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Biomedical subjects

A Jacobson

Publications and source records attributed to A Jacobson.

At least 19 recordsLinked to original sources

An internal open reading frame triggers nonsense-mediated decay of the yeast SPT10 mRNA.

Yeast cells containing a temperature-sensitive mutation in the PRT1 gene were found to selectively stabilize mRNAs harboring early nonsense codons. The similarities between the mRNA decay phenotypes of prt1-1 cells and those lacking the nonsense-mediated mRNA decay (NMD) factor Upf1p led us to determine whether both types of mutations cause the accumulation of the same mRNAs. Differential display analysis and mRNA half-life measurements demonstrated that the HHF2 mRNA increased in abundance in prt1-1 and upf1Delta cells, but did not manifest a change in decay rate. In both mutant strains this increase was attributable to stabilization of the SPT10 transcript, an mRNA encoding a transcriptional regulator of HHF2. Analyses of chimeric mRNAs used to identify the cis-acting basis for NMD of the SPT10 mRNA indicated that ribosomes scan beyond its initiator AUG and initiate at the next downstream AUG, resulting in premature translation termination. By searching a yeast database for transcripts with sequence features similar to those of the SPT10 mRNA, other transcripts that decay by the NMD pathway were identified. Our results demonstrate that mRNAs undergoing leaky scanning are a new class of endogenous NMD substrate, and suggest the existence of a novel cellular regulatory circuit.

5' Untranslated Regions

Linking mRNA turnover and translation: assessing the polyribosomal association of mRNA decay factors and degradative intermediates.

mRNA decay is a multistep process, often dependent on the active translation of an mRNA and on components of the translation apparatus. In Saccharomyces cerevisiae, several trans-acting factors required for mRNA decay associate with polyribosomes. We have explored the specificity of the interactions of these factors with polyribosomes, using sucrose gradient sedimentation analysis of the yeast UPF1 protein to test whether such interactions are altered when polyribosomes are disrupted by treatment with EDTA, digestion with micrococcal nuclease, or shifting of cells containing a temperature-sensitive eIF3 mutation to the nonpermissive temperature. These experiments, as well as others assaying the strength of factor association in high-salt sucrose gradients, lead us to conclude that Upf1p is tightly bound to the smallest polyribosomes, but not to the 40S or 60S ribosomal subunits. Similar experimental approaches were used to determine whether mRNA decay initiates prior to mRNA release from polyribosomes. Using sucrose gradient fractionation and Northern blotting, we can detect the polysomal association of a PGK1 mRNA decay intermediate and conclude that mRNA decay commences while an mRNA is still being translated.

Genetic Techniques

Reduction of cannula-related laparoscopic complications using a radially expanding access device.

STUDY OBJECTIVE: To determine the safety of a new radially expanding access device compared with complication rates associated with sharp laparoscopic cannulas. DESIGN: Prospective, multicenter study (Canadian Task Force classification II-1). SETTING: Free-standing and hospital-based ambulatory surgery centers. PATIENTS: Two hundred twelve women undergoing various laparoscopic procedures and followed over 44 months. INTERVENTION: Five hundred forty-one radially dilating access devices were used exclusively for laparoscopic abdominal wall access. MEASUREMENTS AND MAIN RESULTS: No major vascular injury, abdominal wall bleeding, intestinal injury, bladder or ureteral injury, liver trauma, or postoperative incisional hernia occurred. One patient developed a postoperative mesenteric hematoma probably caused by a venous injury from the Veress needle. Of the 541 radially expanding access cannulas placed, only 6 (1%) slipped, despite absence of fascial anchoring devices. CONCLUSION: Radially dilating abdominal access devices may reduce laparoscopic complications, lessen a surgeon's exposure to liability, and improve patient outcomes while reducing facility costs. (J Am Assoc Gynecol Laparosc 6(1):79-84, 1999)

Adult

Overexpression of truncated Nmd3p inhibits protein synthesis in yeast.

The yeast NMD3 gene was identified in a two-hybrid screen using the nonsense-mediated mRNA decay factor, Upf1p, as bait. NMD3 was shown to encode an essential, highly conserved protein that associated principally with free 60S ribosomal subunits. Overexpression of a truncated form of Nmd3p, lacking 100 C-terminal amino acids and most of its Upf1p-interacting domain, had dominant-negative effects on both cell growth and protein synthesis and promoted the formation of polyribosome half-mers. These effects were eliminated by truncation of an additional 100 amino acids from Nmd3p. Overexpression of the nmd3delta100 allele also led to increased synthesis and destabilization of some ribosomal protein mRNAs, and increased synthesis and altered processing of 35S pre-rRNA. Our data suggest that Nmd3p has a role in the formation, function, or maintenance of the 60S ribosomal subunit and may provide a link for Upf1p to 80S monosomes.

