I know it's a type of capillary electrophoresis, but I don't get how does the separation happen exactly.
Many of us are using isotachophoresis all the time without even realising it. The explanation that follows may not be exact, but I hope that it helps.
Firstly, think about a simple electrophoresis set-up - in agarose electrophoresis of DNA we have a uniformly distributed buffer such as Tris-borate. The current is carried by the borate ions and the DNA molecules run through the homogeneous electric field towards the anode. They separate by size because of the sieving effect of the agarose matrix.
Now let's think about what is happening in an SDS-PAGE separation (a Laemmli gel). Just to remind you:
The running (or reservoir) buffer is Tris-glycine pH 8.3
The stacking gel is in Tris.HCl pH 6.8
The separating gel is in Tris.HCl pH 8.8
When the power supply is turned on, the glycinate ion in the top reservoir begins to move into the stacking gel. When it hits the zone of pH = 6.8 it is much closer to its pKa and so is now only weakly charged. Consequently it slows down. Meanwhile the chloride ions in the stacking gel have begun to move rapidly down through the stacking gel (towards the anode). This creates a discontinuous electric field: the chloride zone has a lower resistance than the glycinate zone so the field strength in the chloride zone is weaker than the field strength in the glycinate zone. This is a stable situation because the ions cannot stray into each other's zones: if a glycinate ion happens to diffuse forwards into the chloride zone it will experience a weaker field and slow down, whereas if a chloride ion diffuses back into the glycinate zone it will hit the stronger field and quickly move ahead again.
What about the SDS-protein complexes that were in the well? (I'll just refer to these as proteins from now on.) Their ionic properties lie between the glycinate and the chloride, and so they eventually end up moving through the stacking gel between the trailing zone of glycinate and the leading zone of chloride. Any protein that finds itself in the glycinate zone will move quickly forward (due to the higher field strength) and any protein that moves ahead by chance into the chloride zone will slow down due to the weak field strength, falling back into the protein zone. And in this way these zones move in a procession through the stacking gel, with the proteins being focussed into a very narrow region in the middle. The glycinate, the proteins and the chloride are all moving at the same speed, and so this is an example of isotachophoresis (isotacho- = "same speed"). The polyacrylamide gel matrix in the stacking gel has no separating function - its role is simply to stabilise against convective effects. The proteins can reach very high local concentrations in the stacking gel, and if you look carefully you will often see refractive effects as your sample runs through the stacking gel. In this way the protein sample is "applied" to the separating gel in a very tight band, perfect for achieving high resolution separation (bands broaden by diffusion in the separating gel so the tighter the bands ar eat the point of loading, the better the final result.)
Once the sample hits the separating gel, all of this breaks down: the pH is now 8.8 so the glycinate becomes strongly charged and zooms off ahead with the chloride through the gel, leaving the proteins to move more slowly due to the sieving effect of the polyacrylamide matrix.
It is possible to set up an isotachophoresis as described above in isolation. Individual proteins will have slightly different ionic properties and will line up in the region between the two buffer ions, allowing for their separation.
Capillary electrophoresis (CE) is a family of electrokinetic separation methods performed in submillimeter diameter capillaries and in micro- and nanofluidic channels. Very often, CE refers to capillary zone electrophoresis (CZE), but other electrophoretic techniques including capillary gel electrophoresis (CGE), capillary isoelectric focusing (CIEF), capillary isotachophoresis and micellar electrokinetic chromatography (MEKC) belong also to this class of methods.  In CE methods, analytes migrate through electrolyte solutions under the influence of an electric field. Analytes can be separated according to ionic mobility and/or partitioning into an alternate phase via non-covalent interactions. Additionally, analytes may be concentrated or "focused" by means of gradients in conductivity and pH.
Two-dimensional gel electrophoresis
|Hyphenated||Capillary electrophoresis mass spectrometry|
A mobility shift assay is electrophoretic separation of a protein–DNA or protein–RNA mixture on a polyacrylamide or agarose gel for a short period (about 1.5-2 hr for a 15- to 20-cm gel).  The speed at which different molecules (and combinations thereof) move through the gel is determined by their size and charge, and to a lesser extent, their shape (see gel electrophoresis). The control lane (DNA probe without protein present) will contain a single band corresponding to the unbound DNA or RNA fragment. However, assuming that the protein is capable of binding to the fragment, the lane with a protein that binds present will contain another band that represents the larger, less mobile complex of nucleic acid probe bound to protein which is 'shifted' up on the gel (since it has moved more slowly).
