03/31/2008

Graduate student Alana Lynes from the Department of Biology and Biochemistry was awarded this year's Teaching Excellence Award for Teaching Assistants. Ms. Lynes received the award in recognition of her outstanding work as instructor in Genetics Laboratory (BIOL 3201). Ms. Lynes studies towards a master degree in ecology under the guidance of Dr. Steven C. Pennings. Her topic is "Centrifugal organization of salt marsh plant communities." Congratulations, Alana!

03/27/2008

By far, the most successful and evolutionarily diverse animals are the beetles (400,000 described species), which can luminesce, spit highly corrosive liquids, and visually, behaviorally, and chemically mimic bees, wasps, and ants. This embarrassment of taxonomic riches has prompted J. B. S. Haldane to state: If one could conclude as to the nature of the Creator from a study of his Creation, it would appear that God has an inordinate fondness for beetles. Many beetle species, such as boll weevils, corn rootworms, potato beetles and longhorn beetles, are associated with billions of dollars of agricultural losses.

The red flour beetle, Tribolium castaneum, a widespread pest for dried commodities such as corn, maize, rice, and flour, and a model organism in population genetics and developmental biology has become the first coleopteran to have its genome sequenced. The sequencing, annotation and analysis of the 200 million nucleotides and 16,000 genes were conducted by an international consortium consisting of 64 research groups from 14 countries and reported in the journal Nature. Drs. Dan Graur and Giddy Landan and graduate student Eran Elhaik from the Department of Biology and Biochemistry at the University of Houston took part in the compositional analyses of this genome.

Tribolium beetles thrive in extremely arid environments  they mostly survive on metabolic water  and have an extremely varied and cosmopolitan palate. This independence of water makes Tribolium a prime-candidate as a research organism during the long-term space flight, such as the one planned for Mars.

12/18/2007

Dr. Xiaolian Gao won the 2007 American Chemistry Society Southwest
Region award. Dr. Gao received the award for her outstanding research in
parallel chemistry synthesis. The ceremony took place at the ACS
Southwest Regional Meeting in Lubbock.

Dr. Gaos lab conducts interdisciplinary research covering important
areas in chemistry and biology, including single-cell molecule DNA
sequencing, bioinformatics of nucleic acids and proteins, and parallel
synthesis and digital photochemistry of bio and organic molecules.

Dr. Gao received her undergraduate degree from Beijing Institute of
Chemical Engineering and a Ph.D. from Rutgers University. After
post-doctorate work at Columbia University, she became a research
scientist with Glaxo Inc. before joining UH in 1992.

11/27/2007

Seven Universities to offer a Graduate Course in Functional Ecology

In Spring 2008 the Department of Biology and Biochemistry will offer a unique Distributed Graduate Seminar, taught at seven universities using video and web-based collaborative tools.

The diversity of life presents a challenge to ecologists because there are too many species to study each individually. One possible solution to this problem is to use traits (e.g., height, seed size, photosynthetic rate) to predict how species will affect and respond to the environment. Seminar students will combine datasets of plant traits with datasets of species abundance across gradients or in environmental change experiments to test the hypothesis that traits can explain the patterns in these datasets.

The seminar will also teach students new tools and expose them to a new culture of collaborative research. As ecologists are moving from single-investigator to more collaborative, multi-investigator approaches, they need to learn the culture that promotes success in large collaborations. At the same time, there is a growing recognition of the need to better document and preserve existing datasets for the benefit of the ecological community. Students will learn both the culture and the software tools required to accomplish these goals.

Distributed Graduate Seminars are partially funded by the National Center for Ecological Analysis and Synthesis (NCEAS), which is located in Santa Barbara, California. This is the second distributed seminar officially funded by NCEAS (a few experimental ones were run on an ad-hoc basis). The seminars include a meeting at NCEAS for selected students from each participating university where the students work on a cross-institutional synthesis project. It is anticipated that scientific publications will result from the seminar.

Graduate students who are not ecologists but who have (or are interested in learning) collaborative, dataset management or analytical skills are welcome to take the seminar. Interested students should contact Dr. Steven Pennings at the Department of Biology and Biochemistry.