Amino Acid Sequence

Temperature-sensitive mutations in the Saccharomyces cerevisiae MRT4, GRC5, SLA2 and THS1 genes result in defects in mRNA turnover.

In a screen for factors involved in mRNA turnover, four temperature-sensitive yeast strains (ts1189, ts942, ts817, and ts1100) exhibited defects in the decay of several mRNAs. Complementation of the growth and mRNA decay defects, and genetic experiments, revealed that ts1189 is mutated in the previously unknown MRT4 gene, ts942 is mutated in GRC5 (encoding the L9 ribosomal protein), ts817 contains a mutation in SLA2 (encoding a membrane protein), and ts1100 contains a mutation in THS1 (encoding the threonyl-tRNA synthetase). Three of the four mutants (mrt4, grc5, and sla2) were not defective in protein synthesis, suggesting that these strains contain mutations in factors that may play a specific role in mRNA decay. The mRNA stabilization observed in the ths1 strain, however, could be due to the significant drop in translation observed in this mutant at 37 degrees. While the three interesting mutants appear to encode novel mRNA decay factors, at least one could be linked to a previously characterized mRNA decay pathway. The growth and mRNA decay defects of ts942 (grc5) cells were suppressed by overexpression of the NMD3 gene, encoding a protein shown to participate in a two-hybrid interaction with the nonsense-mediated decay protein Upf1p.

Amino Acid Sequence

A single amino acid substitution in yeast eIF-5A results in mRNA stabilization.

Most factors known to function in mRNA turnover are not essential for cell viability. To identify essential factors, approximately 4000 temperature-sensitive yeast strains were screened for an increase in the level of the unstable CYH2 pre-mRNA. At the non-permissive temperature, five mutants exhibited decreased decay rates of the CYH2 pre-mRNA and mRNA, and the STE2, URA5 and PAB1 mRNAs. Of these, the mutant ts1159 had the most extensive phenotype. Expression of the TIF51A gene (encoding eIF-5A) complemented the temperature-sensitive growth and mRNA decay phenotypes of ts1159. The tif51A allele was rescued from these cells and shown to encode a serine to proline change within a predicted alpha-helical segment of the protein. ts1159 also exhibited an approximately 30% decrease in protein synthesis at the restrictive temperature. Measurement of amino acid incorporation in wild-type cells incubated with increasing amounts of cycloheximide demonstrated that a decrease in protein synthesis of this magnitude could not account for the full extent of the mRNA decay defects observed in ts1159. Interestingly, the ts1159 cells accumulated uncapped mRNAs at the non-permissive temperature. These results suggest that eIF-5A plays a role in mRNA turnover, perhaps acting downstream of decapping.

Alleles

Obesity, health services use, and health care costs among members of a health maintenance organization.

BACKGROUND: Obesity is an independent risk factor for a variety of chronic diseases and is therefore a potential source of avoidable excess health care expenditures. Previous studies of obesity and health care costs have used group level data, applying estimates of population-attributable risks to estimates of US total costs of care for each obesity-related disease. OBJECTIVE: To quantify the association between body mass index (BMI) and health services use and costs stratified by age and use source at the patient level, a level of detail not previously reported. METHODS: In 17,118 respondents to a 1993 health survey of members of a large health maintenance organization, we ascertained through computerized databases all hospitalizations, laboratory services, outpatient visits, outpatient pharmacy and radiology services, and the direct costs of providing these services during 1993. RESULTS: There was an association between BMI and annual rates of inpatient days, number and costs of outpatient visits, costs of outpatient pharmacy and laboratory services, and total costs (P < or = .003). Relative to BMI of 20 to 24.9, mean annual total costs were 25% greater among those with BMI of 30 to 34.9 (rate ratio, 1.25; 95% confidence interval, 1.10-1.41), and 44% greater among those with BMI of 35 or greater (rate ratio, 1.44; 95% confidence interval, 1.22-1.71). The association between BMI and coronary heart disease, hypertension, and diabetes largely explained these elevated costs. CONCLUSION: Given the high prevalence of obesity and the associated elevated rates of health services use and costs, there is a significant potential for a reduction in health care expenditures through obesity prevention efforts.

