Courses

Last offered Fall 2023

Biology and Social Issues of the Tropics explores the biological dimensions of social and environmental issues in tropical societies, focusing specifically on the tropics of Africa, Asia, Latin America, Oceania, and the Caribbean. Social issues are inextricably bound to human ecologies and their environmental settings. Each section of the course provides the science behind the issues and ends with options for possible solutions, which are debated by the class. The course highlights differences between the tropics and areas at higher latitudes while also emphasizing global interconnectedness. It begins with a survey of the tropical environment, including a global climate model, variation in tropical climates and the amazing biodiversity of tropical biomes. The next section focuses on human population biology, and emphasizes demography and the role of disease particularly malaria, AIDS and Covid-19 (SARS-CoV-2). The final part of the course covers the place of human societies in local and global ecosystems including the challenges of tropical food production, the interaction of humans with their supporting ecological environment, and global climate change. This course fulfills the DPE requirement. Through lectures, debates and readings, students confront social and environmental issues and policies from the perspective of biologists. This builds a framework for lifelong exploration of human diversity in terms of difference, power and equity. [ more ]

Last offered Fall 2022

This course examines evolution as a science and its current and historical importance. Lectures focus on the evidence for evolution, the main evolutionary forces (natural selection and others) and the diversification processes that generate biodiversity. We will also explore recent evolutionary trends and discussions such as human evolution, heritability, personalized genomics, antibiotic and pesticide resistance, climate change, and the conflict between creationists and evolutionists. The course has a required day trip to the American Museum of Natural History in NYC. [ more ]

Last offered Spring 2024

The oceans impact almost all life and processes on Earth. In this course we will explore the astounding diversity of life in the world's oceans, from the smallest photosynthetic microbes on the planet to the largest animals that weigh almost 200 tons. Using an integrative approach that spans from the molecular to the organismal to the ecological levels, we will focus on the biology of marine organisms, and their interactions and interrelationships. Topics including primary production, reproduction, acclimation to stresses, adaptation, and evolution will be discussed in the context of environments such as the open oceans, coastal waters, rocky intertidal zones, coral reefs, and the deep sea. We will emphasize how recent scientific advances have revolutionized our understanding of marine organisms and explore solutions to global challenges, including climate change and ocean acidification, pollution, sustainable fishing and aquaculture, and habitat conservation. [ more ]

Last offered Spring 2024

The fossil record is a direct window into the history of life on Earth and contains a wealth of information on evolution, biodiversity, and climate change. This course investigates the record of ancient life forms, from single-celled algae to snails to dinosaurs. We will explore how, why, when, and where fossils form and learn about the major groups of fossilized organisms and how they have changed through time. In addition, we will cover a range of topics central to modern paleobiology. These include: how the fossil record informs our understanding of evolutionary processes including speciation; the causes and consequences of mass extinctions; how fossils help us tell time and reconstruct the Earth's climactic and tectonic history; statistical analysis of the fossil record to reconstruct biodiversity through time; analysis of fossil morphology to recreate the biomechanics of extinct organisms; and using fossil communities to reconstruct past ecosystems. Laboratory exercises will take advantage of Williams' fossil collections as well as published datasets to provide a broad understanding of fossils and the methods we use to study the history of life on Earth, including using the programming language R (no previous experience is required). We will also view a diversity of fossils in their geologic and paleo-environmental context on our field trip to Eastern New York. This course is in the Sediments and Life group for the Geosciences major. [ more ]

BIOL 214 TUT Mathematical Ecology

Last offered Spring 2016

Using mathematics to study natural phenomena has become ubiquitous over the past couple of decades. In this tutorial, we will study mathematical models comprised of both deterministic and stochastic differential equations that are developed to understand ecological dynamics and, in many cases, evaluate the dynamical consequences of policy decisions. We will learn how to understand these models through both standard analytic techniques such as stability and bifurcation analysis as well as through simulation using computer programs such as MATLAB. Possible topics include fisheries management, disease ecology, control of invasive species, and predicting critical transitions in ecological systems. [ more ]

