Bronchoscopic interventions for plastic bronchitis in children without structural heart disease.

Plastic bronchitis (PB) is a rare and life-threatening complication encountered in several disease states that leads to airway obstruction by branching casts. PB is most often reported in children with cyanotic congenital heart disease where recurrence is common, and mortality is high. There is limited data on optimal management strategies or recurrence of non-structural heart disease-related PB in children. We describe the clinical features, management, and outcomes in our cohort of children with non-structural heart disease-related PB. Among the 12 identified patients, asthma was the most common (67%) diagnosis. Ventilatory requirements ranged from room air to one patient who required extracorporeal membrane oxygenation (ECMO). Most patients (92%) required bronchoscopy, and cryotherapy was successfully utilized in two patients to relieve refractory obstructive airway casts. All patients received chest physiotherapy, and 11 patients were treated with two or more medications. There was one mortality despite ECMO, and one-third had recurrent PB, all of whom had asthma.Conclusion: Asthma is a risk factor for recurrent PB. Bronchoscopic interventions including cryotherapy are safe and effective treatment options in patients with refractory PB. What is Known: • Plastic bronchitis is a rare but life-threatening cause of airway obstruction caused by branching casts that are generally reported in patients with congenital heart disease. What is New: • In children without structural heart disease, asthma is a risk factor for recurrent plastic bronchitis. Cryotherapy via bronchoscopy is a safe and effective intervention in patients with refractory plastic bronchitis.

Alternative splicing of a group II intron in a surface layer protein gene in Clostridium tetani.

Group II introns are ribozymes and retroelements found in bacteria, and are thought to have been the ancestors of nuclear pre-mRNA introns. Whereas nuclear introns undergo prolific alternative splicing in some species, group II introns are not known to carry out equivalent reactions. Here we report a group II intron in the human pathogen Clostridium tetani, which undergoes four alternative splicing reactions in vivo. Together with unspliced transcript, five mRNAs are produced, each encoding a distinct surface layer protein isoform. Correct fusion of exon reading frames requires a shifted 5' splice site located 8 nt upstream of the canonical boundary motif. The shifted junction is accomplished by an altered IBS1-EBS1 pairing between the intron and 5' exon. Growth of C. tetani under a variety of conditions did not result in large changes in alternative splicing levels, raising the possibility that alternative splicing is constitutive. This work demonstrates a novel type of gene organization and regulation in bacteria, and provides an additional parallel between group II and nuclear pre-mRNA introns.

Airway epithelial cell PPARγ modulates cigarette smoke-induced chemokine expression and emphysema susceptibility in mice.

Chronic obstructive pulmonary disease (COPD) is a highly prevalent, chronic inflammatory lung disease with limited existing therapeutic options. While modulation of peroxisome proliferator-activating receptor (PPAR)-γ activity can modify inflammatory responses in several models of lung injury, the relevance of the PPARG pathway in COPD pathogenesis has not been previously explored. Mice lacking Pparg specifically in airway epithelial cells displayed increased susceptibility to chronic cigarette smoke (CS)-induced emphysema, with excessive macrophage accumulation associated with increased expression of chemokines, Ccl5, Cxcl10, and Cxcl15. Conversely, treatment of mice with a pharmacological PPARγ activator attenuated Cxcl10 and Cxcl15 expression and macrophage accumulation in response to CS. In vitro, CS increased lung epithelial cell chemokine expression in a PPARγ activation-dependent fashion. The ability of PPARγ to regulate CS-induced chemokine expression in vitro was not specifically associated with peroxisome proliferator response element (PPRE)-mediated transactivation activity but was correlated with PPARγ-mediated transrepression of NF-κB activity. Pharmacological or genetic activation of PPARγ activity abrogated CS-dependent induction of NF-κB activity. Regulation of NF-κB activity involved direct PPARγ-NF-κB interaction and PPARγ-mediated effects on IKK activation, IκBα degradation, and nuclear translocation of p65. Our data indicate that PPARG represents a disease-relevant pathophysiological and pharmacological target in COPD. Its activation state likely contributes to NF-κB-dependent, CS-induced chemokine-mediated regulation of inflammatory cell accumulation.

