Matching Items (8)

The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species

Description

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

Data Availability: All genomic and transcriptomic sequence files are available from the NIH-NCBI BioProject database (accession numbers PRJNA352725, PRJNA352726, and PRJNA281763). All genome assembly, transcriptome assembly, predicted protein, transcript, genome annotation, repeatmasker, phylogenetic trees, .vcf and GO enrichment files are available on Harvard Dataverse (doi:10.7910/DVN/EH2S9K).

Contributors

Agent

Created

Date Created
  • 2017-05-31

158757-Thumbnail Image.png

Bioinspired Interactions with Complex Granular and Aquatic Environments

Description

August Krogh, a 20th century Nobel Prize winner in Physiology and Medicine, once stated, "for such a large number of problems there will be some animal of choice, or a

August Krogh, a 20th century Nobel Prize winner in Physiology and Medicine, once stated, "for such a large number of problems there will be some animal of choice, or a few such animals, on which it can be most conveniently studied." What developed to be known as the Krogh Principle, has become the cornerstone of bioinspired robotics. This is the realization that solutions to various multifaceted engineering problems lie in nature. With the integration of biology, physics and engineering, the classical approach in solving engineering problems has transformed. Through such an integration, the presented research will address the following engineering solution: maneuverability on and through complex granular and aquatic environments. The basilisk lizard and the octopus are the key sources of inspiration for the anticipated solution. The basilisk lizard is a highly agile reptile with the ability to easily traverse on vast, alternating, unstructured, and complex terrains (i.e. sand, mud, water). This makes them a great medium for pursuing potential solutions for robotic locomotion on such terrains. The octopus, with a nearly soft, yet muscular hydrostat body and arms, is proficient in locomotion and its complex motor functions are vast. Their versatility, "infinite" degrees of freedom, and dexterity have made them an ideal candidate for inspiration in the fields such as soft robotics. Through conducting animal experiments on the basilisk lizard and octopus, insight can be obtained on the question: how does the animal interact with complex granular and aquatic environments so effectively? Following it through by conducting systematic robotic experiments, the capabilities and limitations of the animal can be understood. Integrating the hierarchical concepts observed and learnt through animal and robotic experiments, it can be used towards designing, modeling, and developing robotic systems that will assist humanity and society on a diversified set of applications: home service, health care, public safety, transportation, logistics, structural examinations, aquatic and extraterrestrial exploration, search-and-rescue, environmental monitoring, forestry, and agriculture, just to name a few. By learning and being inspired by nature, there exist the potential to go beyond nature for the greater good of society and humanity.

Contributors

Agent

Created

Date Created
  • 2020

158568-Thumbnail Image.png

Effects of Self-Guided Displays and Associated Interactive Elements on Visitor Knowledge, Attitudes, and Values

Description

Free-choice learning environments provide visitors with unique opportunities to observe and learn voluntarily and can serve as valuable educational opportunities. Incorporating interactive elements into displays have been shown to increase

Free-choice learning environments provide visitors with unique opportunities to observe and learn voluntarily and can serve as valuable educational opportunities. Incorporating interactive elements into displays have been shown to increase visitor dwell time and, ultimately, enhance the displays’ impacts on visitor knowledge and positive attitudes. This is especially important in free-choice learning environments where the visitor controls what display to visit and for how long. Visitors may not benefit from the display if they are not engaged with some attention-holding component. Interactive elements can greatly benefit a display’s potential to strengthen a visitor’s conservation attitudes and values of non-charismatic species that are traditionally less engaging due to their lack of activity or their appearance. This study examined the effect of a self-guided display with or without the incorporation of interactive elements on a visitors knowledge, attitude, and value of rattlesnakes. In Spring 2019, university biology students took surveys before (pre-survey) and after (post-survey) visiting a live animal rattlesnake display on campus. This was repeated in the Fall 2019 except that eight interactive elements were incorporated into the rattlesnakes displays. The pre and post-surveys were designed to evaluate the effect of the displays on student knowledge, attitudes, and values towards rattlesnakes. Paired t-tests revealed that visiting the displays increased student knowledge, attitude, and value of rattlesnakes, but that this effect was not enhanced by adding the interactive elements to the display. The results also showed that visiting the displays increased visitor dwell time, positively influenced one’s interest in revisiting the displays, and, overall provided visitors with enjoyment. These results provide further evidence that self-guided, live animal displays are impactful on increasing visitor knowledge, attitude, and value. However, the results also demonstrate that interactive elements do not necessarily enhance a display’s value, so further research should be conducted to determine key traits of effective interactive elements. This data and that from future related studies can have powerful conservation implications by informing on how displays can be optimized to achieve desired objectives.

