Tracy Johnson - Academia.edu (original) (raw)

Papers by Tracy Johnson

Lab Animal, 2008

One approach to understanding how orally administered drugs are absorbed and metabolized involves... more One approach to understanding how orally administered drugs are absorbed and metabolized involves measuring compound concentrations in portal vein blood and in systemic circulation at various time points. In mice, blood samples are generally collected through terminal bleeding, a process that requires a large number of mice and is susceptible to variation between individuals. The authors developed a portal vein cannulation procedure for serial bleeding in the mouse, using a modified catheter containing a stainless steel stylet that is implanted directly in the portal vein. To demonstrate the technique, they orally administered two different compounds to mice and obtained blood samples from the tail vein and portal vein at different time points. They analyzed compound concentrations using liquid chromatography-tandem mass spectrometry. The technique refines existing methods for pharmacokinetic studies in the mouse and reduces the number of mice required.

Nursing Times, 2003

A project was developed to provide older residents in care homes with hip protectors if they were... more A project was developed to provide older residents in care homes with hip protectors if they were at risk of falling. The aim was to reduce the number of hip fractures sustained through falls. During the project it became apparent that care home staff had little knowledge of hip protectors, and felt unable to take steps to prevent falls. The project extended its scope to raise the awareness of falls-risk assessments and prevention strategies, and developing structures through which best practice could be shared between homes.

Nucleic acids research, 2015

When messenger RNA splicing occurs co-transcriptionally, the potential for kinetic control based ... more When messenger RNA splicing occurs co-transcriptionally, the potential for kinetic control based on transcription dynamics is widely recognized. Indeed, perturbation studies have reported that when transcription kinetics are perturbed genetically or pharmacologically splice patterns may change. However, whether kinetic control is contributing to the control of splicing within the normal range of physiological conditions remains unknown. We examined if the kinetic determinants for co-transcriptional splicing (CTS) might be reflected in the structure and expression patterns of the genome and epigenome. To identify and then quantitatively relate multiple, simultaneous CTS determinants, we constructed a scalable mathematical model of the kinetic interplay of RNA synthesis and CTS and parameterized it with diverse next generation sequencing (NGS) data. We thus found a variety of CTS determinants encoded in vertebrate genomes and epigenomes, and that these combine variously for different ...

Ethnographic Praxis in Industry Conference Proceedings, 2014

Methods in Molecular Biology, 2014

Pre-mRNA splicing is a critical step in eukaryotic gene expression, which involves removal of non... more Pre-mRNA splicing is a critical step in eukaryotic gene expression, which involves removal of noncoding intron sequences from pre-mRNA and ligation of the remaining exon sequences to make a mature message. Splicing is carried out by a large ribonucleoprotein complex called the spliceosome. Since the fi rst description of the pre-mRNA splicing reaction in the 1970s, elegant genetic and biochemical studies have revealed that the enzyme that catalyzes the reaction, the spliceosome, is an exquisitely dynamic macromolecular machine, and its RNA and protein components undergo highly ordered, tightly coordinated rearrangements in order to carry out intron recognition and splicing catalysis. Studies using the genetically tractable unicellular eukaryote budding yeast ( Saccharomyces cerevisiae ) have played an instrumental role in deciphering splicing mechanisms. In this chapter, we discuss how yeast genetics has been used to deepen our understanding of the mechanism of splicing and explore the potential for future mechanistic insights using S. cerevisiae as an experimental tool.

Schizophrenia Research, 2008

Pure and Applied Geophysics PAGEOPH, 1978

Page 1. Pageoph, Vol. 116 (1978), BirkhS.user Verlag, Basel Rupture and Particle Velocity During ... more Page 1. Pageoph, Vol. 116 (1978), BirkhS.user Verlag, Basel Rupture and Particle Velocity During Frictional Sliding 1) By TRACY L. JOHNSON 2) Summary - Laboratory measurements of rupture and particle velocity are in surprisingly ...

