Results for BIO

Introduction to the field of conservation photography and the strategic use of visual communication in addressing issues concerning the environment and conservation. Students will be introduced to basic digital photography, digital image processing, and the theory and application of photographic techniques. Case studies of conservation issues will be examined through photographs and multimedia platforms including images, video, and audio. Lectures, tutorials, demonstrations, and optional field trips will culminate in the production of individual and group projects.

Preference to freshmen. Lack of public understanding of the details of most environmental problems is cited as a cause of environmental deterioration. Good citizenship requires literacy about the elements of the scientific and decision making processes that accompany most environmental issues: what can happen, what are the odds, how can the credibility of sources of expertise be assessed, which components of environmental debates deal with factual and theoretical issues, and which are political value judgments?

Based on the book Extreme Life of the Sea, this course will explore the new science about how marine species thrive in some of the world's most difficult environments. Species that live in the hottest, coldest, deepest and shallowest habitats will be described along with the genetic, biochemical, physiological and behavioral adaptations that allow them to persist. We will also examine the fastest, the oldest, the most archaic, the smallest, biggest and the most numerous species. Emphasis will be on the scientific discoveries about these species that give insight into their lives.

Preference to sophomores. Focus is on two genetic diseases resulting from the production of protein molecules that are unable to fold into their native conformations, called conformational diseases: cystic fibrosis and amyotrophic lateral sclerosis or Lou Gehrig's disease. Hypotheses and controversies surrounding the molecular basis of these disorders, and implications for novel therapeutics. Readings from research literature.

Preference to freshmen. The precious blueprint for life is entrusted to the genomic DNA molecules in all living cells. Multiple strategies have evolved to prevent the deleterious consequences from endogenous DNA alterations and damage from radiation or genotoxic chemicals in the environment. In this seminar you will learn about the remarkable systems that scan cellular DNA for alterations and make repairs to ensure genomic stability. Deficiencies in DNA repair have been implicated in many hereditary diseases involving developmental defects, premature aging, and/or predisposition to cancer. An understanding of DNA repair mechanisms is important for advances in the fields of cancer biology, neurobiology, and gerontology. Background readings, introductory lectures, student presentations, short term paper.

Ever marveled at the imposing trees around campus? This course will explore trees on campus using Bracewell's marvelous "Trees of Stanford" as a rough guide. We will develop tools and explore ideas that will allow the wider community to cherish and appreciate the oft-neglected trees on campus. The course will include guest lectures that focus on the theme of trees: from literature to the physics and biology of trees, to the environmental impact of global forest loss.

Cell structure and function; principles of animal physiology (immunology, renal, cardiovascular, sensory, motor physiology, and endocrinology); neurobiology from cellular basis to neural regulation of physiology. Prerequisites: CHEM 31X (or 31A,B), 33. Recommended: BIO 41; CHEM 35; MATH 19, 20, 21 or 41, 42.

Students enrolled in Bio42 lecture and regular discussion sections attend an additional 75 min section. The objective of the course is to help students to solidify basic concepts, identify areas to work on, and apply core concepts learned that week in Bio42 lecture and section. Space is limited, by application only. Application deadline is December 12, 2014. Co-Requisite: Bio 42.

Investigate yeast strains that are engineered to express the human protein, p53, and use modern molecular methods to identify the functional consequences of p53 mutations isolated from tumor cells. Learn about the protein's role as a tumor suppressor through lectures and by reading and discussing journal articles. Use molecular visualization programs to examine the structure of wild type and mutant p53 proteins. Formulate a testable hypothesis and assay the ability of mutant p53 to direct expression of several reporter genes. During guided reflection, formulate further analyses to determine whether mutant p53 is present in the cell, can bind to DNA, and/or can enter the nucleus. Conduct lab experiments, present findings through a team oral presentation, as well as a scientific poster. Prerequisites: CHEM 31X, or 31A,B, and 33; concurrent or past enrollment in Biology or Human Biology core. 44X,Y should be taken sequentially in the same year, preferably as sophomores, to prepare for internships. Preference given to juniors and seniors in fall quarter, preference given to sophomores in winter quarter. Lab fee. Information about this class is available at http://bio44.stanford.edu.

