Development of twenty-one novel microsatellite loci for Gila topminnow, Poeciliopsis occidentalis occidentalis.

BACKGROUND: Gila topminnow (Poeciliopsis occidentalis occidentalis) was once highly abundant throughout the Lower Colorado River Basin of the southwestern United States. However, this Sonoran Desert endemic suffered extreme population declines over the past century because of habitat degradation and nonnative species introductions. Much of the prior conservation genetic work conducted on the species relied upon a small number of microsatellite loci; many exhibiting low variability in extant populations. Consequently, there was a need for additional microsatellite loci to provide high-resolution delimitation of populations for conservation purposes. METHODS AND RESULTS: Paired-end Illumina sequencing was utilized to screen the Gila topminnow genome for novel microsatellite loci. We identified 21 novel loci that exhibited no deviations from expectations of genetic equilibrium, and cross-amplified in Yaqui topminnow (P. o. sonoriensis). These loci were amplified from 401 samples representing eight populations of Gila topminnow and Yaqui topminnow. Although diversity was low for all populations (observed heterozygosity = 0.12 to 0.45), these novel markers provided ample power to identify population of origin for each individual in Bayesian assignment tests. CONCLUSIONS: This novel set of microsatellite loci provide a useful genetic tool to assess population genetic parameters of the endangered Gila topminnow and delineate populations for identifying conservation priorities. The cross-amplification of these loci in Yaqui topminnow shows promise for application to other Poeciliopsis species of Mexico and Central America.

Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation.

Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis of representative populations across the entire native range of A. sagrei, finding that the species originated in the early Pliocene, with the deepest divergence occurring between western and eastern Cuba. Lineages from these two regions subsequently colonized the northern Caribbean. We find that at the broadest scale, populations colonizing areas with fewer closely related competitors tend to evolve larger body size and more lamellae on their toepads. This trend follows expectations for post-colonization divergence from progenitors and convergence in allopatry, whereby populations freed from competition with close relatives evolve towards common morphological and ecological optima. Taken together, our results show a complex history of ancient and recent Cuban diaspora with populations on competitor-poor islands evolving away from their ancestral Cuban populations regardless of their phylogenetic relationships, thus providing insight into the original diversification of colonist anoles at the beginning of the radiation. Our research also supplies an evolutionary framework for the many studies of this increasingly important species in ecological and evolutionary research.

Comparative tests of the role of dewlap size in Anolis lizard speciation.

Phenotypic traits may be linked to speciation in two distinct ways: character values may influence the rate of speciation or diversification in the trait may be associated with speciation events. Traits involved in signal transmission, such as the dewlap of Anolis lizards, are often involved in the speciation process. The dewlap is an important visual signal with roles in species recognition and sexual selection, and dewlaps vary among species in relative size as well as colour and pattern. We compile a dataset of relative dewlap size digitized from photographs of 184 anole species from across the genus' geographical range. We use phylogenetic comparative methods to test two hypotheses: that larger dewlaps are associated with higher speciation rates, and that relative dewlap area diversifies according to a speciational model of evolution. We find no evidence of trait-dependent speciation, indicating that larger signals do not enhance any role the dewlap has in promoting speciation. Instead, we find a signal of mixed speciational and gradual trait evolution, with a particularly strong signal of speciational change in the dewlaps of mainland lineages. This indicates that dewlap size diversifies in association with the speciation process, suggesting that divergent selection may play a role in the macroevolution of this signalling trait.

Proteomic profiling of bronchoalveolar lavage fluid uncovers protein clusters linked to survival in idiopathic forms of interstitial lung disease.

Background: Idiopathic interstitial pneumonias (IIPs) such as idiopathic pulmonary fibrosis (IPF) and interstitial pneumonia with autoimmune features (IPAF), present diagnostic and therapeutic challenges due to their heterogeneous nature. This study aimed to identify intrinsic molecular signatures within the lung microenvironment of these IIPs through proteomic analysis of bronchoalveolar lavage fluid (BALF). Methods: Patients with IIP (n=23) underwent comprehensive clinical evaluation including pre-treatment bronchoscopy and were compared to controls without lung disease (n=5). Proteomic profiling of BALF was conducted using label-free quantitative methods. Unsupervised cluster analyses identified protein expression profiles which were then analyzed to predict survival outcomes and investigate associated pathways. Results: Proteomic profiling successfully differentiated IIP from controls. k-means clustering, based on protein expression revealed three distinct IIP clusters, which were not associated with age, smoking history, or baseline pulmonary function. These clusters had unique survival trajectories and provided more accurate survival predictions than the Gender Age Physiology (GAP) index (C-index 0.794 vs. 0.709). The cluster with the worst prognosis featured decreased inflammatory signaling and complement activation, with pathway analysis highlighting altered immune response pathways related to immunoglobulin production and B cell-mediated immunity. Conclusions: The unsupervised clustering of BALF proteomics provided a novel stratification of IIP patients, with potential implications for prognostic and therapeutic targeting. The identified molecular phenotypes underscore the diversity within the IIP classification and the potential importance of personalized treatments for these conditions. Future validation in larger, multi-ethnic cohorts is essential to confirm these findings and to explore their utility in clinical decision-making for patients with IIP.