BIOL 219 TUT Dangerous Exposures: Environment, Immunity, and Infectious Disease

Last offered Fall 2020

Global reports of emerging infectious diseases and old diseases with new pathogenic properties incite fears for personal safety as well as national security. The specter of a contagious pandemic has captured the public imagination through the mass news media, movies, and even popular online and board games. In this tutorial course, we will explore the ecology and evolution of several recently emergent diseases such as Ebola hemorrhagic fever, dengue, and AIDS. Topics to be considered include transmission dynamics, epidemiological modeling of vaccination strategies, and wildlife reservoirs that contribute to human virus exposure. We will examine progress in preventing the parasitic disease malaria and why such diseases have proven so refractory. We will also discuss the science behind the recent development of the vaccine against the human papillomavirus, which causes cervical cancer, and the intriguing and highly unusual transmissible cancers in dogs and Tasmanian devils. Finally, we will think about the contributions of inadequate diagnostic capacities world-wide and broader issues of resource shortages in driving the global emergence of drug resistance in tuberculosis and other diseases. One common theme in each of these case studies will be the interplay between the host immune response and the evolution of the pathogen. Although the primary focus of the course is on biology rather than policy, each week's readings will have implications for public health and/or conservation biology. [ more ]

BIOL 222 LEC Essentials of Biochemistry

Last offered Spring 2022

This course will explore the biochemistry of cellular processes and contextualize these processes in healthy and diseased states. Lecture topics in this one semester course will include the structure and function of proteins (enzymes and non-enzymatic proteins), lipids, and carbohydrates. Lectures will also survey the major metabolic pathways (carbohydrates, lipids, and amino acids) with particular attention to enzyme regulation and the integration of metabolism in different tissues and under different metabolic conditions. In the discussion/laboratory component of the course a combination of primary literature, hypothesis-driven exercises, problem solving, and bench work will be used to illustrate how particular techniques and experimental approaches are used in biochemical fields. [ more ]

BIOL 225 TUT Sustainable Food & Agriculture

Last offered Fall 2018

A tutorial course investigating patterns, processes, and stability in human-dominated, food production systems. The course will examine sustainable food and agriculture from an ecological perspective. Topics will include: changes in diversity, concentration, and scale, flows of energy, circulation (or not) of fertilizer nutrients, carbon balances in soils, and stability of food production, processing, and distribution ecosystems. A day-long field experience will take place on a local farm. [ more ]

BIOL 234 TUT Biology of our Sexes: The Genetic and Epigenetic Regulation of Sex Determination

Last offered Spring 2018

Many physical and behavioral characteristics that are associated with male and female anatomy, physiology, and behavior are initially the products molecular choices arising from the action of our chromosomes in early development. The embryonic assignment of sex can also lead to intersex or hermaphroditic outcomes in many different organisms with extraordinary and illuminating biological effects. We will explore the molecular mechanisms and evolutionary basis of sex determination in both plants and animals, as well as the physical and behavioral expression of sex by the organism discussed, and experiments that create and characterize traits and behavior of mosaic/intersex organisms. Additionally, the epigenetic regulation of the X chromosome in mammals has a canonical role in our understanding of sex determination, but whole genome studies and investigations of autosomes and the Y chromosome have raised new layers of complexity for understanding the molecular basis of human sex and sexuality. [ more ]

BIOL 301 LEC Developmental Biology

Last offered Fall 2014

Developmental biology has undergone rapid growth in recent years and is becoming a central organizing discipline that links cells and molecular biology, evolution, anatomy and medicine. We are now beginning to have a molecular understanding of fascinating questions such as how cells decide their fate, how patterns are created, how male and females are distinguished, and how organisms came to be different. We have also discovered how the misregulation of important development regulatory genes can lead to a variety of known cancers and degenerative diseases in humans. In this course we will examine these and related topics combining a rich classical literature with modern genetic and molecular analyses. [ more ]