Molecular mechanisms that govern the replication, recombination, and expression of eukaryotic genomes. Topics: DNA replication, DNA recombination, gene transcription, RNA splicing, regulation of gene expression, protein synthesis, and protein folding. Satisfies Central Menu Area 1. Prerequisite: Biology core.

Formerly 96A - Jasper Ridge Docent Training. First of two-quarter sequence training program to join the Jasper Ridge education/docent program. The scientific basis of ecological research in the context of a field station, hands-on field research, field ecology and the natural history of plants and animals, species interactions, archaeology, geology, hydrology, land management, multidisciplinary environmental education; and research projects, as well as management challenges of the preserve presented by faculty, local experts, and staff. Participants lead research-focused educational tours, assist with classes and research, and attend continuing education classes available to members of the JRBP community after the course.

The variability of the human genome and the role of genomic information in research, drug discovery, and human health. Concepts and interpretations of genomic markers in medical research and real life applications. Human genomes in diverse populations. Original contributions from thought leaders in academia and industry and interaction between students and guest lecturers. Students with a major, minor or coterm in Biology: 109A/209A or 109B/209B may count toward degree program but not both.

Human physiology will be examined by organ systems: respiratory, cardiovascular, renal, and gastrointestinal. Concepts of cell and molecular biology that underlie organ development, pathophysiology and opportunities for regenerative medicine will be introduced. Signaling and integrative control by the endocrine, autonomic and central nervous systems will be introduced. Prerequisite: Biology or Human Biology core.

The inference of key molecular evolutionary processes from DNA and protein sequences. Topics include random genetic drift, coalescent models, effects and tests of natural selection, combined effects of linkage and natural selection, codon bias and genome evolution. Satisfies Central Menu Areas 1 or 4. Prerequisites: Biology core or graduate standing in any department, and consent of instructor.

Fungi are critical, yet often hidden, components of the biosphere. They regulate decomposition, are primary partners in plant symbiosis and strongly impact agriculture and economics. Students will explore the fascinating world of fungal biology, ecology and evolution via lecture, lab, field exercises and Saturday field trips that will provide traditional and molecular experiences in the collection, analysis and industrial use of diverse fungi. Students will chose an environmental niche, collect and identify resident fungi, and hypothesize about their community relationship. Prerequisite: Bio 43 recommended.

The biological causes and consequences of anthropogenic and natural changes in the atmosphere, oceans, and terrestrial and freshwater ecosystems. Topics: glacial cycles and marine circulation, greenhouse gases and climate change, tropical deforestation and species extinctions, and human population growth and resource use. Prerequisite: Biology or Human Biology core or graduate standing.

Focus is on using mutations and genetic analysis to study biological and medical questions. The first portion of the course covers how the identification and analysis of mutations can be used in model systems to investigate biological processes such as development and metabolism. In the second portion of the course, we focus on the use of existing genetic variation in humans and other species to identify disease-associated genes as well as to investigate variation in morphological traits such as body size and shape.

Core course appropriate for advanced undergraduate students and graduate students with prior knowledge of calculus and a college physics course. Introduction to how physical principles offer insights into modern biology, with regard to the structural, dynamical, and functional organization of biological systems. Topics include the roles of free energy, diffusion, electromotive forces, non-equilibrium dynamics, and information in fundamental biological processes.

Cell motility emphasizing role of actin assembly and dynamics coupling actin organization to cell movement. Interaction of cells with extracellular matrix, and remodelling of extracellular matrix in development and disease. Directed cell migration by chemotaxis (neuronal path-finding, immune cells). Cell-cell adhesion, formation of intercellular junctions and mechanisms regulating cell-cell interactions in development and diseases. Emphasis is on experimental logic, methods, problem solving, and interpretation of results. Students present research papers. Satisfies Central Menu Area 2. Prerequisite: Biology core.

