New courses, Fall 2011

New courses offered in the Division of Science in Fall, 2011:

BISC 9B Biology of Cancer (Dore)

Introduces the fundamental aspects of cancer development, progression and treatment with an emphasis on the cellular and molecular changes thought to lead to cancer. Both genetic and lifestyle factors and their impact on the predisposition to develop and recover from cancer will be discussed. Usually offered every year.

CBIO 101A  Chemical Biology (Pontrello)

Chemical biology is not just biochemistry, and the subject involves much more than a simple combination of chemistry and biology topics. This course will explore how recent cutting edge scientific work in chemistry has led to a deeper fundamental understanding of and ability to manipulate biological processes. Emphasis will be placed on the design and chemical synthesis of micro and macromolecular structures that allow scientists to ask unique chemical and biological questions as well as to control biological systems. Both synthetic strategies and characterization as well as biological evaluation and utility will be discussed. The course will consist of scientific literature readings, periodic assignments and exams based on literature and lecture content, as well as group projects and exercises. A textbook is not required, although retention of prerequisite course textbooks is strongly recommended. Topics will range from fluorescent probes, chemical inducers of dimerization, bacterial chemotaxis, controlling stem cell differentiation, solid phase synthesis, synthetic nucleotides, B cell activation, and chemical-inducers of dimerization, just to name a few.

This is not an introductory science course, and the structure will be designed to enhance student understanding of the subject through primary literature and group discussion and review. After several instructor lectures covering general chemistry and biology background, each class will be structured around student presentations of assigned primary scientific literature as a starting point for class discussion about the area of research. The course will also include a project where each student will search chemical biology journals, select a recent article they find interesting, and prepare a report explaining background, fundamental chemistry and biology addressed in the paper, results and applications, and also future directions and implications for the field. The final exam will be based on the content of this collective work.

BCHM 104A Physical Chemistry of Macromolecules I (C.Miller, Oprian)

Covers basics of physical chemistry underpinning applications in BCHM 104b. Focus is placed on quantitative treatments of the probabilistic nature of molecular reality: molecular kinetic theory, basic statistical mechanics, and chemical thermodynamics in aqueous solution. Usually offered every second year

BIOL 107A Data Analysis and Statistics Workshop (Van Hooser)

The interpretation of data is key to making new discoveries, making optimal decisions, and designing experiments. Students will learn skills of data analysis through hands-on, computer-based tutorials and exercises that include experimental data from the biological sciences. Knowledge of very basic statistics (mean, median) will be assumed. Usually offered every second year.

BCHM 172A Cholesterol in Health and Disease (Westover)

In today’s supermarkets, many foods are proudly labeled “cholesterol-free.” 1in 4 Americans over 45 take medicine to lower their cholesterol levels.  Yet, every beginning biology student learns that cholesterol is an essential component of mammalian cell membranes.

This fall, the Biochemistry Department’s Emily Westover will teach a new course called Cholesterol in Health and Disease, BCHM 172a. Drawing from the current literature, students in this course will explore many facets of cholesterol science.  This course will be case study in cholesterol, bringing together concepts from a variety of disciplines, including cell biology, biophysics, biochemistry, physiology and medicine.

The class will address questions such as:

  • How does the body balance production and dietary uptake of cholesterol?
  • What effects does cholesterol have on membrane and protein function?
  • What is the connection between cholesterol and atherosclerosis?

BCHM 172 will meet Tuesdays at 2 pm in the 4th floor Ros-Kos Conference Room.

NBIO 157A Project Laboratory in Neurobiology and Behavior (Vecsey)

What is it like to be a scientist?

Many college science courses don’t help students answer that question. In lecture courses, a host of scientific facts are taught via textbook, but at the end of the course students have read little if any primary research, and would be hard-pressed to explain in detail how those facts were discovered. Courses with labs often have “recipe books” that lay out all of the necessary ingredients and steps required to achieve a desired experimental result. Even students who try to get scientific training by working in a lab may at first be relegated to perform menial tasks that are not fully representative of the scientific process.

With all of this in mind, Brandeis University introduced a series of courses called Project Labs. In these courses, students carry out legitimate research projects in a range of disciplines. No cookbooks, no expected outcomes. We start with an introduction to a biological question, and then set about answering it. We read primary literature to understand the basis for the research we will carry out, and we write up the results in a true journal format.