Under the correct experimental conditions, the interaction between the DNA (or RNA) and protein is stabilized and the ratio of bound to unbound nucleic acid on the gel reflects the fraction of free and bound probe molecules as the binding reaction enters the gel. This stability is in part due to a "caging effect", in that the protein, surrounded by the gel matrix, is unable to diffuse away from the probe before they recombine.  If the starting concentrations of protein and probe are known, and if the stoichiometry of the complex is known, the apparent affinity of the protein for the nucleic acid sequence may be determined.  Unless the complex is very long lived under gel conditions, or dissociation during electrophoresis is taken into account, the number derived is an apparent Kd. If the protein concentration is not known but the complex stoichiometry is, the protein concentration can be determined by increasing the concentration of DNA probe until further increments do not increase the fraction of protein bound. By comparison with a set of standard dilutions of free probe run on the same gel, the number of moles of protein can be calculated. 
An antibody that recognizes the protein can be added to this mixture to create an even larger complex with a greater shift. This method is referred to as a supershift assay, and is used to unambiguously identify a protein present in the protein – nucleic acid complex.
Often, an extra lane is run with a competitor oligonucleotide to determine the most favorable binding sequence for the binding protein. The use of different oligonucleotides of defined sequence allows the identification of the precise binding site by competition (not shown in diagram). Variants of the competition assay are useful for measuring the specificity of binding and for measurement of association and dissociation kinetics. Thus, EMSA might also be used as part of a SELEX experiment to select for oligonucleotides that do actually bind a given protein. [ citation needed ]
Once DNA-protein binding is determined in vitro, a number of algorithms can narrow the search for identification of the transcription factor. Consensus sequence oligonucleotides for the transcription factor of interest will be able to compete for the binding, eliminating the shifted band, and must be confirmed by supershift. If the predicted consensus sequence fails to compete for binding, identification of the transcription factor may be aided by Multiplexed Competitor EMSA (MC-EMSA), whereby large sets of consensus sequences are multiplexed in each reaction, and where one set competes for binding, the individual consensus sequences from this set are run in a further reaction. 
For visualization purposes, the nucleic acid fragment is usually labelled with a radioactive, fluorescent or biotin label. Standard ethidium bromide staining is less sensitive than these methods and can lack the sensitivity to detect the nucleic acid if small amounts of nucleic acid or single-stranded nucleic acid(s) are used in these experiments. When using a biotin label, streptavidin conjugated to an enzyme such as horseradish peroxidase is used to detect the DNA fragment.   While isotopic DNA labeling has little or no effect on protein binding affinity, use of non-isotopic labels including flurophores or biotin can alter the affinity and/or stoichiometry of the protein interaction of interest. Competition between fluorophore- or biotin-labeled probe and unlabeled DNA of the same sequence can be used to determine whether the label alters binding affinity or stoichiometry.
