Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA

1-Methyladenosine modification at position 58 of tRNA is catalyzed by a two-subunit methyltransferase composed of Trm6p and Trm61p in Saccharomyces cerevisiae. Initiator tRNA (tRNAi(Met)) lacking m1A58 (hypomethylated) is rendered unstable through the cooperative function of the poly(A) polymerases, Trf4p/Trf5p, and the nuclear exosome. We provide evidence that a catalytically active Trf4p poly(A) polymerase is required for polyadenylation of hypomethylated tRNAi(Met) in vivo. DNA sequence analysis of tRNAi(Met) cDNAs and Northern hybridizations of poly(A)+ RNA provide evidence that nascent pre-tRNAi(Met) transcripts are targeted for polyadenylation and degradation. We determined that a mutant U6 snRNA and an aberrant form of 5S rRNA are stabilized in the absence of Trf4p, supporting that Trf4p facilitated RNA surveillance is a global process that stretches beyond hypomethylated tRNAi(Met). We conclude that an array of RNA polymerase III transcripts are targeted for Trf4p/ Trf5p-dependent polyadenylation and turnover to eliminate mutant and variant forms of normally stable RNAs.

RNA turnover: unexpected consequences of being tailed

In eukaryotic cells, the 3' poly(A) tails found on mRNA influence their stability and translation. The discovery of a second nuclear poly(A) polymerase complex has fueled a series of reports defining a new and unexpected role for 3' end poly(A) tails in the nuclear surveillance and turnover of noncoding RNAs and intergenic mRNAs of unknown function.

Identification of novel and improved antimitotic agents derived from noscapine

Analogues of the natural product noscapine were synthesized and their potential as antitumor agents evaluated. The discovery of a novel regioselective O-demethylation facilitated the synthesis of the potent aniline 6, which arrests mammalian cells in the G2/M phase of the cell cycle at 0.1 microM and also affects tubulin polymerization. Aniline 6 is orally bioavailable and is 250-fold more potent than noscapine in reducing cell proliferation in rapidly dividing cells.

The bipartite structure of the tRNA m1A58 methyltransferase from S. cerevisiae is conserved in humans

Among all types of RNA, tRNA is unique given that it possesses the largest assortment and abundance of modified nucleosides. The methylation at N(1) of adenosine 58 is a conserved modification, occurring in bacterial, archaeal, and eukaryotic tRNAs. In the yeast Saccharomyces cerevisiae, the tRNA 1-methyladenosine 58 (m(1)A58) methyltransferase (Mtase) is a two-subunit enzyme encoded by the essential genes TRM6 (GCD10) and TRM61 (GCD14). While the significance of many tRNA modifications is poorly understood, methylation of A58 is known to be critical for maintaining the stability of initiator tRNA(Met) in yeast. Furthermore, all retroviruses utilize m(1)A58-containing tRNAs to prime reverse transcription, and it has been shown that the presence of m(1)A58 in human tRNA(3) (Lys) is needed for accurate termination of plus-strand strong-stop DNA synthesis during HIV-1 replication. In this study we have identified the human homologs of the yeast m(1)A Mtase through amino acid sequence identity and complementation of trm6 and trm61 mutant phenotypes. When coexpressed in yeast, human Trm6p and Trm61p restored the formation of m(1)A in tRNA, modifying both yeast initiator tRNA(Met) and human tRNA(3) (Lys). Stable hTrm6p/hTrm61p complexes purified from yeast maintained tRNA m(1)A Mtase activity in vitro. The human m(1)A Mtase complex also exhibited substrate specificity--modifying wild-type yeast tRNA(i) (Met) but not an A58U mutant. Therefore, the human tRNA m(1)A Mtase shares both functional and structural homology with the yeast tRNA m(1)A Mtase, possessing similar enzymatic activity as well as a conserved binary composition.

Discovery of S-phase arresting agents derived from noscapine

Analogues of the natural product noscapine were synthesized, and their potential as antitumor agents were examined. The discovery of a novel regio- and stereoselective O-demethylation led to the synthesis of several O-alkylated analogues that induced an unexpected S-phase arrest of mammalian cells. Compound 4a was the most potent analogue inhibiting cell proliferation at an EC(50) of 1.9 microM.

