Role of TRa in the hemoglobin transition during metamorphosis in Xenopus tropicalis
Metamorphosis and hemoglobin (HB) transition in Xenopus is triggered by thyroid hormone (TH), such as T3. At the climax of metamorphosis T3 reaches its maximum. After the climax of metamorphosis liver morphology changes and larval HB is replaced by new cells, adult HB, produced by adult stem cells. This change happens in all vertebrates. The change is HB is important due to changes of oxygen affinity in adult Xenopus. There are two gene loci in vertebrates for thyroid hormone receptors, TRa and TRb. TRa is expressed in larval red blood cells (RBC) and regulates gene expression. In the absence of TH, TRs repress TH response genes required for metamorphosis, regulating the timing of metamorphosis. Once TH is present TH response genes are transcribed. Our goal was to determine if TRa is required for HB transition. To test this, we used TRÎ± knock out (TRaKO) Xenopus and qPCR to determine gene expression of L5, a larval HB gene and A1, an adult HB gene at stages 54, 58, and 60/62 of metamorphosis. Results showed that TRaKOs had larval RBC death earlier and take longer for adult RBC to be produced to the level of wild type Xenopus. This showed that TRa is not required for TRa transition, but is involved. This could be due to TRÎ² partially compensating for KO of TRa. Future studies would look at development of adult stem cells which may involve TRb, thus showing both receptors involvement in HB switching.
Pyruvate carboxylase controls habituation learning
Animals are constantly bombarded with sensory stimuli and must update their behavior by integrating current sensory input with information stored from prior experiences. To filter irrelevant input and focus attention towards high priority stimuli, all animals exploit a fundamental form of learning, called habituation. Habituation is the progressive response decline to repeatedly experienced, yet insignificant stimuli and provides a behavioral measure of a neural circuit’s ability to balance excitation, inhibition, and plasticity. Habituation deficits are observed in schizophrenia, autism, and addiction, and contribute strongly to the patients’ overall dysfunction. Despite habituation’s behavioral characterization across species and clinical relevance, relatively little is know about the molecular-genetic pathways that regulate habituation.
To gain insight into these pathways we performed an unbiased, genome-wide screen for overtly healthy zebrafish mutants that exhibit reduced habituation of the acoustic startle response. This screen identified pyruvate carboxylase a (pcxa) as a novel, critical regulator of habituation, since mutations in pcxa reduce startle habituation. Pyruvate carboxylase is a mitochondrial enzyme that stimulates the TCA cycle and production of its many biological derivatives by various cell types. Here, we describe results from experiments that aim to determine the critical timing and derivatives of pcxa activity that are required for habituation learning.
MeCP2 promotes GABA circuit development to regulate sensorimotor gating
Dysfunction of the transcriptional regulator methyl-CpG-binding protein 2 (mecp2) is associated with neurological disorders, including Rett Syndrome and schizophrenia. These disorders stem from imbalanced neural circuit activity due to neurodevelopmental defects. Our research shows that mecp2 mutant zebrafish show impaired sensorimotor gating, which we observed through a reduced prepulse inhibition (PPI) of the acoustic startle response. We also found that mecp2 mutant zebrafish develop fewer connections within a GABAergic inhibitory microcircuit that regulates startle PPI. The PPI deficit was improved by chronic, pharmacological enhancement of GABAergic inhibition, and we found that stimulating insulin-like growth factor 1 (IGF1) signaling during development reverses the mutants’ GABA connectivity and PPI deficits. Together, these findings suggest that MeCP2-IGF1 signaling promotes the development of GABAergic microcircuits to control sensorimotor gating.
Integrating a neurally inspired model and applied behavioral analysis to teach joint attention skills to children with autism
Joint Attention (JA) is the ability to coordinate one’s attention with another. Children who have Autism Spectrum Disorder (ASD) tend to have abnormal JA and facial processing compared to typically developing (TD) children. In this work, we will use a neurally grounded model of JA to refine and validate interventions for children with ASD. JA is a particularly good target for intervention because it is a pivotal response class skill, which means that if improved, it will improve other cognitive and behavioral abilities such as language skills. According to the neural model, JA is composed of four steps: 1) Perceiving another as a social partner, which is associated with activation in dorsal medial prefrontal cortex 2) Detecting a shift in the partner’s attention, associated with posterior superior temporal sulcus. 3) Shifting his/her own attention to align with their social partner associated with the dorsolateral frontoparietal network and 4) Continuously monitoring his/her social partner’s attention while ajusting his/her own attention to maintain the interaction, associated with prefrontal cortex and posterior superior temporal sulcus. These distinct areas of neural activation suggest that JA steps can be targeted and taught independently. We will use Applied Behavioral Analysis (ABA) to teach JA skills while tracking the progress of each child. Discrete trial training will be used to determine which of the four JA steps is most difficult for children with ASD so that it can be targeted in an intervention. In addition, we will monitor how language skills change in response to the JA training protocol.
