces deux étapes. Nous montrons que les récepteurs D1/5 sont nécessaires à l'apprentissage du contexte et à celui de la peur. Enfin, nous montrons que la stimulation optogénétique des axones dopaminergiques dans l'hippocampe favorise l'apprentissage contextuel et que leur inhibition empêche l'apprentissage contextuel. Ce travail nous permet de conclure que la voie dopaminergique du mésencéphale vers l'hippocampe a toutes les caractéristiques d'un signal d'apprentissage : elle déclenche la PLT sur les entrées sensorielles co-activées favorisant l'enregistrement d'informations contextuelles dans l'hippocampe indépendamment de toute information de valeur positive ou négative.The hippocampus is the main brain structure involved in episodic memory formation. The role of the hippocampus in learning, memory and their underlying mechanisms has been studied extensively in rodents, in particular by using contextual learning. Long-Term Potentiation (LTP) is an increase in synaptic transmission of glutamatergic afferents that lasts for hours, days or months and is thought to underlie hippocampal memory formation. It can be triggered in the hippocampus by an artificial High frequency Stimulation (HFS). This mechanism helped in deciphering memory mechanisms, showing that both memory and LTP rely firstly on phosphorylation and later on de novo protein synthesis. The link between memory and LTP was confirmed by showing that blocking LTP mechanisms hinders memory formation, and that contextual learning induces LTP in the CA1 of the hippocampus. Since LTP, just like memory, can be saturated, the nervous system cannot store every sensory input that the animal encounters. Moreover, HFS is not compatible with neuronal activity. Hence, there must be a teaching signal that would be the natural molecular trigger of LTP during learning, acting as a filter choosing the pertinent inputs to store. Dopamine is a neuromodulator that has historically been thought of as a value signal, for dopamine gets released during rewarding events. However, dopamine has later been shown to be released whenever a salient unrewarding, or even punishing, event occurs. Dopamine receptors can trigger both phosphorylation and de novo protein formation in most brain structures showing plasticity, and D1/5 Dopaminergic receptors are necessary for LTP maintenance and long-term memory. Moreover, dopaminergic stimulation in vitro can modulate synaptic transmission in CA1. Thus, we hypothesized that dopamine could act as a teaching signal. In this work, we use behavior and electrophysiology coupled with optogenetic manipulations of midbrain dopamine afferents and pharmacology inhibition of D1/5 dopaminergic receptors in order to study the role of dopamine as a teaching signal triggering LTP so that pertinent sensory inputs get stored. Using electrophysiology, we show that coupling optogenetic stimulations of midbrain dopamine with glutamatergic inputs in CA1 induces a progressive LTP that reaches its plateau 90 minutes after the pairing. This LTP endures at least 5 hours, is dependent on D1/5 receptors and partially occludes HFS-triggered LTP. Then, using contextual fear conditioning coupled with auditory cue conditioning we show that intraperitoneal injection of D1/5 receptor inhibitor, SHC23390, hinders both contextual and cue fear memories. Alternatively, intra-hippocampal infusion of SCH23390 blocks contextual memory but preserves cue fear memory intact. These results allowed us to conclude that hippocampal D1/5 receptors are necessary for contextual fear memories and in another brain structure for associative fear memories. Finally, we use a variation of contextual fear conditioning called contextual pre-exposure facilitation effect, which separates contextual learning from fear conditioning since the animal in this task learns each of them on two consecutive days. This allows studying dopamine as a teaching signal without the interference of any value inputs. We show that mice require between 2-8 minutes to encode contextual information. Furthermore, we show that D1/5 receptors are necessary for contextual and fear learning. Finally, we show that optogenetic stimulation of dopaminergic axons in the hippocampus promotes contextual learning and, conversely, their inhibition hinders contextual learning. This work allows us to conclude that the dopaminergic pathway from the midbrain to the hippocampus has all the characteristics of a teaching signal, namely, triggering LTP on co-activated sensory inputs promoting the storage of contextual information in the hippocampus without the need for any value information

Knockout crickets for the study of learning and memory : Dopamine receptor Dop1 mediates aversive but not appetitive reinforcement in crickets