Outpatient Utilization of the RAM Cannula for Nasal Noninvasive Ventilation in Children.

Background: The RAM cannula® consists of nasal prongs that can be used to administer oxygen, continuous, and bilevel positive airway pressure therapies. Studies have reported the efficacy and utility of the RAM cannula in inpatients requiring noninvasive ventilation (NIV); however, there is limited literature on the use of the RAM cannula to provide NIV in the outpatient setting. Objectives: This study aimed to describe the clinical features and outcomes of children who used NIV via RAM cannula in the outpatient setting. Design: Retrospective review. Methods: We conducted a retrospective review of children treated with outpatient NIV via RAM cannula at our institution between January 2010 and March 2023. The analyzed data included age, diagnoses, indications for NIV, duration of RAM cannula use, complications, and outcomes at 6 months. Results: We identified 20 patients who used outpatient NIV via RAM cannula during the study period. The median age at initiation of NIV via RAM cannula was 5.8 months (IQR 2.4-9.9 months). Indications for NIV included sleep-related hypoventilation (15%), restrictive lung disease (25%), obstructive sleep apnea (45%), and chronic respiratory failure (50%), with 6 patients having ⩾2 indications for NIV. RAM cannula was utilized for inability to tolerate conventional NIV interfaces (80%), to alleviate dyspnea (60%), and to avoid tracheostomy (55%). Patients used NIV via RAM cannula for a median duration of 7.7 months (IQR 3.7-20.6 months). Patient outcomes included ongoing usage of RAM cannula (55%), changing to conventional NIV interfaces (15%) or oxygen (10%), weaning off respiratory support (5%), and death (15%). There were no complications related to using the RAM cannula. Conclusion: Our study demonstrates the utility of outpatient NIV via RAM cannula in children with a variety of diagnoses until clinical improvement or tolerance of conventional interfaces, and for avoidance of tracheostomy.

Cryoextraction via flexible bronchoscopy in children with tracheobronchial obstruction.

BACKGROUND: Cryoextraction via flexible bronchoscopy (FB) can be used to alleviate airway obstruction due to blood clots, casts, mucus, and foreign bodies. There is limited literature regarding the utility of cryoextraction to restore airway patency in critically ill children, especially on extracorporeal membrane oxygenation (ECMO). The aims of this study were to describe the clinical course and outcomes of children who underwent cryoextraction via FB. METHODS: A singlecenter retrospective review of children who underwent cryoextraction via FB between 2017 and 2021 was conducted. The analyzed data included diagnoses, indications for cryoextraction, respiratory support modalities, FB and chest imaging results, and outcomes. RESULTS: Eleven patients aged 3-17 years underwent a total of 33 cryoextraction sessions via FB. Patients required ECMO (n = 9) or conventional mechanical ventilation (CMV) for pneumonia, pulmonary hemorrhage, pulmonary embolism, asthma exacerbation, and cardiorespiratory failure following cardiac surgery. One patient underwent elective FB and cryoextraction for plastic bronchitis. Indications for cryoextraction included airway obstruction due to tracheobronchial thrombi (n = 8), mucus plugs (n = 1), or plastic bronchitis (n = 2). Cryoextraction via FB was performed on patients on ECMO (n = 9) and CMV (n = 2) with 6 patients requiring ≥3 cryoextraction sessions for airway obstruction. There were no complications related to cryoextraction. Patient outcomes included partial (n = 5) or complete (n = 6) restoration of airway patency with ECMO decannulation (n = 5) and death (n = 4) due to critical illness. CONCLUSIONS: Cryoextraction via FB is an effective intervention that can be utilized in critically ill children with refractory tracheobronchial obstruction to restore airway patency and to facilitate liberation from ECMO.

External airway splint placement for severe pediatric tracheobronchomalacia.

