The C-terminal WD40 repeats on the TOPLESS co-repressor function as a protein-protein interaction surface.

KEY MESSAGE: The two predicted WD40 propellers on TOPLESS function as protein-protein interaction domains. The 1st WD40 propeller mediates interaction with RAV1, and the 2nd WD40 propeller mediates interaction with VRN5. The TOPLESS/TOPLESS-RELATED (TPL/TPR) co-repressor family proteins are known to interact with a wide variety of proteins including transcription factors, Mediator subunits, histone deacetylases, and histone tails. Through these interactions, TPL/TPR act to repress transcription in an increasingly diverse array of plant pathways. Proteins that bind TPL/TPR typically contain one or more Repression Domains (RDs) that mediate the interaction. For example, the well-characterized Ethylene response factor-associated Amphiphilic Repression (EAR) motif is known to facilitate interaction by binding the TOPLESS Domain (TPD) located in the N-terminus. Here we show that in yeast two-hybrid assays, the non-EAR protein, Related to ABI3/VP1-1 (RAV1), binds a novel region located within the first nine WD40-repeats of TPL. Protein modeling and in silico analysis suggest that these nine WD40 repeats may form the first of two WD40 propellers located on C-terminus of TPL. The interaction between RAV1 and the 1st WD40 propeller is conserved with another RAV family member, TEMPRANILLO1 (TEM1) and is mediated by the B3 Repression Domain (BRD) located on both RAV1 and TEM1. Also, the predicted 2nd WD40 propeller was shown in yeast cells to bind Vernalization 5 (VRN5), which contains several unconfirmed partial RDs. Furthermore, we demonstrate that the 1st WD40 propeller of TPL can form a complex with RAV1 both in yeast and in Arabidopsis protoplasts.

Proteomics dataset containing proteins that obscure identification of TOPLESS interactors in Arabidopsis.

Here we report proteins identified after conducting Tandem Affinity Purification (TAP) of the TOPLESS (TPL) corepressor from Arabidopsis. We generated transgenic plants harboring TPL fused to the GS-TAG, "Boosting tandem affinity purification of plant protein complexes" (Van Leene et al., 2008) [1]. Four independent biological replicates of a selected TPL-GS-TAG line were grown simultaneously, crosslinked with formaldehyde, and proteins were isolated from whole plant tissue via TAP. Purified proteins were treated with trypsin, and the peptides were analyzed via mass spectrometry. Datasets are hosted in the MassIVE public repository (reference number: MSV000082477, https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=f16255fb7080426a9fe1926b4d3d5862). The data in this article has not been published elsewhere and is original to this work.

Decreasing the Preincision Time for Pulmonary Lobectomy: The Process of Lean and Value Stream Mapping.

BACKGROUND: Our objective was to evaluate our results after the implementation of lean (the elimination of wasteful parts of a process). METHODS: After meetings with our anesthesiologists, we standardized our "in the operating room-to-skin incision protocols" before pulmonary lobectomy. Patients were divided into consecutive cohorts of 300 lobectomy patients. Several protocols were slowly adopted and outcomes were evaluated. RESULTS: One surgeon performed 2,206 pulmonary lobectomies, of which 84% were for cancer. Protocols for lateral decubitus positioning changed over time. We eliminated axillary rolls, arm boards, and beanbags. Monitoring devices were slowly eliminated. Central catheters decreased from 75% to 0% of patients, epidurals from 84% to 3%, arterial catheters from 93% to 4%, and finally, Foley catheters were reduced from 99% to 11% (p ≤ 0.001 for all). A protocol for the insertion of double-lumen endotracheal tubes was established and times decreased (mean, 14 minutes to 1 minute; p = 0.001). After all changes were made, the time between operating room entry and incision decreased from a mean of 64 minutes to 37 minutes (p < 0.001). Outcomes improved, mortality decreased from 3.2% to 0.26% (p = 0.015), and major morbidity decreased from 15.2% to 5.3% (p = 0.042). CONCLUSIONS: Lean and value stream mapping can be safely applied to the clinical algorithms of high-risk patient care. We demonstrate that elimination of non-value-added steps can safely decrease preincision time without increasing patient risk in patients who undergo pulmonary lobectomy. Selected centers may be able to adopt some of these lean-driven protocols.