Title: Sample distribution in peak mode isotachophoresis
We present an analytical study of peak mode isotachophoresis (ITP), and provide closed form solutions for sample distribution and electric field, as well as for leading-, trailing-, and counter-ion concentration profiles. Importantly, the solution we present is valid not only for the case of fully ionized species, but also for systems of weak electrolytes which better represent real buffer systems and for multivalent analytes such as proteins and DNA. The model reveals two major scales which govern the electric field and buffer distributions, and an additional length scale governing analyte distribution. Using well-controlled experiments, and numerical simulations, we verify and validate the model and highlight its key merits as well as its limitations. We demonstrate the use of the model for determining the peak concentration of focused sample based on known buffer and analyte properties, and show it differs significantly from commonly used approximations based on the interface width alone. We further apply our model for studying reactions between multiple species having different effective mobilities yet co-focused at a single ITP interface. We find a closed form expression for an effective-on rate which depends on reactants distributions, and derive the conditions for optimizing such reactions. Interestingly, the model reveals thatmore » maximum reaction rate is not necessarily obtained when the concentration profiles of the reacting species perfectly overlap. In addition to the exact solutions, we derive throughout several closed form engineering approximations which are based on elementary functions and are simple to implement, yet maintain the interplay between the important scales. Both the exact and approximate solutions provide insight into sample focusing and can be used to design and optimize ITP-based assays. « less
Sample stacking techniques in electrophoresis are gaining popularity due to their ability to provide improved sensitivity and separation efficiency. The principles behind sample stacking and electrophoretic migration have been studied extensively. Nevertheless, there are still a number of observations and descriptions of ionic boundaries and migration modes for which the underlying principles are not yet fully understood. For example, the behavior of capillary isotachophoresis (cITP) systems that exhibit self-sharpening effects can be complex, especially when the buffer systems contain many ionic components. In this work, cITP coupled with 1 H NMR detection is used to study electrophoretic migration of ions in both anionic and cationic cITP. A significant advantage of 1 H NMR over other detection methods is the high specificity of this method, allowing detection of individual buffer and analyte constituents within the migration zones.
University of California, Riverside.
Current address: Hospira Inc., McPherson, KS 67460.
To whom correspondence should be addressed. Phone: (951) 827-2990. Fax: (951) 827-4713. E-mail: [email protected]
Instrumentation and working
The basic components of an capillary electrochromatograph are a sample vial, source and destination vials, a packed capillary, electrodes, a high voltage power supply, a detector, and a data output and handling device. The source vial, destination vial and capillary are filled with an electrolyte such as an aqueous buffer solution. The capillary is packed with stationary phase. To introduce the sample, the capillary inlet is placed into a vial containing the sample and then returned to the source vial (sample is introduced into the capillary via capillary action, pressure, or siphoning). The migration of the analytes is then initiated by an electric field that is applied between the source and destination vials and is supplied to the electrodes by the high-voltage power supply. The analytes separate as they migrate due to their electrophoretic mobility, and are detected near the outlet end of the capillary. The output of the detector is sent to a data output and handling device such as an integrator or computer. The data is then displayed as an electropherogram, which reports detector response as a function of time. Separated chemical compounds appear as peaks with different migration times in an electropherogram.
Lehninger principles of biochemistry (4th ed.): Nelson, D., and Cox, M.
Nelson, D., and Cox, M. W.H. Freeman and Company, New York, 2005, 1216 pp., ISBN 0-7167-4339-6, $130.95.
In the beginning there was White, Handler, and Smith. (Biochemistry textbooks are almost never referred to by their titles, only by their authors. This point will be revisited shortly.) Then Mahler and Cordes provided competition. In 1970 (we are of course dealing in the distant mists of biochemical time), Lehninger appeared on the scene. It was considered by many to be the first “readable” biochemistry text and quickly became a popular staple in courses. Around the same time, as the inherent importance of biochemistry became obvious, textbooks started multiplying and getting larger. Biochemistry was in an impressive growth phase and authors felt the necessity to include the rapidly accumulating new information in their tomes without eliminating any of the old material.
This growth spurt of biochemistry and the accompanying texts soon resulted in a split of textbook style. Biochemistry was seen as crucial for most life science majors and even engineers needed to be enlightened. However, not all would need the rigorous approach presented by the early generations of texts. New books appeared where the title was now an issue. Volumes that were embossed with Outlines of …, Foundations in …, and Principles of … were aimed at the so-called non-majors sections of biochemistry. In 1982, Albert Lehninger decided that his original efforts had become too dense through two previous editions and opted for a third approach. He titled his new work Principles of Biochemistry but did not direct it toward non-majors. Rather, he saw the need for a book comprehensive enough for an attempt at complete coverage of the field, but not so in-depth that it could suffice as a graduate text. His new book would be designed for undergraduate biochemistry majors and others who needed a majors-level course.