Elucidation of reinforcement mechanisms in associative learning is an important subject in neuroscience. In mammals, dopamine neurons are thought to play critical roles in mediating both appetitive and aversive reinforcement. Our pharmacological studies suggested that octopamine and dopamine neurons mediate reward and punishment, respectively, in crickets, but recent studies in fruit-flies concluded that dopamine neurons mediates both reward and punishment, via the type 1 dopamine receptor Dop1. To resolve the discrepancy between studies in different insect species, we produced Dop1 knockout crickets using the CRISPR/Cas9 system and found that they are defective in aversive learning with sodium chloride punishment but not appetitive learning with water or sucrose reward. The results suggest that dopamine and octopamine neurons mediate aversive and appetitive reinforcement, respectively, in crickets. We suggest unexpected diversity in neurotransmitters mediating appetitive reinforcement between crickets and fruit-flies, although the neurotransmitter mediating aversive reinforcement is conserved. This study demonstrates usefulness of the CRISPR/Cas9 system for producing knockout animals for the study of learning and memory

Frustration in Biomolecules

Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with a finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of "frustration" in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and how structure connects to function. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding, how a large part of the biological functions of proteins are related to subtle local frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. We hope to illustrate how Frustration is a fundamental concept in relating function to structural biology.Comment: 97 pages, 30 figure

Proactive and retroactive interference with associative memory consolidation in the snail Lymnaea is time and circuit dependent

Interference-based forgetting occurs when new information acquired either before or after a learning event attenuates memory expression (proactive and retroactive interference, respectively). Multiple learning events often occur in rapid succession, leading to competition between consolidating memories. However, it is unknown what factors determine which memory is remembered or forgotten. Here, we challenge the snail, Lymnaea, to acquire two consecutive similar or different memories and identify learning-induced changes in neurons of its well-characterized motor circuits. We show that when new learning takes place during a stable period of the original memory, proactive interference only occurs if the two consolidating memories engage the same circuit mechanisms. If different circuits are used, both memories survive. However, any new learning during a labile period of consolidation promotes retroactive interference and the acquisition of the new memory. Therefore, the effect of interference depends both on the timing of new learning and the underlying neuronal mechanisms

Computational investigations of cognitive impairment in Huntington's Disease

Book synopsis: Huntington's Disease is one of the well-studied neurodegenerative conditions, a quite devastating and currently incurable one. It is a brain disorder that causes certain types of neurons to become damaged, causing various parts of the brain to deteriorate and lose their function. This results in uncontrolled movements, loss of intellectual capabilities and behavioural disturbances. Since the identification of the causative mutation, there have been many significant developments in understanding the cellular and molecular perturbations. This book, "Huntington's Disease - Core Concepts and Current Advances", was prepared to serve as a source of up-to-date information on a wide range of issues involved in Huntington's Disease. It will help the clinicians, health care providers, researchers, graduate students and life science readers to increase their understanding of the clinical correlates, genetic aspects, neuropathological findings, cellular and molecular events and potential therapeutic interventions involved in HD. The book not only serves reviewed fundamental information on the disease but also presents original research in several disciplines, which collectively provide comprehensive description of the key issues in the area

Critical role of the circadian clock in memory formation: lessons from Aplysia

Unraveling the complexities of learning and the formation of memory requires identification of the cellular and molecular processes through which neural plasticity arises as well as recognition of the conditions or factors through which those processes are modulated. With its relatively simple nervous system, the marine mollusk Aplysia californica has proven an outstanding model system for studies of memory formation and identification of the molecular mechanisms underlying learned behaviors, including classical and operant associative learning paradigms and non-associative behaviors. In vivo behavioral studies in Aplysia have significantly furthered our understanding of how the endogenous circadian clock modulates memory formation. Sensitization of the tail-siphon withdrawal reflex represents a defensive non-associative learned behavior for which the circadian clock strongly modulates intermediate and long-term memory formation. Likewise, Aplysia exhibit circadian rhythms in long-term memory, but not short-term memory, for an operant associative learning paradigm. This review focuses on circadian modulation of intermediate and long-term memory and the putative mechanisms through which this modulation occurs. Additionally, potential functions and the adaptive advantages of time of day pressure on memory formation are considered. The influence of the circadian clock on learning and memory crosses distant phylogeny highlighting the evolutionary importance of the circadian clock on metabolic, physiological, and behavioral processes. Thus, studies in a simple invertebrate model system have and will continue to provide critical mechanistic insights to complementary processes in higher organisms