Adaptation of the Agrobacterium tumefaciens VirG response regulator to activate transcription in plants.

The Agrobacterium tumefaciens VirG response regulator of the VirA/VirG two-component system was adapted to function in tobacco protoplasts. The subcellular localization of VirG and VirA proteins transiently expressed in onion cells was determined using GFP fusions. Preliminary studies using Gal4DBD-VP16 fusions with VirG and Escherichia coli UhpA, and NarL response regulators indicated compatibility of these bacterial proteins with the eukaryotic transcriptional apparatus. A strong transcriptional activator based on tandem activation domains from the Drosophila fushi tarazu and Herpes simplex VP16 was created. Selected configurations of the two-site Gal4-vir box GUS reporters were activated by chimeric effectors dependent on either the yeast Gal4 DNA-binding domain or that of VirG. Transcriptional induction of the GUS reporter was highest for the VirE19-element promoter with both constitutive and wild-type VirG-tandem activation domain effectors. Multiple VirE19 elements increased the reporter activity proportionately, indicating that the VirG DNA binding domain was functional in plants. The VirG constitutive-Q-VP16 effector was more active than the VirG wild-type. In both the constitutive and wild-type forms of VirG, Q-VP16 activated transcription of the GUS reporter best when located at the C-terminus, i.e. juxtaposed to the VirG DNA binding domain. These results demonstrate the possibility of using DNA binding domains from bacterial response regulators and their cognate binding elements in the engineering of plant gene expression.

Ultrasound-guided femoral vein catheterization in neonates with cardiac disease*.

OBJECTIVE: To describe a novel technique for real-time, ultrasound-guided femoral vein catheterization in neonates with cardiac disease, and to compare it to a contemporaneous cohort of neonates undergoing femoral vein central venous line placement via landmark technique. DESIGN: Retrospective cohort study of data extracted from a quality improvement database. SETTING: Pediatric cardiac intensive care unit and cardiovascular operating room in pediatric tertiary hospital. PATIENTS: One hundred fifteen neonates (mean weight, 3.07 ± 0.41 kg) with cardiac disease who underwent femoral central venous line attempts from January 2009 to September 2011. MEASUREMENTS AND MAIN RESULTS: Study populations were similar in age, weight, and Risk Adjustment for Congenital Heart Surgery-1 category, but differed in intubation status (32% vs. 100%, ultrasound vs. landmark, p < .0001). Central venous line success rate was superior in the ultrasound group: 72 of the 76 (94.7%) vs. 31 of the 39 (79.5%), p = .02. Ultrasound group also had a superior first (75% vs. 30.8 %) and second attempt success rate (90.8% vs. 51.3%), p value for both < .0001. Inadvertent arterial puncture occurred less frequently in the ultrasound group: four of the 76 (5.3%) vs. nine of the 39 (23.1%), p = .01. There was a trend toward more venous thrombosis in the landmark group, 16 of the 39 (41%) vs. 18 of the 76 (23.7%), p = .08. Among all 115 subjects, there was a very strong association between greater than two central venous line attempts and the odds of being diagnosed with a deep venous thrombosis (odds ratio, 9.3; 95% confidence interval 3.5-24.8) and the odds of suffering an inadvertent femoral arterial puncture during the central venous line event (odds ratio, 8.8; 95% confidence interval 10.6-730). CONCLUSIONS: This novel long-axis real-time ultrasound technique facilitates placement of femoral vein central venous line in critically ill neonates with cardiac disease at a higher rate of success with fewer attempts and lower occurrence of complications when compared with the landmark technique.