BIOL 302 LEC Communities and Ecosystems

Last offered Fall 2019

An advanced ecology course that examines how species interact with each other and their environment and how communities are assembled. This course emphasizes phenomena that emerge in complex ecological systems, building on the fundamental concepts of population biology, community ecology, and ecosystem science. This foundation will be used to understand specific topics relevant to conservation including invasibility and the functional significance of diversity for ecosystem stability and processes. Lectures and labs will explore how to characterize the emergent properties of communities and ecosystems, and how theoretical, comparative, and experimental approaches are used to understand their structure and function. The lab component of this course will emphasize hypothesis-oriented field experiments as well as "big-data" analyses using existing data sets.The laboratory component of the course will culminate with a self-designed independent or group project. [ more ]

BIOL 306 LEC Cellular Regulatory Mechanisms

Last offered Spring 2015

This course explores the regulation of cellular function and gene expression from a perspective that integrates current paradigms in molecular genetics, intracellular trafficking, genomics, and synthetic biology. Selected topics include: the contribution of nuclear organization to genome regulation, mechanisms to maintain genomic integrity, transcriptional and post-transcriptional regulation, nuclear export, cell cycle and cell signaling. A central feature of the course will be discussion of articles from the primary literature, with an emphasis on the molecular bases for a variety of human pathologies such as cancer and aging. The laboratory will consist of a semester-long project that incorporates fluorescence-based approaches, quantitative PCR analysis of transcriptional patterns, bioinformatics, and protein analysis. [ more ]

BIOL 311 LEC Neural Systems and Circuits

Last offered Fall 2020

This course will examine the functional organization of the mammalian brain, emphasizing both neuroanatomy and neurophysiology. How do specific populations of neurons and their connections encode sensory information, form perceptions of the external and internal environment, make cognitive decisions, and execute movements? How does the brain produce feelings of reward/motivation and aversion/pain? How does the nervous system regulate homeostatic functions such as sleep, food intake, and thirst? We will explore these questions using a holistic, integrative approach, considering molecular/cellular mechanisms, physiological characterizations of neurons, and connectivity among brain systems. Journal article discussions will complement course topics, providing experience in reading, understanding, and critiquing primary research papers. Writing an original literature review article will provide experience in expository writing and anonymous peer review. Laboratory sessions will provide experience in examining macroscopic and microscopic neural structures, as well as performing experiments to elucidate the structure and function of neural systems using classical and cutting-edge techniques. [ more ]

Last offered Fall 2022

How do animals sense properties of the physical world? How do they convert physical or chemical energy to a signal within a cell that carries information? How is that information represented? What are the limits on what can be sensed? We will look for answers to these questions by investigating the molecular and cellular mechanisms of sensory transduction and how these mechanisms constrain the types of information that the nervous system encodes and processes. We will also ask how natural selection shapes the type of sensory information that animals extract from the world, and what adaptations allow some species to have "special" senses. Some of the examples we will consider are: bat echolocation (hair cells in the ear), detecting visual motion (amacrine cells in the mammalian retina), the constant reshaping of the olfactory system (chemical mapping of odors), what makes a touch stimulus noxious, and enhanced color vision (in birds, bees, and shrimp). Laboratory exercises will focus on the nematode C. elegans, an important model system, to explore and extend how we understand touch, temperature sensation, chemosensation, and light sensation. [ more ]

Last offered Fall 2023

The rapidly evolving field of immunology examines the complex network of interacting molecules and cells that function to recognize and respond to agents foreign to the individual. In this course, we will focus on the biochemical mechanisms that act to regulate the development and function of the immune system and how alterations in different system components can cause disease. Textbook readings will be supplemented with current literature. [ more ]

Last offered Spring 2023

What can computational biology teach us about cancer? In this lab-intensive experience for the Genomics, Proteomics, and Bioinformatics program, computational analysis and wet-lab investigations will inform each other, as students majoring in biology, chemistry, computer science, mathematics/statistics, and physics contribute their own expertise to explore how ever-growing gene and protein data-sets can provide key insights into human disease. In this course, we will take advantage of one well-studied system, the highly conserved Ras-related family of proteins, which play a central role in numerous fundamental processes within the cell. The course will integrate bioinformatics and molecular biology, using database searching, alignments and pattern matching, and phylogenetics to reconstruct the evolution of gene families by focusing on the gene duplication events and gene rearrangements that have occurred over the course of eukaryotic speciation. By utilizing high through-put approaches to investigate genes involved in the inflammatory and MAPK signal transduction pathways in human colon cancer cell lines, students will uncover regulatory mechanisms that are aberrantly altered by siRNA knockdown of putative regulatory components. This functional genomic strategy will be coupled with independent projects using phosphorylation-state specific antisera to test our hypotheses. Proteomic analysis will introduce the students to de novo structural prediction and threading algorithms, as well as data-mining approaches and Bayesian modeling of protein network dynamics in single cells. Flow cytometry and mass spectrometry may also be used to study networks of interacting proteins in colon tumor cells. [ more ]