This 4th edition of that newer Lehninger is the result of the evolution of this approach. Sadly, Albert Lehninger has not been around for recent editions but the book is wisely titled Lehninger Principles of Biochemistry. It still strives and, for the most part, succeeds in being a readable body of work. (On the other hand, it is something of an unfair criticism to say a text is unreadable. Very few will sit and read such a book like a novel. While students would gain the most from this approach—all texts endeavor for a coherent effort at tying biochemistry into a “big picture,” they are most likely to check out a specific section on a topic of misunderstanding, or, more likely, check out the index for the exact item in question.) Authors David Nelson and Michael Cox have built upon their previous edition to generate a smoothly flowing work.
Current users can rest assured that nothing drastic has been changed in style from the 3rd edition. However, there are important additions reflecting our still rapidly changing area of interest. Significant results from the Human Genome Project and other sequencing efforts are included. For example, ABC transporters in all organisms are now discussed. Genomics and proteomics are covered in a separate chapter, and new applications of methods such as atomic force microscopy are described. None of these new inclusions are forced in but seem to be blended nicely with existing material. Also blended in are new insights gained from structural determinations of complexes like bacterial RNA polymerase and large and small ribosomal subunits. The importance of structure in the understanding of biochemical principles was recognized early by Lehninger and is continued by the authors as shown by their inclusion of the Protein Data Bank identification code for each structure shown in the text. The authors have also greatly expanded their coverage of detailed reaction mechanisms.
Instructors should note that the much of the 3rd edition's initial four-chapter section on foundations of biochemistry has been combined and dispersed to other chapters. There is now one initial chapter called “The Foundations of Biochemistry” followed by one devoted to water. The cell biology information in the old chapter two has been placed in the context of other chapters and reduced in scope. Likewise, much of the chemistry found in the old chapter three has been placed in other locations. One presumes the authors have decided to recognize the fact that other courses in fundamentals of chemistry and organic chemistry should be prerequisites for a course using their text. These reductions and combinations are probably ways to get to the meat of the subject more quickly and keep the volume to a manageable size.
With any text of such scope, there are always small things that can be changed. For instance, the authors incorporated essentially intact their section on DNA fingerprinting from the older edition. This shows Southern blotting and RFLP analysis on autoradiograms. This method has long been supplanted by using PCR and capillary electrophoresis.
No modern text book would be complete without the accompanying flock of supplements and this one is no exception. There is a study guide and separate lecture notebook to make life easier for students, a set of transparencies (with bold writing for good projection characteristics) and two test banks to make life easier for the instructor, and a website with graphics and animations to make life easier for both. The website is linked to the appropriate site in the text with an icon of a mouse (computer, not mammalian).
There are too many good biochemistry text books in the market to allow any bad ones to survive. They will all cover essentially the same material in slightly different (and sometimes identical) ways. New editions are ways for books to incorporate new material and feedback from previous versions and it seems that Nelson and Cox have done both in an admirable fashion. This text should continue to please users of the older versions and continue the model that Lehninger himself established with his first efforts.
About the Author
Carlos D. García, PhD, is an Associate Professor of Analytical Chemistry at the University of Texas at San Antonio, USA. His group is currently focused on the development of novel bioanalytical strategies involving microfluidics and nanomaterials.
Karin Y. Chumbimuni-Torres, PhD, is a Research Associate at the University of Texas at San Antonio, USA. She is interested in pursuing the development of electrochemical biosensors and their integration to microchip-based platforms.
Emanuel Carrilho, PhD, is an Associate Professor at the University of Säo Paulo, Brazil. With more than twenty-five years of experience in separation science, his group is focused on the development of analytical methods and instrumentation for bioanalyses.
Hello , we are learning amino acids and proteins.
Our professor did not cover how to name peptides or tripeptides.
Can you please help me understand how to name this tripeptide ?
Kansas State University
Here are some questions from previous first tests, so that you can get some idea about the format, and the logical steps needed to get the right answer.
All organisms must reproduce, use energy, stay organized, and respond to external stimuli. All of these are characteristics of life listed in your textbook. Answer C doesn't appear in your textbook, so you should automatically be a bit suspicious of that. But don't all organisms require oxygen? NO. In fact, some are actually killed by the presence of oxygen. Organisms, as you learned in class, not only include big fuzzy things like your dog, cat or roommate, but also small gooey things like bacteria or yeast (and perhaps your roommate). Some bacteria don't need oxygen. Yeast can get by fine with, or without oxygen. You're on your own with the roommate, sorry. So the answer to this question is C, based on facts you know (the list of characteristics of life in our textbook), and supported by other facts and logic.