Seminar leaders and participating universities are: David Ackerly, University of California, Berkeley; Dan Childers and Tiffany Troxler, Florida International University; Elsa E. Cleland, National Center for Ecological Analysis and Synthesis; Scott L. Collins, University of New Mexico; Shahid Naeem and Dan Bunker, Columbia University; Steven Pennings, University of Houston; Katherine N. Suding, University of California, Irvine.

11/16/2007

What do you do when a naturally occurring hormone in your body turns against you? What do you do when that same hormone  melatonin  is a popular supplement you take to help you sleep? Some intriguing answers were provided by Professors Gregory Cahill and Gregg Roman and their graduate students Oliver Rawashdeh and Nancy Hernandez de Borsetti from the Department of Biology and Biochemistry at the University of Houston.

Frequently called the hormone of darkness, melatonin is a hormone the body produces that may regulate sleep patterns. In almost all organisms tested, the natural levels of this hormone are high during the night and low during the day. Melatonin is also a very powerful antioxidant.
Unlike vitamin C or glutathione, which are only active in aqueous
(watery) phase and vitamin E, which is only active in lipid (oily) phase, melatonin is effective in both aqueous and lipid phases. Thus, many people take melatonin supplements to fight jetlag, balance out seasonal affective disorder, and regulate dementia.

Melatonin, however, turned out to have a dark side after dark. The University of Houston used a model organism, the zebrafish (Danio rerio), and found that melatonin directly inhibits memory formation at night. The study was initially concerned with the mechanism by which the biological clock controls the formation of new memories. The researchers found the zebrafish capable of learning very well during the day, but a very slow learner at night. The experiments were performed using zebrafish for several reasons. Theyre small and breed in large numbers (thereby being inexpensive to use), and they are diurnal, having the same activity rhythms as people. Zebrafish are most active during the day and less active at night, whereas many other vertebrate model systems, such as rodents, are nocturnal. Thus if one is interested in how the biological clock regulates cognitive function in humans, one should use a model system that reacts to the clock the same way people do.

More than two years worth of work, including the discovery that the ability to learn and remember was controlled by an endogenous (or
internal) clock originating within the zebrafish, led Cahill and his colleagues to hypothesize that melatonin may be responsible for poor learning and memory formation during the night. In order to test whether melatonin was involved in inhibiting nighttime learning and memory formation, they treated the zebrafish during the day with melatonin.
Interestingly, melatonin failed to affect learning, but dramatically inhibited the formation of new memories.

The next step was to inhibit melatonin signaling during the night with a melatonin receptor antagonist and test for effects on memory formation.
According to Dr. Roman, The results were, excuse the expression, like night and day. We saw dramatic improvements in nighttime memory formation by inhibiting melatonin signaling, indicating that the reason the zebrafish did not form memories at night was because of the melatonin hormone.

Next, with the pineal gland being the primary source of melatonin in fish and in people, Graduate student Oliver Rawashdeh removed the gland from the fish and found they could now form memories during the night.
Removing this melatonin-producing gland allowed the researchers to alleviate the hormones negative side effects, further demonstrating that melatonin inhibits the formation of new memories during the night.

With these findings, the University of Houston researchers hope to have a handle on separating the beneficial effects of melatonin (the antioxidant properties) from its negative effects. The benefits include the slowing down of some forms of neurodegeneration, such as in Parkinsons and Alzheimers, and stopping DNA damage, which may prevent certain cancers. And, since the positive antioxidant effects are direct and independent of receptor signaling, there is hope that by removing the melatonin receptor signaling mechanism, one may be able to combat the negative effects of melatonin on cognitive function without affecting the benefits.

Additionally, the University of Houston scientists hope that by inhibiting melatonin signaling with receptor antagonists may help many people who need to perform nighttime cognitive tasks. Among the people that may benefit from this study are students studying for finals, airplane pilots, ER physicians, and nightshift workers.

The value of melatonin as a supplement is largely due to its antioxidant properties, Roman said. The use of melatonin receptor antagonists will not affect this attribute, but may alleviate an important side effect on nighttime cognitive function.

The article was published in the journal Science on November 16, 2007, and is entitled Melatonin Suppresses Nighttime Memory Formation in Zebrafish."

