Su-jin Ha

Bioinformatics involves the use of techniques including applied mathematics, informatics, statistics, computer science, chemistry, and biochemistry to solve biological problems. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and protein-protein interactions, and the modeling of evolution.

 

Contents

Overview

The scientific study of the nervous systems underwent a significant increase in the second half of the twentieth century, principally due to revolutions in molecular biology, neural networks and computational neuroscience. It has become possible to understand, in exquisite detail, the complex processes occurring inside a single neuron and in a network that eventually produces the intellectual behavior, cognition, emotion and physiological responses.

stained neuron

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The task of neural science is to explain behavior in terms of the activities of the brain. How does the brain marshal its millions of individual nerve cells to produce behavior, and how are these cells influenced by the environment...? The last frontier of the biological sciences--their ultimate challenge--is to understand the biological basis of consciousness and the mental processes by which we perceive, act, learn, and remember. — Eric Kandel, Principles of Neural science, fourth edition

”

The nervous system is composed of a network of neurons and other supportive cells (such as glial cells). Neurons form functional circuits, each responsible for specific tasks to the behaviors at the organism level. Thus, neuroscience can be studied at many different levels, ranging from molecular level to cellular level to systems level to cognitive level.

At the molecular level, the basic questions addressed in molecular neuroscience include the mechanisms by which neurons express and respond to molecular signals and how axons form complex connectivity patterns. At this level, tools from molecular biology and genetics are used to understand how neurons develop and die, and how genetic changes affect biological functions. The morphology, molecular identity and physiological characteristics of neurons and how they relate to different types of behavior are also of considerable interest. (The ways in which neurons and their connections are modified by experience are addressed at the physiological and cognitive levels.)

At the cellular level, the fundamental questions addressed in cellular neuroscience are the mechanisms of how neurons process signals physiologically and electrochemically. They address how signals are processed by the dendrites, somas and axons, and how neurotransmitters and electrical signals are used to process signals in a neuron.

At the systems level, the questions addressed in systems neuroscience include how the circuits are formed and used anatomically and physiologically to produce the physiological functions, such as reflexes, sensory integration, motor coordination, emotional responses, learning and memory, et cetera. In other words, they address how these neural circuits function and the mechanisms through which behaviors are generated. For example, systems level analysis addresses questions concerning specific sensory and motor modalities: how does vision work? How do songbirds learn new songs and bats localize with ultrasound? The related field of neuroethology, in particular, addresses the complex question of how neural substrates underlies specific animal behavior.

Animation of a stack of horizontal MRI sections of a normal adult human brain

At the cognitive level, cognitive neuroscience addresses the questions of how psychological/cognitive functions are produced by the neural circuitry. The emergence of powerful new measurement techniques such as neuroimaging (e.g.,fMRI, PET, SPECT), electrophysiology and human genetic analysis combined with sophisticated experimental techniques from cognitive psychology allows neuroscientists and psychologists to address abstract questions such as how human cognition and emotion are mapped to specific neural circuitries.

Neuroscience is also beginning to become allied with social sciences, and burgeoning interdisciplinary fields of neuroeconomics, decision theory, social neuroscience are starting to address some of the most complex questions involving interactions of brain with environment.

Neuroscience generally includes all scientific studies involving the nervous system. Psychology, as the scientific study of mental processes, may be considered a sub-field of neuroscience, although some mind/body theorists argue that the definition goes the other way — that psychology is a study of mental processes that can be modeled by many other abstract principles and theories, such as behaviorism and traditional cognitive psychology, that are independent of the underlying neural processes. The term neurobiology is sometimes used interchangeably with neuroscience, though the former refers to the biology of nervous system, whereas the latter refers to science of mental functions that form the foundation of the constituent neural circuitries. In Principles of Neural Science, nobel laureate Eric Kandel contends that cognitive psychology is one of the pillar disciplines for understanding the brain in neuroscience.

Neurology and Psychiatry are medical specialties and are generally considered, in academic research, subfields of neuroscience that specifically address the diseases of the nervous system. These terms also refer to clinical disciplines involving diagnosis and treatment of these diseases. Neurology deals with diseases of the central and peripheral nervous systems such as amyotrophic lateral sclerosis (ALS) and stroke, while psychiatry focuses on mental illnesses. The boundaries between the two have been blurring recently and physicians who specialize in either generally receive training in both. Both neurology and psychiatry are heavily involved in and influenced by basic research in neuroscience.