Adult

An in vivo comparison between a visible light-cured bonding system and a chemically cured bonding system.

Direct bonding of brackets has become a routine procedure in clinical orthodontics. Many techniques and materials are currently advocated and used, the most recent being light-cured composites. Advantages of the light-cured systems are their relative ease of use, improved bracket placement, and more rapid set of the composite. For a new system to be clinically viable, it must possess properties that are at least as reliable as existing systems. The purpose of this longitudinal clinical study was to evaluate and compare the rate of success and/or failure between a visible light-cured bonding material (Sequence) and a chemically cured bonding material (System 1+), using both systems in every patient. Contralateral quadrants were bonded with each system respectively. A total of 32 patients were followed for a mean period of 11 months (range of 3 to 21 months), with a total of 531 brackets bonded, 265 with visible light-cured and 266 with chemically cured resins. Failures for each system were recorded and failure rates calculated. The failure rate of the visible light-cured composite was 11.3% and that of the chemically cured composite was 12%. A Chi-squared (chi2) test did not reveal any statistically significant differences between the failure rates of the two systems, (chi2 = 0.014, df-1, P > 0.9).

Acid Etching, Dental

Viral escape from antisense RNA.

RNA coliphage SP was propagated for several generations on a host expressing an inhibitory antisense RNA complementary to bases 31-270 of the positive-stranded genome. Phages evolved that escaped inhibition. Typically, these escape mutants contained 3-4 base substitutions, but different sequences were observed among different isolates. The mutations were located within three different types of structural features within the predicted secondary structure of SP genomic RNA: (i) hairpin loops; (ii) hairpin stems; and (iii) the 5' region of the phage genome complementary to the antisense molecule. Computer modelling of the mutant genomic RNAs showed that all of the substitutions within hairpin stems improved the Watson-Crick pairing of the stem. No major structural rearrangements were predicted for any of the mutant genomes, and most substitutions in coding regions did not alter the amino acid sequence. Although the evolved phage populations were polymorphic for substitutions, many substitutions appeared independently in two selected lines. The creation of a new, perfect, antisense RNA against an escape mutant resulted in the inhibition of that mutant but not of other escape mutants nor of the ancestral, unevolved phage. Thus, at least in this system, a population of viruses that evolved to escape from a single antisense RNA would require a cocktail of several antisense RNAs for inhibition.

Antiviral Agents

Pbp1p, a factor interacting with Saccharomyces cerevisiae poly(A)-binding protein, regulates polyadenylation.

The poly(A) tail of an mRNA is believed to influence the initiation of translation, and the rate at which the poly(A) tail is removed is thought to determine how fast an mRNA is degraded. One key factor associated with this 3'-end structure is the poly(A)-binding protein (Pab1p) encoded by the PAB1 gene in Saccharomyces cerevisiae. In an effort to learn more about the functional role of this protein, we used a two-hybrid screen to determine the factor(s) with which it interacts. We identified five genes encoding factors that specifically interact with the carboxy terminus of Pab1p. Of a total of 44 specific clones identified, PBP1 (for Pab1p-binding protein) was isolated 38 times. Of the putative interacting genes examined, PBP1 promoted the highest level of resistance to 3-aminotriazole (>100 mM) in constructs in which HIS3 was used as a reporter. We determined that a fraction of Pbp1p cosediments with polysomes in sucrose gradients and that its distribution is very similar to that of Pab1p. Disruption of PBP1 showed that it is not essential for viability but can suppress the lethality associated with a PAB1 deletion. The suppression of pab1Delta by pbp1Delta appears to be different from that mediated by other pab1 suppressors, since disruption of PBP1 does not alter translation rates, affect accumulation of ribosomal subunits, change mRNA poly(A) tail lengths, or result in a defect in mRNA decay. Rather, Pbp1p appears to function in the nucleus to promote proper polyadenylation. In the absence of Pbp1p, 3' termini of pre-mRNAs are properly cleaved but lack full-length poly(A) tails. These effects suggest that Pbp1p may act to repress the ability of Pab1p to negatively regulate polyadenylation.

Amino Acid Sequence

Fission yeast rad12+ regulates cell cycle checkpoint control and is homologous to the Bloom's syndrome disease gene.