Last offered Spring 2024

This course will focus on how multi-protein complexes are assembled to control key cellular processes in eukaryotic systems: 1) protein sorting and trafficking, 2) establishment and maintenance of cell architecture, and 3) mitosis, cell migration and tissue morphogenesis that require coordination of the membrane transport and cytoskeleton. The course will highlight involvement of these processes in pathological conditions. Laboratories will use mammalian tissue culture as a model system to study cellular functions. Important techniques in cell biology will be introduced in the first half of the semester; in the second half of the term, students will conduct a multi-week independent project. Textbook readings will be supplemented with primary literature. [ more ]

Last offered Fall 2023

Conservation Biology focuses on protection of the Earth's biodiversity. This course starts with an overview of biodiversity including patterns of species richness, causes of species loss (extinction), and the critical contributions of biodiversity to ecosystem function and human welfare. Then we analyze ways to conserve biodiversity at the genetic, population, species and community/ecosystem levels. Labs are field oriented, and focus on local New England communities and ecosystems. Labs emphasize knowing the dominant species in each system; they also stress how to collect and analyze the field data on ecological community structure and function that are critical to test hypotheses that relate to different conservation goals. [ more ]

Last offered Spring 2023

Genome sequencing technologies have opened the "book of life" to biologists. But making sense of genomes is still a work in progress. This course will examine central features of genomes, their evolution, and their contribution to human diseases such as cancer. Genome biology is a new field, and this presents the opportunity to learn science as it is being done. Biologists working today started out knowing nothing about core features of genomes, such as why most of the DNA is repetitive, or why segments of genes get removed in the RNA, or why silenced genes wake up in cancer cells. They began to find meaning by adopting dual perspectives of function and neutral evolution. Students will learn to walk these same paths and learn to evaluate for themselves what genome complexity means. In lab, students will develop hands-on and computational skills for investigating genome structural variation, then apply them in the second half of the semester in independent lab investigations. [ more ]

Last offered Fall 2022

Evolutionary ecology is an interdisciplinary field that integrates concepts in genetics, adaptation, and ecology to understand how evolution operates in the context of ecological communities. This course provides an overview of the discipline including foundational concepts in evolutionary demography, phenotypic plasticity, and population genetics. It also explores how breakthroughs in these topics provide a framework for advances in our understanding of the evolution of reproductive timing and ageing, interspecific interactions (e.g. competition, predation), cooperation, and altruism. The course combines lectures, readings, in-class discussion, and a lab section that includes a mixture of field, computer, and lab projects. Laboratories will give students practical, hands-on experience in how to develop, plan, and carry out evolutionary ecology research from start to finish. [ more ]

BIOL 405 TUT Sociobiology

Last offered Fall 2014

Sociobiology, or the study of social behavior, has challenged the limits of evolutionary theory since Darwin described the non-reproducing castes among social insects (i.e., eusociality) as "one special difficulty." Inclusive fitness theory and Hamilton's rule--that an altruistic act can evolve where the benefit to related individuals exceeds the cost to the actor--potentially resolves Darwin's paradox. Nevertheless, explanations including delayed fitness benefits and ecological constraints have been suggested as alternatives to inclusive fitness theory. Moreover, the theoretical justification for inclusive fitness theory has recently been vigorously challenged. This course will use readings from the primary literature to examine the evidence for inclusive fitness as a potential explanation for topics including the evolution of helping behavior, eusociality and its relationship to extraordinary sex ratios, and spiteful behavior. Other topics that we will cover include the evolution of deceit and self deception. [ more ]