This figure is based on a figure from a previous textbook (there is likely to be a similar one in your current textbook). The exact figure isn't important what is important is that you understand that both the figures and the text in your book can contain information that we want you to know. Are you getting the idea that we would like you to read the textbook as well as go to class? Good! At any rate, if you read the textbook, this question should be very simple. But even if you didn't read it, or don't remember the material very well, you can use logic to go through the choices and eliminate the obviously wrong ones. You should know that typically the scientific method uses available data to generate hypotheses experiments are performed to test the hypotheses. So some sort of DATA should be the starting point (box 1). Based on that, you should eliminate answers A, C, and E. That leaves B and D, which are very similar. At this stage you need to remember the difference between THEORY and CONCLUSION, which are the two terms that are different in answers B and D. Once again you find out that we need you to understand the definitions of the words used in this course! So if you know that many similar conclusions allow scientists to arrive at a THEORY, or that one set of observations is not nearly enough to support a THEORY, you should eliminate answer B. Thus the correct answer is D.
This question comes directly from an exercise that you will do in the PoB studio. Exercises that you do in the studio are fair game for exam questions, just in case you were wondering about that. And questions involving simple math (dividing or multiplying by 10, for example) are also going to show up on exams. If we ask you more complicated math questions, we will inform you ahead of time and allow you to bring a calculator just in case you feel that you need it. But this question doesn't require a calculator. An absorbance of 0.2 is one-third that of an absorbance of 0.6. That means that there will be one-third the number of yeast cells in a solution with this absorbance, compared to a solution with an absorbance of 0.6. One-third of 300 = 100. The correct answer is therefore (C).
More definitions. Note that the bold-faced term SUGGESTED EXPLANATION is a pretty good synonym for one of the answers, i.e. HYPOTHESIS. You can also eliminate DOGMA because it was never mentioned in your book or in your studio material as a part of the scientific method. So even if you are just guessing (which is not a recommended strategy), we often give you answers so ridiculous that you are able to guess from fewer choices! Funny how nobody ever thanks us for these easy questions they just complain about the ones that are hard. The correct answer is D.
Here is a classic case where haste and careless reading will result in poor test performance. You probably knew that Dendroica is the genus name, and petechiae and pennsylvanica are species names. So the correct answer must be B, right? Well, B is correct, but it is also incomplete. If you recall the arrangement of taxonomic divisions, you will remember that organisms in the same genus are also in the same FAMILY (as well as the same ORDER, CLASS, KINGDOM etc.) So if you read a bit further down the list of choices, the real answer appears. These organisms belong to the same FAMILY and the same GENUS the answer is E. I hope that this example reinforces the notion that you need to READ THE ENTIRE QUESTION AND ALL THE ANSWERS before you make a mark on your answer card.
6. Here is a picture of a chromosome. The box labeled "A" outlines a structure called a(n)___1___ the structure labeled "B" is a(n)__2____. (blanks 1 and 2 should be filled respectively with:)
A. 1- aster, 2-chromatid
B. 1- chromatid, 2- centromere
C. 1- kinetochore, 2- chromatid
D. 1- telomere, 2- centromere
E. 1- nucleolus, 2- kinetochore
Here is an example of a question from the Cell Biology Module, which illustrates that we often expect you to label certain structures in figures taken almost directly from your text or from the computer material. Again, it is obvious that you need to know and remember very specific terms. And again, at least one answer (E) is ridiculous if you read the material or went to class the NUCLEOLUS is a part of the NUCLEUS of a cell, and not a part of a CHROMOSOME. After eliminating that one, you are left with four choices. And unfortunately, unless you understand the DEFINITION of all of those terms, you may not get the right answer, which is B.