Fluorous Effect in Proteins: De Novo Design and Characterization of a Four-α-Helix Bundle Protein Containing Hexafluoroleucine

Several studies have demonstrated that proteins incorporating fluorinated analogues of hydrophobic amino acids such as leucine and valine into their hydrophobic cores exhibit increased stability toward thermal denaturation and unfolding by guanidinium chloride. However, estimates for the increase in the thermodynamic stability of a protein (DeltaDeltaG(unfold)) afforded by the substitution of a hydrophobic amino acid with its fluorinated analogue vary quite significantly. To address this, we have designed a peptide that adopts an antiparallel four-helix bundle structure in which the hydrophobic core is packed with leucine, and investigated the effects of substituting the central two layers of the core with L-5,5,5,5',5',5'-hexafluoroleucine (hFLeu). We find that DeltaDeltaG(unfold) is increased by 0.3 kcal/mol per hFLeu residue. This is in good agreement with the predicted increase in DeltaDeltaG(unfold) of 0.4 kcal/mol per residue arising from the increased hydrophobicity of the hFLeu side chain, which we determined experimentally from partitioning measurements on hFLeu and leucine. The increased stability of this fluorinated protein may therefore be ascribed to simple hydrophobic effects, rather than specific "fluorous" interactions between the hFLeu residues.

Effects of pneumoperitoneum on intraoperative pulmonary mechanics and gas exchange during laparoscopic gastric bypass

BACKGROUND

Hypercarbia and elevated intraabdominal pressure resulting from carbon dioxide (CO2) pneumoperitoneum can adversely affect respiratory mechanics. This study examined the changes in mechanical ventilation, CO2 homeostasis, and pulmonary gas exchange in morbidly obese patients undergoing a laparoscopic or open gastric bypass (GBP) procedure.

METHODS

In this study, 58 patients with a body mass index (BMI) of 40 to 60 kg/m2 were randomly allocated to laparoscopic ( n = 31) or open ( n = 27) GBP. Minute ventilation was adjusted to maintain a low normal arterial partial pressure of CO2 (PaCO2), low normal end-tidal partial pressure of CO2 (ETCO2), and low airway pressure. Respiratory compliance, ETCO2, peak inspiratory pressure (PIP), total exhaled CO2 per minute (VCO2), and pulse oximetry (SO2) were measured at 30-min intervals. The acid-base balance was determined by arterial blood gas analysis at 1-h intervals. The pulmonary gas exchange was evaluated by calculation of the alveolar dead space-to-tidal volume ratio (V(Dalv)/V(T)) and alveolar-arterial oxygen gradient (PAO2-PaO2).

RESULTS

The two groups were similar in age, gender, and BMI. As compared with open GBP, laparoscopic GBP resulted in higher ETCO2, PIP, and VCO2, and a lower respiratory compliance. Arterial blood gas analysis demonstrated higher PaCO2 and lower pH during laparoscopic GBP than during open GBP ( p < 0.05). The V(Dalv)/V(T) ratio and PAO2-PaO2 gradient did not change significantly during laparoscopic GBP. Intraoperative oxygen desaturation (SO2 < 90%) did not develop in any of the patients in either group.

CONCLUSIONS

Laparoscopic GBP alters intraoperative pulmonary mechanics and acid-base balance but does not significantly affect pulmonary oxygen exchange. Changes in pulmonary mechanics are well tolerated in morbidly obese patients when proper ventilator adjustments are maintained.

A short and efficient synthesis of L-5,5,5,5',5',5'-hexafluoroleucine from N-Cbz-L-serine

[reaction: see text] 5,5,5,5',5',5'-Hexafluoroleucine (6), a fluorous analogue of leucine, is of considerable interest as a building block in the design of fluorous proteins and peptides. We report a short and efficient synthesis of 6, which is obtained from N-Cbz-L-serine (1) in 50% overall yield, 99% enantiomeric excess, and in multigram quantities. Key steps are addition of a serine-derived organozincate to hexafluoroacetone to construct the hexafluoroleucine side chain, followed by radical-mediated deoxygenation of the resulting tertiary alcohol.