BIOL 406 SEM Dynamics of Internal Membrane Systems

Last offered Fall 2014

Eukaryotic cells build and maintain a diverse set of internal membrane compartments, such as the endoplasmic reticulum, the Golgi compartment, and lysosomes, which exist as parts of an interconnected and dynamic membrane system. Each of these membrane compartments has unique functions despite a high rate of exchange between the different organelles. This course will mechanistically examine how the identity of organelles is achieved via highly regulated membrane trafficking events and investigate the importance of membrane trafficking in specialized biological processes including neurotransmission, glucose homeostasis, and immune cell killing. We will read classic and current primary literature articles and discuss the essential techniques, experimental design, and models of cell biology. [ more ]

Last offered Spring 2024

Emotion is influenced and governed by a number of neural circuits and substrates, and emotional states can be influenced by memory, cognition, and many external stimuli. We will read and discuss articles about mammalian neuroanatomy associated with emotion as defined by classic lesion studies, pharmacology, electrophysiology, fMRI imaging, knockout and optogenetic mouse studies, for investigating neural circuit function in order to gain an understanding of the central circuits and neurotransmitter systems that are implicated in emotional processing. We will focus initially on the neural circuits involved in fear, as a model for how human and animal emotion and physiology is studied, with special sessions on emotional responses to music and art, as well as discussions about burgeoning neurobiological research into the emotion of disgust. The larger goal of the course is to give students opportunities and experience in critical evaluation and discussion of primary scientific literature, and to develop and refine strategies on how to use scientific evidence in building arguments in essays. [ more ]

BIOL 409 TUT Cultural Evolution in Biological Systems

Last offered Fall 2017

The evolution of genetically transmitted traits has been the subject of extensive study since the "modern synthesis" combined Darwin's and Mendel's ideas--later enriched by molecular approaches to developmental biology. More recently, the study of evolution has been extended to traits that are transmitted via social learning. The cultural evolution that occurs in such behavioral traits has many parallels with evolution based on genes: errors and innovation correspond to genetic mutations, immigration may bring in new forms of the behavior, and population bottlenecks can result in loss of behavioral traits. However, there is also a crucial difference between genetic and social transmission of traits: social learners can potentially acquire traits from many members of their population, including unrelated individuals. This difference has many implications, including the acceleration of the evolutionary time scale. We will explore the ways socially learned behaviors evolve, using systems such as tool use (primates, crows), vocal learning (songbirds, orcas), and social organization (baboons). Among the topics we will consider are the role of neutral models and random processes, how neural constraints guide social learning, how social status influences the choice of tutors, and how competition and sexual selection drive changes in learned behavior. We will also consider how these processes interact and how they generate differences as well as parallels between cultural and genetic evolution. [ more ]

BIOL 410 SEM Nanomachines in Living Systems

Last offered Spring 2021

Through reading and discussing the primary literature, this course will explore how nanometer-sized biological molecules like proteins perform functions that require integration of information and transmission of force at much larger scales, microns and above. These nanoscale proteins will be considered as nanomachines that can transform a chemical energy into a mechanical one. We will focus on the cytoskeleton, which gives cells their shape, organizes the internal parts of cells and provides mechanical support for essential cellular processes like cell division and movement. An emphasis will be placed on how the biochemical properties of actin, actin-binding proteins and motors are used to generate mechanical force necessary for the respective biological function. Topics will include some controversial and emerging hypotheses in the field: sliding versus depolymerizing hypotheses for constriction of the contractile ring in cytokinesis, roles of cytoskeleton in pathogen entry and propagation, organelle dynamics, polarity establishment in cell migration, immunological synapse and neuronal function. [ more ]

BIOL 411 TUT Developmental Biology: From Patterning to Pathogenesis

Last offered Fall 2020

A small number of developmental regulators coordinate the interplay between cell proliferation and specification of cell fates during animal development. The genetic basis of many of the cancer and degenerative diseases are, in fact, due to these same developmental regulators whose expression is misregulated in the adult. Through the reading of primary literature, this course in developmental biology will examine the mechanisms of gene expression of key regulators, the biological processes they mediate in the embryo, and how they become misregulated in proliferative and degenerative diseases. [ more ]