The Role of Peroxidases in Plant Biology During Spaceflight
A thorough understanding of how spaceflight affects plant biology is critical to the advancement of space travel. Botany and horticulture systems will be an essential part of life support for extended space missions. The effects of microgravity, oxygen stress, cold stress, and ionizing radiation are obstacles that stand in the way of maintaining plant life. This research uses genomic data obtained from International Space Station Mission SpaceX CRS-4 to target the genes of arabidopsis manipulated by spaceflight. The peroxidase family of enzymes are genes of interest that were down-regulated during spaceflight and previous literature has shown manipulation. Peroxidase function in plant biology has been shown to play a role in response to abiotic stress as well as cell wall modeling. 4 peroxidase genes (PRX22, PRX32, PRX39 and RCI3) are identified and will be genotyped for homozygous mutants. In-silica molecular biology provides the primer design and in-silica simulation of ligation will allow these gensto be cloned for knockout, over-expression and rescue. These transgenic seeds will be subject to experimentation that mimics components of spaceflight.
Nurr1 knockdown in substantia nigra proposed to result in cognitive deficits in Rattus norvegicus
Many Parkinson’s disease (PD) patients suffer from cognitive impairment. Reduced secretion of dopamine (DA) from substantia nigra (SN) to striatum results in motor deficits in PD patients, but little is known about its effects on cognition. Nurr1 is a nuclear receptor expressed in SN neurons and regulates DA expression. The role of Nurr1 in PD-related cognitive deficits has not yet been studied. We hypothesize that reduced levels of Nurr1 in the SN, leading to decreased DA in striatum, will result in cognitive deficits in Rattus norvegicus. Knockdown of Nurr1 in SN with an anti-Nurr1 ribozyme was unsuccessful. CRISPR/Cas9 will be used to knockout Nurr1 before performing cognitive and behavioral testing to help reveal the role of Nurr1 in the cognitive behavior of PD patients.
Fine mapping for domestication traits using recombinant chromosome nearly isogenic lines
There are many morphological differences between maize (Zea mays ssp. mays) and its evolutionary ancestor teosinte (Zea mays ssp. parviglumis). Some of these traits have already been characterized at the genetic level which has provided valuable insights into the domestication process but at this point differences in ear structure have not been fully explained. In past work the Doebley Lab used maize-teosinte hybrid recombinant inbred lines (RILs) to find various quantitative trait loci (QTL) for ear size. Of particular interest was a significant large effect QTL on chromosome 5 for ear diameter which was found using a maize-teosinte BC2S3 line. This QTL also co-localized to a second large effect QTL for kernel row number. Further work was done with a different set of maize teosinte BC6Â¬S6 lines and end results narrowed down that same QTL to a 2.654 Mbp region. Markers were used to find recombination points in the region of interest on the short arm of chromosome 5. With this information new recombinant chromosome nearly isogenic lines (RC-NILs) were created that were meant to be homozygous at every point except for the across the region. The RC-NILs were made with two separate lines, B11b and B46, that both showed presence of the QTL. Both phenotypic and genotypic data was collected for the RC-NILs and results showed a shadow peak for the QTL on chromosome 5. Additionally an unanticipated region on chromosome 7 appeared to be segregating for the kernels per rank trait as well as ear diameter and kernels per row. Next a portion of the RC-NILs that did not segregate on chromosome 7 will be used to determine the gene or transcription factor responsible for the large effect QTL on chromosome 5.
Analysis of endochondral ossification at the epiphyseal plate using CT scans
Many studies have identified similarities between skeletal growth and nutrition in humans and animals. However, current research has yet to establish a protocol to effectively analyze variability in subchondral primary and secondary bone mineral density, a critical measurement when analyzing the relationship between skeletal growth and diet. Previous studies have experimented with the capabilities of MIMICS software on the scale of clinical and micro computed tomography (micro-CT) scans to fill this analytical gap. Even with these advances in technological use, a fully tested method has yet to be developed to quantitatively analyze the variance of bone density as it forms along the epiphyseal plate. We plan to test the abilities of a previously created method to see how accurate it is at discerning between various dietary treatments based off the amount of primary and secondary bone present in regions of interest at the epiphyseal plate.
