The osmotic controlled passage of polar water through fundamentally nonpolar biologic lipid bilayers (membranes) wasn't understood until the work of Peter Agre and Roderick MacKinnon on aquaporins resulting in the Nobel prize in Chemistry in 2003. We decided to examine conservation in aquaporins. A Google search provided us with both the PDB id (1h6i) of the human aquaporin A chain from RBCs, and a clearer understanding that the aquaprorins represent a related group of proteins present in multiple species. At http://www.rcsb.org/pdb/ we conducted an initial investigation of the structure of 1h6i. At consurf (http://consurf.tau.ac.il/) we were able to obtain the protein sequences for the best 20 matches in nearly FASTA form. After text editing we ran Clustalw and retrieved both rooted and unrooted trees. In the trees, it is easy to see the families of aquaporins (type 1, 2 etc; see tree.doc below).
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Actively learn about chimpanzee conservation. The way it works: you ask your own questions, we give you tools to find credible answers and then you share your results for future users of this website.
This problem space will allow you to actively learn about chimpanzee conservation. The way it works: you aks your own questions; we give you tools to find credible answers; and then you share your results for future users of this website.
Dogs are known for their acute sense of smell. Humans are not. Do dogs have a higher percentage of functional olfactory receptors as compared to humans and other primates? Students will be assigned to obtain the full length genetic sequence of five olfactory receptor (OR) genes from their assigned OR family. (See website below.) Students will determine if a functional orthologous gene is present in the human genome, in the genome of a great ape, and in the sequence of a monkey. The class will pool their data and analyze for the percentage of pseudogenes present in each group.
Brief Overview: Hypotheses 1) arsC evolved after araA/araB since a reducing environment existed pre-dating the necessity for the reductase activity encoded by arsC. 2) ArsA, arsB and arsC should be highly conserved given their ubiquity in all three domains. 3) Non-ATP dependent AraB should be structurally different from ATP-dependent AraB. 4) The phlyogenetic relationships between ara genes should reflect the 16S rRNA phylogenies.
This problem space is designed to allow exploration of the remarkable ability of some plants to undergo desiccation and revive with the addition of water. This ability is ancient, and modern day descendants of the earliest land plants, such as mosses, retain this ability. Vascular plants have lost desiccation tolerance in all tissues (with the exception of seeds, pollen and spores), but it has re-evolved in a few species. The problem space includes gene expression data for desiccation sensitive and tolerant plants. It also includes information on the evolutionary relationships of genes involved in desiccation tolerance.
Two sister species of monkey flower are pollinated by different pollinators; this difference is a major factor in their reproductive isolation. One species Mimulus cardinalis has small red flowers with high nectar levels and is pollinated by hummingbirds while the other species, Mimulus lewisii, has large pink flowers with low levels of nectar and is pollinated by bumblebees. Although the mechanism of species maintenance is clear, what is less clear is the process that led to the speciation in the first place. We have developed an Excel spreadsheet that models the interaction of the two pollinators with monkeyflowers that have varying color and nectar production phenotypes. Users can specify: * the starting color and nectar genotypes of the population * the color and nectar preferences of the birds * the color and nectar preferences of the bees * the relative visitation rates of the birds and bees The spreadsheet then runs a standard Hardy-Weinberg simulation for 20 generations under the specified conditions and plots the results. This model follows the frequencies of the alleles in two "gene pools": the alleles carried by the bees and the alleles carried by the birds. At each generation, each pool is calculated, used to produce offspring, and the resulting offspring are then pooled.