Psychopathology, 2008

Background: While the problem of significant comorbidity in first-episode psychosis (FEP) is well... more Background: While the problem of significant comorbidity in first-episode psychosis (FEP) is well known, little is known about the pattern of onset of disorder prior to and during FEP. The current study examined Axis I psychiatric comorbidity in 62 people being treated for FEP. Method: Morbidity in the years prior to the diagnosis of psychosis was assessed retrospectively, while comorbidities during the 15 months after psychosis diagnosis were investigated prospectively via structured clinical interview. Results: Prevalence of morbidity was high, with 84% of patients having an Axis I psychiatric disorder during at least one phase (i.e. either prior to, during or following the FEP). Sixty-nine percent had one or more psychiatric diagnoses in their lifetime prior to admission for FEP and 47% had one or more comorbid disorder concurrently with FEP. Substance use disorders were most prevalent prior to admission and at 15-month follow-up, while mood disorders were most prevalent during acute psychosis. Conclusions: The study shows the large amount of Axis I comorbidity in young people with FEP. Issues for treatment of comorbidities are discussed.

PLoS ONE, 2011

There is mounting evidence to suggest that the synthesis of pre-mRNA transcripts and their subseq... more There is mounting evidence to suggest that the synthesis of pre-mRNA transcripts and their subsequent splicing are coordinated events. Previous studies have implicated the mammalian spliceosomal U2 snRNP as having a novel role in stimulating transcriptional elongation in vitro through interactions with the elongation factors P-TEFb and Tat-SF1; however, the mechanism remains unknown [1]. These factors are conserved in Saccharomyces cerevisiae, a fact that suggests that a similar interaction may occur in yeast to stimulate transcriptional elongation in vivo. To address this possibility we have looked for evidence of a role for the yeast Tat-SF1 homolog, Cus2, and the U2 snRNA in regulating transcription. Specifically, we have performed a genetic analysis to look for functional interactions between Cus2 or U2 snRNA and the P-TEFb yeast homologs, the Bur1/2 and Ctk1/2/3 complexes. In addition, we have analyzed Cus2-deleted or -overexpressing cells and U2 snRNA mutant cells to determine if they show transcription-related phenotypes similar to those displayed by the P-TEFb homolog mutants. In no case have we been able to observe phenotypes consistent with a role for either spliceosomal factor in transcription elongation. Furthermore, we did not find evidence for physical interactions between the yeast U2 snRNP factors and the P-TEFb homologs. These results suggest that in vivo, S. cerevisiae do not exhibit functional or physical interactions similar to those exhibited by their mammalian counterparts in vitro. The significance of the difference between our in vivo findings and the previously published in vitro results remains unclear; however, we discuss the potential importance of other factors, including viral proteins, in mediating the mammalian interactions.

PLoS Genetics, 2009

In the last several years, a number of studies have shown that spliceosome assembly and splicing ... more In the last several years, a number of studies have shown that spliceosome assembly and splicing catalysis can occur cotranscriptionally. However, it has been unclear which specific transcription factors play key roles in coupling splicing to transcription and the mechanisms through which they act. Here we report the discovery that Gcn5, which encodes the histone acetyltransferase (HAT) activity of the SAGA complex, has genetic interactions with the genes encoding the heterodimeric U2 snRNP proteins Msl1 and Lea1. These interactions are dependent upon the HAT activity of Gcn5, suggesting a functional relationship between Gcn5 HAT activity and Msl1/Lea1 function. To understand the relationship between Gcn5 and Msl1/Lea1, we carried out an analysis of Gcn5's role in co-transcriptional recruitment of Msl1 and Lea1 to pre-mRNA and found that Gcn5 HAT activity is required for co-transcriptional recruitment of the U2 snRNP (and subsequent snRNP) components to the branchpoint, while it is not required for U1 recruitment. Although previous studies suggest that transcription elongation can alter co-transcriptional pre-mRNA splicing, we do not observe evidence of defective transcription elongation for these genes in the absence of Gcn5, while Gcn5-dependent histone acetylation is enriched in the promoter regions. Unexpectedly, we also observe Msl1 enrichment in the promoter region for wild-type cells and cells lacking Gcn5, indicating that Msl1 recruitment during active transcription can occur independently of its association at the branchpoint region. These results demonstrate a novel role for acetylation by SAGA in co-transcriptional recruitment of the U2 snRNP and recognition of the intron branchpoint.

