Biomedical subjects

Lakshmi Ramachandran

Publications and source records attributed to Lakshmi Ramachandran.

8 recordsLinked to original sources

PubMed2006

Non-random clustering of stress-related genes during evolution of the S. cerevisiae genome.

BACKGROUND: Coordinately regulated genes often physically cluster in eukaryotic genomes, for reasons that remain unclear. RESULTS: Here we provide evidence that many S. cerevisiae genes induced by starvation and other stresses reside in non-random clusters, where transcription of these genes is repressed in the absence of stress. Most genes essential for growth or for rapid, post-transcriptional responses to stress in cycling cells map between these gene clusters. Genes that are transcriptionally induced by stresses include a large fraction of rapidly evolving paralogues of duplicated genes that arose during an ancient whole genome duplication event. Many of these rapidly evolving paralogues have acquired new or more specialized functions that are less essential for growth. The slowly evolving paralogues of these genes are less likely to be transcriptionally repressed in the absence of stress, and are frequently essential for growth or for rapid stress responses that may require constitutive expression of these genes in cycling cells. CONCLUSION: Our findings suggest that a fundamental organizing principle during evolution of the S. cerevisiae genome has been clustering of starvation and other stress-induced genes in chromosome regions that are transcriptionally repressed in the absence of stress, from which most genes essential for growth or rapid stress responses have been excluded. Chromatin-mediated repression of many stress-induced genes may have evolved since the whole genome duplication in parallel with functions for proteins encoded by these genes that are incompatible with growth. These functions likely provide fitness effects that escape detection in assays of reproductive capacity routinely employed to assess evolutionary fitness, or to identify genes that confer stress-resistance in cycling cells.

Evolution, Molecular↗

PubMed2006

Evidence for ORC-dependent repression of budding yeast genes induced by starvation and other stresses.

The highly conserved origin recognition complex (ORC) is required for repressing genes in the silent mating type loci of budding yeast. Here we report that at a non-permissive temperature, the temperature-sensitive orc2-1 mutation induces the expression of more than 500 genes, the majority of which are also induced during starvation of wild-type cells. Many genes induced by starvation or by the orc2-1 mutation are also induced by inactivation of proteins required for chromatin-mediated repression of transcription. Genes induced by the orc2-1 mutation, starvation, or inactivation of repressor proteins, map near ORC-binding loci significantly more frequently compared to all genes. Genes repressed by starvation map near ORC-binding sites less frequently compared to all genes, which suggests they have been evolutionarily excluded from regions of repressive chromatin near ORC-binding sites. Deletion of sequences containing ORC-binding sites near the DAL2 and DAL4 genes in the DAL gene cluster, which are induced by either the orc2-1 mutation or by starvation, constitutively activates these genes and abolishes their activation by the orc2-1 mutation. Our findings suggest a role for ORC in the repression of a large number of budding yeast genes induced by starvation or other aspects of a deleterious environment.

Apoptosis↗

PubMed2005

A comparison of the aging and apoptotic transcriptome of Saccharomyces cerevisiae.

In this paper, we present the results of global transcript analysis by the microarray technique of senescent and apoptotic yeast cells. We compared young daughter and old mother cells isolated by elutriation centrifugation, and non-apoptotic and apoptotic cells induced either by a temperature shift of the cdc48(S565G) temperature-sensitive mutant or of the orc2-1 temperature-sensitive mutant. The majority of all genes found to be differentially regulated in these three physiological situations was upregulated, indicating that a cellular death process was initiated rather than an unspecific shut-down of gene expression due to immediate killing. The functional classes of genes upregulated in all three conditions were largely the same, although individual genes were in many cases not identical. The largest group of genes involved were nuclear genes coding for mitochondrial components or functions, which is understandable given the fact that apoptosis can be triggered by mitochondrially generated oxygen radicals and that mitochondria play an important role in the execution of apoptosis. Other functional classes consisted of genes involved in DNA damage response, in cell cycle regulation and checkpoints, in DNA repair, and in membrane lipid and cell wall synthesis. These functional classes represent the response of the cell to the known cellular insults, which occur during aging and apoptosis. As we have shown previously, final-stage senescent yeast mother cells (of the wild-type) are apoptotic.

Apoptosis↗

PubMed2005

Apoptosis in budding yeast caused by defects in initiation of DNA replication.

Apoptosis in metazoans is often accompanied by the destruction of DNA replication initiation proteins, inactivation of checkpoints and activation of cyclin-dependent kinases, which are inhibited by checkpoints that directly or indirectly require initiation proteins. Here we show that, in the budding yeast Saccharomyces cerevisiae, mutations in initiation proteins that attenuate both the initiation of DNA replication and checkpoints also induce features of apoptosis similar to those observed in metazoans. The apoptosis-like phenotype of initiation mutants includes the production of reactive oxygen species (ROS) and activation of the budding-yeast metacaspase Yca1p. In contrast to a recent report that activation of Yca1p only occurs in lysed cells and does not contribute to cell death, we found that, in at least one initiation mutant, Yca1p activation occurs at an early stage of cell death (before cell lysis) and contributes to the lethal effects of the mutation harbored by this strain. Apoptosis in initiation mutants is probably caused by DNA damage associated with the combined effects of insufficient DNA replication forks to completely replicate the genome and defective checkpoints that depend on initiation proteins and/or replication forks to restrain subsequent cell-cycle events until DNA replication is complete. A similar mechanism might underlie the proapoptotic effects associated with the destruction of initiation and checkpoint proteins during apoptosis in mammals, as well as genome instability in initiation mutants of budding yeast.