OBJECTIVE: To present external airway splinting with bioabsorbable airway supportive devices (ASD) for severe, life-threatening cases of pediatric tracheomalacia (TM) or tracheobronchomalacia (TBM). METHODS: A retrospective cohort was performed for 5 pediatric patients with severe TM or TBM who underwent ASD placement. Devices were designed and 3D-printed from a bioabsorbable material, polycaprolactone (PCL). Pre-operative planning included 3-dimensional airway modeling of tracheal collapse and tracheal suture placement using nonlinear finite element (FE) methods. Pre-operative modeling revealed that triads along the ASD open edges and center were the most effective suture locations for optimizing airway patency. Pediatric cardiothoracic surgery and otolaryngology applied the ASDs by suspending the trachea to the ASD with synchronous bronchoscopy. Respiratory needs were trended for all cases. Data from pediatric patients with tracheostomy and diagnosis of TM or TBM, but without ASD, were included for discussion. RESULTS: Five patients (2 Females, 3 Males, ages 2-9 months at time of ASD) were included. Three patients were unable to wean from respiratory support after vascular ring division; all three weaned to room air post-ASD. Two patients received tracheostomies prior to ASD placement, but continued to experience apparent life-threatening events (ALTE) and required ventilation with supraphysiologic ventilator settings. One patient weaned respiratory support successfully after ASD placement. The last patient died post-ASD due to significant respiratory co-morbidity. CONCLUSION: ASD can significantly benefit patients with severe, unrelenting tracheomalacia or tracheobronchomalacia. Proper multidisciplinary case deliberation and selection are key to success with ASD. Pre-operative airway modeling allows proper suture placement to optimally address the underlying airway collapse.

Thiol redox disturbances in children with severe asthma are associated with posttranslational modification of the transcription factor nuclear factor (erythroid-derived 2)-like 2.

BACKGROUND: Airway thiol redox disturbances, including depletion of the antioxidant, glutathione, are differentiating features of severe asthma in children. OBJECTIVES: Given the role of the transcription factor nuclear factor (erythroid-derived 2)-like 2 (Nrf2) in maintaining glutathione homeostasis and antioxidant defense, we quantified expression and activity of Nrf2 and its downstream targets in the airways and systemic circulation of children with asthma. We hypothesized that Nrf2 activation and function would be impaired in severe asthma, resulting in depletion of thiol pools and insufficient glutathione synthesis and conjugation. METHODS: PBMCs and airway lavage cells were collected from children 6 to 17 years with severe (n = 51) and mild-to-moderate asthma (n = 38). The thiols glutathione and cysteine were quantified, and expression and activity of Nrf2 and its downstream targets were assessed. RESULTS: Children with severe asthma had greater oxidation and lower concentrations of glutathione and cysteine in the plasma and airway lavage. Although Nrf2 mRNA and protein increased in severe asthma as a function of increased thiol oxidation, the Nrf2 expressed was highly dysfunctional. Nrf2 activation and downstream targets of Nrf2 binding, including glutathione-dependent enzymes, were not different between groups. The duration of asthma was a key factor associated with Nrf2 dysfunction in severe asthma. CONCLUSION: Children with severe asthma have a global disruption of thiol redox signaling and control in both the airways and systemic circulation that is associated with posttranslational modification of Nrf2. We conclude that the Nrf2 pathway is disrupted in severe asthma as a function of chronic oxidative stress, which ultimately inhibits glutathione synthesis and antioxidant defense.

Ventilator change in children on home mechanical ventilation affected by the Philips respironics trilogy ventilator recall.

The Philips Respironics recall notification issued in June 2021 affected many of their positive airway pressure devices and mechanical ventilators including the Trilogy 100 and 200 ventilators that are often utilized in children using home positive pressure ventilation via tracheostomy (PPV-T). Optimal strategies to replace ventilators in children using home PPV-T affected by the Philips recall are unknown. We conducted a retrospective study of children using home PPV-T with recalled Trilogy ventilators who underwent inpatient ventilator change to non-recalled portable home ventilators (PHV) using our collaborative institutional protocol. During the study period, there were 40 children using PPV-T with recalled Trilogy ventilators and 19 patients underwent inpatient ventilator change either during an elective hospitalization (n = 8) or during an unscheduled or postoperative hospitalization (n = 11). The median duration of hospitalization for ventilator change was 2 days (interquartile range: 6 days) and generally 1 day for patients admitted solely for ventilator change. In children using PPV-T with recalled Trilogy ventilators, a systematic protocol collaborating with the patients, physicians, and durable medical equipment companies may optimize transition to nonrecalled PHVs.