BIOL 412 SEM Neural and Hormonal Basis of Hunger

Last offered Spring 2018

Hunger and satiety are highly regulated behavioral states that maintain energy homeostasis in animals. This course will focus on readings from the primary literature to track numerous recent advances in how the brain and endocrine systems regulate appetite. Topics include how organ systems communicate with the brain to regulate appetite, how different populations of neurons in the brain interact to regulate appetite, how brain systems that regulate appetite affect other behaviors, and how the neural and hormonal basis of hunger compare with brain systems that regulate other homeostatic systems such as thirst. By tracing the advances in appetite regulation within the past decade, we will also trace the advent of cutting-edge molecular, genetic, and optical-based tools that are transforming multiple fields within physiology and neuroscience. Students in this class will have the opportunity to improve skills in written and oral scientific presentation. [ more ]

BIOL 413 SEM Global Change Ecology

Last offered Fall 2019

Plants and animals are increasingly faced with rapid environmental change driven by human activities across the globe. How do they cope with challenges imposed by climate change, altered nutrient cycling, biological invasions, and increased urbanization? What are the impacts of organismal responses at the population and community level? This course uses an integrative approach to understand the impacts of global change at multiple levels of biological organization in both aquatic and terrestrial environments. We examine how global-scale environmental changes affect the distribution and abundance of species and alter community organization. We also consider the physiological and behavioural mechanisms underlying species responses and the role of acclimation versus adaptation in coping with rapid environmental change. Finally, we learn the analytical tools used to predict future responses to global change. Class discussions will focus on readings drawn from the primary literature. [ more ]

Last offered Fall 2023

All organisms face variability in their environments, and the molecular and cellular responses to stresses induced by environmental change often illuminate otherwise hidden facets of normal physiology. Moreover, many organisms have evolved unique molecular mechanisms, such as novel cellular compounds or macromolecular structural modifications, which contribute to their ability to survive continuous exposure to extreme conditions, such as high temperatures or low pH. This course will examine how chaperonins, proteases, and heat- and cold-shock proteins are regulated in response to changes in the external environment. We will then consider how these and other molecular mechanisms function to stabilize DNA and proteins- and, ultimately, cells and organisms. Other extreme environments, such as hydrothermal vents on the ocean floor, snow fields, hypersaline lakes, the intertidal zone, and acid springs provide further examples of cellular and molecular responses to extreme conditions. Biotechnological applications of these molecular mechanisms in areas such as protein engineering will also be considered. Class discussions will focus upon readings from the primary literature. [ more ]

Last offered Spring 2024

Recent advances in the field of immunology have led to the development of new approaches to prevent and treat diseases that affect millions of people worldwide. Drugs that modulate the body's natural immune response have become powerful tools in treating major diseases--infection, autoimmunity and cancer. This course will use readings from the primary literature to explore central themes involved in translating basic research to new clinical and therapeutic approaches. Topics will include vaccine development, autoimmunity and cancer immunotherapy. [ more ]

BIOL 418 SEM Signal Transduction to Cancer

Last offered Spring 2020

Division of normal cells is a highly regulated process based on input from both intrinsic and extrinsic signals. The cell's response to its environment affects all aspects of cell behavior: proliferation, death, differentiation and migration. The goal of the course is to understand the molecular mechanisms of signal transduction that guide normal cell behavior and how disruptions in this process can lead to cancer. We will focus on the Hedgehog-Gli signaling pathway that is activated in 30% of all known cancers. Genetic studies will serve as an introduction to the components of the pathway, followed by an examination of the molecular mechanisms of signal reception, transduction of intracellular information, scaffolding and transcriptional targets. The final section of the course will investigate how high throughput screens, medicinal chemistry studies and mouse models are used to identify small molecular inhibitors of pathway components. We will consider the effectiveness of these inhibitors in pharmacological studies, clinical trials and potential cancer treatments. [ more ]