Development of an effective chiral auxiliary for hydroxyalkyl radicals

The development of an effective chiral auxiliary for hydroxyalkyl radicals is delineated. Both the 2-tetrahydropyranyl (THP) and tri-O-benzyl-2-deoxy-alpha-D-glucopyranosyl (GLU) auxiliaries resulted in diastereoselective radical additions to methyl acrylate at -78 degrees C (ds = 6/1 and 11/1, respectively). The developing stereochemistry at the radical center was completely under auxiliary control. Correlation experiments showed that the D-GLU auxiliary led to attack on the radical Si-face. The selectivity of these radical additions dropped-off considerably when the more reactive 2-nitropropene trap was employed. Computational studies suggested that the observed facial selectivity was due primarily to entropic factors in the transition state but that a smaller temperature-dependent enthalpic contribution was also involved. It was hypothesized that incorporation of a quaternary center at C-6 (THP numbering) would restore the facial selectivity with more reactive radical traps by restricting the orientations available to the incoming alkene. In the event, the trans-6-tert-butyltetrahydropyranyl (tBu-THP) auxiliary resulted in very good diastereoselection with 2-nitropropene (ds = 35/1 at -78 degrees C, 15/1 at 0 degrees C, and 8/1 at RT) as did the tri-O-benzyl-6,6-dimethyl-2-alpha-D-deoxyglucopyranosyl (diMe-GLU) auxiliary during additions to ethyl alpha-trifluoroacetoxyacrylate (ds = 10/1 at 0 degrees C). A protocol for recovery of the sugar-derived chiral auxiliaries was also established. This work sets the stage for the development of a novel approach to 1, 3, 5.(2n + 1) polyols based on iterative radical homologation as well as the application of these pyranosidic auxiliaries to other synthetically important reactions.

Dual requirement for yeast hnRNP Nab2p in mRNA poly(A) tail length control and nuclear export

Recent studies of mRNA export factors have provided additional evidence for a mechanistic link between mRNA 3'-end formation and nuclear export. Here, we identify Nab2p as a nuclear poly(A)-binding protein required for both poly(A) tail length control and nuclear export of mRNA. Loss of NAB2 expression leads to hyperadenylation and nuclear accumulation of poly(A)(+) RNA but, in contrast to mRNA export mutants, these defects can be uncoupled in a nab2 mutant strain. Previous studies have implicated the cytoplasmic poly(A) tail-binding protein Pab1p in poly(A) tail length control during polyadenylation. Although cells are viable in the absence of NAB2 expression when PAB1 is overexpressed, Pab1p fails to resolve the nab2Delta hyperadenylation defect even when Pab1p is tagged with a nuclear localization sequence and targeted to the nucleus. These results indicate that Nab2p is essential for poly(A) tail length control in vivo, and we demonstrate that Nab2p activates polyadenylation, while inhibiting hyperadenylation, in the absence of Pab1p in vitro. We propose that Nab2p provides an important link between the termination of mRNA polyadenylation and nuclear export.

Multiinstitutional experience with the management of superior mesenteric artery injuries

BACKGROUND

Superior mesenteric artery (SMA) injuries are rare and often lethal injuries incurring very high morbidity and mortality. The purposes of this study are to review a multiinstitutional experience with these injuries; to analyze Fullen's classification based on anatomic zone and ischemia grade for its predictive value; to correlate the American Association for the Surgery of Trauma-Organ Injury Scale (AAST-OIS) for abdominal vascular injury with mortality; and to identify independent risk factors predictive of mortality, describing current trends for the management of this injury in America.

DESIGN

We performed a retrospective multiinstitutional study of patients sustaining SMA injuries involving 34 trauma centers in the US over 10 years. Outcomes variables, both continuous and dichotomous, were analyzed initially with univariate methods. For the subsequent multivariate analysis, stepwise logistic regression was used to identify a set of risk factors significantly associated with mortality.

RESULTS

There were 250 patients enrolled, with a mean Revised Trauma Score (RTS) of 6.44 and a mean Injury Severity Score (ISS) of 25. Surgical management consisted of ligation in 175 of 244 patients (72%), primary [corrected] repair in 53 of 244 patients (22%), autogenous grafts were used in 10 of 244 (4%), and prosthetic grafts of PTFE in 6 of 244 patients (2%). Overall mortality was 97 of 250 patients (39%). Mortality versus Fullen's zones: zone I, 39 of 51 (76.5%); zone II, 15 of 34 (44.1%); zone III, 11 of 40 (27.5%); and zone IV, 25 of 108 (23.1%). Mortality versus Fullen's ischemia grade: grade 1, 22 of 34 (64.7%). Mortality versus AAST-OIS for abdominal vascular injury: grade I, 9 of 55 (16.4%); grade II, 13 of 51 (25.5%); grade III, 8 of 20 (40%); grade IV, 37 of 69 (53.6%); and grade V, 17 of 19 (89.5%). Logistic regression analysis identified as independent risk factors for mortality the following: transfusion of greater than 10 units of packed RBCs, intraoperative acidosis, dysrhythmias, injury to Fullen's zone I or II, and multisystem organ failure.