This problem space enables investigators to explore data from a published study by Markham et al on HIV evolution within individual patients. The study involved 15 injection drug users in Baltimore, Maryland (USA) who became infected with HIV between 1989 and 1992. Patients came in at approximately six-month intervals ("visits") to have blood samples taken. From these samples, the researchers extracted and sequenced multiple copies of proviral DNA. Patients' CD4 counts were also measured at each visit to assess their level of immune function. In this problem space, you will have access to the following materials: * background information on HIV/AIDS, * the original Markham et al. reference and other primary literature, * viral sequences from each visit of each patient, * patients' CD4 counts at each visit, * phylogenetic trees of the virus sequences from each patient, * a phylogenetic tree of each patient's starting consensus viral sequence, * a published activity using this data from the book Microbes Count!, * and additional materials prepared by other users of the problem space. You can use this data to explore a number of different questions. Here are a few general questions to get you started: * Does the virus evolve the same way in different patients? * Are there any specific mutations that cause rapid immune decline? * What types of natural selection might be influencing HIV evolution? * Is HIV being transmitted between patients after initial infection?
In this problem space, you will have access to the following materials: background information on HIV/AIDS, the original Markham et al. reference and other primary literature, viral sequences from each visit of each patient, patients' CD4 counts at each visit, phylogenetic trees of the virus sequences from each patient, a phylogenetic tree of each patient's starting consensus viral sequence, a published activity using this data from the book Microbes Count!, and additional materials prepared by other users of the problem space. You can use this data to explore a number of different questions. Here are a few general questions to get you started: Does the virus evolve the same way in different patients? Are there any specific mutations that cause rapid immune decline? What types of natural selection might be influencing HIV evolution? Is HIV being transmitted between patients after initial infection?
This exercise is intended to engage students to design, model, visualize and evaluate the theoretical three dimensional image of a protein whose structure has not yet been determined. The phylogenetic analysis in Biology Workbench of paralogs and orthologs to alphafetoprotein reveals more divergent sequences within active site domains of related proteins without biological activity and greater conservation of the alphafetoprotein active domain between different species.
Leptin is a hormone secreted by adipose cells. Are there structural differences in the leptin molecules in terrestrial mammals and aquatic mammals? Do the leptin molecules reflect the phylogenetic relations of marine mammals and terrestrial ones. How do leptin molecules compare between desert organisms (camel, dromedary, fat-tailed dunnart) and temperate organisms. Does the evolutionary conservation of a leptin molecule reflect functional regions of the hormone? If the mouse leptin is more similar to chickens than rabbits, what about human leptin?
We are contributing to the problem space for the lactase persistence case study presented in the mini-workshop by Waterman, Stanley, and Jenkins. We are also using this as an example case for modifications to the Case It software that will run microarray simulations using published data, and allow students to connect directly to online bioinformatics tools and databases. After reviewing the case scenario and research articles, students will run the microarray simulation and use the results to formulate questions regarding molecular evolution of lactase and related genes.
This highly detailed investigation into microbes was designed for a wide range of students, from AP biology to college seniors. The authors have provided detailed background material, lab notes, discussion questions and references.
Cellulases are enzymes that digest the common polysaccharide cellulose using one of several enzymatic strategies (EC 18.104.22.168). A variety of organisms, ranging from marine to terrestrial, aerobic to anaerobic, possess enzymes with this activity. Cellulases may prove to be of significant economic importance to the process of converting cellulose to ethanol, in other words, the burgeoning biofuel industry. We propose a multi-institutional effort to identify cellulolytic organisms by enrichment, create transposon mutants lacking cellulase activity (via screening of mutants), obtain DNA sequence from these mutants, and to compare the recovered cellulase-specific gene sequences to known cellulase genes. The 16S rRNA sequence from each cellulolytic isolate will also be obtained, and the phylogenetics of the organism and the cellulases will be examined and compared. Cellulase specific oligonucleotide primers can be designed to locate cellulase sequences from microbially diverse environments without cultivation and mutagenesis. Students can also search publically-available metagenomic data sets for cellulase sequences to explore cellulase diversity from geographically distinct environments. Such sequences will provide useful information regarding the diversity and phylogeny of cellulase-like genes from a variety of environments. Finally research on the regulation of cellulase can be investigated on the isolated strains. Different institutions will carry out these procedures from a variety of environments, such as marine sediments, estuaries, and agricultural soils. The strains, mutants, and sequences recovered will be a resource available to participating investigators and their students. A website will be maintained for easy access to data and current investigations. Students will also present their data at annual group meetings among the participating institutions.