A strategy for building an amplified transcriptional switch to detect bacterial contamination of plants.

We have designed and tested a transcriptional autofeedback loop that could be used to engineer plants to sense the presence of bacteria. The signal amplification circuit was built based on the biological switch responsive to the presence of bacterial flagellin. Several flagellin- and E. coli-inducible Arabidopsis promoters were cloned and tested in transient expression assays in Arabidopsis and lettuce protoplasts using a flagellin-based peptide. These were investigated either as direct drivers of a reporter gene, or as a component of a transcriptional autofeedback loop. Arabidopsis promoters from the xyloglucan endotransglucosylase/hydrolase 18 (ATXTH18) and cytochrome P450 family CYP82C3 monooxygenase worked well as biological switches. These promoters were incorporated into our feedback loop system for signal amplification. The inclusion of a transcriptional repressor reduced basal expression, thereby increasing fold-amplification of signal detection and fine-tuning the positive autofeedback loop regulation.

Parabolic flight induces changes in gene expression patterns in Arabidopsis thaliana.

Our primary objective was to evaluate gene expression changes in Arabidopsis thaliana in response to parabolic flight as part of a comprehensive approach to the molecular biology of spaceflight-related adaptations. In addition, we wished to establish parabolic flight as a tractable operations platform for molecular biology studies. In a succession of experiments on NASA's KC-135 and C-9 parabolic aircraft, Arabidopsis plants were presented with replicated exposure to parabolic flight. Transcriptome profiling revealed that parabolic flight caused changes in gene expression patterns that stood the statistical tests of replication on three different flight days. The earliest response, after 20 parabolas, was characterized by a prominence of genes associated with signal transduction. After 40 parabolas, this prominence was largely replaced by genes associated with biotic and abiotic stimuli and stress. Among these responses, three metabolic processes stand out in particular: the induction of auxin metabolism and signaling, the differential expression of genes associated with calcium-mediated signaling, and the repression of genes associated with disease resistance and cell wall biochemistry. Many, but not all, of these responses are known to be involved in gravity sensing in plants. Changes in auxin-related gene expression were also recorded by reporter genes tuned to auxin signal pathways. These data demonstrate that the parabolic flight environment is appropriate for molecular biology research involving the transition to microgravity, in that with replication, proper controls, and analyses, gene expression changes can be observed in the time frames of typical parabolic flight experiments.

Yeast two-hybrid map of Arabidopsis TFIID.

General transcription factor IID (TFIID) is a multisubunit protein complex involved in promoter recognition and is fundamental to the nucleation of the RNA polymerase II transcriptional preinitiation complex. TFIID is comprised of the TATA binding protein (TBP) and 12-15 TBP-associated factors (TAFs). While general transcription factors have been extensively studied in metazoans and yeast, little is known about the details of their structure and function in the plant kingdom. This work represents the first attempt to compare the structure of a plant TFIID complex with that determined for other organisms. While no TAF3 homolog has been observed in plants, at least one homolog has been identified for each of the remaining 14 TFIID subunits, including both TAF14 and TAF15 which have previously been shown to be unique to either yeast or humans. The presence of both TAFs 14 and 15 in plants suggests ancient roles for these proteins that were lost in metazoans and fungi, respectively. Yeast two-hybrid interaction assays resulted in a total of 65 binary interactions between putative subunits of Arabidopsis TFIID, including 26 contacts unique to plants. The interaction matrix of Arabidopsis TAFs is largely consistent with the three-lobed topological map for yeast TFIID, which suggests that the structure and composition of TFIID have been highly conserved among eukaryotes.

The hemostatic history of a 15-month-old child implanted with a Berlin heart left ventricular assist device.