 

History of Neuroscience

Evidence of trepanation, the surgical practice of either drilling or scraping a hole into the skull with the aim of curing headaches or mental disorders or relieving cranial pressure, being performed on patients dates back to Neolithic times and has been found in various cultures throughout the world. Manuscripts dating back to 5000BC indicated that the Egyptians had some knowledge about symptoms of brain damage.

Early views on the function of the brain regarded it to be a "cranial stuffing" of sorts. In Egypt, from the late Middle Kingdom onwards, the brain was regularly removed in preparation for mummification. It was believed at the time that the heart was the seat of intelligence. According to Herodotus, during the first step of mummification: 'The most perfect practice is to extract as much of the brain as possible with an iron hook, and what the hook cannot reach is mixed with drugs.'

The view that the heart was the source of consciousness was not challenged until the time of Hippocrates. He believed that the brain was not only involved with sensation, since most specialized organs (e.g., eyes, ears, tongue) are located in the head near the brain, but was also the seat of intelligence. Aristotle, however, believed that the heart was the center of intelligence and that the brain served to cool the blood. This view was generally accepted until the Roman physician Galen, a follower of Hippocrates and physician to Roman gladiators, observed that his patients lost their mental faculties when they had sustained damage to their brains.

In Al-Andalus, Abulcasis, the father of modern surgery, developed material and technical designs which are still used in neurosurgery. Averroes suggested the existence of Parkinson's disease and attributed photoreceptor properties to the retina. Avenzoar described meningitis, intracranial thrombophlebitis, mediastinal tumours and made contributions to modern neuropharmacology. Maimonides wrote about neuropsychiatric disorders and described rabies and belladonna intoxication.

Studies of the brain were became more sophisticated after the invention of the microscope and the development of a staining procedure by Camillo Golgi during the late 1890s that used a silver chromate salt to reveal the intricate structures of single neurons. His technique was used by Santiago Ramón y Cajal and led to the formation of the neuron doctrine, the hypothesis that the functional unit of the brain is the neuron. Golgi and Ramón y Cajal shared the Nobel Prize in Physiology or Medicine in 1906 for their extensive observations, descriptions and categorizations of neurons throughout the brain. The hypotheses of the neuron doctrine were supported by experiments following Galvani's pioneering work in the electrical excitability of muscles and neurons. In the late 19th century, DuBois-Reymond, Müller, and von Helmholtz showed neurons were electrically excitable and that their activity predictably affected the electrical state of adjacent neurons.

In parallel with this research, work with brain-damaged patients by Paul Broca suggested that certain regions of the brain were responsible for certain functions. This hypothesis was supported by observations of epileptic patients conducted by John Hughlings Jackson, who correctly deduced the organization of motor cortex by watching the progression of seizures through the body. Wernicke further developed the theory of the specialization of specific brain structures in language comprehension and production. Modern research still uses the Brodmann cytoarchitectonic (referring to study of cell structure) anatomical definitions from this era in continuing to show that distinct areas of the cortex are activated in the execution of specific tasks.

ref: Principles of Neural Science, 4th ed. Eric R. Kandel, James H. Schwartz, Thomas M. Jessel, eds. McGraw-Hill:New York, NY. 2000.

Andrea Vesalius (1514-1564) René Descartes (1596-1650)

 

Major Branches of Neuroscience

Current neuroscience research activities can be very roughly categorized into the following major branches, based on the subject and scale of the system in examination as well as distinct experimental approaches. Individual neuroscientists, however, often work on questions that span several distinct subfields.

