The role of splicing factors and small nuclear RNAs in spliceosomal formation

Protein coding genes are comprised of protein-coding exons and non-protein-coding introns. The process of splicing involves removal of the introns and joining of the exons to form a mature messenger RNA, which subsequently undergoes translation into polypeptide. The spliceosome is a large, RNA/protein assembly of five small nuclear RNAs as well as over 300 proteins, which catalyzes intron removal and exon ligation. The selection of specific exons for inclusion in the mature messenger RNA is spatiotemporally regulated and results in production of an enormous diversity of polypeptides from a single gene locus. This phenomenon, known as alternative splicing, is regulated, in part, by protein splicing factors, which target the spliceosome to exon/intron boundaries. The first part of my dissertation (Chapters II and III) focuses on the discovery and characterization of the 45 kilodalton FK506 binding protein (FKBP45), which I discovered in the silk moth, Bombyx mori, as a U1 small nuclear RNA binding protein. This protein family binds the immunosuppressants FK506 and rapamycin and contains peptidyl-prolyl cis-trans isomerase activity, which converts polypeptides from cis to trans about a proline residue. This is the first time that an FKBP has been identified in the spliceosome. The second section of my dissertation (Chapters IV, V, VI and VII) is an investigation of the potential role of small nuclear RNA sequence variants in the control of splicing. I identified 46 copies of small nuclear RNAs in the 6X whole genome shotgun of the Bombyx mori p50T strain. These variants may play a role in differential binding of specific proteins that mediate alternative splicing. Along these lines, further investigation of U2 snRNA sequence variants in Bombyx mori demonstrated that some U2 snRNAs preferentially assemble into high molecular weight spliceosomal complexes over others. Expression of snRNA variants may represent another mechanism by which the cell is able to fine tune the splicing process.

Estrogen and lithium: Facilitating factors involved in brain cell signaling pathways

Learning and memory in adult females decline during menopause and estrogen replacement therapy is commonly prescribed during menopause. Post-menopausal women tend to suffer from depression and are prescribed antidepressants – in addition to hormone therapy. Estrogen replacement therapy is a topic that engenders debate since several studies contradict its efficacy as a palliative therapy for cognitive decline and neurodegenerative diseases. Signaling transduction pathways can alter brain cell activity, survival, and morphology by facilitating transcription factor DNA binding and protein production. The steroidal hormone estrogen and the anti-depressant drug lithium interact through these signaling transduction pathways facilitating transcription factor activation. The paucity of data on how combined hormones and antidepressants interact in regulating gene expression led me to hypothesize that in primary mixed brain cell cultures, combined 17β-estradiol (E2) and lithium chloride (LiCl) (E2/LiCl) will alter genetic expression of markers involved in synaptic plasticity and neuroprotection. Results from these studies indicated that a 48 h treatment of E2/LiCl reduced glutamate receptor subunit genetic expression, but increased neurotrophic factor and estrogen receptor genetic expression. Combined treatment also failed to protect brain cell cultures from glutamate excitotoxicity. If lithium facilitates protein signaling pathways mediated by estrogen, can lithium alone serve as a palliative treatment for post-menopause? This question led me to hypothesize that in estrogen-deficient mice, lithium alone will increase episodic memory (tested via object recognition), and enhance expression in the brain of factors involved in anti-apoptosis, learning and memory. I used bilaterally ovariectomized (bOVX) C57BL/6J mice treated with LiCl for one month. Results indicated that LiCl-treated bOVX mice increased performance in object recognition compared with non-treated bOVX. Increased performance in LiCl-treated bOVX mice coincided with augmented genetic and protein expression in the brain. Understanding the molecular pathways of estrogen will assist in identifying a palliative therapy for menopause-related dementia, and lithium may serve this purpose by acting as a selective estrogen-mediated signaling modulator.

Factors Affecting Current and Future Treeline Locations and Dynamics in the Peruvian Andes

The elevational distributions of tropical treelines are thought to be determined by temperature, and are predicted to shift upslope in response to global warming. In contrast to this hypothesis, global-scale studies have shown that only half of all studied treelines are shifting upslope. Understanding how treelines will respond to climate change has important implications for global biodiversity, especially in the tropics, because tropical treelines generally represent the upper-elevation distribution limit of the hyper-diverse cloudforest ecosystem. In Chapter 1, I introduce the idea that grasslands found above tropical treelines may represent a potential grass ceiling which forest species cannot cross or invade. I use an extensive literature review to outline potential mechanisms which may be acting to stabilize treeline and prevent forest expansion into high-elevation grasslands. In Chapters 2-4, I begin to explore these potential mechanisms through the use of observational and experimental methods. In Chapter 2, I show that there are significant numbers of seedlings occurring just outside of the treeline in the open grasslands and that seed rain is unlikely to limit seedling recruitment above treeline. I also show that microclimates outside of the closed-canopy cloudforest are highly variable and that mean temperatures are likely a poor explanation of tropical treeline elevations. In Chapter 3, I show that juvenile trees maintain freezing resistances similar to adults, but nighttime radiative cooling near the ground in the open grassland results in lower cold temperatures relative to the free atmosphere, exposing seedlings of some species growing above treeline to lethal frost events. In Chapter 4, I use a large-scale seedling transplant experiment to test the effects of mean temperature, absolute low temperature and shade on transplanted seedling survival. I find that increasing mean temperature negatively affects seedling survival of two treeline species while benefiting another. In addition, low temperature extremes and the presence of shade also appear to be important factors affecting seedling survival above tropical treelines. This work demonstrates that mean temperature is a poor predictor of tropical treelines and that temperature extremes, especially low temperatures, and non-climatic variables should be included in predictions of current and future tropical treeline dynamics.