We documented the hemostatic changes associated with placement of a EXCOR Berlin Heart left ventricular assist device in a 15-month-old child before heart transplantation. The development of hypercoagulability was rapid, manifested first by a plasmatic and subsequently platelet-mediated increase in coagulation kinetics and strength that persisted for weeks. The patient had no thrombotic complications for 6 wk before transplant but required extraordinary blood product administration to achieve hemostasis secondary to aggressive, multimodal anticoagulation. In summary, when proscribing anesthetic and surgical management of patients with a Berlin Heart, consideration of hypercoagulable features and anticoagulant therapy must be made to maximize patient safety.

Contact activation prolongs clot lysis time in human plasma: role of thrombin-activatable fibrinolysis inhibitor and Factor XIII.

BACKGROUND: Contact activation system proteins (e.g., Factor XII, kallikrein) have been implicated as direct or indirect activators of plasminogen. However, contact activation and Factor XI have enhanced thrombin-activatable fibrinolysis inhibitor (TAFI) activation and decreased fibrinolysis, and Factor XIII (FXIII) also delays fibrinolysis via alpha(2)-anti-plasmin deposition on fibrin polymers. Thus, the goals of this study were to define how fibrinolysis is modulated in human plasma by contact or tissue factor (TF) activation, and what role TAFI and FXIII plays in this system. METHODS: Normal, TAFI-deficient and TAFI-deficient/FXIII-supplemented plasma was exposed to tissue-type plasminogen activator and activated with either celite or TF. Clot growth/disintegration kinetics were documented with thrombelastography. RESULTS: Normal plasma activated with celite had significantly prolonged onset and duration of clot lysis compared with samples activated with TF. TAFI-deficient plasma activated with celite was noted to have a duration of clot lysis not different from samples activated with TF, but a significant difference in time to onset of lysis persisted. Celite activation of TAFI-deficient/FXIII-supplemented plasma showed significantly prolonged onset and duration of clot lysis compared with samples activated with TF. CONCLUSIONS: Primarily TAFI, and to a lesser extent FXIII, contributed to contact system protein-mediated attenuation of fibrinolysis. Clinical investigation of these phenomena is warranted in clinical settings involving contact activation (e.g., intra-aortic balloon pumps and ventricular assist devices) to determine whether these devices modulate fibrinolysis and perhaps contribute to thromboembolic morbidity.

Argatroban, bivalirudin, and lepirudin do not decrease clot propagation and strength as effectively as heparin-activated antithrombin in vitro.

BACKGROUND: Heparin-induced thrombocytopenia is a potentially limb- and life-threatening response to heparin exposure. Direct thrombin inhibitors (DTIs) have been reported to provide anti-coagulation for cardiopulmonary bypass; however, clot formation within the cardiopulmonary bypass circuit has been reported after the administration of DTIs. We present a case of thrombosis of the cardiopulmonary bypass circuit and, ultimately, death after argatroban administration. An in vitro thrombelastographic assessment of the effects of DTIs on clot kinetics was consequently performed to determine potential causes for this complication. METHODS: Normal human plasma was unmodified or exposed to heparin (1, 2, 3 U/ml), argatroban (5, 10, 50 microg/ml), bivalirudin (12, 20, 120 microg/ml), or lepirudin (3, 6, 10 microg/ml) before activation with tissue factor/kaolin in a thrombelastograph. Clot initiation (R, reaction time), propagation (MTG, maximum thrombus generation), and strength (MG, maximum elastic modulus) were determined. Analysis of variance was performed, with p < 0.05 considered significant. RESULTS: Compared with unmodified plasma, heparin significantly prolonged R and essentially reduced MTG and MG to the limits of detection in an activity-dependent fashion. In general, the DTIs tested prolonged R in a concentration-dependent fashion but did not diminish MTG or MG nearly as well as heparin. The only exception was 10 microg/ml lepirudin, which eliminated coagulation. CONCLUSIONS: DTIs demonstrated a significant prolongation of clot initiation but poor attenuation of propagation and strength. Further in vitro and clinical investigations to design a heparin-equivalent regimen to provide anti-coagulation for patients with heparin-induced thrombocytopenia are indicated.