Applications of complex systems will be explored in thisnseminar through lectures, discussions, and a class project. Lecture topicsninclude a discussion of chaos in weather modeling and aircraft turbulence,napplication of network science to understand Ebola and the ALS ice bucketnchallenge, and self-organized processes such as crowd dynamics andnWikipedia. The first half of the course will emphasize complex systemsnapplications. Students will apply complex systems analysis techniques tontheir personal research, a current event, or repeat a classic complexnsystems experiment. Projects can include topics such as calculating thenfractal dimension of a forest, simulating crowd dynamics, studying thendegree distribution of social networks, or making a Van der Pol oscillator.nGraduate student led seminar. Can be repeated for credit.

How birds interact with their environments and each other, emphasizing studies that had impact in the fields of population biology, community ecology, and evolution. Local bird communities. Emphasis is on field research. Enrollment limited to 20. Prerequisites: 43 or equivalent, and consent of instructor. Recommended: birding experience.

Series of talks by distinguished speakers introducing approaches to population and resource studies.

Preference to seniors and graduate students. The neurochemistry and neurophysiology of changes in brain activity and conscious awareness associated with changes in the sleep/wake state. Behavioral and neurobiological phenomena including sleep regulation, sleep homeostasis, circadian rhythms, sleep disorders, sleep function, and the molecular biology of sleep. Enrollment limited to 16.

Survey of instruments which use light and other radiation for analysis of cells in biological and medical research. Topics: basic light microscopy through confocal fluorescence and video/digital image processing. Lectures on physical principles; involves partial assembly and extensive use of lab instruments. Lab. Prerequisites: some college physics, Biology core.

Neural interactions underlying behavior. Prerequisites: PSYCH 1 or basic biology.

Continuation of BIO 160A. Focus is on the molecular mechanisms underlying the generation of diverse cell types and tissues during embryonic and post-embryonic animal development. The role of cell-cell communication in controlling key developmental decisions. The topics include sexual control of development, tissue polarity and growth, cell migration, regeneration, and the evolution of developmental mechanisms. Experimental logic and methods of research in developmental biology. Discussions of research papers. Satisfies Central Menu Areas 1 or 2. Prerequisites: Biology Core and 160A, or consent of instructor.

Study of the human skeleton (a. k. a. human osteology), as it bears on other disciplines, including medicine, forensics, archaeology, and paleoanthropology (human evolution). Basic bone biology, anatomy, and development, emphasizing hands-on examination and identification of human skeletal parts, their implications for determining an individual¿s age, sex, geographic origin, and health status, and for the evolutionary history of our species. Three hours of lecture and at least three hours of supervised and independent study in the lab each week.

For advanced undergraduates and first-year graduate students. Critical reading of the research literature in prokaryotic genetics and molecular biology, with particular applications to the study of major human pathogens. Classic and foundational papers in pathogenesis, genetics, and molecular biology; recent literature on bacterial pathogens such as Salmonella, Vibrio, and/or Yersinia. Diverse experimental approaches: biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: Biology Core and two upper-division courses in genetics, molecular biology, or biochemistry.

Models in population genetics and evolution. Selection, random drift, gene linkage, migration, and inbreeding, and their influence on the evolution of gene frequencies and chromosome structure. Models are related to DNA sequence evolution. Prerequisites: calculus and linear algebra, or consent of instructor.

Focus on metabolic biochemistry: the study of chemical reactions that provide the cell with the energy and raw materials necessary for life. Topics include glycolysis, gluconeogenesis, the citric acid cycle, oxidative phosphorylation, photosynthesis, the pentose phosphate pathway, and the metabolism of glycogen, fatty acids, amino acids, and nucleotides as well as the macromolecular machines that synthesize RNA, DNA, and proteins. Medical relevance is emphasized throughout. Satisfies Central Menu Area 1 for Bio majors. Prerequisite: BIO 188/288 or CHEM 181 or CHEMENG 181/281 (formerly 188/288).