Fibroblast growth factor receptors control epithelial-mesenchymal interactions necessary for alveolar elastogenesis.

RATIONALE: The mechanisms contributing to alveolar formation are poorly understood. A better understanding of these processes will improve efforts to ameliorate lung disease of the newborn and promote alveolar repair in the adult. Previous studies have identified impaired alveogenesis in mice bearing compound mutations of fibroblast growth factor (FGF) receptors (FGFRs) 3 and 4, indicating that these receptors cooperatively promote postnatal alveolar formation. OBJECTIVES: To determine the molecular and cellular mechanisms of FGF-mediated alveolar formation. METHODS: Compound FGFR3/FGFR4-deficient mice were assessed for temporal changes in lung growth, airspace morphometry, and genome-wide expression. Observed gene expression changes were validated using quantitative real-time RT-PCR, tissue biochemistry, histochemistry, and ELISA. Autocrine and paracrine regulatory mechanisms were investigated using isolated lung mesenchymal cells and type II pneumocytes. MEASUREMENTS AND MAIN RESULTS: Quantitative analysis of airspace ontogeny confirmed a failure of secondary crest elongation in compound mutant mice. Genome-wide expression profiling identified molecular alterations in these mice involving aberrant expression of numerous extracellular matrix molecules. Biochemical and histochemical analysis confirmed changes in elastic fiber gene expression resulted in temporal increases in elastin deposition with the loss of typical spatial restriction. No abnormalities in elastic fiber gene expression were observed in isolated mesenchymal cells, indicating that abnormal elastogenesis in compound mutant mice is not cell autonomous. Increased expression of paracrine factors, including insulin-like growth factor-1, in freshly-isolated type II pneumocytes indicated that these cells contribute to the observed pathology. CONCLUSIONS: Epithelial/mesenchymal signaling mechanisms appear to contribute to FGFR-dependent alveolar elastogenesis and proper airspace formation.

Mortality and Outcomes of Pediatric Tracheostomy Dependent Patients.

Objective: To describe clinical factors associated with mortality and causes of death in tracheostomy-dependent (TD) children. Methods: A retrospective study of patients with a new or established tracheostomy requiring hospitalization at a large tertiary children's hospital between 2009 and 2015 was conducted. Patient groups were developed based on indication for tracheostomy: pulmonary, anatomic/airway obstruction, and neurologic causes. The outcome measures were overall mortality rate, mortality risk factors, and causes of death. Results: A total of 187 patients were identified as TD with complete data available for 164 patients. Primary indications for tracheostomy included pulmonary (40%), anatomic/airway obstruction (36%), and neurologic (24%). The median age at tracheostomy and duration of follow up were 6.6 months (IQR 3.5-19.5 months) and 23.8 months (IQR 9.9-46.7 months), respectively. Overall, 45 (27%) patients died during the study period and the median time to death following tracheostomy was 9.8 months (IQR 6.1-29.7 months). Overall survival at 1- and 5-years following tracheostomy was 83% (95% CI: 76-88%) and 68% (95% CI: 57-76%), respectively. There was no significant difference in mortality based on indication for tracheostomy (p = 0.35), however pulmonary indication for tracheostomy was associated with a shorter time to death (HR: 1.9; 95% CI: 1.04-3.4; p = 0.04). Among the co-morbid medical conditions, children with seizure disorder had higher mortality (p = 0.04). Conclusion: In this study, TD children had a high mortality rate with no significant difference in mortality based on indication for tracheostomy. Pulmonary indication for tracheostomy was associated with a shorter time to death and neurologic indication was associated with lower decannulation rates.

An instructional definition and assessment rubric for bioinformatics instruction.