Isolation and characterization of class A4 heat shock transcription factor from alfalfa.

Plant heat shock transcription factors (HSFs) regulate transcription of heat shock (HS) genes. In Arabidopsis thaliana, 21 HSFs have been classified into groups A-C. Members of class A act as typical transcriptional activators, whereas B HSFs function as coactivators or repressors depending on promoter context. The function of class C HSFs is still unclear. Here, we present the isolation and characterization of the first HSF from alfalfa (Medicago sativa L.) and designate it MsHSFA4 based on amino acid sequence analysis. The MsHSFA4 gene was determined to be single copy and was detected at two separate genetic loci in the tetraploid Medicago sativa. Overexpression of MsHSFA4 in tobacco mesophyll protoplasts resulted in weak transcriptional activity, similar to that exhibited by Arabidopsis AtHSFA4a. The MsHSFA4 proximal promoter contains three putative HSE elements, and the gene itself is activated both by heat and cold stress.

Identification and characterization of GIP1, an Arabidopsis thaliana protein that enhances the DNA binding affinity and reduces the oligomeric state of G-box binding factors.

Environmental control of the alcohol dehydrogenase (Adh) and other stress response genes in plants is in part brought about by transcriptional regulation involving the G-box cis-acting DNA element and bZIP G-box Binding Factors (GBFs). The mechanisms of GBF regulation and requirements for additional factors in this control process are not well understood. In an effort to identify potential GBF binding and control partners, maize GBF1 was used as bait in a yeast two-hybrid screen of an A. thaliana cDNA library. GBF Interacting Protein 1 (GIP1) arose from the screen as a 496 amino acid protein with a predicted molecular weight of 53,748 kDa that strongly interacts with GBFs. Northern analysis of A. thaliana tissue suggests a 1.8-1.9 kb GIP1 transcript, predominantly in roots. Immunolocalization studies indicate that GIP1 protein is mainly localized to the nucleus. In vitro electrophoretic mobility shift assays using an Adh G-box DNA probe and recombinant A. thaliana GBF3 or maize GBF1, showed that the presence of GIP1 resulted in a tenfold increase in GBF DNA binding activity without altering the migration, suggesting a transient association between GIP1 and GBF. Addition of GIP1 to intentionally aggregated GBF converted GBF to lower molecular weight macromolecular complexes and GIP1 also refolded denatured rhodanese in the absence of ATP. These data suggest GIP1 functions to enhance GBF DNA binding activity by acting as a potent nuclear chaperone or crowbar, and potentially regulates the multimeric state of GBFs, thereby contributing to bZIP-mediated gene regulation.

Plant class B HSFs inhibit transcription and exhibit affinity for TFIIB and TBP.

Plant heat shock transcription factors (HSFs) are capable of transcriptional activation (class A HSFs) or both, activation and repression (class B HSFs). However, the details of mechanism still remain unclear. It is likely, that the regulation occurs through interactions of HSFs with general transcription factors (GTFs), as has been described for numerous other transcription factors. Here, we show that class A HSFs may activate transcription through direct contacts with TATA-binding protein (TBP). Class A HSFs can also interact weakly with TFIIB. Conversely, class B HSFs inhibit promoter activity through an active mechanism of repression that involves the C-terminal regulatory region (CTR) of class B HSFs. Deletion analysis revealed two sites in the CTR of soybean GmHSFB1 potentially involved in protein-protein interactions with GTFs: one is the repressor domain (RD) located in the N-terminal half of the CTR, and the other is a TFIIB binding domain (BD) that shows affinity for TFIIB and is located C-terminally from the RD. A Gal4 DNA binding domain-RD fusion repressed activity of LexA-activators, while Gal4-BD proteins synergistically activated strong and weak transcriptional activators. In vitro binding studies were consistent with this pattern of activity since the BD region alone interacted strongly with TFIIB, and the presence of RD had an inhibitory effect on TFIIB binding and transcriptional activation.