Contributors

Agent

Created

Date Created
  • 2020

151260-Thumbnail Image.png

Social snakes?: non-random association patterns detected in a population of Arizona black rattlesnakes (Crotalus cerberus)

Description

Social structure affects many aspects of ecology including mating systems, dispersal, and movements. The quality and pattern of associations among individuals can define social structure, thus detailed behavioral observations are

Social structure affects many aspects of ecology including mating systems, dispersal, and movements. The quality and pattern of associations among individuals can define social structure, thus detailed behavioral observations are vital to understanding species social structure and many other aspects of their ecology. In squamate reptiles (lizards and snakes), detailed observations of associations among individuals have been primarily limited to several lineages of lizards and have revealed a variety of social structures, including polygynous family group-living and monogamous pair-living. Here I describe the social structure of two communities within a population of Arizona black rattlesnakes (Crotalus cerberus) using association indices and social network analysis. I used remote timelapse cameras to semi-continuously sample rattlesnake behavior at communal basking sites during early April through mid-May in 2011 and 2012. I calculated an association index for each dyad (proportion of time they spent together) and used these indices to construct a weighted, undirected social network for each community. I found that individual C. cerberus vary in their tendency to form associations and are selective about with whom they associate. Some individuals preferred to be alone or in small groups while others preferred to be in large groups. Overall, rattlesnakes exhibited non-random association patterns, and this result was mainly driven by association selection of adults. Adults had greater association strengths and were more likely to have limited and selected associates. I identified eight subgroups within the two communities (five in one, three in the other), all of which contained adults and juveniles. My study is the first to show selected associations among individual snakes, but to my knowledge it is also the first to use association indices and social network analysis to examine association patterns among snakes. When these methods are applied to other snake species that aggregate, I anticipate the `discovery' of similar social structures.

Contributors

Agent

Created

Date Created
  • 2012

157626-Thumbnail Image.png

Variations in Menopause Etiology Affect Cognitive Outcomes: How Age, Menopause Type, and Exogenous Ovarian Hormone Exposures Across the Lifespan Impact the Trajectory of Brain Aging

Description

Reproductive hormones are recognized for their diverse functions beyond reproduction itself, including a vital role in brain organization, structure, and function throughout the lifespan. From puberty to reproductive senescence, the

Reproductive hormones are recognized for their diverse functions beyond reproduction itself, including a vital role in brain organization, structure, and function throughout the lifespan. From puberty to reproductive senescence, the female is characterized by inherent responsiveness to hormonal cyclicity. For most women, a natural transition to menopause occurs in midlife, wherein the endogenous hormonal milieu undergoes significant changes and marks the end of the reproductive life stage. Although most women experience natural menopause, many women will undergo gynecological surgery during their lifetime, which can lead to an abrupt surgical menopause. It is of critical importance to better understand how endogenous and exogenous reproductive hormone exposures across the lifespan influence cognitive and brain aging, as women are at a greater risk for developing a variety of diseases after menopause, including dementia. Using rodent models, this dissertation explores how the etiology of reproductive senescence, that is, whether it is transitional or surgical, influences the female phenotype to result in divergent cognitive outcomes dependent upon a variety of factors, with an emphasis on age at the time of intervention playing a key role in brain outcomes. Furthermore, the impact of exogenous hormone therapy on cognition is evaluated in the context of surgical menopause. A novel rat model of hysterectomy is also presented, with results demonstrating for the first time that the nonpregnant uterus, which is typically considered to be a quiescent organ, may play a unique, direct role in modulating cognitive outcomes. Neurobiological mechanisms associated with reproductive hormones and aging are assessed to better recognize neural correlates underlying the observed behavior changes. The overarching goal of this dissertation was to elucidate novel factors contributing to cognitive aging outcomes in females. Collectively, the data presented herein indicate that the age at the onset of reproductive senescence has significant implications for learning and memory outcomes, and that variations in gynecological surgery can have unique, long-lasting effects on the brain and cognition. Translationally, this series of experiments moves the field forward toward the goal of improving the health and quality of life for women throughout the lifespan.

Contributors

Agent

Created

Date Created
  • 2019

153959-Thumbnail Image.png

Chameleon color change communicates conquest and capitulation

Description

Sexual and social signals have long been thought to play an important role in speciation and diversity; hence, investigations of intraspecific communication may lead to important insights regarding key processes

Sexual and social signals have long been thought to play an important role in speciation and diversity; hence, investigations of intraspecific communication may lead to important insights regarding key processes of evolution. Though we have learned much about the control, function, and evolution of animal communication by studying several very common signal types, investigating rare classes of signals may provide new information about how and why animals communicate. My dissertation research focused on rapid physiological color change, a rare signal-type used by relatively few taxa. To answer longstanding questions about this rare class of signals, I employed novel methods to measure rapid color change signals of male veiled chameleons Chamaeleo calyptratus in real-time as seen by the intended conspecific receivers, as well as the associated behaviors of signalers and receivers. In the context of agonistic male-male interactions, I found that the brightness achieved by individual males and the speed of color change were the best predictors of aggression and fighting ability. Conversely, I found that rapid skin darkening serves as a signal of submission for male chameleons, reducing aggression from winners when displayed by losers. Additionally, my research revealed that the timing of maximum skin brightness and speed of brightening were the best predictors of maximum bite force and circulating testosterone levels, respectively. Together, these results indicated that different aspects of color change can communicate information about contest strategy, physiology, and performance ability. Lastly, when I experimentally manipulated the external appearance of chameleons, I found that "dishonestly" signaling individuals (i.e. those whose behavior did not match their manipulated color) received higher aggression from unpainted opponents. The increased aggression received by dishonest signalers suggests that social costs play an important role in maintaining the honesty of rapid color change signals in veiled chameleons. Though the color change abilities of chameleons have interested humans since the time of Aristotle, little was previously known about the signal content of such changes. Documenting the behavioral contexts and information content of these signals has provided an important first step in understanding the current function, underlying control mechanisms, and evolutionary origins of this rare signal type.