The lack of an instructional definition of bioinformatics delays its effective integration into biology coursework. Using an iterative process, our team of biologists, a mathematician/computer scientist, and a bioinformatician together with an educational evaluation and assessment specialist, developed an instructional definition of the discipline: Bioinformatics is "an interdisciplinary field that is concerned with the development and application of algorithms that analyze biological data to investigate the structure and function of biological polymers and their relationships to living systems." The field is defined in terms of its two primary foundational disciplines, biology and computer science, and its interdisciplinary nature. At the same time, we also created a rubric for assessing open-ended responses to a prompt about what bioinformatics is and how it is used. The rubric has been shown to be reliable in successive rounds of testing using both common percent agreement (89.7%) and intraclass correlation coefficient (0.620) calculations. We offer the definition and rubric to life sciences instructors to help further integrate bioinformatics into biology instruction, as well as for fostering further educational research projects.

Heterogeneous Pulmonary Phenotypes in Filamin A Mutation-Related Lung Disease.

Background: Interstitial lung disease (ILD) has been recently reported in a few patients with pathogenic variants in the Filamin A (FLNA) gene with variable presentation and prognosis. This study evaluated the respiratory manifestations and clinical features in children with FLNA disease. Methods: We conducted a retrospective review of pediatric patients with variants in FLNA in a tertiary children's hospital. The clinical features, genotype, management, and outcomes were analyzed. Results: We identified 9 patients with variants in FLNA aged 15 months to 24 years, 4 females and 5 males. Six patients had abnormal chest imaging ranging from mild interstitial prominence to atelectasis, interstitial densities, and hyperinflation. Three patients with ILD presented during the neonatal period or early infancy with respiratory distress or respiratory failure requiring supplemental oxygen or assisted ventilation via tracheostomy. We report male twins with the same FLNA variant and lung disease, but different ages and clinical features at presentation eventually culminating in respiratory failure requiring assisted ventilation. All patients had FLNA variants identified by FLNA sequencing, had abnormal echocardiograms, and none of the patients underwent lung biopsy or lung transplantation. The outcomes were variable and could be as severe as chronic respiratory failure. Conclusion: The wide spectrum of respiratory manifestations and abnormal chest imaging in our study highlights the importance of evaluation for lung disease in patients with variants in FLNA. FLNA sequencing in suspected cases with ILD may obviate the need for a lung biopsy, prompt surveillance for progressive lung disease, and evaluation for associated clinical features.

A broadscale phylogenetic analysis of group II intron RNAs and intron-encoded reverse transcriptases.

Group II introns are self-splicing RNAs that are frequently assumed to be the ancestors of spliceosomal introns. They are widely distributed in bacteria and are also found in organelles of plants, fungi, and protists. In this study, we present a broadscale phylogenetic analysis of group II introns using sequence data from both the conserved RNA structure and the intron-encoded reverse transcriptase (RT). Two similar phylogenies are estimated for the RT open reading frame (ORF), based on either amino acid or nucleotide sequence, whereas one phylogeny is produced for the RNA. In making these estimates, we confronted nearly all the classic challenges to phylogenetic inference, including positional saturation, base composition heterogeneity, short internodes with low support, and sensitivity to taxon sampling. Although the major lineages are well-defined, robust resolution of topology is not possible between these lineages. The approximately unbiased (AU) and Shimodaira-Hasegawa topology tests indicated that the RT ORF and RNA ribozyme data sets are in significant conflict under a variety of models, revealing the possibility of imperfect coevolution between group II introns and their intron-encoded ORFs. The high level of sequence divergence, large timescale, and limited number of alignable characters in our study are representative of many RTs and group I introns, and our results suggest that phylogenetic analyses of any of these sequences could suffer from the same sources of error and instability identified in this study.

The Puf family of RNA-binding proteins in plants: phylogeny, structural modeling, activity and subcellular localization.