Nucleic Acids Research, 2011

Alternative pre-mRNA splicing allows dramatic expansion of the eukaryotic proteome and facilitate... more Alternative pre-mRNA splicing allows dramatic expansion of the eukaryotic proteome and facilitates cellular response to changes in environmental conditions. The Saccharomyces cerevisiae gene SUS1, which encodes a protein involved in mRNA export and histone H2B deubiquitination, contains two introns; non-canonical sequences in the first intron contribute to its retention, a common form of alternative splicing in plants and fungi. Here we show that the pattern of SUS1 splicing changes in response to environmental change such as temperature elevation, and the retained intron product is subject to nonsense-mediated decay. The activities of different splicing factors determine the pattern of SUS1 splicing, including intron retention and exon skipping. Unexpectedly, removal of the 3 0 intron is affected by splicing of the upstream intron, suggesting that cross-exon interactions influence intron removal. Production of different SUS1 isoforms is important for cellular function, as we find that the temperature sensitivity and histone H2B deubiquitination defects observed in sus1D cells are only partially suppressed by SUS1 cDNA, but SUS1 that is able to undergo splicing complements these phenotypes. These data illustrate a role for S. cerevisiae alternative splicing in histone modification and cellular function and reveal important mechanisms for splicing of yeast genes containing multiple introns.

Molecular BioSystems, 2010

Pre-mRNA splicing, the removal of noncoding intron sequences from the pre-mRNA, is a critical rea... more Pre-mRNA splicing, the removal of noncoding intron sequences from the pre-mRNA, is a critical reaction in eukaryotic gene expression. Pre-mRNA splicing is carried out by a remarkable macromolecular machine, the spliceosome, which undergoes dynamic rearrangements of its RNA and protein components to assemble its catalytic center. While significant progress has been made in describing the "moving parts" of this machine, the mechanisms by which spliceosomal proteins mediate the ordered rearrangements within the spliceosome remain elusive. Here we explore recent evidence from proteomics studies revealing extensive post-translational modification of splicing factors. While the functional significance of most of these modifications remains to be characterized, we describe recent studies in which the roles of specific post-translational modifications of splicing factors have been characterized. These examples illustrate the importance of post-translational modifications in spliceosome dynamics.

Molecular Biology of the Cell, 2013

The central dogma uniquely positions RNA as the key molecular player for translating genetic soft... more The central dogma uniquely positions RNA as the key molecular player for translating genetic software into protein hardware. But it has become increasingly clear that RNA also plays an essential regulatory role within cells. MicroRNAs in particular have emerged as ubiquitous and still poorly understood molecules involved in the control of a wide variety of biological processes. RNA has also recently been shown to have important roles in structural assembly within cells. A diverse set of speakers at the Minisymposium on Micro-and Coding RNA highlighted some of these new and often unexpected roles of RNA across a range of length scales.

Molecular and Cellular Biology, 2013

Recent studies have revealed a close relationship between transcription, histone modification, an... more Recent studies have revealed a close relationship between transcription, histone modification, and RNA processing. In fact, genome-wide analyses that correlate histone marks with RNA processing signals raise the possibility that specific RNA processing factors may modulate transcription and help to "write" chromatin marks. Here we show that the nuclear cap binding complex (CBC) directs recruitment of transcription elongation factors and establishes proper histone marks during active transcription. A directed genetic screen revealed that deletion of either subunit of the CBC confers a synthetic growth defect when combined with deletion of genes encoding either Ctk2 or Bur2, a component of the Saccharomyces cerevisiae ortholog of P-TEFb. The CBC physically associates with these complexes to recruit them during transcription and mediates phosphorylation at Ser-2 of the C-terminal domain (CTD) of RNA polymerase II. To understand how these interactions influence downstream events, histone H3K36me3 was examined, and we demonstrate that CBC⌬ affects proper Set2-dependent H3K36me3. Consistent with this, the CBC and Set2 have similar effects on the ability to rapidly induce and sustain activated gene expression, and these effects are distinct from other histone methyltransferases. This work provides evidence for an emerging model that RNA processing factors can modulate the recruitment of transcription factors and influence histone modification during elongation.