Capstone course series for seniors. Creative, self-reflective and scientifically relevant projects conceived, produced and exhibited over the course of three quarters. Explore scientific content of personal interest through creative forms including but not limited to writing, music, fine arts, performing arts, photography, film or new media. A written essay on the creative process and scientific significance of the selected topic will accompany the creative work. Completed projects may be included in a creative portfolio. Required enrollment in 196A,B,C.

Individually arranged under the supervision of members of the faculty.

Individually arranged under the supervision of members of the faculty. Credit for work arranged with out-of-department faculty is restricted to Biology majors and requires department approval. See http://biohonors.stanford.edu for information and petitions. May be repeated for credit.

Individual research taken by arrangement with in-department instructors. See http://biohonors.stanford.edu for information on research sponsors, units, and credit for summer research. May be repeated for credit.

Workshop. For seniors pursuing an honors thesis in a biology-focused major or program. Focus on improving scientific writing and synthesizing in the context of students' individual research projects. Complete literature review which will form the basis for the thesis introduction. Develop methods section of the thesis. Small seminar-style discussion sections with research-based discussions, student led PowerPoint presentations, and writing workshops. Co-requisite: Concurrent enrollment in 199 or 199X or equivalent. Satisfies WIM in Biology.

Individual research by arrangement with out-of-department instructors. Credit for 199X is restricted to declared Biology majors and requires department approval. See http://biohonors.stanford.edu for information on research sponsors, units, petitions, deadlines, credit for summer research, and out-of-Stanford research. May be repeated for credit.

Molecular mechanisms that govern the replication, recombination, and expression of eukaryotic genomes. Topics: DNA replication, DNA recombination, gene transcription, RNA splicing, regulation of gene expression, protein synthesis, and protein folding. Satisfies Central Menu Area 1. Prerequisite: Biology core.

For Ph.D. students. Current research on cell structure, function, and dynamics. Topics include complex cell phenomena such as cell division, apoptosis, compartmentalization, transport and trafficking, motility and adhesion, and differentiation. Weekly reading of current papers from the primary literature. Preparation of an original research proposal. Prerequisite for advanced undergraduates: BIO 129A,B, and consent of instructor.

Seminar. The logic of how neural circuits control behavior; how neural circuits are assembled during development and modified by experience. Emphasis is on primary literature. Topics include: neurons as information processing units; simple and complex circuits underlying sensory information processing and motor control; and development and plasticity of neural circuits. Advanced undergraduates and graduate students with background in physical science, engineering, and biology may apply to enroll. Recommended: background in neuroscience.

Core course appropriate for advanced undergraduate students and graduate students with prior knowledge of calculus and a college physics course. Introduction to how physical principles offer insights into modern biology, with regard to the structural, dynamical, and functional organization of biological systems. Topics include the roles of free energy, diffusion, electromotive forces, non-equilibrium dynamics, and information in fundamental biological processes.

The inference of key molecular evolutionary processes from DNA and protein sequences. Topics include random genetic drift, coalescent models, effects and tests of natural selection, combined effects of linkage and natural selection, codon bias and genome evolution. Satisfies Central Menu Areas 1 or 4. Prerequisites: Biology core or graduate standing in any department, and consent of instructor.

Preference to seniors and graduate students. The neurochemistry and neurophysiology of changes in brain activity and conscious awareness associated with changes in the sleep/wake state. Behavioral and neurobiological phenomena including sleep regulation, sleep homeostasis, circadian rhythms, sleep disorders, sleep function, and the molecular biology of sleep. Enrollment limited to 16.

Study of the human skeleton (a. k. a. human osteology), as it bears on other disciplines, including medicine, forensics, archaeology, and paleoanthropology (human evolution). Basic bone biology, anatomy, and development, emphasizing hands-on examination and identification of human skeletal parts, their implications for determining an individual¿s age, sex, geographic origin, and health status, and for the evolutionary history of our species. Three hours of lecture and at least three hours of supervised and independent study in the lab each week.

For advanced undergraduates and first-year graduate students. Critical reading of the research literature in prokaryotic genetics and molecular biology, with particular applications to the study of major human pathogens. Classic and foundational papers in pathogenesis, genetics, and molecular biology; recent literature on bacterial pathogens such as Salmonella, Vibrio, and/or Yersinia. Diverse experimental approaches: biochemistry, genomics, pathogenesis, and cell biology. Prerequisites: Biology Core and two upper-division courses in genetics, molecular biology, or biochemistry.