Here is another type of question which you will grow to appreciate during a semester in BIOL 198. We will have discussed a process (in this case transport of materials in plants) in class this will also be covered in the textbook. Now we are testing to see if you understand that process enough so that you can place the steps in the process in the correct sequence. So try to remember the sequences of steps in some of the major processes (photosynthesis, oxidative phosphorylation, mitosis, etc.) that we discuss in this course, because you may be called upon to place them in the correct order. In this case, the correct answer is D. Sugar is actively transported into the phloem from the leaf cells which make the sugar. This change in osmotic potential causes water to diffuse into the phloem (this concept will also be covered in Module 4), creating a positive pressure potential. At the other end of the plant, the sugar molecules are transported out of the phloem to provide nutrition for the non-photosynthetic root cells.
We often ask you some matching questions, because it allows us to test over a lot of material with one question. In this case, you are asked to match specific structures with a specific level of organization (TISSUE OR ORGAN) of animals. So you need to know the levels of organization as well as the specific structures. Again, this is not a hard question if you have read the material and attended class, but it probably looks pretty hard to you right now if you haven't covered this material yet! But you don't have to panic. You probably know that the liver is an organ, and that the skin is an organ. You may not know that epithelium is a type of tissue, and that nerves are another type of tissue, so we'll go on to the final choice. You probably already knew that the stomach is an organ, not a tissue, so the answer must be E. And that would be right!
Another common type of question on our exam is this one, where you need to fill in the blanks in order from a list of choices. As before, some of the answers are ridiculous. Red blood cells don't change to white blood cells or to tissue cells as they pass through capillaries, so you can eliminate answers B and C. And we won't even get started on why answer A is absurd!
You also get a clue from the information in the question (didn't we tell you to read the questions carefully?), when you note that the correct answers would be things that behave in the bloodstream in an analogous manner to oxygen and carbon dioxide, respectively. Since oxygen is needed by animal cells, and since carbon dioxide is a waste product of animal cells, you probably can figure out that some necessary nutrient should go in the first blank, and some waste product should go in the second blank. Based on that logic, you can eliminate D, leading to the conclusion that the only possible answer is E. This question is probably too easy, don't you think?
11. Passage of water-soluble molecules across biological membranes is restricted by the membrane structural component known as
D) nucleic acids.
E) none of the above.
Here is an example of a question which was written to be as clear and simple as possible, but was missed by a significant proportion of the class. The answer is A lipids (including phospholipids and cholesterol) are hydrophobic and thus automatically are the only logical choice for a membrane component that can restrict passage of hydrophilic (water-soluble) molecules across membranes. But that logical and simple answer was missed by many. Why? As one student wrote, "the way that it is worded indicates that you want the answer for a membrane structural component and what you have listed as choices for the answer are the four major classes of biological polymers, not membrane structural components--therefore E is the correct answer."
This could be an example of looking for the "trick" in the question (where there is none). But actually if the answer E was correct as this student assumed, it would be a trick question! Think about it. By looking for the "trick", she mentally changed the question from a simple one to a tricky, complicated one. She changed her perspective to one that is different from that of the person who wrote the question, who wanted it to be as clear and simple as possible. And when you are not thinking along the same lines as the person who wrote the question, you probably will get it wrong.
Alternatively, it could be an example of memorization-driven blinders memorizing the four basic biological polymers and not thinking about them in another context. This student obviously memorized the fact that there are four biological polymers. Great! But she should also know that three of the four (lipids, proteins, and carbohydrates) ARE also membrane structural components. Just because they are "biological polymers" does not mean that they automatically are excluded from any memory bin that holds the information for "membrane structural components". As noted before, memorization is not enough, and in this case, memorization of a list, in the absence of additional understanding, may have acted as a set of blinders and actually hurt the student's performance on the test.
The Biology of Hunger
The biological mechanisms behind hunger, appetite, and satiety are mysterious. What processes cause us to feel hunger and then tell us when to stop eating? Why are we attracted to particular foods more than others? What are the biological roots of eating disorders like binge eating and anorexia?
For Nilay Yapici, Neurobiology and Behavior, the answers lie in our brains. “I’ve always been fascinated by how our brains control our behaviors,” she says. “I want to understand how genes regulate our brain functions, which then control our behaviors, especially our daily life decisions like eating.”