Branch	Major Topics and Concepts	Experimental and Theoretical Methods
Molecular and Cellular Neuroscience	behavioral genetics, neurocytology, glia, protein trafficking, ion channel, synapse, action potential, neurotransmitters, neuroimmunology	PCR, immunohistochemistry, patch clamp, voltage clamp, molecular cloning, gene knockout, biochemical assays, linkage analysis, fluorescent in situ hybridization, Southern blots, DNA microarray, green fluorescent protein, calcium imaging, two-photon microscopy, HPLC, microdialysis
Behavioral Neuroscience	biological psychology, circadian rhythms, neuroendocrinology, hypothalamic-pituitary-gonadal axis, hypothalamic-pituitary-adrenal axis, neurotransmitters, homeostasis, dimorphic sexual-behavior, motor control, sensory processing, photo reception, organizational/activational effects of hormones, drug/alcohol effects	animal models (gene knockout), in-situ hybridization, golgi stain, fMRI, immunohistochemistry, functional genomics, PET, pattern recognition, EEG, MEG
Systems Neuroscience	primary visual cortex, perception, audition, sensory integration, population coding, pain, spontaneous and evoked activity, color vision, olfaction, taste, motor system, spinal cord, sleep, homeostasis, arousal, attention	single unit recording, intrinsic signal imaging, microstimulation, voltage sensitive dyes, fMRI, patch clamp, genomics, training awake behaving animals, local field potential, ROC, cortical cooling, calcium imaging, two-photon microscopy
Developmental Neuroscience	axon guidance, neural crest, growth factors, growth cone, neuromuscular junction, cell proliferation, neuronal differentiation, cell survival and apoptosis, synaptic formation, motor differentiation, injury and regeneration	Xenopus oocyte, protein chemistry, genomics, Drosophila, Hox gene
Cognitive Neuroscience	attention, cognitive control, behavioral genetics, decision making, emotion, language, memory, motivation, motor learning, perception, sexual behavior, social neuroscience	experimental designs from cognitive psychology, psychometrics, EEG, MEG, fMRI, PET, SPECT, single unit recording, human genetics
Computational and Theoretical Neuroscience	cable theory, Hodgkin-Huxley model, neural networks, voltage-gated currents, Hebbian learning	Markov chain Monte Carlo, simulated annealing, high performance computing, partial differential equations, self-organizing nets, pattern recognition
Neuroscience of Diseases and Aging	dementia, peripheral neuropathy, spinal cord injury, autonomic nervous system, depression, anxiety, Parkinson's disease, addiction, memory loss	clinical trials, neuropharmacology, deep brain stimulation, neurosurgery
Neural engineering	Neuroprosthetic, brain-computer interface
Neurolinguistics	language, Broca's area, generative grammar, language acquisition, syntax

 

Major Themes of Research

Neuroscience research from different areas can also be seen as focusing on a set of specific themes and questions. (Some of these are taken from http://www.northwestern.edu/nuin/fac/index.htm)

• Behavior/Cognition/Language
• Biological Rhythms
• Brain Imaging or neuroimaging
• Cell Biology
• Cell Imaging & Electrophysiology
• Computational neuroscience
• Development
• Hearing Sciences
• language
• Learning/Memory
• Mechanisms of Drug Action
• Molecular Neuroscience
• Motor Control
• Neurobiology of Disease
• Neuroendocrinology
• Neuroimmunology
• Signal transduction
• Systems Neuroscience
• Universal Grammar
• Vision Sciences

• Neurobiology of the neuron
• Sensation and perception
• Sleep
• Autonomic systems and homeostasis
• Arousal, attention and emotion
• Genetics of the nervous system
• Injury of the nervous systems

 

Allied and Overlapping Fields

Neuroscience, by its very interdiciplinary nature, overlaps with and encompasses many different subjects. Below is a list of related subjects and fields.

Aphasiology Cognitive Science Generative grammar Machine Learning Neural Networks Evolutionary neuroscience Neural engineering Neuroanatomy Neurobiology Neurochemistry Neuroeconomics Neuroergonomics Neuroendocrinology Neuroesthetics Neuroethics Neuroethology Neurogenetics Neurogenomics Neuroheuristic Neuroimaging

Neurolinguistics Neuromarketing Neuropharmacology Neurophenomenology Neurophilosophy Neurophysiology Neuroproteomics Neuroprosthetics Neuropsychiatry Neuropsychology Neuropsychopharmacology Neurotheology (also Biotheology) Psychiatry Psychoneuroimmunology Psychopharmacology Psychobiology (also Biopsychology, also Biological psychology) Vision

 

 

See also

 

 

List of neuroscience topics

• List of neuroscientists
• Important publications in neuroscience
• Mind scientist
• Neuroscience journals

 

References

 

Citations

 