Models in population genetics and evolution. Selection, random drift, gene linkage, migration, and inbreeding, and their influence on the evolution of gene frequencies and chromosome structure. Models are related to DNA sequence evolution. Prerequisites: calculus and linear algebra, or consent of instructor.

Focus on metabolic biochemistry: the study of chemical reactions that provide the cell with the energy and raw materials necessary for life. Topics include glycolysis, gluconeogenesis, the citric acid cycle, oxidative phosphorylation, photosynthesis, the pentose phosphate pathway, and the metabolism of glycogen, fatty acids, amino acids, and nucleotides as well as the macromolecular machines that synthesize RNA, DNA, and proteins. Medical relevance is emphasized throughout. Satisfies Central Menu Area 1 for Bio majors. Prerequisite: BIO 188/288 or CHEM 181 or CHEMENG 181/281 (formerly 188/288).

Open to upper-division undergraduates and graduate students. Practical experience in teaching lab biology or serving as an assistant in a lecture course. May be repeated for credit. Prerequisite: consent of instructor.

Preparation for teaching the core experimental courses (44X and 44Y). Emphasis is on lab, speaking, and writing skills. Focus is on updating the lab to meet the changing technical needs of the students. Taken prior to teaching either of the above courses. May be repeated for credit. Prerequisite: selection by instructor.

Limited to first year Biology PhD students. Lab rotations with Biosciences faculty.

For graduate students only. Individual research by arrangement with in-department instructors.

Individual research by arrangement with out-of-department instructors. Master's students: credit for work arranged with out-of-department instructors is restricted to Biology students and requires approved department petition. See http://biohonors.stanford.edu for more information. May be repeated for credit.

Limited to and required of first-year Ph.D. students in molecular, cellular, and developmental biology. Current research in molecular, cellular, and developmental biology emphasizing primary research literature. Held in conjunction with the department's Monday seminar series. Students and faculty meet weekly before the seminar for a student presentation and discussion of upcoming papers.

Required of first-year PhD students in population biology, and ecology and evolution. Major conceptual issues and developing topics. This course isnnopen only to Biology PhD students and is not open to auditors."

Topics announced at the beginning of each quarter. Current literature. May be repeated for credit. See http://carnegiedpb.stanford.edu/seminars/seminars.php.

Water is an essential ingredient for life. While the Mediterranean climate of California draws immigrants and tourists to our mild dry climate, infrequent rain and prized water rights have led to a tumultuous history behind how water is currently distributed. In this freshman seminar we will discuss water in California from multiple perspectives that span weather, history, art and plant physiology. The implications of climate change on agriculture and the Californian economy and lifestyle will also be discussed.

Feeding ever-growing populations is a constant challenge to mankind. In the second half of the 20th century, the breeding of improved varieties combined with the use of chemical fertilizers and pesticides led to crop yield increases labeled the Green Revolution. Modern technologies in genetic engineering are expected to bring the second green revolution. Meeting the current and future global food needs without further damaging the fragile environment requires innovative effort from scientists and the society.

Literature review, research, and current problems in the theory and practice of population genetics and molecular evolution. May be repeated for credit. Prerequisite: consent of instructor.

Seminar. Topics in biology ranging from neurobiology to ecology.

Students register through their affiliated department; otherwise register for CHEMENG 459. For specialists and non-specialists. Sponsored by the Stanford BioX Program. Three seminars per quarter address scientific and technical themes related to interdisciplinary approaches in bioengineering, medicine, and the chemical, physical, and biological sciences. Leading investigators from Stanford and the world present breakthroughs and endeavors that cut across core disciplines. Pre-seminars introduce basic concepts and background for non-experts. Registered students attend all pre-seminars; others welcome. See http://biox.stanford.edu/courses/459.html. Recommended: basic mathematics, biology, chemistry, and physics.