BACKGROUND: Puf proteins have important roles in controlling gene expression at the post-transcriptional level by promoting RNA decay and repressing translation. The Pumilio homology domain (PUM-HD) is a conserved region within Puf proteins that binds to RNA with sequence specificity. Although Puf proteins have been well characterized in animal and fungal systems, little is known about the structural and functional characteristics of Puf-like proteins in plants. RESULTS: The Arabidopsis and rice genomes code for 26 and 19 Puf-like proteins, respectively, each possessing eight or fewer Puf repeats in their PUM-HD. Key amino acids in the PUM-HD of several of these proteins are conserved with those of animal and fungal homologs, whereas other plant Puf proteins demonstrate extensive variability in these amino acids. Three-dimensional modeling revealed that the predicted structure of this domain in plant Puf proteins provides a suitable surface for binding RNA. Electrophoretic gel mobility shift experiments showed that the Arabidopsis AtPum2 PUM-HD binds with high affinity to BoxB of the Drosophila Nanos Response Element I (NRE1) RNA, whereas a point mutation in the core of the NRE1 resulted in a significant reduction in binding affinity. Transient expression of several of the Arabidopsis Puf proteins as fluorescent protein fusions revealed a dynamic, punctate cytoplasmic pattern of localization for most of these proteins. The presence of predicted nuclear export signals and accumulation of AtPuf proteins in the nucleus after treatment of cells with leptomycin B demonstrated that shuttling of these proteins between the cytosol and nucleus is common among these proteins. In addition to the cytoplasmically enriched AtPum proteins, two AtPum proteins showed nuclear targeting with enrichment in the nucleolus. CONCLUSIONS: The Puf family of RNA-binding proteins in plants consists of a greater number of members than any other model species studied to date. This, along with the amino acid variability observed within their PUM-HDs, suggests that these proteins may be involved in a wide range of post-transcriptional regulatory events that are important in providing plants with the ability to respond rapidly to changes in environmental conditions and throughout development.

Group II introns in eubacteria and archaea: ORF-less introns and new varieties.

Group II introns are a major class of ribozymes found in bacteria, mitochondria, and plastids. Many introns contain reverse transcriptase open reading frames (ORFs) that confer mobility to the introns and allow them to persist as selfish DNAs. Here, we report an updated compilation of group II introns in Eubacteria and Archaea comprising 234 introns. One new phylogenetic class is identified, as well as several specialized lineages. In addition, we undertake a detailed search for ORF-less group II introns in bacterial genomes in order to find undiscovered introns that either entirely lack an ORF or encode a novel ORF. Unlike organellar group II introns, we find only a handful of ORF-less introns in bacteria, suggesting that if a substantial number exist, they must be divergent from known introns. Together, these results highlight the retroelement character of bacterial group II introns, and suggest that their long-term survival is dependent upon retromobility.

PPARgamma deficiency results in reduced lung elastic recoil and abnormalities in airspace distribution.

BACKGROUND: Peroxisome proliferator-activated receptor (PPAR)-gamma is a nuclear hormone receptor that regulates gene expression, cell proliferation and differentiation. We previously described airway epithelial cell PPARgamma deficient mice that develop airspace enlargement with decreased tissue resistance and increased lung volumes. We sought to understand the impact of airspace enlargement in conditionally targeted mice upon the physio-mechanical properties of the lung. METHODS: We measured elastic recoil and its determinants, including tissue structure and surface forces. We measured alveolar number using radial alveolar counts, and airspace sizes and their distribution using computer-assisted morphometry. RESULTS: Air vs. saline-filled pressure volume profiles demonstrated loss of lung elastic recoil in targeted mice that was contributed by both tissue components and surface tension, but was proportional to lung volume. There were no significant differences in surfactant quantity/function nor in elastin and collagen content between targeted animals and littermate controls. Importantly, radial alveolar counts were significantly reduced in the targeted animals and at 8 weeks of age there were 18% fewer alveoli with 32% more alveolar ducts. Additionally, the alveolar ducts were 19% larger in the targeted animals. CONCLUSIONS: Our data suggest that the functional abnormalities, including loss of recoil are secondary to altered force transmission due to differences in the structure of alveolar ducts, rather than changes in surfactant function or elastin or collagen content. These data further define the nature of abnormal lung maturation in the absence of airway epithelial cell PPARgamma and identify a putative genetic determinant of dysanapsis, which may serve as a precursor to chronic lung disease.

A diversity of uncharacterized reverse transcriptases in bacteria.

