Marianne Huebner

Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways

BackgroundThe heat shock response of Arabidopsis thaliana is dependent upon a complex regulatory network involving twenty-one known transcription factors and four heat shock protein families. It is known that heat shock proteins (Hsps) and transcription factors (Hsfs) are involved in cellular response to various forms of stress besides heat. However, the role of Hsps and Hsfs under cold and non-thermal stress conditions is not well understood, and it is unclear which types of stress interact least and most strongly with Hsp and Hsf response pathways. To address this issue, we have analyzed transcriptional response profiles of Arabidopsis Hsfs and Hsps to a range of abiotic and biotic stress treatments (heat, cold, osmotic stress, salt, drought, genotoxic stress, ultraviolet light, oxidative stress, wounding, and pathogen infection) in both above and below-ground plant tissues.ResultsAll stress treatments interact with Hsf and Hsp response pathways to varying extents, suggesting considerable cross-talk between heat and non-heat stress regulatory networks. In general, Hsf and Hsp expression was strongly induced by heat, cold, salt, and osmotic stress, while other types of stress exhibited family or tissue-specific response patterns. With respect to the Hsp20 protein family, for instance, large expression responses occurred under all types of stress, with striking similarity among expression response profiles. Several genes belonging to the Hsp20, Hsp70 and Hsp100 families were specifically upregulated twelve hours after wounding in root tissue, and exhibited a parallel expression response pattern during recovery from heat stress. Among all Hsf and Hsp families, large expression responses occurred under ultraviolet-B light stress in aerial tissue (shoots) but not subterranean tissue (roots).ConclusionOur findings show that Hsf and Hsp family member genes represent an interaction point between multiple stress response pathways, and therefore warrant functional analysis under conditions apart from heat shock treatment. In addition, our analysis revealed several family and tissue-specific heat shock gene expression patterns that have not been previously described. These results have implications regarding the molecular basis of cross-tolerance in plant species, and raise new questions to be pursued in future experimental studies of the Arabidopsis heat shock response network.

Association between early surgical intervention vs watchful waiting and outcomes for mitral regurgitation due to flail mitral valve leaflets.

IMPORTANCE The optimal management of severe mitral valve regurgitation in patients without class I triggers (heart failure symptoms or left ventricular dysfunction) remains controversial in part due to the poorly defined long-term consequences of current management strategies. In the absence of clinical trial data, analysis of large multicenter registries is critical. OBJECTIVE To ascertain the comparative effectiveness of initial medical management (nonsurgical observation) vs early mitral valve surgery following the diagnosis of mitral regurgitation due to flail leaflets. DESIGN, SETTING, AND PARTICIPANTS The Mitral Regurgitation International Database (MIDA) registry includes 2097 consecutive patients with flail mitral valve regurgitation (1980-2004) receiving routine cardiac care from 6 tertiary centers (France, Italy, Belgium, and the United States). Mean follow-up was 10.3 years and was 98% complete. Of 1021 patients with mitral regurgitation without the American College of Cardiology (ACC) and the American Heart Association (AHA) guideline class I triggers, 575 patients were initially medically managed and 446 underwent mitral valve surgery within 3 months following detection. MAIN OUTCOMES AND MEASURES Association between treatment strategy and survival, heart failure, and new-onset atrial fibrillation. RESULTS There was no significant difference in early mortality (1.1% for early surgery vs 0.5% for medical management, P=.28) and new-onset heart failure rates (0.9% for early surgery vs 0.9% for medical management, P=.96) between treatment strategies at 3 months. In contrast, long-term survival rates were higher for patients with early surgery (86% vs 69% at 10 years, P < .001), which was confirmed in adjusted models (hazard ratio [HR], 0.55 [95% CI, 0.41-0.72], P < .001), a propensity-matched cohort (32 variables; HR, 0.52 [95% CI, 0.35-0.79], P = .002), and an inverse probability-weighted analysis (HR, 0.66 [95% CI, 0.52-0.83], P < .001), associated with a 5-year reduction in mortality of 52.6% (P < .001). Similar results were observed in relative reduction in mortality following early surgery in the subset with class II triggers (59.3 after 5 years, P = .002). Long-term heart failure risk was also lower with early surgery (7% vs 23% at 10 years, P < .001), which was confirmed in risk-adjusted models (HR, 0.29 [95% CI, 0.19-0.43], P < .001), a propensity-matched cohort (HR, 0.44 [95% CI, 0.26-0.76], P = .003), and in the inverse probability-weighted analysis (HR, 0.51 [95% CI, 0.36-0.72], P < .001). Reduction in late-onset atrial fibrillation was not observed (HR, 0.85 [95% CI, 0.64-1.13], P = .26). CONCLUSION AND RELEVANCE Among registry patients with mitral valve regurgitation due to flail mitral leaflets, performance of early mitral surgery compared with initial medical management was associated with greater long-term survival and a lower risk of heart failure, with no difference in new-onset atrial fibrillation.