Lab Animal, 2008

One approach to understanding how orally administered drugs are absorbed and metabolized involves... more One approach to understanding how orally administered drugs are absorbed and metabolized involves measuring compound concentrations in portal vein blood and in systemic circulation at various time points. In mice, blood samples are generally collected through terminal bleeding, a process that requires a large number of mice and is susceptible to variation between individuals. The authors developed a portal vein cannulation procedure for serial bleeding in the mouse, using a modified catheter containing a stainless steel stylet that is implanted directly in the portal vein. To demonstrate the technique, they orally administered two different compounds to mice and obtained blood samples from the tail vein and portal vein at different time points. They analyzed compound concentrations using liquid chromatography-tandem mass spectrometry. The technique refines existing methods for pharmacokinetic studies in the mouse and reduces the number of mice required.

Journal of Geophysical Research, 1972

Ninety-six new focal mechanisms were determined for earthquakes on the belt of seismic activity s... more Ninety-six new focal mechanisms were determined for earthquakes on the belt of seismic activity separating the Pacific and Australian plates. The direction of convergence of these plates varies from Ntg•-SW to E-W. The Australian plate underthrusts the Pacific plate to the ENE under the Solomon and New Hebrides islands and overthrusts the Pacific to the east along the Tonga-Kermadec arc and the North Island of New Zealand. The data for the Macquarie ridge concur with the idea that. the pole of rotation for the Pacific and Australian pla.tes is nearby and to the east of this feature. The data also suggest a. NNE-SSW convergence of the Pacific and Australian plates in northwestern New Guinea. The relative motions of the plates near the Bismarck Archipelago are complex because of the presence of at least three additional small plates. The south Bismarck plate, the best defined, underlies the southern part of the Bismarck Sea. It is bounded on the north by a.n E-W belt of seismicity at about 3øS defining a left-lateral strike-slip fault. The New Britain arc forms the southern boundary, where the Solomon Sea floor underthrusts the south Bismarck plate to the NNW. There is some evidence for SW convergence of the south Bismarck and Australian plates in northeastern New Guinea. Small plates, less well-defined seismically, are also proposed under the northern part of the Bismarck Sea and under the Solomon Sea. The plate under}ying the Solomon Sea floor is bounded by the Solomon and New Britain arcs and by eastern New Guinea. The southern boundary is not sharply defined by seismic data. The Solomon Sea plate is moving approximately NW with respect to the Australian plate and underthrusting the Pacific plate to the NE along the Solomon arc. The consistent pattern of relative motions of these three small plates allows quantitative estimates of relative rates of motion between them. These data demonstrate that plate tectonics is applicable even for regions with dimensions of only a few hundred kilometers. Geologic data from New Guinea are used to speculate about earlier plate motions in that area. Many recent studies have demonstrated that most shallow earthquakes, especially in oceanic areas, indicate relative motion of two lithospheric plates [e.g., Isacks et al., 1968; Mc-Kenzie and Parker, 1967]. Data from 96 new focal mechanisms for shallow earthquakes and 29 published mechanisms from other studies are used to analyze relative plate motions in the southwest Pacific. This region is important because it includes a long boundary between two of the larger plates of the world. In general, the seismic data as well as other geologic data in this region are consistent with convergence of the Pacific and Australian plates about a pole of rotation determined to be south of New • Lamont-Doherty Geological Observatory contribution 1837.

Journal of Geophysical Research, 1975

JB_description.

Journal of Geophysical Research, 1972

Journal of Allergy and Clinical Immunology, 2006

RATIONALE: Paraneoplastic pemphigus (PNP) is a potentially rare complication usually associated w... more RATIONALE: Paraneoplastic pemphigus (PNP) is a potentially rare complication usually associated with a neoplasm and is characterized by intractable ulcerative stomatitis, mucosal surface erosions and polymorphic cutaneous eruptions. METHODS/CASE: A 50-year-old African-American female with invasive breast carcinoma and supraclavicular lymph node metastasis was treated with a chemotherapeutic regimen of Cyclophosphamide and Doxorubicin. During her multiple cycle course she developed severe oral mucositis leading to the discontinuation of chemotherapy. The oral lesions progressed and she developed a diffuse polymorphic cutaneous eruption represented by erythematous papules, bullae and erosions that responded to oral corticosteroid treatment with Prednisone 60 mg/day for 2 weeks and tapered down to 20 mg everyday. Oral mucosal and skin lesion biopsies were performed and interpreted as consistent with PNP.