Confirming antibiotic induced bacterial knockout in leaf-cutter ant fungus gardens using genus-specific primers and qPCR
Leaf-cutter ants utilize a fungal cultivar as an external gut to break down plant polysaccharides into simpler monomers. A community of bacteria lives in consortium with this fungus, and the composition of this community is conserved between different ant colonies. These bacteria have several possible functions, such as nitrogen fixation and vitamin production, but their exact role remains uncertain. To gain insight into the possible role of this community, we conducted an experiment with the goal of knocking out particular groups of bacteria. We fed leaf-cutter ant colonies leaves infused with antibiotics and measured leaf intake and visually monitored garden health. While the ants incorporated fewer antibiotic-infused leaves than control leaves, we could not detect any visual differences between groups, suggesting that the bacterial community may not serve an essential function. We are now analyzing these samples using genus specific qPCR primers to confirm bacterial knockout within samples. The five genera targeted by these primers are heavily prevalent within the bacterial community of the fungus garden, and four of the five genera belong to the Enterobacteria family. The results of this qPCR analysis will be cross-referenced with previous observations taken on treatment groups to identify genera that may serve functional importance within the bacterial community that could not be detected based on our prior experimental setup. This genus-specific primer and qPCR methodology can also be used in future studies that aim to elucidate the role of bacteria in leaf-cutter ant fungus gardens.
Improving graft-versus-tumor effects of ex vivo activated NK cells through JAK/STAT and BCL2 inhibition
For many people who are resistant to standard chemotherapy regimens, allogeneic bone marrow transplantations (alloBMT) provide a valuable second line therapy that are used to replace a patientâ€™s immune system after high dose radiation or chemotherapy. Recently, infusion of ex vivo expanded Natural Killer (NK) cells after alloBMT has increased graft versus tumor (GVT) effects. However, we have also observed that highly activated NK cells can induce graft versus host disease (GVHD) after alloBMT. Studies have shown that NK cell activation can be controlled through Janus Activating Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) and B-cell lymphoma 2 (BCL2) signaling inhibition. Our lab has previously shown JAK/STAT inhibitor, Ruxolitinib, and BCL2 inhibitor, Venetoclax, synergistically target these overlapping signal cascades. This study will determine the impact of Ruxolitinib and Venetoclax on NK cell activation as a means of enhancing GVT after alloBMT. We intend, for the first time, to pretreat NK cells with Ruxolitinib and Venetoclax, optimize their activation, and test the pretreated NK cells in an in vivo model of alloBMT. Success of this proposal will be a step forward in enhancing immunotherapeutic treatment options for people with chemo-resistant cancers.
Effect of Cultivation on "Illite-like" Material in Relation to Potassium and Ammonium Dynamics
Illite, or “illite-like” material, – a collective term for 2:1 phyllosilicate clay minerals identified by a 10Ã… interlayer spacing – has been established to function as a K reservoir in soils. What is not known is how the relative amount of illite changes under different cultivation conditions and fertilization regimes and the effects it has on potassium and ammonium soil dynamics. This study seeks to explore these relationships by tracking clay mineralogical changes via modern X-ray diffraction techniques in response to mono-ionic saturation treatments.
Prion Domain in the Luminidependens Gene of Solanum tuberosum
Abstract: Prions are an interesting class of proteins that can take on unique conformations within an organism. In animals, these proteins are associated with degenerative neural diseases such as chronic wasting disease in deer. However, in plants, these proteins are much less devastating and have actually been associated with epigenetic plant memory during development in response to environmental cues (ex. Vernalization). Prion domains can be found in a number of genes, but is best characterized in the Luminidependens gene of the autonomous flowering pathway. To better understand how prions function within plants, it is first necessary to determine which species include prion domains. So far, these proteins have been described in Arabidopsis thaliana and a distant relative of tomato (Solanum lycopersicum). In this project, I have extracted the Luminidependens gene from potato (Solanum tuberosum) and described a prion domain.
Forests, historic competition, and the genetic structure of American black bear (Ursus americanus) populations in the southern Rocky Mountains
Large and wide-ranging carnivores typically display much genetic connectivity across their distributional range. American black bears (Ursus americanus) are vagile carnivores and habitat generalists. However, they are typically associated with forested habitats, consequently, habitat fragmentation and interspecific competition with brown bears has the potential to alter connectivity between black bear subpopulations and resultant genetic structure. Our analysis of genetic structure of black bears in the southern Rocky Mountains of Wyoming and Colorado (n = 296) revealed two discrete populations. Bears in northern Wyoming were distinct (FST = 0.217) from bears in southern Wyoming and in Colorado, despite higher densities of anthropogenic development within Colorado. Structure appeared driven by the amount of contiguous forest, rather than the simple distance between populations. We hypothesize that forested habitat mediated historic competitive interactions with brown bears and governed genetic connectivity. Our work suggests that the interaction of habitat and interspecific competition could be an important force in structuring the populations of highly vagile carnivores, possibly overwhelming the effects of anthropogenic development.
