Molecular coding of memory

The central importance of nuclear mechanisms in the storage of memory

The neurobiological nature of the memory trace (engram) remains controversial. The most widely accepted hypothesis at present is that long-term memory is stored as stable, learning-induced changes in synaptic connections. This hypothesis, the synaptic plasticity hypothesis of memory, is supported by extensive experimental data gathered from over 50 years of research. Nonetheless, there are important mnemonic phenomena that the synaptic plasticity hypothesis cannot, or cannot readily, account for. Furthermore, recent work indicates that epigenetic and genomic mechanisms play heretofore underappreciated roles in memory. Here, we critically assess the evidence that supports the synaptic plasticity hypothesis and discuss alternative non-synaptic, nuclear mechanisms of memory storage, including DNA methylation and retrotransposition. We argue that long-term encoding of memory is mediated by nuclear processes; synaptic plasticity, by contrast, represents a means of relatively temporary memory storage. In addition, we propose that memories are evaluated for their mnemonic significance during an initial period of synaptic storage; if assessed as sufficiently important, the memories then undergo nuclear encoding.

Can memory exist outside of brain and be transferred? Historical review, issues & ways forward

Learning and memory are among the executive functions attributed to intelligent forms of life. Unfortunately, there is a lack of clear understanding regarding the underlying mechanisms governing these functions. Most of the modern day scientists attribute these functions solely to brain. However, in the latter half of last century, a number of reports suggested existence of extra-cranial memory and potential of its transfer between animals. Some have linked this phenomenon to RNA while others believed that peptides were responsible. The terms like "educated RNA" and "scotophobin" were coined. This atypical work involving flatworms, yeast RNA and scotophobin was received with deep skepticism and ultimately disregarded. However, the recent reproduction of some of this earlier work by scientists at Tufts University has reignited the debate on the mechanisms of learning and memory. Keeping this in view, we believe it is high time to summarize this historical work and discuss the possibilities to delineate these atypical claims. The objective is to incite the present day researchers to explore this opportunity under the perspective of newer advancements in science.

On Having No Head: Cognition throughout Biological Systems

The central nervous system (CNS) underlies memory, perception, decision-making, and behavior in numerous organisms. However, neural networks have no monopoly on the signaling functions that implement these remarkable algorithms. It is often forgotten that neurons optimized cellular signaling modes that existed long before the CNS appeared during evolution, and were used by somatic cellular networks to orchestrate physiology, embryonic development, and behavior. Many of the key dynamics that enable information processing can, in fact, be implemented by different biological hardware. This is widely exploited by organisms throughout the tree of life. Here, we review data on memory, learning, and other aspects of cognition in a range of models, including single celled organisms, plants, and tissues in animal bodies. We discuss current knowledge of the molecular mechanisms at work in these systems, and suggest several hypotheses for future investigation. The study of cognitive processes implemented in aneural contexts is a fascinating, highly interdisciplinary topic that has many implications for evolution, cell biology, regenerative medicine, computer science, and synthetic bioengineering.

The stability of memories during brain remodeling: A perspective

One of the most important features of the nervous system is memory: the ability to represent and store experiences, in a manner that alters behavior and cognition at future times when the original stimulus is no longer present. However, the brain is not always an anatomically stable structure: many animal species regenerate all or part of the brain after severe injury, or remodel their CNS toward a new configuration as part of their life cycle. This raises a fascinating question: what are the dynamics of memories during brain regeneration? Can stable memories remain intact when cellular turnover and spatial rearrangement modify the biological hardware within which experiences are stored? What can we learn from model species that exhibit both, regeneration and memory, with respect to robustness and stability requirements for long-term memories encoded in living tissues? In this Perspective, we discuss relevant data in regenerating planaria, metamorphosing insects, and hibernating ground squirrels. While much remains to be done to understand this remarkable process, molecular-level insight will have important implications for cognitive science, regenerative medicine of the brain, and the development of non-traditional computational media in synthetic bioengineering.