CONCLUSION

SMA injuries are highly lethal. Fullen's anatomic zones, ischemia grade, and AAST-OIS abdominal vascular injuries correlate well with mortality. Injuries to Fullen's zones I and II, Fullen's maximal ischemia grade, and AAST-OIS injury grades IV and V, high-intraoperative transfusion requirements, and presence of acidosis and disrhythmias are significant predictors of mortality. All of these predictive factors for mortality must be taken into account in the surgical management of these injuries.

Practical utility of the D-dimer assay for excluding thromboembolism in severely injured trauma patients

BACKGROUND

We have advocated the use of a D-dimer assay to exclude the diagnosis of pulmonary embolism (PE) and deep venous thrombosis (DVT) in surgical and trauma patients suspected of having these diagnoses. Injury is known to increase D-dimer levels independent of thromboembolism. The purpose of this study was to assess the period after injury over which the D-dimer assay remains positive because of injury exclusive of thromboembolism.

METHODS

We prospectively sampled the plasma of severely injured patients for D-dimer using an enzyme-linked immunosorbent assay method at admission; at hours 8, 16, 24, and 48; and at days 3, 4, 5, and 6. Patients were then screened for DVT with a routine duplex Doppler at day 7. Patients were followed for PE, adult respiratory distress syndrome, and disseminated intravascular coagulation.

RESULTS

One hundred fifty-four patients (mean Injury Severity Score of 23) underwent a total of 1,230 D-dimer assays. Twenty-six (17%) had thromboembolism. Nine (6%) patients developed DVT, 2 (1%) developed PE, 13 (8%) developed disseminated intravascular coagulation, and 11 (7%) developed severe adult respiratory distress syndrome. None of the trauma patients with thromboembolism had a (false) negative D-dimer at or after the time of their thromboembolic complication. True-negative D-dimer results as a function of time from injury are: 0 hours, 18%; 8 hours, 16%; 16 hours, 17%; 24 hours, 22%; 48 hours, 37%; day 3, 34%; day 4, 32%; day 5, 30%; and day 6, 30%. The negative predictive value of the assay was 100%. D-dimer levels were significantly higher in those who developed a thromboembolic complication than in those who did not (independent of Injury Severity Score).

CONCLUSION

These data serve to validate D-dimer as a means of excluding thromboembolism, specifically in patients with severe injury (100% negative predictive value). Before 48 hours after injury, however, the vast majority of these patients without thromboembolism had positive D-dimer assays. Because of the high false-positive rate early after severe injury, the D-dimer assay may be of little value before postinjury hour 48.

Evaluation of intra-abdominal pressure after laparoscopic and open gastric bypass

BACKGROUND

Increased intra-abdominal pressure (IAP) postoperatively can adversely affect cardiovascular, pulmonary, and renal function. In this prospective, randomized trial, we compared the IAP in morbidly obese patients after laparoscopic and open gastric bypass (GBP) surgery.

METHODS

64 patients with a body mass index of 40 to 60 kg/m2 were randomized to undergo laparoscopic or open GBP. IAPs were obtained at baseline (after induction of anesthesia), immediately after the operation, and on post-operative day (POD) 1, 2, and 3. Intraoperative and postoperative fluid requirements, urine output, and creatinine clearance were recorded.

RESULTS

Demographics of the two groups were similar. IAP increased from baseline immediately after laparoscopic and open GBP (p < 0.05). IAP returned to baseline by POD 2 after laparoscopic GBP but remained elevated through POD 3 after open GBP. In fact, IAP was lower after laparoscopic GBP than after open GBP on POD 1, 2 and 3 (p < 0.05). The amount of intraoperative IV fluid was similar between groups, but laparoscopic GBP required less IV fluid and facilitated higher urine output postoperatively than open GBP. There was no significant difference in creatinine clearance between groups.

CONCLUSIONS

Laparoscopic GBP resulted in significantly lower IAP, less postoperative fluid required, and greater postoperative urine output than open GBP.