The Role of Splicing Factors and Small Nuclear RNAS in Spliceosomal Formation

Protein coding genes are comprised of protein-coding exons and non-protein-coding introns. The process of splicing involves removal of the introns and joining of the exons to form a mature messenger RNA, which subsequently undergoes translation into polypeptide. The spliceosome is a large, RNA/protein assembly of five small nuclear RNAs as well as over 300 proteins, which catalyzes intron removal and exon ligation. The selection of specific exons for inclusion in the mature messenger RNA is spatio-temporally regulated and results in production of an enormous diversity of polypeptides from a single gene locus. This phenomenon, known as alternative splicing, is regulated, in part, by protein splicing factors, which target the spliceosome to exon/intron boundaries. The first part of my dissertation (Chapters II and III) focuses on the discovery and characterization of the 45 kilodalton FK506 binding protein (FKBP45), which I discovered in the silk moth, Bombyx mori, as a U1 small nuclear RNA binding protein. This protein family binds the immunosuppressants FK506 and rapamycin and contains peptidyl-prolyl cis-trans isomerase activity, which converts polypeptides from cis to trans about a proline residue. This is the first time that an FKBP has been identified in the spliceosome. The second section of my dissertation (Chapters IV, V, VI and VII) is an investigation of the potential role of small nuclear RNA sequence variants in the control of splicing. I identified 46 copies of small nuclear RNAs in the 6X whole genome shotgun of the Bombyx mori p50T strain. These variants may play a role in differential binding of specific proteins that mediate alternative splicing. Along these lines, further investigation of U2 snRNA sequence variants in Bombyx mori demonstrated that some U2 snRNAs preferentially assemble into high molecular weight spliceosomal complexes over others. Expression of snRNA variants may represent another mechanism by which the cell is able to fine tune the splicing process.

Estrogen and Lithium: Facilitating Factors Involved in Brain Cell Signaling Pathways

Learning and memory in adult females decline during menopause and estrogen replacement therapy is commonly prescribed during menopause. Post-menopausal women tend to suffer from depression and are prescribed antidepressants – in addition to hormone therapy. Estrogen replacement therapy is a topic that engenders debate since several studies contradict its efficacy as a palliative therapy for cognitive decline and neurodegenerative diseases. Signaling transduction pathways can alter brain cell activity, survival, and morphology by facilitating transcription factor DNA binding and protein production. The steroidal hormone estrogen and the anti-depressant drug lithium interact through these signaling transduction pathways facilitating transcription factor activation. The paucity of data on how combined hormones and antidepressants interact in regulating gene expression led me to hypothesize that in primary mixed brain cell cultures, combined 17beta-estradiol (E2) and lithium chloride (LiCl) (E2/LiCl) will alter genetic expression of markers involved in synaptic plasticity and neuroprotection. Results from these studies indicated that a 48 h treatment of E2/LiCl reduced glutamate receptor subunit genetic expression, but increased neurotrophic factor and estrogen receptor genetic expression. Combined treatment also failed to protect brain cell cultures from glutamate excitotoxicity. If lithium facilitates protein signaling pathways mediated by estrogen, can lithium alone serve as a palliative treatment for post-menopause? This question led me to hypothesize that in estrogen-deficient mice, lithium alone will increase episodic memory (tested via object recognition), and enhance expression in the brain of factors involved in anti-apoptosis, learning and memory. I used bilaterally ovariectomized (bOVX) C57BL/6J mice treated with LiCl for one month. Results indicated that LiCl-treated bOVX mice increased performance in object recognition compared with non-treated bOVX. Increased performance in LiCl-treated bOVX mice coincided with augmented genetic and protein expression in the brain. Understanding the molecular pathways of estrogen will assist in identifying a palliative therapy for menopause-related dementia, and lithium may serve this purpose by acting as a selective estrogen-mediated signaling modulator.

Factors affecting current and future treeline locations and dynamics in the Peruvian Andes

The elevational distributions of tropical treelines are thought to be determined by temperature, and are predicted to shift upslope in response to global warming. In contrast to this hypothesis, global-scale studies have shown that only half of all studied treelines are shifting upslope. Understanding how treelines will respond to climate change has important implications for global biodiversity, especially in the tropics, because tropical treelines generally represent the upper-elevation distribution limit of the hyper-diverse cloudforest ecosystem. In Chapter 1, I introduce the idea that grasslands found above tropical treelines may represent a potential grass ceiling which forest species cannot cross or invade. I use an extensive literature review to outline potential mechanisms which may be acting to stabilize treeline and prevent forest expansion into high-elevation grasslands. In Chapters 2-4, I begin to explore these potential mechanisms through the use of observational and experimental methods. In Chapter 2, I show that there are significant numbers of seedlings occurring just outside of the treeline in the open grasslands and that seed rain is unlikely to limit seedling recruitment above treeline. I also show that microclimates outside of the closed-canopy cloudforest are highly variable and that mean temperatures are likely a poor explanation of tropical treeline elevations. In Chapter 3, I show that juvenile trees maintain freezing resistances similar to adults, but nighttime radiative cooling near the ground in the open grassland results in lower cold temperatures relative to the free atmosphere, exposing seedlings of some species growing above treeline to lethal frost events. In Chapter 4, I use a large-scale seedling transplant experiment to test the effects of mean temperature, absolute low temperature and shade on transplanted seedling survival. I find that increasing mean temperature negatively affects seedling survival of two treeline species while benefiting another. In addition, low temperature extremes and the presence of shade also appear to be important factors affecting seedling survival above tropical treelines. This work demonstrates that mean temperature is a poor predictor of tropical treelines and that temperature extremes, especially low temperatures, and non-climatic variables should be included in predictions of current and future tropical treeline dynamics.^