Identifying Food Intake Neurons
Yapici explores how the food intake circuits in the brain are regulated in different behavioral states. Her lab seeks to identify neurons that mediate food intake decisions and trace their activity during various behaviors, such as foraging or resting.
Yapici began her research career focusing on Drosophila melanogaster, the fruit fly. She wanted to explore the genetics behind behavior, and she was drawn to drosophila because it has a smaller brain with 1000-fold fewer neurons than the mouse brain, yet approximately 80 percent of the protein-coding genes in drosophila are the same as in other species, such as mice and humans.
Early on, the Yapici lab identified excitatory interneurons, which they called Ingestion Neurons 1 (IN1), in the taste-processing center of the drosophila brain. “These neurons change activity when the fly is hungry,” Yapici says. “They have a higher firing rate when the fly is actively eating. We think the activity of these neurons is controlling the persistence of food intake.”
A Gut-Brain Positive Feedback Loop?
In their quest to understand the role of IN1 in food intake in drosophila, the researchers began to look at the interaction between the fly’s brain and its gut. “We have preliminary evidence that the duration of food intake may be regulated by information coming from the gut,” Yapici says. “It’s like a positive feedback loop. If the fly is eating something good, neurons in the gut seem to be activated and send impulses to the IN1 neurons in the brain. We think that’s why the IN1 neurons are persistently active while the fly is eating. It’s almost like the gut is telling the brain, ‘This is good. Keep on eating.’”
Recent research from other labs appears to show that these gut-brain neurons also exist in mice, Yapici explains. “This is encouraging to me because it seems similar mechanisms exist in both drosophila and mice, which makes the fly model more promising in terms of using it to understand the neural circuits that regulate food intake in the brain,” she says.
“The duration of food intake may be regulated by information coming from the gut. It’s like a positive feedback loop . It’s almost like the gut is telling the brain, ‘This is good. Keep on eating.’”
Yapici and her lab are planning to use the fly model to identify specific genes of interest, and then to take those findings and apply them to more complicated mouse models. “We’ll be going back and forth between the two models, and learning from both at the same time,” she says.
Imaging Deep Regions of the Brain
To peer into the deep regions of the mouse brain, Yapici has an ongoing collaboration with Chris Xu, Applied and Engineering Physics. Xu is the lead principle investigator (PI) and Yapici is a co-PI for the Cornell Neurotechnology Hub, which is dedicated to developing new brain-imaging technologies and making them known to the neuroscience community. Yapici and Xu worked together to develop a method to image deep regions of the living fly brain without surgery. Recently they extended that work further, seeking to create new methods to image the mouse brain stem.
“We are trying to image really deep regions in the brain,” Yapici says. “These regions are very important for taste processing and also probably for communicating with the gut. In addition, they contain other neural circuits that regulate physiological functions, like sleep and motor behaviors. No one can access them in behaving animals because of the technical difficulties of imaging them, but if we can develop this new imaging method using three-photon microscopy, there will be a lot of applications for its use. I’m very excited about that.”
What Is the Volume of One Fly Gulp?
Although she is not a trained engineer, Yapici is no stranger to inventing new tools to address scientific questions in the lab. Some years ago, she developed an ingenious one, called Expresso, to measure food intake for individual flies. Expresso is made up of many tiny glass capillaries that contain an exact measure of liquid food and a sensor that can detect the meniscus in the glass capillaries. The researchers put one fly in a chamber with one capillary to feed from.
“We can determine the volume of each gulp a fly takes,” Yapici says. “At the same time, we can track the flies. So, we know how much a fly eats and then what they do before and after they eat. Do they hang out in a corner? Do they stay close to the food? Do they forage for other food? It’s a very quantitative way of measuring fly feeding and foraging.”
A Passion for Understanding the Brain
In college, Yapici considered studying engineering but was always fascinated more by biology. “I even almost became a neurosurgeon,” she says. “But my passion was for understanding the brain rather than curing it. The research I do is basic science, but I like working on a question that has some kind of applied goal in the future. I don’t think I’m going to develop a therapy for an eating disorder, but I might actually identify a mechanism that can be used by someone else to develop a therapy. That’s the way science is. It’s a group effort. You need a lot of complementary scientific knowledge and expertise to reach a final goal.”