Surgical treatment of atrial fibrillation using radiofrequency energy

BACKGROUND

The Maze III procedure for atrial fibrillation (AF) is effective but has not been used widely due to its complexity, bleeding risk, and added operative time. Surgical radiofrequency ablation may simplify the procedure and make intraoperative correction of AF more accessible and widely performed.

METHODS

Endocardial pulmonary venous isolation was performed on 48 patients with AF undergoing concurrent operation using temperature-controlled radiofrequency energy delivered through a hand-held flexible probe. Additional right-sided lesions were made at the surgeon's discretion.

RESULTS

Forty-two patients were appropriate for analysis (6 died). These patients had an AF duration of 4.8 +/- 6.4 years. At a mean follow-up of 138 +/- 96 days, 34 patients were in sinus rhythm. We were unable to demonstrate a difference in outcome based on AF duration, left atrial size, or addition of right-sided lesions.

CONCLUSIONS

Radiofrequency atrial ablation was effective in 81% of patients with AF at restoring sinus rhythm at an average follow-up of 4 months. This procedure is simple to perform and should broaden the number of patients that receive an AF treatment procedure during concurrent cardiac operation.

Pathologic femoral shaft fractures comparing fixation techniques using cement

To determine the most stable mode of internal fixation for the pathologic femoral shaft fracture with extensive cortical destruction, 2 fixation techniques incorporating methylmethacrylate were compared. Osteotomies through standardized cortical defects were created in intact embalmed femora to simulate a standard pathologic fracture. Fixation obtained with either intramedullary Schneider rods or 28-hold ASIF plates, both using bone cement, was compared in torsion and bending. In torsion, plate-fixed femora failed at a mean load of 71.2 newton-meters compared to 26.8 newton-meters for the Schneider rod counterparts. In bending, plate-fixed bones at a mean load of 8133.9 newtons compared to 1921.4 newtons for rod-fixed femora. Fixation with double plates and methylmethacrylate was clearly more stable and allowed for immediate pain-free ambulation.

Injury surveillance in construction: injuries to laborers

Construction is one of the largest industries in the United States, employing over 7.5 million people. It accounts for 3 times as many accidents as might be expected on a per capita basis. Laborers represent one of 15 job classifications participating in this industry. They have a higher risk of death or injury from a number of causes than do other construction workers.

Whole blood D-dimer assay: an effective noninvasive method to rule out pulmonary embolism

BACKGROUND

The whole blood D-dimer assay has gained recognition as a noninvasive test to rule out pulmonary embolism (PE) in medical patients.

METHODS

We performed a whole blood D-dimer assay in medical and surgical patients undergoing either pulmonary angiogram or pulmonary ventilation perfusion scan for suspected PE or duplex Doppler or venogram for suspected deep venous thrombosis (DVT).

RESULTS

A total of 483 patients were enrolled; 16 were excluded because of an equivocal pulmonary ventilation perfusion scan. The 467 remaining patients had a mean age of 56 +/- 27 years. There were 258 women and 209 men. A total of 353 patients were admitted to a medical service and 114 to surgery/ trauma. A total of 82 patients (18%) developed thromboembolism: 20 had PE, and 62 had DVT.

CONCLUSION

No surgical patient with PE or DVT (n = 27) had a negative D-dimer. A negative D-dimer result in a stable surgical patient should be considered conclusive evidence to rule out thromboembolism and, thus, negate the need for further diagnostic studies. In our surgical patients suspected of DVT or PE, had D-dimer been used, one third of the patients would have avoided an expensive or invasive diagnostic test.

Injury and employment patterns among Hispanic construction workers

This article describes non-fatal injuries among Hispanic construction workers treated at an emergency department from 1990 to 1998. Medical and interview data were analyzed to evaluate and explain the workers' apparently inflated risk of injury. The majority of the injured Hispanic workers were employed in the less-skilled trades. Compared with other injured workers, Hispanics had a higher proportion of serious injuries and were disadvantaged in terms of training and union status. With the exception of union status, these differences largely disappeared after controlling for trade. The physical, financial, and emotional consequences were more apparent 1 year later for injured Hispanics, even after controlling for trade. These observations suggest that minority status is a predictor of trade and that trade is a predictor of injury risk. In addition to reducing injury hazards, interventions should address the limited employment and union membership options that are available to minority workers in the construction industry.