Last offered Spring 2023

Thermal physiology involves the study of molecular events, organ systems, and organism-environmental interactions that are involved with heat production and temperature maintenance. The area of thermal physiology has been around for over 100 years. However, only in the last 5-7 years has the science progressed to understanding basic fundamental mechanisms for generating and regulating heat production. This tutorial will focus on four questions: 1) how do organisms generate heat? 2) how do organisms sense the temperature in the environment? 3) how do organisms integrate information about the environment (temperature, humidity, time of day, etc.) with internal information (deep body temperature, energy stores, etc.) to regulate their metabolic production of heat? 4) how do animals make "the decision" to enter a state of torpor? [ more ]

BIOL 425 TUT Coevolution

Last offered Fall 2021

Coevolution, defined as reciprocal adaptation between species, is central to understanding biological phenomena ranging from global patterns of biodiversity to the molecular mechanisms of evolution. The focus of this tutorial will be on coevolution as a paradigm for understanding species diversification. [ more ]

BIOL 426 TUT Frontiers in Muscle Physiology: Controversies

Last offered Fall 2013

While an active muscle produces force, contraction of muscle is far from the only function of this intriguing organ system. Muscle plays a major role in metabolic regulation of organisms, acts as a glucose storage facility, regulates blood pressure in mammals, and produces numerous hormones. The mechanism for contractile activity varies not only among different organisms, but also among different muscles within the same organism. Controversies, disagreements, and arguments pervade the muscle biology literature perhaps because of the integrative nature of the science. In this tutorial course, we will utilize molecular, physiological, comparative, and evolutionary aspects of muscle biology to address current controversies of this dynamic tissue. Some questions that will be addressed include: 1) Lactic acid generated by skeletal muscle is / is not involved with fatigue at high exercise intensity, 2) Satellite cells are / are not obligatory for skeletal muscle hypertrophy, 3) Do mammals possess the same "stretch activation" of skeletal muscle as seen in insect flight muscle?, 4) Are smooth and skeletal muscles from the same lineage of cells, or do they represent convergent evolution on the tissue level? After an initial group meeting, students meet weekly with a tutorial partner and the instructor for an hour each week. Every other week at this tutorial meeting, students present a written and oral critical analysis of the assigned research articles. Students not making a presentation question and critique the work of their colleague. [ more ]

BIOL 428 SEM Forests of the Future--Understanding Global Change through 'Big Science' Experiments

Last offered Spring 2021

Increases in atmospheric CO2 and warming temperatures associated with global climate change affect the growth and physiology of plants and microorganisms and the cycling and storage of carbon and nutrients within terrestrial ecosystems. These changes cross scale and encompass complex feedbacks that are challenging to predict and understand. Over the past several decades, scientists have used large-scale global change experiments to depict the future of organisms and ecosystems in a CO2-enriched, warmer world. In this course, we will trace the progress of these experiments and evaluate our understanding of the effect of global changes on plant growth and physiology, microbial community composition and activity, and ecosystem nutrient cycling processes. We will then consider the interactive effects of multi-factor global changes and assess the promises and challenges of interpreting biological responses at the ecosystem level. Finally, we will investigate how experimental results can be integrated within models that describe and predict ecosystem function at a global scale. Throughout the course, we will consider how understanding gained from manipulative experiments can be used to inform and prioritize climate change mitigation strategies. Discussions and writing assignments will focus on reading and critiquing the scientific literature. Writing assignments will include two short writing assignments (3 pages each) and a final research proposal (6 pages), as well as formal written peer review. Students will gain experience revising scientific writing. [ more ]

BIOL 430 TUT Genome Sciences: At the Cutting Edge

Last offered Spring 2020

Research in genomics has integrated and revolutionized the field of biology, including areas of medicine, plant biology, microbiology, and evolutionary biology. Moreover, recent developments in "metagenomics" (genomic studies of entire communities of microorganisms in natural environments, such as the mammalian gut and the deep sea) and "metatranscriptomics" (studies of genome wide changes in expression and mRNA levels in natural communities of organisms) have generated unprecedented knowledge about the genomic potential of a community and the in situ biological activity of different ecological niches. In this course we will explore how research in these and related areas, including proteomics, have advanced our fundamental understanding of (1) organisms in the three domains of life, and their interactions and evolutionary relationships; (2) biological systems and environments, such as the human body, extreme environments, and the oceans; (3) strategies for solving global challenges in medicine, agriculture, energy resources, and environmental sciences. During the course, students will meet each week for one hour with a tutorial partner and the instructor. Every other week, students will present a written and oral critical analysis of the assigned research articles. On alternate weeks, students will question/critique the work of their colleague. [ more ]