The newest installment in the Project Lab series is Bio157a, the Project Lab in Neurobiology and Behavior. In this course, the ultimate goal is to understand how an animal like the fruit fly senses and responds to temperature. Specifically, we will examine temperature preference behavior in Drosophila melanogaster and several related species. Some of those species are native to cold climates, whereas others hail from deserts such as the Mojave. Have these species evolved to prefer different temperatures? Or are they simply more tolerant of those temperatures? These are some of the core questions that we will address. What the results will be we can only guess – and that’s what it’s like to be a scientist!

The next chapter in space flight

Brandeis NOW has a new story on the Graybiel Lab and its role in the privatization of space flight.

Microtubules and Molecular Motors Do The Wave

Most people are familiar with audiences in crowded arenas performing “the wave,” raising their hands in sync to produce a pattern that propagates around the whole stadium.  This self-organized motion appears seemingly out of nowhere.  It is not produced by any external control, but is rather emerges from thousands of individuals interacting only with their neighbors.  A similar principle of self-organization might also be relevant on length scales that are billion times smaller.  On this scale, nanometer-sized proteins interact with each other to produce dynamical structures and patterns that are essential for life—and some of these processes are reminiscent of waves in crowded stadiums.  For example, thousands of nano-sized molecular motors located within a single eukaryotic flagellum or cilium coordinate their activity to produce wave-like beating patterns.  Furthermore, dense arrays of cilia spontaneously synchronize their beating to produce metachronal waves.

Proper functioning of cilia is essential for health; for example, cilia determine the correct polarity and location of our organs during development.  Defective cilia can cause a serious condition called situs inversus, in which the positions of the heart and lungs are mirrored from the normal state.  In another example, thousands of cilia in our lungs function to clear airways of microscopic debris such as dust or smoke by organizing their beating into coordinated, wave-like patterns.  Despite the importance of ciliar function, the exact mechanisms that lead to spontaneous wave-like patterns within isolated cilia, as well as in dense ciliary fields, is not well understood.

In a paper published in the journal Science this week, an interdisciplinary team consisting of physics graduate student Timothy Sanchez and biochemistry graduate student David Welch working with biophysicist Zvonimir Dogic and biologist Daniela Nicastro present a striking finding: the first example of a simple microscopic system that self-organizes to produce cilia-like beating patterns.  Their experimental system consists of three main components: 1) microtubule filaments; 2) motor proteins called kinesin, which consume chemical fuel to move along microtubules; and (3) a bundling agent that induces assembly of filaments into bundles.  Sanchez et al. found that under a certain set of conditions, these very simple components are able to self-organize into active bundles that spontaneously beat in a periodic manner.  One large spontaneously beating bundle is featured below:

In addition to observing the beating of isolated bundles, the researchers were also able to assemble a dense field of bundles that spontaneously synchronized their beating patterns into traveling waves.  An example of this higher-level organization is shown here:

The significance of these observations is several-fold. First, due to the importance of ciliar function for health, there is great interest in elucidating the mechanism that controls the beating patterns of isolated cilia as well as dense ciliary fields.  However, the complexity of these structures presents a major challenge.  Each eukaryotic flagellum and cilium contains more than 600 different proteins.  For this reason, most previous studies of cilia and flagella have employed a top-down approach; they have attempted to elucidate the beating mechanism by deconstructing the fully functioning organelles through the systematic elimination ­­­of constituent proteins. In this study, the researchers utilize an alternative bottom-up approach and demonstrate for the first time that it is possible to construct artificial cilia-like structures from a “minimal system,” comprised of only three components.  These observations suggest that emergent properties, spontaneously arising when microscopic molecular motors interact with each other, might play a role in formation of ciliary beating patterns.

Second, self-organizing processes in general have recently become the focus of considerable interest in the physics community.  These processes range in scale from microscopic cellular functions and swarms of bacteria to macroscopic phenomena such as flocking of birds and manmade traffic jams. Theoretical models indicate that these vastly different phenomena can be described using similar theoretical formalisms.  However, controllable experiments with flocks of birds or crowds at football stadiums are virtually impossible to conduct.  The experiments described by Sanchez et al. could serve as a model system to test a broad range of theoretical predictions. Third, the reproduction of such an essential biological functionality in a simple in vitro system will be of great interest to the fields of cellular and evolutionary biology. Finally, these findings open the door for the development of one of the major goals of nanotechnology: to design motile nano-scale objects.