Lab Animal, 2008

One approach to understanding how orally administered drugs are absorbed and metabolized involves... more One approach to understanding how orally administered drugs are absorbed and metabolized involves measuring compound concentrations in portal vein blood and in systemic circulation at various time points. In mice, blood samples are generally collected through terminal bleeding, a process that requires a large number of mice and is susceptible to variation between individuals. The authors developed a portal vein cannulation procedure for serial bleeding in the mouse, using a modified catheter containing a stainless steel stylet that is implanted directly in the portal vein. To demonstrate the technique, they orally administered two different compounds to mice and obtained blood samples from the tail vein and portal vein at different time points. They analyzed compound concentrations using liquid chromatography-tandem mass spectrometry. The technique refines existing methods for pharmacokinetic studies in the mouse and reduces the number of mice required.

Nursing Times, 2003

A project was developed to provide older residents in care homes with hip protectors if they were... more A project was developed to provide older residents in care homes with hip protectors if they were at risk of falling. The aim was to reduce the number of hip fractures sustained through falls. During the project it became apparent that care home staff had little knowledge of hip protectors, and felt unable to take steps to prevent falls. The project extended its scope to raise the awareness of falls-risk assessments and prevention strategies, and developing structures through which best practice could be shared between homes.

Nucleic acids research, 2015

When messenger RNA splicing occurs co-transcriptionally, the potential for kinetic control based ... more When messenger RNA splicing occurs co-transcriptionally, the potential for kinetic control based on transcription dynamics is widely recognized. Indeed, perturbation studies have reported that when transcription kinetics are perturbed genetically or pharmacologically splice patterns may change. However, whether kinetic control is contributing to the control of splicing within the normal range of physiological conditions remains unknown. We examined if the kinetic determinants for co-transcriptional splicing (CTS) might be reflected in the structure and expression patterns of the genome and epigenome. To identify and then quantitatively relate multiple, simultaneous CTS determinants, we constructed a scalable mathematical model of the kinetic interplay of RNA synthesis and CTS and parameterized it with diverse next generation sequencing (NGS) data. We thus found a variety of CTS determinants encoded in vertebrate genomes and epigenomes, and that these combine variously for different ...

Ethnographic Praxis in Industry Conference Proceedings, 2014

Methods in Molecular Biology, 2014

Pre-mRNA splicing is a critical step in eukaryotic gene expression, which involves removal of non... more Pre-mRNA splicing is a critical step in eukaryotic gene expression, which involves removal of noncoding intron sequences from pre-mRNA and ligation of the remaining exon sequences to make a mature message. Splicing is carried out by a large ribonucleoprotein complex called the spliceosome. Since the fi rst description of the pre-mRNA splicing reaction in the 1970s, elegant genetic and biochemical studies have revealed that the enzyme that catalyzes the reaction, the spliceosome, is an exquisitely dynamic macromolecular machine, and its RNA and protein components undergo highly ordered, tightly coordinated rearrangements in order to carry out intron recognition and splicing catalysis. Studies using the genetically tractable unicellular eukaryote budding yeast ( Saccharomyces cerevisiae ) have played an instrumental role in deciphering splicing mechanisms. In this chapter, we discuss how yeast genetics has been used to deepen our understanding of the mechanism of splicing and explore the potential for future mechanistic insights using S. cerevisiae as an experimental tool.

Schizophrenia Research, 2008

Pure and Applied Geophysics PAGEOPH, 1978

Page 1. Pageoph, Vol. 116 (1978), BirkhS.user Verlag, Basel Rupture and Particle Velocity During ... more Page 1. Pageoph, Vol. 116 (1978), BirkhS.user Verlag, Basel Rupture and Particle Velocity During Frictional Sliding 1) By TRACY L. JOHNSON 2) Summary - Laboratory measurements of rupture and particle velocity are in surprisingly ...