11/12/2007

Microorganisms are unavoidable in spacecrafts and their presence has, at times, been a source of problems. Astronauts spend months in the same quarters, breathe recycled air and drink recycled water; conditions that create a bacterial breeding ground. Additionally, the space environment has been shown to suppress the human immune system, making the body more susceptible to infection. Further, weightlessness and higher levels of radiation may increase the mutation rate in bacteria. This could result in the emergence of some organisms more resistant to antibiotics or in the change of normally harmless organisms into pathogenic life forms.

Because of unidentified effects of space on bacteria and the immune system, we do not know which organisms will cause problems. A group of researchers led by Drs. George E. Fox and Richard C. Wilson from the Department of Biology and Biochemistry at the University of Houston and Maia Larios-Sanz, then at the University of Houston and currently at the University of St. Thomas, have developed a technique to determine the approximate identity of organisms in space.

Their approach is phylogenetic, i.e., the approximate identity of a bacterium is based on the similarity of its DNA to known bacteria. Organisms whose DNA sequences are closely matched are more closely related than organisms whose DNA sequences are less similar. Fox, Willson, Larios-Sanz and their collaborators have developed a method to identify the DNA sequences that are diagnostic of small groups of bacteria.

Current detection systems mandate that one tests for an exact organism. If a problem organism is similar but not identical to the organism one is testing for, the test will show up negative. However, with the system developed by the University of Houston researchers, astronauts would be able to pinpoint an organisms rough taxonomic affiliation and significantly narrow down the possibilities of its identity. Once the device identifies the problem organism, scientists can predict the bacterial source, like a faulty air filter or a water purifier, and fix the defective instrument for future missions.

Because of limited laboratory space and chemical availability in spacecrafts, the University of Houston researchers are designing an easy-to-use monitoring method. Astronauts would filter the air or water, or swab a surface, to obtain the bacterial sample, and then they would test the sample for high levels of certain organisms that would indicate contamination. The tool will provide an early warning that the air or water purification system might not be working properly. The routine monitoring system and the bacterial identification device will help astronauts stay healthy during their time in space.

Larios-Sanz M, Kourentzi KD, Warmflash D, Jones J, Pierson DL, Willson RC, and Fox GE. 2007.16S rRNA beacons for bacterial monitoring during human space missions. Aviation, Space and Environmental Medicine 78:A43A47.

02/05/2007

Put a fruit fly on a near-starvation diet, and it is likely to live much longer than its well-fed relatives. But if it smells food, some of the life-stretching effects of the diet disappear. In a recent report in the journal Science, Dr. Gregg Roman from the Department of Biology and Biochemistry at the University of Houston and colleagues from Baylor College of Medicine and New Mexico State University report on a link between smell and life span in Drosophila. The scientists placed fruit flies on an ascetic diet known as calorie restriction, which slashes food intake and can extend an animal's life by up to 50%. The researchers then planted enticing (at least to a Drosophila) yeast paste in a screened-off end of the insects' home tubes; the flies could smell and see the goodies but not eat them. Although the calorie-restricted flies lived longer than normal, they died sooner than similarly hungry insects not exposed to the yeast scent. The smell had no impact on survival in well-fed Drosophila.

Further support that the sense of smell affects life span came when the researchers measured survival in flies harboring a mutant form of the protein Or83b. This molecule helps direct odor receptors into position in the fly's olfactory organs on the antennae. A faulty Or83b dulls the sense of smell. Interestingly, the inability to smell food stretches longevity by more than to 50%. Like many long-lived organisms, flies with mutant Or83b showed increased resistance to starvation. Restoring functional Or83b by genetic engineering restored fly longevity to normal. This study, thus, establishes that some component of the response to caloric restriction is olfactory.

"Not only can they not have their cake -- they can't smell their cake" without shortening their lifespans, said Wayne Van Voorhees, a faculty member in the Molecular Biology Program at New Mexico State University and a member of the research collaboration.

"It's incredibly exciting that the group has been able to show a link between the olfactory system and life span," says molecular geneticist Stephen Helfand of Brown University. The work reveals that the brain has control over the life span.

11/10/2006

The Honeybee Genome Sequencing Consortium announced that it had finished sequencing the genome of Apis mellifera. The honeybee is the third insect to have its genome fully sequenced, preceded by the fruitfly, Drosophila melanogaster and the malaria mosquito, Anopheles gambiae. A flour beetle, an aphid and a wasp are next in line. The work was done by 150 scientists from about 20 countries over the past three years. Dr. Dan Graur and graduate student Eran Elhaik from the Department of Biology and Biochemistry at the University of Houston took part in the compositional analyses of this uniquely AT-rich genome.