A second-generation device for automated training and quantitative behavior analyses of molecularly-tractable model organisms

A deep understanding of cognitive processes requires functional, quantitative analyses of the steps leading from genetics and the development of nervous system structure to behavior. Molecularly-tractable model systems such as Xenopus laevis and planaria offer an unprecedented opportunity to dissect the mechanisms determining the complex structure of the brain and CNS. A standardized platform that facilitated quantitative analysis of behavior would make a significant impact on evolutionary ethology, neuropharmacology, and cognitive science. While some animal tracking systems exist, the available systems do not allow automated training (feedback to individual subjects in real time, which is necessary for operant conditioning assays). The lack of standardization in the field, and the numerous technical challenges that face the development of a versatile system with the necessary capabilities, comprise a significant barrier keeping molecular developmental biology labs from integrating behavior analysis endpoints into their pharmacological and genetic perturbations. Here we report the development of a second-generation system that is a highly flexible, powerful machine vision and environmental control platform. In order to enable multidisciplinary studies aimed at understanding the roles of genes in brain function and behavior, and aid other laboratories that do not have the facilities to undergo complex engineering development, we describe the device and the problems that it overcomes. We also present sample data using frog tadpoles and flatworms to illustrate its use. Having solved significant engineering challenges in its construction, the resulting design is a relatively inexpensive instrument of wide relevance for several fields, and will accelerate interdisciplinary discovery in pharmacology, neurobiology, regenerative medicine, and cognitive science.

Automated analysis of behavior: a computer-controlled system for drug screening and the investigation of learning

Efforts to understand cognition will be greatly facilitated by computerized systems that enable the automated analysis of animal behavior. A number of controversies in the invertebrate learning field have resulted from difficulties inherent in manual experiments. Driven by the necessity to overcome these problems during investigation of neural function in planarian flatworms and frog larvae, we designed and developed a prototype for an inexpensive, flexible system that enables automated control and analysis of behavior and learning. Applicable to a variety of small animals such as flatworms and zebrafish, this system allows automated analysis of innate behavior, as well as of learning and memory in a plethora of conditioning paradigms. We present here the schematics of a basic prototype, which overcomes experimenter effects and operator tedium, enabling a large number of animals to be analyzed with transparent on-line access to primary data. A scaled-up version of this technology represents an efficient methodology to screen pharmacological and genetic libraries for novel neuroactive reagents of basic and biomedical relevance.

Georges Ungar and memory transfer

The idea that memories could be transferred from one organism to another by administration of a "trained" donor brain to a naive recipient seized both scientific and public attention in the 1960's and early 1970's. Georges Ungar was one of the earliest and strongest proponents of this idea, and he provided it extensive theoretical and experimental support. This paper reviews Ungar's work on memory transfer (and in particular on the scotophobin molecule), with an analysis of its successes and failures.

Patterns of peptides and protein-associated-peptide complexes in psychiatric disorders

Peptidic neurones may be considered as multisignal intergrators and transducers. When formation or release of peptide outstrips genetically determined breakdown capacity, overflow of peptides to the body fluids and urine may be expected. In this paper, pathological urinary chromatographic patterns of peptides are shown for genetic, functional and mixed disorders. Part symptoms of the disorders may be induced with the biologically isolated and purified peptides as well as with chemically synthesized peptides.

Relations between immunological and neurological memory: learning ability in rats during immunostimulation

The effect of an immunostimulator, Freund's complete adjuvant (FCA), on the ability of Wistar rats to learn in a visual discrimination test was studied by foodgetting and electric-shock avoidance methods. A significant improvement in learning ability was demonstrated under the influence of FCA when the negative reinforcement method was used, but a worsening when the positive reinforcement method was used. Analysis of the dynamics of extinction of the reflexes formed gave similar results. The possible relations between immunogenesis and memory forming processes are discussed.

Isolation and identification of two learning-induced brain peptides

Goldfish were trained either to avoid the blue compartment of a tank and swim into the green compartment or, conversely, to avoid green and prefer blue. Preliminary experiments indicated that acquisition of the avoidance behavior was associated with the presence in the brain of two peptides, one found in blue avoiding (BA), another in green avoiding (GA) fish. With the help of behavioral bioassays, the peptides were isolated and purified, and their structure was determined by ultrasmicroanalytical techniques. The sequence of the BA peptide, pglu-ile-gly-ala-val-phe-pro-leu-lys-tyr-gly-ser-lys-OH was reproduced by synthesis. Sequential analysis of the GA peptide gave two alternative structures, NAc-lys-gly-gln-ile-ala-val-phe-pro-leu-lys-tyr-gly-ser-OH or NAc-lys-gly-ala-val-gln-ile-phe-pro-lys-tyr-gly-ser-OH, both of which are being synthetized to be compared with the natural compound. Overlapping sequences between the BA and GA peptides suggest the existence of a family of peptides associated with behavior based on color discrimination.

The synthesis of a peptide having the structure attributed to a sound habituating material

A peptide isolated from rats habituated to a sound stimulus has been given the structure (see article) Glu-Ala-Gly-Tyr-Ser-Lys-OH. A synthesis of this compound afforded a product that different from the natural material on the basis of chromatographic and physiological comparisons. The proposed sequence must therefore be in error.