Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation

MOTIVATION

The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being surpassed by structurally constrained substitution (SCS) models. The SCS models often consider site-dependent evolution, a process that provides realism but complicates their implementation into likelihood functions that are commonly used for substitution model selection.

RESULTS

We present a method to perform selection among site-dependent SCS models, also among empirical and site-dependent SCS models, based on the approximate Bayesian computation (ABC) approach and its implementation into the computational framework ProteinModelerABC. The framework implements ABC with and without regression adjustments and includes diverse empirical and site-dependent SCS models of protein evolution. Using extensive simulated data, we found that it provides selection among SCS and empirical models with acceptable accuracy. As illustrative examples, we applied the framework to analyze a variety of protein families observing that SCS models fit them better than the corresponding best-fitting empirical substitution models.

AVAILABILITY AND IMPLEMENTATION

ProteinModelerABC is freely available from https://github.com/DavidFerreiro/ProteinModelerABC, can run in parallel and includes a graphical user interface. The framework is distributed with detailed documentation and ready-to-use examples.

Consequences of the Last Glacial Period on the Genetic Diversity of Southeast Asians

The last glacial period (LGP) promoted a loss of genetic diversity in Paleolithic populations of modern humans from diverse regions of the world by range contractions and habitat fragmentation. However, this period also provided some currently submersed lands, such as the Sunda shelf in Southeast Asia (SEA), that could have favored the expansion of our species. Concerning the latter, still little is known about the influence of the lowering sea level on the genetic diversity of current SEA populations. Here, we applied approximate Bayesian computation, based on extensive spatially explicit computer simulations, to evaluate the fitting of mtDNA data from diverse SEA populations with alternative evolutionary scenarios that consider and ignore the LGP and migration through long-distance dispersal (LDD). We found that both the LGP and migration through LDD should be taken into consideration to explain the currently observed genetic diversity in these populations and supported a rapid expansion of first populations throughout SEA. We also found that temporarily available lands caused by the low sea level of the LGP provided additional resources and migration corridors that favored genetic diversity. We conclude that migration through LDD and temporarily available lands during the LGP should be considered to properly understand and model the first expansions of modern humans.

Evaluating Causes of Current Genetic Gradients of Modern Humans of the Iberian Peninsula

The history of modern humans in the Iberian Peninsula includes a variety of population arrivals sometimes presenting admixture with resident populations. Genetic data from current Iberian populations revealed an overall east–west genetic gradient that some authors interpreted as a direct consequence of the Reconquista, where Catholic Kingdoms expanded their territories toward the south while displacing Muslims. However, this interpretation has not been formally evaluated. Here, we present a qualitative analysis of the causes of the current genetic gradient observed in the Iberian Peninsula using extensive spatially explicit computer simulations based on a variety of evolutionary scenarios. Our results indicate that the Neolithic range expansion clearly produces the orientation of the observed genetic gradient. Concerning the Reconquista (including political borders among Catholic Kingdoms and regions with different languages), if modeled upon a previous Neolithic expansion, it effectively favored the orientation of the observed genetic gradient and shows local isolation of certain regions (i.e., Basques and Galicia). Despite additional evolutionary scenarios could be evaluated to more accurately decipher the causes of the Iberian genetic gradient, here we show that this gradient has a more complex explanation than that previously hypothesized.

Analysis of selection in protein-coding sequences accounting for common biases

The evolution of protein-coding genes is usually driven by selective processes, which favor some evolutionary trajectories over others, optimizing the subsequent protein stability and activity. The analysis of selection in this type of genetic data is broadly performed with the metric nonsynonymous/synonymous substitution rate ratio (dN/dS). However, most of the well-established methodologies to estimate this metric make crucial assumptions, such as lack of recombination or invariable codon frequencies along genes, which can bias the estimation. Here, we review the most relevant biases in the dN/dS estimation and provide a detailed guide to estimate this metric using state-of-the-art procedures that account for such biases, along with illustrative practical examples and recommendations. We also discuss the traditional interpretation of the estimated dN/dS emphasizing the importance of considering complementary biological information such as the role of the observed substitutions on the stability and function of proteins. This review is oriented to help evolutionary biologists that aim to accurately estimate selection in protein-coding sequences.