Students will look at their chef salad and 1) classify species according to their own list of criteria 2) perhaps develop a phylogeny based on published morphological data 3) download sequences (ideally of 3-4 genes) and make a molecular phylogeny
This problem space can be used to explore concepts related to metabolism. It is based on an article by Causey et al. (2004), entitled "Engineering Escherichia coli for Efficient Conversion of Glucose to Pyruvate". Students can use the original data from the article and various tools to visualize metabolic pathways to explore questions about bioengineering.
Students will examine an important plant enzyme, Rubisco, and learn about its function and evolution in higher plants. The primary activity will be one or two lab periods to introduce students to resources. The overview will be will be a "prelab" using the write-up at the Protein Database, www.pdb.org,where extensive information about the function and structure of this enzyme is included. Students will be given a specific access protocol and ask to capture specific images to be mailed to the instructor prior to class meeting. In class student will access a list of RbcL sequences in Fasta format and insert them into Workbench. An alignment will be prepared by each student and mapped onto a structural map of spinach RbcL.
The Phylogenetic Tree Constructor (PTC) is an easy-to-use web-based interface that students can use to explore molecular phylogeny within a defined set of DNA or protein sequences.
This problem space introduces basic skills in protein structure exploration, utilizing prions -- relatively small proteins that display dramatically alternate conformations for similar primary structures. We will learn to search databases for protein structures, explore the Cn3D software, and propose questions that may be answered with these tools.
Prions are relatively small proteins that display dramatically alternate conformations for similar primary structures. Abnormal conformations appear to cause fatal neurological diseases in a wide variety of mammals. Researchers are discovering the mechanisms behind these conformational changes, including differences that may lead to species barriers (or lack thereof) among exposed animals. How do these conformations differ?
How do small sequence differences affect susceptibility to conformational change? This problem space introduces basic skills in protein structure exploration. We will learn to search databases for protein structures, explore the Cn3D software, and propose questions that may be answered with these tools.
Prions are infectious protein particles associated with various neurodegenerative diseases in humans and animals. This problem space introduces basic skills in protein structure and sequence exploration that can be used to analyze some unusual properties of prions, and develop testable hypotheses that can be explored through these tools. Students will be challenged to use a systems-biology approach to link structure, evolution and function of proteins.
A unique tool to enable students to discuss and research problems posed in the context of protein structure and function, using Trpcage, a 20 residue polypeptide that is one of the smallest model proteins synthesized to date:
This project provides a case study introducing students to patterns of relationships and evolution among economically important dinoflagellates, the causative agents of red tides. Using nucleotide sequences, students build a tree of relationships among dinoflagellate taxa. They use their tree (along with phylogenetic hypotheses derived from the literature) to explore the evolution of morphological and/or ecological characters in dinoflagellates. As broader applications, students learn to compare and evaluate hypotheses of evolutionary relationships. Additionally, because the case study focuses on dinoflagellates that have evolved toxicity, it can be used to further explore the biological and economic impacts of red tides.
This problem space provides resources for going beyond the discussions of whale evolution presented in biology textbooks to look at how different types of data can be used to resolve this set of phylogenetic puzzles and to explore other related questions. In addition to providing some background on this topic the problem space has: * rich data resources for examining evolutionary relationships * curricular materials focusing on tree reading and interpretation * some suggestions for ways to extend this problem space with related research projects
What! You haven't ever seen a Whippo? What about a Whammel? Well, how do you think that whales evolved? Which mammals do you think are their closest living relatives? Trying to make sense of whale evolution is a great place to engage in some evolutionary reasoning and look closely at the way scientists work through difficult historical problems. By the way, the term Whippo is used as a sort of shorthand for the hypothesis that whale and hippos represent sister groups—that is, they are each other's closest living relatives. This problem space provides a collection of resources for going beyond the discussions of whale evolution presented in biology textbooks to look at how different types of data can be used to resolve this set of phylogenetic puzzles and to explore other related questions.