Neutrophil extracellular traps linked to idiopathic pulmonary fibrosis severity and survival.

Background: Idiopathic pulmonary fibrosis (IPF) leads to progressive loss of lung function and mortality. Understanding mechanisms and markers of lung injury in IPF is paramount to improving outcomes for these patients. Despite the lack of systemic involvement in IPF, many analyses focus on identifying circulating prognostic markers. Using a proteomic discovery method followed by ELISA validation in multiple IPF lung compartments and cohorts we explored novel markers of IPF survival. Methods: In our discovery analysis, agnostic label-free quantitative proteomics differentiated lung tissue protein expression based on survival trajectory (n=10). Following selection of the candidate pathway (neutrophil extracellular trap (NET) formation), we subsequently validated the presence of NETs in the IPF lung microenvironment using fully quantitative assays of known NET remnants in separate IPF cohorts (n=156 and n=52) with bronchoalveolar lavage fluid. We then assessed the correlation of these markers with baseline pulmonary function and survival. Results: Discovery lung tissue proteomics identified NET formation as significantly associated with poor IPF survival. Using fully quantitative confirmatory tests for reproducibility we confirmed the presence of NET markers in IPF BALF and found significant correlations with worse pulmonary function in both cohorts (p<0.03 and p = 0.04 respectively). In the survival cohort, higher levels of NET markers predicted worse survival after adjusting for gender, age, and baseline physiologic severity (hazard ratio range: 1.79-2.19). Conclusions: NET markers were associated with disease severity and worse survival in IPF. These findings suggest NET formation contributes to lung injury and decreased survival in IPF and may represent a potential therapeutic target.

Highly accelerated real-time cardiac cine MRI using k-t SPARSE-SENSE.

For patients with impaired breath-hold capacity and/or arrhythmias, real-time cine MRI may be more clinically useful than breath-hold cine MRI. However, commercially available real-time cine MRI methods using parallel imaging typically yield relatively poor spatio-temporal resolution due to their low image acquisition speed. We sought to achieve relatively high spatial resolution (∼2.5 × 2.5 mm(2)) and temporal resolution (∼40 ms), to produce high-quality real-time cine MR images that could be applied clinically for wall motion assessment and measurement of left ventricular function. In this work, we present an eightfold accelerated real-time cardiac cine MRI pulse sequence using a combination of compressed sensing and parallel imaging (k-t SPARSE-SENSE). Compared with reference, breath-hold cine MRI, our eightfold accelerated real-time cine MRI produced significantly worse qualitative grades (1-5 scale), but its image quality and temporal fidelity scores were above 3.0 (adequate) and artifacts and noise scores were below 3.0 (moderate), suggesting that acceptable diagnostic image quality can be achieved. Additionally, both eightfold accelerated real-time cine and breath-hold cine MRI yielded comparable left ventricular function measurements, with coefficient of variation <10% for left ventricular volumes. Our proposed eightfold accelerated real-time cine MRI with k-t SPARSE-SENSE is a promising modality for rapid imaging of myocardial function.

Rapid ungated myocardial perfusion cardiovascular magnetic resonance: preliminary diagnostic accuracy.