Psychopathology, 2008

Background: While the problem of significant comorbidity in first-episode psychosis (FEP) is well... more Background: While the problem of significant comorbidity in first-episode psychosis (FEP) is well known, little is known about the pattern of onset of disorder prior to and during FEP. The current study examined Axis I psychiatric comorbidity in 62 people being treated for FEP. Method: Morbidity in the years prior to the diagnosis of psychosis was assessed retrospectively, while comorbidities during the 15 months after psychosis diagnosis were investigated prospectively via structured clinical interview. Results: Prevalence of morbidity was high, with 84% of patients having an Axis I psychiatric disorder during at least one phase (i.e. either prior to, during or following the FEP). Sixty-nine percent had one or more psychiatric diagnoses in their lifetime prior to admission for FEP and 47% had one or more comorbid disorder concurrently with FEP. Substance use disorders were most prevalent prior to admission and at 15-month follow-up, while mood disorders were most prevalent during acute psychosis. Conclusions: The study shows the large amount of Axis I comorbidity in young people with FEP. Issues for treatment of comorbidities are discussed.

PLoS ONE, 2011

There is mounting evidence to suggest that the synthesis of pre-mRNA transcripts and their subseq... more There is mounting evidence to suggest that the synthesis of pre-mRNA transcripts and their subsequent splicing are coordinated events. Previous studies have implicated the mammalian spliceosomal U2 snRNP as having a novel role in stimulating transcriptional elongation in vitro through interactions with the elongation factors P-TEFb and Tat-SF1; however, the mechanism remains unknown [1]. These factors are conserved in Saccharomyces cerevisiae, a fact that suggests that a similar interaction may occur in yeast to stimulate transcriptional elongation in vivo. To address this possibility we have looked for evidence of a role for the yeast Tat-SF1 homolog, Cus2, and the U2 snRNA in regulating transcription. Specifically, we have performed a genetic analysis to look for functional interactions between Cus2 or U2 snRNA and the P-TEFb yeast homologs, the Bur1/2 and Ctk1/2/3 complexes. In addition, we have analyzed Cus2-deleted or -overexpressing cells and U2 snRNA mutant cells to determine if they show transcription-related phenotypes similar to those displayed by the P-TEFb homolog mutants. In no case have we been able to observe phenotypes consistent with a role for either spliceosomal factor in transcription elongation. Furthermore, we did not find evidence for physical interactions between the yeast U2 snRNP factors and the P-TEFb homologs. These results suggest that in vivo, S. cerevisiae do not exhibit functional or physical interactions similar to those exhibited by their mammalian counterparts in vitro. The significance of the difference between our in vivo findings and the previously published in vitro results remains unclear; however, we discuss the potential importance of other factors, including viral proteins, in mediating the mammalian interactions.

PLoS Genetics, 2009

In the last several years, a number of studies have shown that spliceosome assembly and splicing ... more In the last several years, a number of studies have shown that spliceosome assembly and splicing catalysis can occur cotranscriptionally. However, it has been unclear which specific transcription factors play key roles in coupling splicing to transcription and the mechanisms through which they act. Here we report the discovery that Gcn5, which encodes the histone acetyltransferase (HAT) activity of the SAGA complex, has genetic interactions with the genes encoding the heterodimeric U2 snRNP proteins Msl1 and Lea1. These interactions are dependent upon the HAT activity of Gcn5, suggesting a functional relationship between Gcn5 HAT activity and Msl1/Lea1 function. To understand the relationship between Gcn5 and Msl1/Lea1, we carried out an analysis of Gcn5's role in co-transcriptional recruitment of Msl1 and Lea1 to pre-mRNA and found that Gcn5 HAT activity is required for co-transcriptional recruitment of the U2 snRNP (and subsequent snRNP) components to the branchpoint, while it is not required for U1 recruitment. Although previous studies suggest that transcription elongation can alter co-transcriptional pre-mRNA splicing, we do not observe evidence of defective transcription elongation for these genes in the absence of Gcn5, while Gcn5-dependent histone acetylation is enriched in the promoter regions. Unexpectedly, we also observe Msl1 enrichment in the promoter region for wild-type cells and cells lacking Gcn5, indicating that Msl1 recruitment during active transcription can occur independently of its association at the branchpoint region. These results demonstrate a novel role for acetylation by SAGA in co-transcriptional recruitment of the U2 snRNP and recognition of the intron branchpoint.