Simulation-based mastery learning improves patient outcomes in laparoscopic inguinal hernia repair: A randomized controlled trial

Objective:To evaluate a mastery learning, simulation-based curriculum for laparoscopic, totally extraperitoneal (TEP) inguinal hernia repair. Background:Clinically relevant benefits from improvements in operative performance, time, and errors after simulation-based training are not clearly established. Methods:After performing a baseline TEP in the OR, general surgery residents randomized to mastery learning (ML) or standard practice (SP) were reassessed during subsequent TEPs. The ML curriculum involved Web-based modules followed by training on a TEP simulator until expert performance was achieved. Operative time, performance, and patient outcomes adjusted for staff, resident participation, difficulty of repair, PGY-level, and patient comorbidities were compared between groups with mixed effects-ANOVA and generalized linear models. Results:Fifty residents (PGY1-5) performed 219 TEP repairs on 146 patients. Baseline operative time, performance, and demographics were similar between groups. To achieve mastery, ML-residents (n = 26) required a median of 16 (range 7–27) simulated repairs. After training, TEPs performed by ML-residents were faster than those by SP-residents, with time corrected for participation (mean ± SD, 34 ± 8 minutes vs. 48 ± 14 minutes; difference –13; 95%CI, –18 to –8; P < 0.001). Operative performance scores (GOALS, scale 6–30) were better for ML residents (21.9 ± 2.8 vs. 18.3 ± 3.8; P = 0.001). Intraoperative complications (peritoneal tear, procedure conversion), postoperative complications (urinary retention, seroma), and need for overnight stay were less likely in the ML group (adjusted odds ratios 0.14, 0.04, and 0, respectively; all P < 0.05). Conclusions:A simulation-based ML curriculum decreased operative time, improved trainee performance, and decreased intra- and postoperative complications and overnight stays after laparoscopic TEP inguinal hernia repair. ClinicalTrials.gov Identifier: NCT01085500

Small, nonfunctioning, asymptomatic pancreatic neuroendocrine tumors (PNETs): Role for nonoperative management

BACKGROUND Controversy exists regarding the optimal management of incidentally discovered, small pancreatic neuroendocrine tumors (PNETs). Our aim was to review the outcomes of patients who underwent nonoperative and operative management. METHODS We retrospectively reviewed patients with nonfunctioning PNETs at our institution from January 1, 2000 to June 30, 2011. Patients were included if the tumor was sporadic and <4 cm without radiographic evidence of local invasion or metastases. RESULTS Nonoperative patients (n = 77, median age, 67 years; range, 31-94) had a median tumor size of 1.0 cm (range, 0.3-3.2). Mean follow-up (F/U) was 45 months (max. 153 months). Median tumor size did not change throughout F/U; there was no disease progression or disease specific mortality. In the operative group (n = 56, median age, 60 years; range, 27-82), median neoplasm size was 1.8 cm (range, 0.5-3.6). Mean F/U was 52 months (max. 138 months). A total of 46% of the operative patients had some type of complication, more than half due to a clinically significant pancreatic leak. No recurrence or disease specific mortality was seen in the operative group, including 5 patients with positive lymph nodes. CONCLUSION Small nonfunctioning PNETs usually exhibit minimal or no growth over many years. Nonoperative management may be advocated when serial imaging demonstrates minimal or no growth without suspicious features.

Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: A genome and transcriptome approach

BackgroundMany microorganisms have a wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments, however not many have been fully explored over their entire growth temperature range through a holistic view of its physiology, genome, and transcriptome. We used Exiguobacterium sibiricum strain 255-15, a psychrotrophic bacterium from 3 million year old Siberian permafrost that grows from -5°C to 39°C to study its thermal adaptation.ResultsThe E. sibiricum genome has one chromosome and two small plasmids with a total of 3,015 protein-encoding genes (CDS), and a GC content of 47.7%. The genome and transcriptome analysis along with the organisms known physiology was used to better understand its thermal adaptation. A total of 27%, 3.2%, and 5.2% of E. sibiricum CDS spotted on the DNA microarray detected differentially expressed genes in cells grown at -2.5°C, 10°C, and 39°C, respectively, when compared to cells grown at 28°C. The hypothetical and unknown genes represented 10.6%, 0.89%, and 2.3% of the CDS differentially expressed when grown at -2.5°C, 10°C, and 39°C versus 28°C, respectively.ConclusionThe results show that E. sibiricum is constitutively adapted to cold temperatures stressful to mesophiles since little differential gene expression was observed between 4°C and 28°C, but at the extremities of its Arrhenius growth profile, namely -2.5°C and 39°C, several physiological and metabolic adaptations associated with stress responses were observed.

Outcomes following surgery without radiotherapy for rectal cancer

This study determined survival and recurrence rates following curative resection of rectal cancer without radiotherapy.

IL13 gene polymorphisms modify the effect of exposure to tobacco smoke on persistent wheeze and asthma in childhood, a longitudinal study.

BackgroundTobacco smoke and genetic susceptibility are risk factors for asthma and wheezing. The aim of this study was to investigate whether there is a combined effect of interleukin-13 gene (IL13) polymorphisms and tobacco smoke on persistent childhood wheezing and asthma.MethodsIn the Isle of Wight birth cohort (UK, 1989–1999), five IL13 single nucleotide polymorphisms (SNPs): rs1800925 (-1112C/T), rs2066960, rs1295686, rs20541 (R130Q) and rs1295685 were genotyped. Parents were asked whether their children had wheezed in the last 12 months at ages 1, 2, 4 and 10 years. Children who reported wheeze in the first 4 years of life and also had wheezing at age 10 were classified as early-onset persistent wheeze phenotype; non-wheezers never wheezed up to age 10. Persistent asthma was defined as having a diagnosis of asthma both during the first four years of life and at age 10. Logistic regression methods were used to analyze data on 791 children with complete information. Potential confounders were gender, birth weight, duration of breast feeding, and household cat or dog present during pregnancy.ResultsMaternal smoking during pregnancy was associated with early-onset persistent wheeze (OR 2.93, p < 0.0001); polymorphisms in IL13 were not (OR 1.15, p = 0.60 for the common haplotype pair). However, the effect of maternal smoking during pregnancy was stronger in children with the common IL13 haplotype pair compared to those without it (OR 5.58 and OR 1.29, respectively; p for interaction = 0.014). Single SNP analysis revealed a similar statistical significance for rs20541 (p for interaction = 0.02). Comparable results were observed for persistent childhood asthma (p for interaction = 0.03).ConclusionThis is the first report that shows a combined effect of in utero exposure to smoking and IL13 on asthma phenotypes in childhood. The results emphasize that genetic studies need to take environmental exposures into account, since they may explain contradictory findings.