Textbooks

• Bear, M.F.; B.W. Connors, and M.A. Paradiso (2001). Neuroscience: Exploring the Brain. Baltimore: Lippincott. ISBN 0-7817-3944-6. 
• Kandel, ER; Schwartz JH, Jessell TM (2000). Principles of Neural Science, 4th ed., New York: McGraw-Hill. ISBN 0-8385-7701-6. 
• Squire, L. et al. (2003). Fundamental Neuroscience, 2nd edition. Academic Press; ISBN 0-12-660303-0
• Byrne and Roberts (2004). From Molecules to Networks. Academic Press; ISBN 0-12-148660-5
• Sanes, Reh, Harris (2005). Development of the Nervous System, 2nd edition. Academic Press; ISBN 0-12-618621-9
• Siegel et al. (2005). Basic Neurochemistry, 7th edition. Academic Press; ISBN 0-12-088397-X
• Rieke, F. et al. (1999). Spikes: Exploring the Neural Code. The MIT Press; Reprint edition ISBN 0-262-68108-0

 

Online textbooks

• Neuroscience 2nd ed. Dale Purves, George J. Augustine, David Fitzpatrick, Lawrence C. Katz, Anthony-Samuel LaMantia, James O. McNamara, S. Mark Williams. Published by Sinauer Associates, Inc., 2001.
• Basic Neurochemistry: Molecular, Cellular, and Medical Aspects 6th ed. by George J. Siegel, Bernard W. Agranoff, R. Wayne Albers, Stephen K. Fisher, Michael D. Uhler, editors. Published by Lippincott, Williams & Wilkins, 1999.

 

Popular works

• Andreasen, Nancy C. (March 4 2004). Brave New Brain: Conquering Mental Illness in the Era of the Genome. Oxford University Press. 392 pages, 56 halftones & line illus.; 8 color plates, 234x154 mm. ISBN 9780195145090. 
• Damasio, A. R. (1994). Descartes' Error: Emotion, Reason, and the Human Brain. New York, Avon Books. ISBN 0-399-13894-3 (Hardcover) ISBN 0-380-72647-5 (Paperback)
• Gardner, H. (1976). The Shattered Mind: The Person After Brain Damage. New York, Vintage Books, 1976 ISBN 0-394-71946-8
• Goldstein, K. (2000). The Organism. New York, Zone Books. ISBN 0-942299-96-5 (Hardcover) ISBN 0-942299-97-3 (Paperback)
• Llinas R. (2001)." I of the Vortex: From Neurons to Self" MIT Press. ISBN 0-262-12233-2 (Hardcover) ISBN 0-262-62163-0 (Paperback)
• Luria, A. R. (1997). The Man with a Shattered World: The History of a Brain Wound. Cambridge, Massachusetts, Harvard University Press. ISBN 0-224-00792-0 (Hardcover) ISBN 0-674-54625-3 (Paperback)
• Luria, A. R. (1998). The Mind of a Mnemonist: A Little Book About A Vast Memory. New York, Basic Books, Inc. ISBN 0-674-57622-5
• Pinker, S. (1999). "How the Mind Works." W. W. Norton & Company. ISBN 0-393-31848-6
• Pinker, S. (2002). "The Blank Slate: The Modern Denial of Human Nature." Viking Adult. ISBN 0-670-03151-8
• Ramachandran, V.S. (1998). Phantoms in the Brain. New York, New York Harper Collins. ISBN 0-688-15247-3 (Paperback)
• Rose, S. (2006). "21st Century Brain: Explaining, Mending & Manipulating the Mind" ISBN 0099429772 (Paperback)
• Sacks, O. The Man Who Mistook His Wife for a Hat. Summit Books ISBN 0-671-55471-9 (Hardcover) ISBN 0-06-097079-0 (Paperback)
• Sacks, O. (1990). Awakenings. New York, Vintage Books. (See also Oliver Sacks) ISBN 0-671-64834-9 (Hardcover) ISBN 0-06-097368-4 (Paperback)
• Sternberg, E. (2007) Are You a Machine? The Brain, the Mind and What it Means to be Human. Amherst, NY: Prometheus Books.

 

Notes From Online Courses

• Intro to Neuroscience - Smith College Spring 2005

External links

 

 

• Neurome.org
• High-Resolution Cytoarchitectural Primate Brain Atlases
• Society for Neuroscience
• Neural Plasticity-Open Access Journal (Hindawi Publishing)
• Neuroscience. 2nd ed. by Purves et al (online textbook)
• Neuroscience News, Books, Links, Forum and Gifts
• Neuroscience for Kids
• Brain Research and Information Network B.R.A.I.N.
• Undergraduate Neuroscience major at Carthage College rca ieftin

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