Contributors

Agent

Created

Date Created
  • 2015

157036-Thumbnail Image.png

Water as a physiological currency: hydration state impacts immune function, metabolic substrates, and reproductive investment

Description

Environmental changes are occurring at an unprecedented rate, and these changes will undoubtedly lead to alterations in resource availability for many organisms. To effectively predict the implications of such changes,

Environmental changes are occurring at an unprecedented rate, and these changes will undoubtedly lead to alterations in resource availability for many organisms. To effectively predict the implications of such changes, it is critical to better understand how organisms have adapted to coping with seasonally limited resources. The vast majority of previous work has focused on energy balance as the driver of changes in organismal physiology. While energy is clearly a vital currency, other resources can also be limited and impact physiological functions. Water is essential for life as it is the main constituent of cells, tissues, and organs. Yet, water has received little consideration for its role as a currency that impacts physiological functions. Given the importance of water to most major physiological systems, I investigated how water limitations interact with immune function, metabolism, and reproductive investment, an almost entirely unexplored area. Using multiple species and life stages, I demonstrated that dehydrated animals typically have enhanced innate immunity, regardless of whether the dehydration is a result of seasonal water constraints, water deprivation in the lab, or high physiological demand for water. My work contributed greatly to the understanding of immune function dynamics and lays a foundation for the study of hydration immunology as a component of the burgeoning field of ecoimmunology. While a large portion of my dissertation focused on the interaction between water balance and immune function, there are many other physiological processes that may be impacted by water restrictions. Accordingly, I recently expanded the understanding of how reproductive females can alter metabolic substrates to reallocate internal water during times of water scarcity, an important development in our knowledge of reproductive investments. Overall, by thoroughly evaluating implications and responses to water limitations, my dissertation, when combined previous acquired knowledge on food limitation, will enable scientists to better predict the impacts of future climate change, where, in many regions, rainfall events are forecasted to be less reliable, resulting in more frequent drought.

Contributors

Agent

Created

Date Created
  • 2019

149679-Thumbnail Image.png

Intra-offspring tradeoffs of python egg-brooding behavior

Description

Though it is a widespread adaptation in humans and many other animals, parental care comes in a variety of forms and its subtle physiological costs, benefits, and tradeoffs related to

Though it is a widespread adaptation in humans and many other animals, parental care comes in a variety of forms and its subtle physiological costs, benefits, and tradeoffs related to offspring are often unknown. Thus, I studied the hydric, respiratory, thermal, and fitness dynamics of maternal egg-brooding behavior in Children's pythons (Antaresia childreni). I demonstrated that tight coiling detrimentally creates a hypoxic developmental environment that is alleviated by periodic postural adjustments. Alternatively, maternal postural adjustments detrimentally elevate rates of egg water loss relative to tight coiling. Despite ventilating postural adjustments, the developmental environment becomes increasingly hypoxic near the end of incubation, which reduces embryonic metabolism. I further demonstrated that brooding-induced hypoxia detrimentally affects offspring size, performance, locomotion, and behavior. Thus, parental care in A. childreni comes at a cost to offspring due to intra-offspring tradeoffs (i.e., those that reflect competing offspring needs, such as water balance and respiration). Next, I showed that, despite being unable to intrinsically produce body heat, A. childreni adjust egg-brooding behavior in response to shifts in nest temperature, which enhances egg temperature (e.g., reduced tight coiling during nest warming facilitated beneficial heat transfer to eggs). Last, I demonstrated that A. childreni adaptively adjust their egg-brooding behaviors due to an interaction between nest temperature and humidity. Specifically, females' behavioral response to nest warming was eliminated during low nest humidity. In combination with other studies, these results show that female pythons sense environmental temperature and humidity and utilize this information at multiple time points (i.e., during gravidity [egg bearing], at oviposition [egg laying], and during egg brooding) to enhance the developmental environment of their offspring. This research demonstrates that maternal behaviors that are simple and subtle, yet easily quantifiable, can balance several critical developmental variables (i.e., thermoregulation, water balance, and respiration).

Contributors

Agent

Created

Date Created
  • 2011