Apoptosis↗

PubMed2003

Apoptosis-like yeast cell death in response to DNA damage and replication defects.

In budding (Saccharomyces cerevisiae) and fission (Schizosaccharomyces pombe) yeast and other unicellular organisms, DNA damage and other stimuli can induce cell death resembling apoptosis in metazoans, including the activation of a recently discovered caspase-like molecule in budding yeast. Induction of apoptotic-like cell death in yeasts requires homologues of cell cycle checkpoint proteins that are often required for apoptosis in metazoan cells. Here, we summarize these findings and our unpublished results which show that an important component of metazoan apoptosis recently detected in budding yeast-reactive oxygen species (ROS)-can also be detected in fission yeast undergoing an apoptotic-like cell death. ROS were detected in fission and budding yeast cells bearing conditional mutations in genes encoding DNA replication initiation proteins and in fission yeast cells with mutations that deregulate cyclin-dependent kinases (CDKs). These mutations may cause DNA damage by permitting entry of cells into S phase with a reduced number of replication forks and/or passage through mitosis with incompletely replicated chromosomes. This may be relevant to the frequent requirement for elevated CDK activity in mammalian apoptosis, and to the recent discovery that the initiation protein Cdc6 is destroyed during apoptosis in mammals and in budding yeast cells exposed to lethal levels of DNA damage. Our data indicate that connections between apoptosis-like cell death and DNA replication or CDK activity are complex. Some apoptosis-like pathways require checkpoint proteins, others are inhibited by them, and others are independent of them. This complexity resembles that of apoptotic pathways in mammalian cells, which are frequently deregulated in cancer. The greater genetic tractability of yeasts should help to delineate these complex pathways and their relationships to cancer and to the effects of apoptosis-inducing drugs that inhibit DNA replication.

Alkylating Agents↗

PubMed2003

Apoptosis in yeasts.

Although yeasts lack some elements of the complex apoptotic machinery of metazoan cells, recent studies show that many features of apoptosis, including a caspase-like activity, can be induced in these organisms by DNA damage and other apoptotic triggers. These remarkable findings provide a compelling argument for increased efforts to bring the powerful genetic approaches available to yeast researchers more directly to bear on questions related to apoptosis and its induction or inhibition by drugs. Yeasts may provide a particularly useful model for understanding connections between DNA damage, cell cycle regulation and apoptosis. Here we summarize these recent findings and explore their implications, particularly for the development of more effective therapeutic strategies for treating cancer.

Antineoplastic Agents↗

PubMed2003

Clinical characterization of corneal infiltrative events observed with soft contact lens wear.

PURPOSE: Corneal infiltrates are commonly observed during adverse reactions associated with contact lens wear. Broad ranges of presentations are encountered, and there is no well-established classification system. The aim of this paper is to categorize corneal infiltrates associated with soft lens wear and present the typical clinical characteristics associated with each type of event. METHODS: All events of corneal infiltrates occurring in soft contact lens clinical trials over 10 years (9 years retrospective and 1 year prospective) and conducted at two contact lens research centers were reviewed by a panel of experts comprising ophthalmologists, optometrists, and other biologic scientists. Classification of each event was based on assessment of a range of signs and symptoms by the review panel. RESULTS: A classification scheme was devised to distinguish infiltrative events that were serious and symptomatic (microbial keratitis), clinically significant and symptomatic (contact lens-induced peripheral ulcer, contact lens-induced acute red eye, infiltrative keratitis), and clinically nonsignificant and asymptomatic (asymptomatic infiltrative keratitis and asymptomatic infiltrates). CONCLUSION: Corneal infiltrates can be classified into six distinct categories. This classification scheme, based on clinical characteristics, should aid diagnosis, management, and treatment of corneal infiltrates as well as assisting investigations into the etiology of each of these conditions.

Contact Lenses, Hydrophilic↗

PubMed2003

Altered conjunctival response after contact lens-related corneal inflammation.

PURPOSE: Corneal inflammation in overnight contact lens (CL) wear is not fully understood. We designed a masked study to examine the impact of overnight CL wear on clinical variables in subjects who had previously experienced corneal inflammatory disease. METHODS: Forty-four subjects were entered into the study: Nine subjects who had previously experienced CL-associated acute red eye (CLARE) and nine controls; 13 subjects who had previously experienced CL-induced peripheral ulceration (CLPU) and 13 controls, respectively. Controls were matched for age, gender, CL wear experience, and refractive error. Subjects wore bilateral disposable CLs (-3.00 DS). Corneal, conjunctival, and CL fitting variables were assessed prior to sleep, after a single night of CL wear, at 1, 2, and 4 hours after waking by clinicians who were masked to group membership. Retrospective analysis of prewear corneal and conjunctival variables for CLARE subjects and their respective controls was also performed. RESULTS: Contact lens-associated acute red eye subjects consistently showed higher limbal redness (p < 0.05), bulbar redness (p < 0.05), and conjunctival staining (p < 0.005) compared with controls. Lens fitting and corneal variables were not significantly different at any time point for CLARE subjects. Contact lens-induced peripheral ulceration subjects were not different from matched controls for any variable at any time point. Limbal redness varied significantly over time among controls, with highest values measured at eye opening (p < 0.05). Retrospective analysis of prewear variables showed no significant differences between CLARE and control subjects. CONCLUSIONS: Wearers who previously experienced CLARE had a greater conjunctival response to CL wear compared with wearers who had no previous inflammatory disease. Clinical observations, however, were not helpful in predicting wearers who were predisposed to CLARE.

Adult↗