Nucleic Acids Research, 2011

Alternative pre-mRNA splicing allows dramatic expansion of the eukaryotic proteome and facilitate... more Alternative pre-mRNA splicing allows dramatic expansion of the eukaryotic proteome and facilitates cellular response to changes in environmental conditions. The Saccharomyces cerevisiae gene SUS1, which encodes a protein involved in mRNA export and histone H2B deubiquitination, contains two introns; non-canonical sequences in the first intron contribute to its retention, a common form of alternative splicing in plants and fungi. Here we show that the pattern of SUS1 splicing changes in response to environmental change such as temperature elevation, and the retained intron product is subject to nonsense-mediated decay. The activities of different splicing factors determine the pattern of SUS1 splicing, including intron retention and exon skipping. Unexpectedly, removal of the 3 0 intron is affected by splicing of the upstream intron, suggesting that cross-exon interactions influence intron removal. Production of different SUS1 isoforms is important for cellular function, as we find that the temperature sensitivity and histone H2B deubiquitination defects observed in sus1D cells are only partially suppressed by SUS1 cDNA, but SUS1 that is able to undergo splicing complements these phenotypes. These data illustrate a role for S. cerevisiae alternative splicing in histone modification and cellular function and reveal important mechanisms for splicing of yeast genes containing multiple introns.

Molecular BioSystems, 2010

Pre-mRNA splicing, the removal of noncoding intron sequences from the pre-mRNA, is a critical rea... more Pre-mRNA splicing, the removal of noncoding intron sequences from the pre-mRNA, is a critical reaction in eukaryotic gene expression. Pre-mRNA splicing is carried out by a remarkable macromolecular machine, the spliceosome, which undergoes dynamic rearrangements of its RNA and protein components to assemble its catalytic center. While significant progress has been made in describing the "moving parts" of this machine, the mechanisms by which spliceosomal proteins mediate the ordered rearrangements within the spliceosome remain elusive. Here we explore recent evidence from proteomics studies revealing extensive post-translational modification of splicing factors. While the functional significance of most of these modifications remains to be characterized, we describe recent studies in which the roles of specific post-translational modifications of splicing factors have been characterized. These examples illustrate the importance of post-translational modifications in spliceosome dynamics.

Molecular Biology of the Cell, 2013

The central dogma uniquely positions RNA as the key molecular player for translating genetic soft... more The central dogma uniquely positions RNA as the key molecular player for translating genetic software into protein hardware. But it has become increasingly clear that RNA also plays an essential regulatory role within cells. MicroRNAs in particular have emerged as ubiquitous and still poorly understood molecules involved in the control of a wide variety of biological processes. RNA has also recently been shown to have important roles in structural assembly within cells. A diverse set of speakers at the Minisymposium on Micro-and Coding RNA highlighted some of these new and often unexpected roles of RNA across a range of length scales.

Molecular and Cellular Biology, 2013

Recent studies have revealed a close relationship between transcription, histone modification, an... more Recent studies have revealed a close relationship between transcription, histone modification, and RNA processing. In fact, genome-wide analyses that correlate histone marks with RNA processing signals raise the possibility that specific RNA processing factors may modulate transcription and help to "write" chromatin marks. Here we show that the nuclear cap binding complex (CBC) directs recruitment of transcription elongation factors and establishes proper histone marks during active transcription. A directed genetic screen revealed that deletion of either subunit of the CBC confers a synthetic growth defect when combined with deletion of genes encoding either Ctk2 or Bur2, a component of the Saccharomyces cerevisiae ortholog of P-TEFb. The CBC physically associates with these complexes to recruit them during transcription and mediates phosphorylation at Ser-2 of the C-terminal domain (CTD) of RNA polymerase II. To understand how these interactions influence downstream events, histone H3K36me3 was examined, and we demonstrate that CBC⌬ affects proper Set2-dependent H3K36me3. Consistent with this, the CBC and Set2 have similar effects on the ability to rapidly induce and sustain activated gene expression, and these effects are distinct from other histone methyltransferases. This work provides evidence for an emerging model that RNA processing factors can modulate the recruitment of transcription factors and influence histone modification during elongation.