Retroelements are usually considered to be eukaryotic elements because of the large number and variety in eukaryotic genomes. By comparison, reverse transcriptases (RTs) are rare in bacteria, with only three characterized classes: retrons, group II introns and diversity-generating retroelements (DGRs). Here, we present the results of a bioinformatic survey that aims to define the landscape of RTs across eubacterial, archaeal and phage genomes. We identify and categorize 1021 RTs, of which the majority are group II introns (73%). Surprisingly, a plethora of novel RTs are found that do not belong to characterized classes. The RTs have 11 domain architectures and are classified into 20 groupings based on sequence similarity, phylogenetic analyses and open reading frame domain structures. Interestingly, group II introns are the only bacterial RTs to exhibit clear evidence for independent mobility, while five other groups have putative functions in defense against phage infection or promotion of phage infection. These examples suggest that additional beneficial functions will be discovered among uncharacterized RTs. The study lays the groundwork for experimental characterization of these highly diverse sequences and has implications for the evolution of retroelements.

The natural history of group I introns.

There are four major classes of introns: self-splicing group I and group II introns, tRNA and/or archaeal introns and spliceosomal introns in nuclear pre-mRNA. Group I introns are widely distributed in protists, bacteria and bacteriophages. Group II introns are found in fungal and land plant mitochondria, algal plastids, bacteria and Archaea. Group II and spliceosomal introns share a common splicing pathway and might be related to each other. The tRNA and/or archaeal introns are found in the nuclear tRNA of eukaryotes and in archaeal tRNA, rRNA and mRNA. The mechanisms underlying the self-splicing and mobility of a few model group I introns are well understood. By contrast, the role of these highly distinct processes in the evolution of the 1500 group I introns found thus far in nature (e.g. in algae and fungi) has only recently been clarified. The explosion of new sequence data has facilitated the use of comparative methods to understand group I intron evolution in a broader context and to generate hypotheses about intron insertion, splicing and spread that can be tested experimentally.

Patterns of Bird-Bacteria Associations.

Birds, with their broad geographic ranges and close association with humans, have historically played an important role as carriers of human disease and as reservoirs for drug-resistant bacteria. Here, we examine scientific literature over a 15-year timespan to identify reported avian-bacterial associations and factors that may impact zoonotic disease emergence by classifying traits of bird species and their bacteria. We find that the majority of wild birds studied were migratory, in temperate habitats, and in the order Passeriformes. The highest diversity of bacteria was found on birds in natural habitats. The most frequently reported bacteria were Escherichia coli, Salmonella enterica, and Campylobacter jejuni. Of the bacteria species reported, 54% have shown pathogenicity toward humans. Percentage-wise, more pathogens were found in tropical (vs. temperate) habitats and natural (vs. suburban, urban, or agricultural) habitats. Yet, only 22% were tested for antibiotic resistance, and of those tested, 75% of bacteria species were resistant to at least one antibiotic. There were no significant patterns of antibiotic resistance in migratory versus non-migratory birds, temperate versus tropical areas, or different habitats. We discuss biases in detection and representation, and suggest a need for increased sampling in non-temperate zones and in a wider range of avian species.

Epithelial cell PPAR[gamma] contributes to normal lung maturation.

Peroxisome proliferator-activated receptor (PPAR)-gamma is a member of the nuclear hormone receptor superfamily that can promote cellular differentiation and organ development. PPARgamma expression has been reported in a number of pulmonary cell types, including inflammatory, mesenchymal, and epithelial cells. We find that PPARgamma is prominently expressed in the airway epithelium in the mouse lung. In an effort to define the physiological role of PPARgamma within the lung, we have ablated PPARgamma using a novel line of mice capable of specifically targeting the airway epithelium. Airway epithelial cell PPARgamma-targeted mice display enlarged airspaces resulting from insufficient postnatal lung maturation. The increase in airspace size is accompanied by alterations in lung physiology, including increased lung volumes and decreased tissue resistance. Genome-wide expression profiling reveals a reduction in structural extracellular matrix (ECM) gene expression in conditionally targeted mice, suggesting a disruption in epithelial-mesenchymal interactions necessary for the establishment of normal lung structure. Expression profiling of airway epithelial cells isolated from conditionally targeted mice indicates PPARgamma regulates genes encoding known PPARgamma targets, additional lipid metabolism enzymes, and markers of cellular differentiation. These data reveal airway epithelial cell PPARgamma is necessary for normal lung structure and function.