Integrating Ecology and Evolution to Study Hypothetical Dynamics of Algal Blooms and Mullers Ratchet Using Evolvix
Algal blooms reoccur over various temporal and spatial scales. They occasionally carry toxins that can be very disruptive to their ecosystem. Therefore, algal blooms have been the subject of considerable research. Many algal blooms are governed by the availability of nutrients or other limiting growth factors. However, other limitations could exist. For example, algae are primary producers that can be subject to predation. This trophic relationship could result in typical predator-prey dynamics, where predation pressure keeps algal populations at levels below those supported by available nutrients. If a prey algae develops the ability to produce a toxin, that deters predators and thereby increases survival rates, then such algae might form blooms if supported by their environment. It is also clear that such algae will experience mutations that occasionally could knock-out DNA repair mechanisms, which could increase the probability of acquiring the necessary mutations for producing a predator deterring toxin.
Here we investigate the hypothetical scenario above. In our simulation model, we implement a sequence of steps that allows an asexual healthy algal population to escape predation pressure and form a bloom with the help of mutators. However, the bloom is then driven to extinction by the very cause of its initial success. The necessary steps are: (1) Loss of enough important DNA repair genes by random mutation. (2) The resulting increased mutation rate makes it more likely to acquire a mutation that alters algal metabolism to produce a toxin. (3) As a result, predators avoid toxic algae and provide them with a substantial growth advantage that can mask other deleterious mutational effects in the algal genome. (4) The continued lack of predation pressure caused by the toxin results in an algal bloom if sufficient nutrients are available and predation is strong enough on non-toxic algae. (5) The lack of recombination in these blooming mutators-algae inevitably causes a fast accumulation of slightly deleterious mutations as predicted by Mullers ratchet. (6) If such mutations accumulate fast enough they will eventually lead to the mutational meltdown of the toxic blooming algae, albeit without affecting the healthy algal population that remains under predation pressure. We simulate a corresponding model of algal blooms that integrates the ecological continuous time dynamics of a predator-prey system with the population genetics of a simplified Mullerâ€™s ratchet model using the Evolvix modeling language. Even if our simulated model might be hypothetical, the need to simulate ecological and population dynamics and evolutionary genetics in the same integrate model is more wide spread.
Effect of cell culture media and substrate stiffness on hMSC differentiation and growth factor secretion
Human mesenchymal stem cells (hMSCs) are clinically-relevant cell sources due to their multipotency and ability to secrete immune-modulating cytokines and growth factors (GFs). A novel way to modulate hMSC differentiation and GF secretion profiles is to alter the stiffness of the underlying cell-culture substrate. Here, we demonstrate the ability to alter hMSC adipogenic differentiation and vascular endothelial growth factor (VEGF) secretion via culture on polyethylene glycol (PEG) hydrogels of varying stiffness. We demonstrate that these changes in cell behavior are highly dependent on not only the underlying cell culture substrate, but also on the culture media in which the cells are grown.
Does the common symbiosis pathway play a role during the colonization of poplar by ectomycorrhizal fungi?
The symbiotic relationship between mycorrhizal fungi and the plants they colonize is one of the most important types of mutualistic associations that take place in our world. The two most ecologically important types of mycorrhizal associations are arbuscular mycorrhizal (AM) fungi and ectomycorrhizal (ECM) fungi. Extensive studies on AM fungal associations have provided a significant understanding of the molecular signaling pathway in the plant utilized by the fungus for colonization. However, little is known about how ECM colonize plants. To discover more about ECM colonization, we looked at if the gene CCaMK, which is required for AM symbiosis, is also required for ECM symbiosis. We also looked at if molecular signals like lipochitooligosaccharides (LCOs) enhance lateral root formation in a CCaMK-dependent manner. From these observations, we hypothesis that we will see a similar pathway in colonization and signaling by AM fungi and ECM fungi. To test this hyphothesis, we performed lateral root assays on wild-type poplar treated with non-sulfated (ns), sulfated LCOs (s), and fucsosylated (fuc) LCOs compared to a negative control. We calculated the lateral roots per centimeter of primary root for all treatments. We colonized wild-type and CCaMK-RNAi poplar lines with the ECM fungus Laccaria bicolor and measured Hartig net formation. From the data, we analyzed, we concluded that CCaMK is required for complete Hartig net formation and stimulation of lateral root formation induced by nsLCOs. These results indicate that CCaMK likely is an important gene in the symbiotic pathway between ECM fungi and the plants they colonize.