The effect of dilution on plasma coagulation kinetics determined by thrombelastography is dependent on antithrombin activity and mode of activation.

Hemodilution-associated hypercoagulability has been the focus of several investigations because significant morbidity and mortality have been associated with perioperative thrombophilia. Because most investigations implicate imbalances in procoagulant/anticoagulant activity as the etiology of hemodilution-associated hypercoagulability, we determined the effects of dilution on coagulation kinetics and clot strength with thrombelastography (TEG(R)). Control plasma (+/-celite activation) and antithrombin (AT)-deficient (<10% activity) plasma were diluted 0%, 10%, 20%, and 30% with saline. TEG(R) variables measured included time to clot initiation (reaction time, R), speed of clot propagation (angle, alpha), and clot strength (amplitude, A; or shear elastic modulus, G). Dilution of control plasma (10%-30%) resulted in a significant (P < 0.05) 16% decrease in R values, no change in alpha values, and decrease in A and G values. AT-deficient plasma had significantly smaller R values compared with control, and dilution did not change R values in AT-deficient plasma. Celite activation eliminated dilution-associated changes in R values in control plasma but resulted in linear decreases (R(2) = 0.88-0.96, P < 0.0001) in alpha, A, and G in response to dilution. Thus, our data indirectly support the concept that decreases in AT activity cause dilution-mediated hypercoagulability in plasma. Finally, celite activation permits quantification of dilution with TEG.

The impact of factor XIII on coagulation kinetics and clot strength determined by thrombelastography.

Fibrinogen has been shown to be responsible for most protein-mediated clot strength via thrombelastography. However, factor XIII (FXIII) activity also plays a prominent role in the development of clot strength. Thus, we hypothesized that changes in FXIII activity would significantly increase clot strength. FXIII (0%, 1%, 6.25%, 12.5%, 25%, 50%, and 100% normal activity) was placed in a fixed volume of citrated FXIII-deficient plasma with 1% tissue factor and calcium chloride and underwent thrombelastography for 10 min. We measured the variables reaction time (R; a measurement of clot initiation), alpha (a measure of the rate of clot formation), amplitude (A; a measure of clot strength), and shear elastic modulus (G; a measure of clot strength). FXIII activity significantly decreased R in a pattern of exponential decay (R2 = 0.77; P < 0.001). FXIII activity significantly increased alpha, following a sigmoidal pattern (R2 = 0.88; P < 0.001). Finally, increases in FXIII activity significantly increased A and G in a sigmoidal pattern (R = 0.89; P < 0.001). We concluded that FXHI significantly affects R, alpha, A, and G. Thus, transfusion decision making with protein-mediated thrombelastographic patterns must account for the contribution of both fibrinogen and FXIII.

Plant adaptation to low atmospheric pressures: potential molecular responses.

There is an increasing realization that it may be impossible to attain Earth normal atmospheric pressures in orbital, lunar, or Martian greenhouses, simply because the construction materials do not exist to meet the extraordinary constraints imposed by balancing high engineering requirements against high lift costs. This equation essentially dictates that NASA have in place the capability to grow plants at reduced atmospheric pressure. Yet current understanding of plant growth at low pressures is limited to just a few experiments and relatively rudimentary assessments of plant vigor and growth. The tools now exist, however, to make rapid progress toward understanding the fundamental nature of plant responses and adaptations to low pressures, and to develop strategies for mitigating detrimental effects by engineering the growth conditions or by engineering the plants themselves. The genomes of rice and the model plant Arabidopsis thaliana have recently been sequenced in their entirety, and public sector and commercial DNA chips are becoming available such that thousands of genes can be assayed at once. A fundamental understanding of plant responses and adaptation to low pressures can now be approached and translated into procedures and engineering considerations to enhance plant growth at low atmospheric pressures. In anticipation of such studies, we present here the background arguments supporting these contentions, as well as informed speculation about the kinds of molecular physiological responses that might be expected of plants in low-pressure environments.