SNP interaction detection with Random Forests in high-dimensional genetic data

BackgroundIdentifying variants associated with complex human traits in high-dimensional data is a central goal of genome-wide association studies. However, complicated etiologies such as gene-gene interactions are ignored by the univariate analysis usually applied in these studies. Random Forests (RF) are a popular data-mining technique that can accommodate a large number of predictor variables and allow for complex models with interactions. RF analysis produces measures of variable importance that can be used to rank the predictor variables. Thus, single nucleotide polymorphism (SNP) analysis using RFs is gaining popularity as a potential filter approach that considers interactions in high-dimensional data. However, the impact of data dimensionality on the power of RF to identify interactions has not been thoroughly explored. We investigate the ability of rankings from variable importance measures to detect gene-gene interaction effects and their potential effectiveness as filters compared to p-values from univariate logistic regression, particularly as the data becomes increasingly high-dimensional.ResultsRF effectively identifies interactions in low dimensional data. As the total number of predictor variables increases, probability of detection declines more rapidly for interacting SNPs than for non-interacting SNPs, indicating that in high-dimensional data the RF variable importance measures are capturing marginal effects rather than capturing the effects of interactions.ConclusionsWhile RF remains a promising data-mining technique that extends univariate methods to condition on multiple variables simultaneously, RF variable importance measures fail to detect interaction effects in high-dimensional data in the absence of a strong marginal component, and therefore may not be useful as a filter technique that allows for interaction effects in genome-wide data.

Warmer does not have to mean sicker: temperature and predators can jointly drive timing of epidemics.

Ecologists and epidemiologists worry that global warming will increase disease prevalence. These fears arise because several direct and indirect mechanisms link warming to disease, and because parasite outbreaks are increasing in many taxa. However, this outcome is not a foregone conclusion, as physiological and community-interaction-based mechanisms may inhibit epidemics at warmer temperatures. Here, we explore this thermal-community-ecology-based mechanism, centering on fish predators that selectively prey upon Daphnia infected with a fungal parasite. We used an interplay between a simple model built around this systems biology and laboratory experiments designed to parameterize the model. Through this data-model interaction, we found that a given density of predators can inhibit epidemics as temperatures rise when thermal physiology of the predator scales more steeply than that of the host. This case is met in our fish-Daphnia-fungus system. Furthermore, the combination of steeply scaling parasite physiology and predation-induced mortality can inhibit epidemics at lower temperatures. This effect may terminate fungal epidemics of Daphnia as lakes cool in autumn. Thus, predation and physiology could constrain epidemics to intermediate temperatures (a pattern that we see in our system). More generally, these results accentuate the possibility that warmer temperatures might actually enhance predator control of parasites.

Quality of Life After Early Mitral Valve Repair Using Conventional and Robotic Approaches

BACKGROUND Early mitral valve (MV) repair of degenerative mitral regurgitation is associated with superior clinical outcomes compared with prosthetic replacement and restores normal life expectancy, even in those without symptoms. Although current guidelines recommend prompt referral for effective MV repair in those with severe mitral regurgitation, some are reluctant to pursue early correction due to the perception that short-term quality of life (QOL) may be adversely affected by the operation. METHODS Between January 2008 and November 2009, 202 patients underwent conventional transsternotomy or minimally invasive port-access robot-assisted MV repair, with or without patent foramen ovale closure or left Maze, and were mailed a postsurgical QOL survey. RESULTS Unadjusted QOL scores for patients undergoing MV repair were excellent early after the operation using both approaches. Robotic repair was associated with slightly improved scores on the Duke Activity Status Index, the Short Form-12 Item Health Survey Physical domain, and the Linear Analogue Self-Assessment frequency of chest pain and fatigue indices during the first postoperative year; however, differences between treatment groups became indistinguishable after 1 year. Robotic repair patients returned to work slightly quicker (median, 33 vs 54 days, p<0.001). CONCLUSIONS Functional QOL outcomes within the first 2 years after early MV repair are excellent using open and robotic platforms. A robotic approach may be associated with slightly improved early QOL and return to employment-based activities. These results may have implications regarding future evolution of clinical guidelines and economic health care policy.