BACKGROUND: Myocardial perfusion cardiovascular magnetic resonance (CMR) is a well-established method for detection of ischemic heart disease. However, ECG gating problems can result in image degradation and non-diagnostic scans, particularly in patients with arrhythmias. METHODS: A turboFLASH saturation recovery pulse sequence was used without any ECG triggering. One saturation pulse followed by 4-5 slices of undersampled radial k-space images was acquired rapidly, on the order of 40-50 msec per image. The acquisition of the set of 4-5 slices was continuously repeated approximately 4 times per second. An iterative constrained reconstruction method was used to reconstruct the ungated images. The ungated perfusion images were post-processed into three different sets of images (ungated, self-gated to near systole, and self-gated to near diastole). To test the ungated approach and compare the different processing methods, 8 patients scheduled for coronary angiography underwent stress and rest perfusion imaging with the ungated acquisition. Six patients had a history of atrial fibrillation (AF). Three blinded readers assessed image quality and presence/absence of disease. RESULTS: All 8 subjects successfully completed the perfusion CMR protocol and 7/8 underwent coronary angiography. Three patients were in atrial fibrillation during CMR. Overall, the CMR images were of high quality as assessed by the three readers. There was little difference in image quality between patients in AF compared to those in sinus rhythm (3.6±0.7 vs. 3.3±0.5). Stress/rest perfusion imaging showed normal perfusion in 4 patients, fixed perfusion defects in 2 patients, and reversible perfusion defects in 2 patients, corresponding with angiographic results. Pooled results from the independent readers gave a sensitivity of 0.92 (CI 0.65-0.99) and specificity of 0.92 (CI 0.65-0.99) for the detection of coronary artery disease using ungated perfusion imaging. The same sensitivity, and a specificity of 1 (CI 0.76-1), was achieved when the images were self-gated after acquisition into near systole or near diastole. CONCLUSIONS: Ungated radial dynamic perfusion CMR can give high quality imaging in patients in sinus rhythm and during atrial fibrillation. In this small cohort, high diagnostic accuracy was possible with this rapid perfusion imaging sequence. An ungated approach simplifies the acquisition and could expand the role of perfusion CMR to include patients with arrhythmia and those with gating problems.

PCCA: a program for phylogenetic canonical correlation analysis.

UNLABELLED: PCCA (phylogenetic canonical correlation analysis) is a new program for canonical correlation analysis of multivariate, continuously valued data from biological species. Canonical correlation analysis is a technique in which derived variables are obtained from two sets of original variables whereby the correlations between corresponding derived variables are maximized. It is a very useful multivariate statistical method for the calculation and analysis of correlations between character sets. The program controls for species non-independence due to phylogenetic history and computes canonical coefficients, correlations and scores; and conducts hypothesis tests on the canonical correlations. It can also compute a multivariate version of Pagel's lambda, which can then be used in the phylogenetic transformation. AVAILABILITY: PCCA is distributed as DOS/Windows, Mac OS X and Linux/Unix executables with a detailed program manual and is freely available on the World Wide Web at: http://anolis.oeb.harvard.edu/~liam/programs/.

Detection of late radiation damage on left atrial fibrosis using cardiac late gadolinium enhancement magnetic resonance imaging.

PURPOSE: This is a proof-of-principle study investigating the feasibility of using late gadolinium enhancement magnetic resonance imaging (LGE-MRI) to detect left atrium (LA) radiation damage. METHODS AND MATERIALS: LGE-MRI data were acquired for 7 patients with previous external beam radiation therapy (EBRT) histories. The enhancement in LA scar was delineated and fused to the computed tomography images used in dose calculation for radiation therapy. Dosimetric and normal tissue complication probability analyses were performed to investigate the relationship between LA scar enhancement and radiation doses. RESULTS: The average LA scar volume for the subjects was 2.5 cm3 (range, 1.2-4.1 cm3; median, 2.6 cm3). The overall average of the mean dose to the LA scar was 25.9 Gy (range, 5.8-49.2 Gy). Linear relationships were found between the amount of radiation dose (mean dose) (R2 = 0.8514, P = .03) to the LA scar-enhanced volume. The ratio of the cardiac tissue change (LA scar/LA wall) also demonstrated a linear relationship with the level of radiation received by the cardiac tissue (R2 = 0.9787, P < .01). Last, the normal tissue complication probability analysis suggested a dose response function to the LA scar enhancement. CONCLUSIONS: With LGE-MRI and 3-dimensional dose mapping on the treatment planning system, it is possible to define subclinical cardiac damage and distinguish intrinsic cardiac tissue change from radiation induced cardiac tissue damage. Imaging myocardial injury secondary to EBRT using MRI may be a useful modality to follow cardiac toxicity from EBRT and help identify individuals who are more susceptible to EBRT damage. LGE-MRI may provide essential information to identify early screening strategy for affected cancer survivors after EBRT treatment.

The right ventricle under pressure: evaluating the adaptive and maladaptive changes in the right ventricle in pulmonary arterial hypertension using echocardiography (2013 Grover Conference series).

The importance of the right ventricle (RV) in pulmonary arterial hypertension (PAH) has been gaining increased recognition. This has included a reconceptualization of the RV as part of an RV-pulmonary circulation interrelated unit and the observation that RV function is a major determinant of prognosis in PAH. Noninvasive imaging of RV size and function is critical to the longitudinal management of patients with PAH, and continued understanding of the pathophysiology of pulmonary vascular disease relies on the response of the RV to pulmonary vascular remodeling. Echocardiography, in particular the newer echocardiographic measurements and techniques, allows easy, readily accessible means to assess and follow RV size and function.