The honeybee has 10,000 to 15,000 genes arrayed on 16 chromosomes, compared with humans' estimated 24,000 genes and 24 chromosomes. Comparisons with the fruitfly and mosquito genomes suggest that bees evolved more slowly than either of those other insects. Curiously, some bee genes -- notably the ones responsible for internal "clocks" and circadian rhythms -- are more similar to mammalian genes than dipteran genes.

Compared with other insects, honeybees have only one-third as many genes involved in recognizing and killing bacterial pathogens. This is a surprise for an organism that spends 95 percent of its life in a crowded, moist, and warm indoor environment hospitable to bacteria and parasites. This may be due to bees being extremely hygienic and practicing preventive medicine. For example, when a larva dies, it is removed from its cell in the honeycomb immediately and the carcass is flown a distance from the hive before it is discarded. Nurse bees secrete antimicrobial substances into the food they provide the larvae. Honey, the principal source of food over the winter, does not support microbial growth because of its high-sugar, low-water makeup. Overall, it appears that compared with other insects, a bee's genome is less concerned with protecting the individual and more concerned with protecting the larger organism -- the colony. Bees also have fewer genes encoding exoskeletal proteins. It is thought that this paucity may be due to the fact that beesspend their larval stage and much of their early adulthood inside the hive, protected from ultraviolet light and other stresses.

But what is lost in the immune system and the skin is gained in the bee equivalent of the nose. The bee genome contains 170 olfactory-receptor genes, of which 157 are in a gene family so far found only in honeybees. In comparison, fruitflies and mosquitoes have 62 and 79 genes, respectively. Smell seems to be of extreme importance in helping bees find flowers and communicate with one another, including with their queen, through pheromones. At the same time, honeybees have a paucity of taste receptors -- 10, compared with the fruitfly's 68 and the mosquito's 76.

But there is no genomic smoking gun that explains the species' most remarkable behavior - its eusociality. Nor can we yet identify the genes responsible for communication, most famously for the ritualized "dance" that is used to communicate food location among bees. There is no cluster of brain genes possessed only by bees.

03/07/2006

Scientists have long wondered why organisms bother with sexual reproduction. It makes a whole lot more sense to just have a bunch of individuals that can clone themselves. In the March 2 issue of the journal Nature, a team headed by Dr. Ricardo Azevedo from the Department of Biology and Biochemistry at the University of Houston proposed that sexual reproduction actually selects for conditions that favor its own maintenance - a case of evolution forging its own path.

One advantage of sex is that it can help rid the genome of harmful mutations. When, as a result of sexual reproduction, organisms shuffle their genes, harmful mutations can be brought together in the same genome, making them more susceptible to the cleansing action of natural selection. But for this to work, mutations must be more harmful when combined in the same genome than when separated - a phenomenon known as negative epistasis. If negative epistasis were true, it would provide a powerful explanation for why sex has managed to persist for so long despite its numerous costs. But the phenomenon has yet to be widely demonstrated in nature and scientists have yet to figure out how such a thing evolved in the first place.

An experiment run in an artificial gene network model shows that negative epistasis is a natural byproduct of sex itself. The researchers created digital organisms that reproduced through sex in the same manner as real organisms. And like a regular organism, the virtual ones developed a natural buffer to resist change by mutations. This ability, called "genetic robustness," is thought to be one of the main benefits of sex. By shuffling genes, sex allows a population to spread its mutations across many individuals within a group. The mutations become diluted and can be effectively dealt with by an individual's genetic repair system.

But the researchers found that the protection only works when the digital organisms were facing a few mutations at a time. When assaulted by many at once, their repair systems became overwhelmed and the organisms died. Dr. Azevedo thinks this happens in real life, too.

10/14/2005

Dr. George Fox was awarded the 2005 Faculty Research Award by The University of Houston Chapter of the Sigma Xi Scientific Research Society. Dr. Fox is best known for the formulation of the archaebacterial concept and the fundamental tripartite taxonomic division of life on Earth. Dr. Fox is fellow of the American Academy of Microbiology, the American Association for the Advancement of Science, and the American Institute of Medical and Biological Engineering. He won the University of Houston Research Award in 1997.