Lab Animal, 2008

One approach to understanding how orally administered drugs are absorbed and metabolized involves... more One approach to understanding how orally administered drugs are absorbed and metabolized involves measuring compound concentrations in portal vein blood and in systemic circulation at various time points. In mice, blood samples are generally collected through terminal bleeding, a process that requires a large number of mice and is susceptible to variation between individuals. The authors developed a portal vein cannulation procedure for serial bleeding in the mouse, using a modified catheter containing a stainless steel stylet that is implanted directly in the portal vein. To demonstrate the technique, they orally administered two different compounds to mice and obtained blood samples from the tail vein and portal vein at different time points. They analyzed compound concentrations using liquid chromatography-tandem mass spectrometry. The technique refines existing methods for pharmacokinetic studies in the mouse and reduces the number of mice required.

Journal of Geophysical Research, 1972

Ninety-six new focal mechanisms were determined for earthquakes on the belt of seismic activity s... more Ninety-six new focal mechanisms were determined for earthquakes on the belt of seismic activity separating the Pacific and Australian plates. The direction of convergence of these plates varies from Ntg•-SW to E-W. The Australian plate underthrusts the Pacific plate to the ENE under the Solomon and New Hebrides islands and overthrusts the Pacific to the east along the Tonga-Kermadec arc and the North Island of New Zealand. The data for the Macquarie ridge concur with the idea that. the pole of rotation for the Pacific and Australian pla.tes is nearby and to the east of this feature. The data also suggest a. NNE-SSW convergence of the Pacific and Australian plates in northwestern New Guinea. The relative motions of the plates near the Bismarck Archipelago are complex because of the presence of at least three additional small plates. The south Bismarck plate, the best defined, underlies the southern part of the Bismarck Sea. It is bounded on the north by a.n E-W belt of seismicity at about 3øS defining a left-lateral strike-slip fault. The New Britain arc forms the southern boundary, where the Solomon Sea floor underthrusts the south Bismarck plate to the NNW. There is some evidence for SW convergence of the south Bismarck and Australian plates in northeastern New Guinea. Small plates, less well-defined seismically, are also proposed under the northern part of the Bismarck Sea and under the Solomon Sea. The plate under}ying the Solomon Sea floor is bounded by the Solomon and New Britain arcs and by eastern New Guinea. The southern boundary is not sharply defined by seismic data. The Solomon Sea plate is moving approximately NW with respect to the Australian plate and underthrusting the Pacific plate to the NE along the Solomon arc. The consistent pattern of relative motions of these three small plates allows quantitative estimates of relative rates of motion between them. These data demonstrate that plate tectonics is applicable even for regions with dimensions of only a few hundred kilometers. Geologic data from New Guinea are used to speculate about earlier plate motions in that area. Many recent studies have demonstrated that most shallow earthquakes, especially in oceanic areas, indicate relative motion of two lithospheric plates [e.g., Isacks et al., 1968; Mc-Kenzie and Parker, 1967]. Data from 96 new focal mechanisms for shallow earthquakes and 29 published mechanisms from other studies are used to analyze relative plate motions in the southwest Pacific. This region is important because it includes a long boundary between two of the larger plates of the world. In general, the seismic data as well as other geologic data in this region are consistent with convergence of the Pacific and Australian plates about a pole of rotation determined to be south of New • Lamont-Doherty Geological Observatory contribution 1837.

Journal of Geophysical Research, 1975

JB_description.

Journal of Geophysical Research, 1972

Journal of Allergy and Clinical Immunology, 2006

RATIONALE: Paraneoplastic pemphigus (PNP) is a potentially rare complication usually associated w... more RATIONALE: Paraneoplastic pemphigus (PNP) is a potentially rare complication usually associated with a neoplasm and is characterized by intractable ulcerative stomatitis, mucosal surface erosions and polymorphic cutaneous eruptions. METHODS/CASE: A 50-year-old African-American female with invasive breast carcinoma and supraclavicular lymph node metastasis was treated with a chemotherapeutic regimen of Cyclophosphamide and Doxorubicin. During her multiple cycle course she developed severe oral mucositis leading to the discontinuation of chemotherapy. The oral lesions progressed and she developed a diffuse polymorphic cutaneous eruption represented by erythematous papules, bullae and erosions that responded to oral corticosteroid treatment with Prednisone 60 mg/day for 2 weeks and tapered down to 20 mg everyday. Oral mucosal and skin lesion biopsies were performed and interpreted as consistent with PNP.