The human BLM gene is a member of the Escherichia coli recQ helicase family, which includes the Saccharomyces cerevisiae SGS1 and human WRN genes. Defects in BLM are responsible for the human disease Bloom's syndrome, which is characterized in part by genomic instability and a high incidence of cancer. Here we describe the cloning of rad12+, which is the fission yeast homolog of BLM and is identical to the recently reported rhq1+ gene. We showed that rad12 null cells are sensitive to DNA damage induced by UV light and gamma radiation, as well as to the DNA synthesis inhibitor hydroxyurea. Overexpression of the wild-type rad12+ gene also leads to sensitivity to these agents and to defects associated with the loss of the S-phase and G2-phase checkpoint control. We showed genetically and biochemically that rad12+ acts upstream from rad9+, one of the fission yeast G2 checkpoint control genes, in regulating exit from the S-phase checkpoint. The physical chromosome segregation defects seen in rad12 null cells combined with the checkpoint regulation defect seen in the rad12+ overproducer implicate rad12+ as a key coupler of chromosomal integrity with cell cycle progression.

Adenosine Triphosphatases

Haemorrhage from a duodenal ulcer in a neonate

A 7-week-old boy born at 32 weeks' gestation developed massive upper gastrointestinal bleeding from a duodenal ulcer. The base of the ulcer had eroded into the hepatic artery. Haemorrhage was only controlled following operation.

Journal Article

Low-dose aspirin for oocyte donation recipients with a thin endometrium: prospective, randomized study.

OBJECTIVE: To evaluate the effect of low-dose aspirin use in oocyte donation recipients with an endometrial thickness of < 8 mm. DESIGN: A prospective, randomized study. SETTING: An oocyte donation program in a private infertility practice. PATIENT(S): Twenty-eight recipients undergoing oocyte donation who failed to develop an endometrial thickness of at least 8 mm in a previous evaluation cycle. INTERVENTION(S): Fifteen recipients received low-dose aspirin (81 mg/d) in addition to standard hormone replacement for an oocyte donation cycle. The remaining 13 recipients did not receive aspirin. MAIN OUTCOME MEASURE(S): Clinical pregnancy rates, delivery rates, implantation rates, and change in endometrial thickness were compared in the aspirin and nonaspirin groups. RESULT(S): There was no demonstrable increase in endometrial thickness in the aspirin-treated group. However, there was a statistically significant increase in implantation rates in the aspirin-treated group (24% versus 9%) and in implantation rates and clinical pregnancy rates in the aspirin-treated group when the final endometrial thickness was < 8 mm. CONCLUSION(S): Low-dose aspirin therapy improves implantation rates in oocyte donation recipients with a thin endometrium.

Adult

Apoptosis in lymphoid and parenchymal cells during sepsis: findings in normal and T- and B-cell-deficient mice.

OBJECTIVES: To determine if apoptosis (programmed cell death) occurs systemically in lymphoid and parenchymal cells during sepsis. To examine the potential role of T and B cells in the apoptotic process using knockout mice deficient in mature T and B lymphocytes. DESIGN: Prospective, randomized, controlled trial. SETTING: Animal laboratory in a university medical setting. INTERVENTIONS: Cecal ligation and puncture (CLP) (n = 34) or sham surgery (n = 13) was performed in female ND4 mice and, 15 to 22 hrs postoperatively, thymus, lung, heart, spleen, ileum, colon, liver, kidney, brain, and muscle were obtained and examined for apoptosis. A second group of mice (Rag-1) which are totally deficient in mature T and B cells also underwent CLP (n = 14) or sham surgery (n = 14) and had examination of tissues for apoptosis. MEASUREMENTS AND MAIN RESULTS: Four methods with varying sensitivities and specificities were used to detect apoptosis, including: a) DNA agarose gel electrophoresis; b) terminal deoxynucleotidyl transferase mediated dUTP nick end labeling (TUNEL); c) electron microscopy; and d) light microscopy. In CLP mice, multiple methods demonstrated apoptosis in lymphocytes in thymus, spleen, ileum, colon, lung, and skeletal muscle. In addition to lymphocytes, parenchymal cells in ileum, colon, lung, and to a lesser extent, in skeletal muscle and kidney were apoptotic in CLP mice. There was no evidence of apoptosis by any method of detection in liver, brain, or heart. Results in Rag-1 mice which are deficient in T and B cells demonstrated extensive apoptosis in thymus, spleen, and ileum with less degrees of apoptosis in colon and lung. Both lymphoid cells and parenchymal cells were apoptotic. Rag-1 mice which underwent CLP did not die prematurely and there were no apparent observable differences in the physical response (tachypnea, piloerection, lethargy, etc), or intra-abdominal bowel inflammation/adhesions compared with CLP mice with normal T and B cells. CONCLUSIONS: Apoptosis is an important mechanism of cell death in lymphocytes and parenchymal cells in sepsis and occurs systemically in many organs. Apoptosis may be an important cause of immunologic suppression in sepsis by inducing widespread lymphocyte depletion. Alternately, apoptosis may be beneficial to host survival by down-regulating the inflammatory response which accompanies sepsis. The degree to which parenchymal cell apoptosis is contributing to multiple organ failure cannot be determined from the present study. Findings in Rag-1 mice demonstrate that mature T and B cells and their secretory products are not necessary for apoptosis to occur during sepsis and that apoptotic cell death is not restricted to T or B cells. Apoptosis may be a key regulator of the balance between the pro- and anti-inflammatory process.