09/12/2005

Multiple hereditary exostoses (MHE) is an inherited disorder of bone growth. People who have MHE, grow exostoses, or bony bumps, on their bones, which can vary in size, location and number. The long bones (legs, arms, fingers, toes), as well as the pelvis and shoulder blades are the most commonly affected. At a ceremony on September 18, 2005 in New York, Dan Wells, Professor of Biology and Biochemistry, was awarded the MHE Coalition Humanitarian Scientific Award. Dr. Wells was selected from an outstanding pool of international scientists. Congratulations!

04/12/2005

Costa M. Colbert, Associate Professor of Biology and Biochemistry, is the 2005 recipient of the College of Natural Sciences and Mathematics John Butler teaching excellence award. This award recognizes one faculty member each year for their contribution to the teaching mission of the college. Dr. Colbert, who has been a member of the department since 1997, has taught Human Physiology, Anatomy and Physiology, Neuroscience, and a graduate course in Advanced Neurophysiology. Congratulations!

02/02/2005

In an article published in the January 2005 issue of the open-access journal PLoS Biology, Drs. Gregory M. Cahill and Maki Kaneko report on the creation of a zebrafish that glows in sync with the periodicity of its circadian clock. To the genome of the fish, Drs. Cahill and Kaneko added a recombinant gene called per3-luc. This gene produces luciferase, a protein responsible for the flash of fireflies in the mating season. Whenever per3-luc expression is turned on, the cells of the transgenic fish also produce luciferase, and the fish glow slightly in the dark. Dr. Cahill anticipates that these transgenic fish will be useful in examining the molecular machinery of the vertebrate circadian clock. For example, it may be possible to identify mutations affecting the circadian rhythm through the isolation of fish that "blink" irregularly. Since luminescence can be measured quickly and noninvasively, these transgenic animals are ideal candidates for high-throughput screening aimed at identifying components of the circadian clock. It is hoped that Dr. Cahill's luminescent fish will help make jetlag a thing of the past.

01/12/2005

"Everything should be made as simple as possible but no simpler," Albert Einstein once said. Nature seems to agree. Cells become specialized by following a certain predetermined lineage, but they take a developmental path that is simpler than that expected by chance alone. In the January 13, 2005 issue of the prestigious journal Nature (433: 152-156), Dr. Ricardo Azevedo and colleagues present a study in which the known cell lineages of three different nematodes and a sea squirt are compared with those generated by a computer simulation. The algorithm allowed Dr. Azevedo to contrast the developmental complexity in different organisms with the simplest systems having the least number of steps. The study showed that the specialization processes were significantly simpler than that predicted by chance, but still not as basic as they could be. These findings should help shed light on developmental processes that are currently at the forefront of biological research in evolutionary developmental biology.

10/08/2004

Not yet as popular as Pasteurization, Gaussian, Salmonella and Fahrenheit, the Eskinogram (see left) is gaining currency in professional circles. The Eskinogram is a useful heuristic for understanding the circadian timekeeping system. It has only three components input, clock mechanism, and output but encapsulates fundamental concepts in circadian timekeeping. The core clock mechanism is discrete, both anatomically and genetically; the input mechanism is also discrete, separate from the core timekeeping mechanism, and the same clock mechanism influences many "outputs," including sleep and wakefulness, hormone secretion, and activity rhythms. For students of circadian rhythms, the Eskinogram is the central dogma, and like molecular biology's central dogma, the core heuristic retains its essential truth despite many modifications to its schematic structure.

03/29/2004

Susan H. Hardin, an associate professor of biology and biochemistry at the University of Houston, has been chosen one of Houston's top women in technology. Hardin will be recognized with a group of her peers at a gala June 12 when she receives one of the Top Houston Women in Technology awards for 2004.

10/23/2003

Dr. Paul Hardin, Professor in the UH Department of Biology and Biochemistry, will receive the Aschoff-Honma Prize for 2003 at a ceremony to be held on September 8 in Sapporo, Japan. This international prize is given every other year to a young scientist who has made groundbreaking contributions in biological rhythms research. It is considered the top individual honor given to scientists working in biological rhythms research. Dr. Hardin will receive an award of ¥1,000,000 (approximately $10,000 US), and will give a special plenary lecture at the Sapporo Symposium on Biological Rhythms in Japan.