These encouraging results are only the first from this very new model system.  The Dogic lab is currently planning refinements to the system to study these topics in greater depth.

UPDATE: Today, this publication was additionally featured on NPR Science Friday as the video pick of the week:

 

Nicolas Rohleder — ISPNE 2011 Curt P. Richter Award

Nicolas Rohleder, of the Department of Psychology, Brandeis University, is the recipient of the 2011 Curt P. Richter Award of the International Society for Psychoneuroendocrinology (ISPNE) for his original manuscript entitled “Acute and chronic stress induced changes in sensitivity of peripheral inflammatory pathways to the signals of multiple stress systems”. The award, which has been given by the ISPNE for over 25 years to a distinguished line of young investigators in the field of psychoneuroendocrinology, consists of an honorarium, an award certificate and plaque, a travel grant of up to $ 1,000 to attend the Society’s annual meeting, the publication of the manuscript in the society’s journal ‘Psychoneuroendocrinology‘, and well as a year’s complimentary access to ScienceDirect and Scopus.  Dr. Rohleder will receive the award, and make a presentation of his research findings, at the ISPNE annual meeting to be held in Berlin, Germany on August 4-6.

  • Rohleder N. Acute and chronic stress induced changes in sensitivity of peripheral inflammatory pathways to the signals of multiple stress systems – 2011 Curt Richter Award Winner. Psychoneuroendocrinology. 2012

and more and more papers

More papers appearing recently, not otherwise mentioned:

  • Standfuss J, Edwards PC, D’Antona A, Fransen M, Xie G, Oprian DD, Schertler GF. The structural basis of agonist-induced activation in constitutively active rhodopsin. Nature. 2011;471(7340):656-60.
  • Rim Noh S, Lohani M, Isaacowitz DM. Deliberate real-time mood regulation in adulthood: The importance of age, fixation and attentional functioning. Cogn Emot. 2011:1-16.
  • Zemskov EP, Kassner K, Tsyganov MA, Epstein IR. Speed of traveling fronts in a sigmoidal reaction-diffusion system. Chaos. 2011;21(1):013115.
  • and MORE…

Dynamic Coding in Neural Signals Workshop on July 29

The Center of Excellence for Learning in Education, Science and Technology (CELEST) is holding a workshop on its cross-function initiative Dynamic Coding in Neural Signals at Boston University (677 Beacon Street, Room B02) on July 29, 2011. from 1:00 – 5:45 pm. The workshop is free and open to the public. There will be talks by invited speakers from 1 – 4:15, including presentations by Don Katz (“Perceptual processing via coherent sequences of ensemble states”) and Paul Miller (“Stochastic transitions between discrete states in models of taste processing and decision-making”). a student and postdoc poster session will follow, with ample opportunity for discussion between presenters and workshop attendees.

CELEST is a joint venture of scientists at four Boston-area universities including Brandeis and is sponspored by the National Science Foundation. Robert Sekuler, Louis and Frances Salvage Professor of Psychology at Brandeis, is a co-Principal Investigator, and Biology and Neuroscience faculty Gina Turrigiano and Paul Miller are also involved in the center.

More postdocs than ever

and still not paid very well. The annual nationwide Survey of Earned Doctorates from a group of US government agencies shows that an increasing majority of Ph.D. recipients in the sciences go on to postdoctoral positions, as do the majority of Brandeis Ph.D. recipients in the life sciences, the only disciplines for which I  have statistics handy. The average salaries for postdocs are, as you might expect, less than luxurious when compared to other career paths taken by Ph.D. recipients.

What’s behind the curtain

Thanks to a gift from Vertica, an HP company, the Department of Computer Science is doing some remodeling in the Volen Center, creating a modern computer laboratory lounge for our students. Classroom 105 is being moved to Volen 119, formerly known as the Berry Patch; Rooms 104 and 105 are being combined and fit with soft furniture, workstations, and group work tables as a comfortable place to sit and work individually and on group projects. We are also upgrading the furniture in the Volen lobby itself.

 

 

 

The CS Systems Operations page says:

2011-06-15: The Berry Patch […] will be closing for renovations on 6/17/2011. The workstations in room 118 next door will remain available, as will the remote shell servers (coeus and themis); several other workstations will also be accessible for remote-only use.

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