BIOL 432 SEM Evolutionary Genetics

Last offered Fall 2017

The synthesis of evolutionary processes with the mechanistic understanding of genetics has lent insight into many mysteries of life. The goal of this course is to explore the interface between evolution and genetics to make sense of fundamental biological processes. For example, why do we expect that male and female offspring occur in 50:50 ratios? How and why do unusual sex-ratios occur? Other topics include: conflict among genes, evolution of allelic dominance, adaptation at the molecular level, and genetics of speciation. Class discussion and written assignments will emphasize critical evaluation and synthesis of the scientific literature. [ more ]

Last offered Fall 2023

Beyond the genome, transcriptome, and proteome is the metabolome, the suite of small-molecule metabolites present in a biological sample. These molecules are not simply the products of the proteome nor a collection of cellular fuels and wastes. In this seminar, we will investigate metabolites as signals that influence cellular processes. Biochemistry and molecular biology textbooks often emphasize the proteins that mediate cellular communication. Of course, specialized metabolites like neurotransmitters and certain hormones are well known to regulate information flow between cells. But what about molecules that participate in the metabolic processes of almost every cell--how can these intermediary metabolites be used as signals? How do they communicate acutely and with specificity? What role do they play in sensing (or promoting) environmental change? And how can metabolites be regulated to override their typical fates in metabolic pathways and serve as signals? We'll examine these questions and more at the levels of inter-organellar, intercellular, and inter-organismal metabolic communication by reading the primary scientific literature together. Familiarity with typical mechanisms of cellular communication and/or physiology (BIOL 205) is recommended but not required. [ more ]

BIOL 454 SEM Climate Change Physiology

Last offered Fall 2020

Animals are increasingly faced with rapid climate change driven by human activities across the globe. How do they cope with challenges imposed by increasing temperature? And, how might physiological mechanisms at the organismal level scale up to influence population processes? This course uses an integrative approach to understand the impacts of climate change at multiple levels of biological organization in both terrestrial and aquatic environments. We examine physiological mechanisms underlying animal responses and the role of acclimation versus adaptation in coping with rapidly shifting thermal environments. We then consider the impacts of these mechanisms on whole organism performance and their consequences for population persistence. Finally, we learn the analytical tools used to incorporate physiological mechanisms into ecological models to predict future responses to global climate change. Class discussions will focus on readings drawn from the primary literature. [ more ]

BIOL 455 SEM Neural Regeneration

Last offered Spring 2021

Injury to the human nervous system can cause lasting impairment, but non-mammalian animals have prodigious capacity to regenerate neurons, regrow axons, and repair scars. What accounts for these differences? Regeneration can occur in multiple modes: replacement of injured neurons, repairs such as axonal regrowth to reconnect to a target structure, or repurposing existing neurons for new tasks through neural plasticity. We will explore the molecular foundations that underlie neuronal proliferation, neural plasticity, and inflammatory responses. We will consider the potential for translating these findings to inform treatments for humans who suffer from neural injury or neurodegenerative disease. Class discussions will focus on readings from the primary literature. [ more ]

Last offered Spring 2023

How can two or more species coexist if they compete for the same resources? Or when one preys on the other? Understanding species coexistence has been central to ecology since its inception. The question is important because species diversity is a defining characteristic of natural ecosystems. This course provides an in depth look into the theoretical and empirical evidence for species coexistence. It also explores how the evolution of interacting species can change the identity and number of species in a community thereby playing a key role in determining and maintaining species diversity. Finally, the course will address how this body of theory and empirical evidence can be used to predict how we might expect diversity to change with increases in human-caused disruptions to the natural environment. [ more ]