Animals

Upf1p, Nmd2p, and Upf3p are interacting components of the yeast nonsense-mediated mRNA decay pathway.

Rapid turnover of nonsense-containing mRNAs in Saccharomyces cerevisiae is dependent on Upf1p, Nmd2p, and Upf3p, the products of the UPF1, NMD2/UPF2, and UPF3 genes, respectively. We showed previously that Upf1p and Nmd2p interact and that this interaction is required for nonsense-mediated mRNA decay (F. He and A. Jacobson, Genes Dev. 9:437-454, 1995; F. He, A. H. Brown, and A. Jacobson, RNA 2:153-170, 1996). In this study we have used the yeast two-hybrid system to define other protein-protein interactions among the essential components of this decay pathway. Nmd2p-Upf3p and Upf1p-Upf3p interactions were identified, and the respective domains involved in these interactions were delineated by deletion analysis. The domains of Upf1p and Upf3p putatively involved in their mutual interaction were found to correspond to the domains on the two proteins which interact with Nmd2p, suggesting that Nmd2p bridges Upf1p and Upf3p. This conclusion was reinforced by experiments showing that: (i) deletion of NMD2 completely abolishes interactions between Upf1p and Upf3p and (ii) overexpression of full-length Nmd2p or Nmd2p fragments that retain Upf1p- and Upf3p-interacting domains promotes 10- to 200-fold enhancement of Upf1p-Nmd2p-Upf3p complex formation. These results; the observation that cells harboring either single or multiple deletions of UPF1, NMD2, and UPF3 inhibit nonsense-mediated mRNA decay to the same extent; and an analysis of the possible targets of a dominant-negative NMD2 allele indicate that Upf1p, Nmd2p, Upf3p, and at least one other factor are functionally dependent, interacting components of the yeast nonsense-mediated mRNA decay pathway.

Adaptor Proteins, Signal Transducing

Polysome-associated mRNAs are substrates for the nonsense-mediated mRNA decay pathway in Saccharomyces cerevisiae.

In eukaryotic cells, premature termination of translation at nonsense codons has been implicated as the cause of a variety of posttranscriptional events, including rapid mRNA decay in the cytoplasm or the nucleus, altered splice site selection, and exon skipping. In the yeast Saccharomyces cerevisiae, nonsense codons promote accelerated mRNA decay, and we sought to determine the cellular location in which this degradation occurs. In this report, we demonstrate that six different mRNAs, including nonsense-containing transcripts of the LEU2, HIS4, PGK1, and CYH2 genes, and two wild-type mRNAs (the MAT(alpha)1 and CYH2 mRNAs), were stabilized when the translation elongation inhibitor cycloheximide was added to cellular growth media. Subsequent removal of cycloheximide resulted in resumption of translation and degradation of wild-type and nonsense-containing mRNAs. A significant fraction of the CYH2 pre-mRNA that accumulated in the presence of cycloheximide was associated with polysomes, but disappeared from that fraction when decay resumed in the absence of the drug. Moreover, the abundance of the spliced and unspliced forms of the untranslated U3 snRNA was shown to be unaffected in strains harboring mutations that stabilize nonsense-containing mRNAs. Taken together, these observations indicate that nonsense-containing mRNAs in yeast are degraded within the polysome compartment of the cell.

Codon, Nonsense

Haemorrhage from a duodenal ulcer in a neonate.

A 7-week-old boy born at 32 weeks' gestation developed massive upper gastrointestinal bleeding from a duodenal ulcer. The base of the ulcer had eroded into the hepatic artery. Haemorrhage was only controlled following operation.

Duodenal Ulcer