Gene Flow in the African Baobab inferred from parentage analysis
Adansonia is an iconic genus of trees native to mainland Africa, Madagascar, and Australia. This research investigates spatial patterns of genetic variation in the African baobab, Adansonia digitata, a species historically documented to be bat pollinated. However, in South Africa researchers suspect bat pollination is being supplemented in their absence by hawkmoths. Using one population in South Africa as a case study, I am quantifying patterns of contemporary pollen flow by paternity analysis from ten seeds of a single focal tree and each potential pollen donor within a 350meter radius. We are also testing if geographic distance corresponds with genetic distance by genotyping additional trees 2-3km from this focal tree. Parentage analysis and genetic differentiation will be analyzed from nine microsatellite markers. Using this info predictions can be made about distance of gene flow given the uncertain dominant pollinators in South Africa.
Unraveling the TCH2 interaactome
Plants exhibit many mechanical stresses that are present in everyday biological processes such as the impact of wind, touch and gravity. Calcium (Ca2+) signaling ion fluxes are one of the most important mechanisms when it comes to rapid, long-distance response signaling, including in response to these mechanical stimuli. Ca2+ binding proteins within the cell senses the Ca2+ signals. In the model plant Arabidopsis thaliana, there exist seven calmodulin (CAM) and fifty CAM-like (CML) genes, which encode potential calcium sensors (McCormack et al., 2005). One of these genes, CML24 (also known as TOUCH2, or TCH2) is rapidly switched on by touch. This project is to test if 8 other genes predicted to interact with TCH2 are also involved in touch sensing. This will be tested through the use of mutants in these genes and analysis of their growth responses and gene expression patterns using quantitative PCR. The results from this work should help understand the poorly studied plant touch-sensing network.
MGAT2 deficiency alters bile acid metabolism
Mice deficient in the enzyme MGAT2 (Mogat2â€“/â€“) exhibit protection from obesity. Bile acids are known to modulate energy metabolism. This study investigates whether Mogat2â€“/â€“ mice have altered bile acid metabolism. Tissue, plasma, and fecal samples from Mogat2â€“/â€“ and control mice were analyzed by enzymatic bile acid quantification. Characterization of bile acid species in plasma was accomplished by HPLC-TMS and mRNA expression of bile acid signaling genes in the liver and distal intestine were analyzed by quantitative PCR. Mogat2 deficiency alters concentration and composition of plasma bile acids, and expression levels of multiple bile acid signaling genes are altered at the mRNA level. These findings merit further investigation of the role of bile acid signaling in the metabolic phenotype of Mogat2 deficiency.
Quantification of interneurons present in postmortem adult Down Syndrome Brain
Down syndrome (DS) is caused by the presence of three copies of chromosome 21 and is the most common genetic cause of intellectual disability. For such a common genetic disorder, little is known about the neuroanatomical differences in DS relative to a normal brain. However, studies have consistently revealed fewer neurons in the frontal and temporal regions of the DS cerebral cortex. Our aim is to test the hypothesis that there are fewer of a specific neuronal type, interneurons, in regions of the cerebral cortex of mature human DS brain. Our methods determine whether there are fewer GABAergic interneurons present in regions of the DS cortex through identification by interneuron specific markers in immunohistochemistry and quantification by stereology.
Comparison of Plant Polymer Degrading Microbes Enriched from Fecal Samples
Extensive studies have been done on understanding the ecology of cellulose and hemicellulose degrading microbes in various bovine species, yet little is known about how these communities compare to organisms with different digestive environments. By understanding these systems better, we will be able to use this knowledge for the improvement of biofuels and provision of a better context about the role of the gut microbiota with regards to plant polymer degradation. I hypothesize that the bacteria responsible for plant polymer degradation derived from species with similar digestive tracts are more closely related to each other than they are to species with different digestive tracts. Furthermore, I believe this trend will hold for each of the plant polymers used in this study: xylan and cellulose. To test this hypothesis, I inoculated fecal samples from five individuals of each host species (horse, cow, chicken, pig) in triplicates in a liquid media with either xylan or cellulose as the sole carbon source. Various colonies were isolated through serial dilutions on TSA plates. The 16S rRNA gene of these isolates are being sequenced via Sanger sequencing. Sequences will be classified using the Silva database and a maximum likelihood tree will be generate to observe the phylogenetic relatedness between strains from different host species.