Atrial fibrillation ablation outcome is predicted by left atrial remodeling on MRI.

BACKGROUND: Although catheter ablation therapy for atrial fibrillation (AF) is becoming more common, results vary widely, and patient selection criteria remain poorly defined. We hypothesized that late gadolinium enhancement MRI (LGE-MRI) can identify left atrial (LA) wall structural remodeling (SRM) and stratify patients who are likely or not to benefit from ablation therapy. METHODS AND RESULTS: LGE-MRI was performed on 426 consecutive patients with AF without contraindications to MRI before undergoing their first ablation procedure and on 21 non-AF control subjects. Patients were categorized by SRM stage (I-IV) based on the percentage of LA wall enhancement for correlation with procedure outcomes. Histological validation of SRM was performed comparing LGE-MRI with surgical biopsy. A total of 386 patients (91%) with adequate LGE-MRI scans were included in the study. After ablation, 123 patients (31.9%) experienced recurrent atrial arrhythmias during the 1-year follow-up. Recurrent arrhythmias (failed ablations) occurred at higher SRM stages with 28 of 133 (21.0%) in stage I, 40 of 140 (29.3%) in stage II, 24 of 71 (33.8%) in stage III, and 30 of 42 (71.4%) in stage IV. In multivariate analysis, ablation outcome was best predicted by advanced SRM stage (hazard ratio, 4.89; P<0.0001) and diabetes mellitus (hazard ratio, 1.64; P=0.036), whereas increased LA volume and persistent AF were not significant predictors. LA wall enhancement was significantly greater in patients with AF versus non-AF controls (16.6±11.2% versus 3.1±1.9%; P<0.0001). Histological evidence of remodeling from surgical biopsy specimens correlated with SRM on LGE-MRI. CONCLUSIONS: Atrial SRM is identified on LGE-MRI, and extensive LGE (≥30% LA wall enhancement) predicts poor response to catheter ablation therapy for AF.

Asynchronous evolution of physiology and morphology in Anolis lizards.

Species-rich adaptive radiations typically diversify along several distinct ecological axes, each characterized by morphological, physiological, and behavioral adaptations. We test here whether different types of adaptive traits share similar patterns of evolution within a radiation by investigating patterns of evolution of morphological traits associated with microhabitat specialization and of physiological traits associated with thermal biology in Anolis lizards. Previous studies of anoles suggest that close relatives share the same "structural niche" (i.e., use the same types of perches) and are similar in body size and shape, but live in different "climatic niches" (i.e., use habitats with different insolation and temperature profiles). Because morphology is closely tied to structural niche and field active body temperatures are tied to climatic niches in Anolis, we expected phylogenetic analyses to show that morphology is more evolutionarily conservative than thermal physiology. In support of this hypothesis, we find (1) that thermal biology exhibits more divergence among recently diverged Anolis taxa than does morphology; and (2) diversification of thermal biology among all species often follows diversification in morphology. These conclusions are remarkably consistent with predictions made by anole biologists in the 1960s and 1970s.

MARCKS is a natively unfolded protein with an inaccessible actin-binding site: evidence for long-range intramolecular interactions.

Myristoylated alanine-rich C kinase substrate (MARCKS) is an unfolded protein that contains well characterized actin-binding sites within the phosphorylation site domain (PSD), yet paradoxically, we now find that intact MARCKS does not bind to actin. Intact MARCKS also does not bind as well to calmodulin as does the PSD alone. Myristoylation at the N terminus alters how calmodulin binds to MARCKS, implying that, despite its unfolded state, the distant N terminus influences binding events at the PSD. We show that the free PSD binds with site specificity to MARCKS, suggesting that long-range intramolecular interactions within MARCKS are also possible. Because of the unusual primary sequence of MARCKS with an overall isoelectric point of 4.2 yet a very basic PSD (overall charge of +13), we speculated that ionic interactions between oppositely charged domains of MARCKS were responsible for long-range interactions within MARCKS that sterically influence binding events at the PSD and that explain the observed differences between properties of the PSD and MARCKS. Consistent with this hypothesis, chemical modifications of MARCKS that neutralize negatively charged residues outside of the PSD allow the PSD to bind to actin and increase the affinity of MARCKS for calmodulin. Similarly, both myristoylation of MARCKS and cleavage of MARCKS by calpain are shown to increase the availability of the PSD so as to activate its actin-binding activity. Because abundant evidence supports the conclusion that MARCKS is an important protein in regulating actin dynamics, our data imply that post-translational modifications of MARCKS are necessary and sufficient to regulate actin-binding activity.