Influence of Paleolithic range contraction, admixture and long-distance dispersal on genetic gradients of modern humans in Asia

Cavalli-Sforza and coauthors originally explored the genetic variation of modern humans throughout the world and observed an overall east-west genetic gradient in Asia. However, the specific environmental and population genetics processes causing this gradient were not formally investigated and promoted discussion in recent studies. Here we studied the influence of diverse environmental and population genetics processes on Asian genetic gradients and identified which could have produced the observed gradient. To do so, we performed extensive spatially-explicit computer simulations of genetic data under the following scenarios: (a) variable levels of admixture between Paleolithic and Neolithic populations, (b) migration through long-distance dispersal (LDD), (c) Paleolithic range contraction induced by the last glacial maximum (LGM), and (d) Neolithic range expansions from one or two geographic origins (the Fertile Crescent and the Yangzi and Yellow River Basins). Next, we estimated genetic gradients from the simulated data and we found that they were sensible to the analysed processes, especially to the range contraction induced by LGM and to the number of Neolithic expansions. Some scenarios were compatible with the observed east-west genetic gradient, such as the Paleolithic expansion with a range contraction induced by the LGM or two Neolithic range expansions from both the east and the west. In general, LDD increased the variance of genetic gradients among simulations. We interpreted the obtained gradients as a consequence of both allele surfing caused by range expansions and isolation by distance along the vast east-west geographic axis of this continent.

P770 Does intraoperative transesophageal match postoperative echocardiography in mitral valve surgery?

BACKGROUND

Intraoperative transesophageal echocardiography (iTEE) has an important role in mitral valve (MV) surgery, but may have dissimilar parameters from postoperative echocardiography (post-TTE). We aimed to evaluate iTTE Doppler flow profile and compare with the post-TTE in MV surgery.

METHODS

We conducted a prospective, observational study of 126 patients that underwent MVsurgery during 2 years. iTEE evaluated mean pressure gradient (MPG) and functional area. Patients were re-evaluated with TTE, 72 hours after surgery (post-TTE). iTEE and post-TTE Doppler values were compared and correlated. Preoperative TTE (pre-TTE) parameters were also determined.

RESULTS

The mean age was 59 ± 18 years and 55% were female. The prevalence of severe mitral regurgitation (MR) was 77.6% and severe mitral stenosis (MS) 23.7%. Globally, mitral valve repair was performed in 71%cases (83% for MR and 15% for MS) and replacement in 29% (64% for MR and 46% for MS). Left ventricular ejection fraction (LVEF), systolic pulmonary artery pressure (sPAP), tricuspid annular plane systolic excursion (TAPSE) assessed in pre-TTE and post-TTE, as also MPG and functional area in post-TTE and iTEE are depicted on table 1. There was a higher numerical difference in iTEE vs post-TTE MPG values in mechanical valves (n = 5) (3.5 ± 1.2 to 5.2 ± 1.6, difference of 1.65 ± 2.4mmHg), than in biological valves (n = 17) (3.1 ± 1.1 to 3.9 ± 1.5, difference of 0.8 ± 1.7mmHg). Globally, iTEE-derived MPG and functional area were strongly correlated with their post-TTE values (r2 0.7 and 0.8,p < 0.001).

CONCLUSIONS

iTEE Doppler parameters were strongly correlated with postoperative TTE parameters, with minimal differences: postoperative MPG were +0.4 ± 1mmHg higher in MV repair and +1.0 ± 1.8mmHg in MV replacement. There was a global improvement in sPAP. Our study demonstrates the usefulness of iTEE and its importance in stablishing possible reference values for postoperative follow-up.

MR MS pre-TTE post-TTE P value pre-TTE post-TTE P value LVEF (± SD,%) 57 ± 9 52 ± 10 <0.001 58 ± 6 56 ± 7 <0.001 sPAP (± SD,mmHg) 42 ± 17 33 ± 9 <0.001 47 ± 18 35 ± 6 <0.001 TAPSE (± SD,mm) 18 ± 2 14 ± 3 <0.001 18 ± 2 14 ± 3 <0.001 MV repair MV replacement iTEE post-TTE P value iTEE post-TTE P value MPG (± SD, mmHg) 2.8 ± 1.5 3.1 ± 1.4 0.084 3.2 ± 1.4 4.2 ± 1.6 0.016 Functional Area (± SD, cm2) 2.8 ± 0.6 2.8 ± 0.7 0.665 2.8 ± 0.6 2.7 ± 0.8 0.653

Consequences of diverse evolutionary processes on american genetic gradients of modern humans

European genetic gradients of modern humans were initially interpreted as a consequence of the demic diffusion of expanding Neolithic farmers. However, recent studies showed that these gradients may also be influenced by other evolutionary processes such as population admixture or range contractions. Genetic gradients were observed in the Americas, although their specific evolutionary causes were not investigated. Here we extended the approach used to study genetic gradients in Europe to analyze the influence of diverse evolutionary scenarios on American genetic gradients. Using extensive computer simulations, we evaluated the impact of (i) admixture between expansion waves of modern humans, (ii) the presence of ice-sheets during the last glacial maximum (LGM) and (iii) long-distance dispersal (LDD) events, on the genetic gradients (detected by principal component analysis) of the entire continent, North America and South America. The specific simulation of North and South America showed that genetic gradients are usually orthogonal to the direction of range expansions-either expansions from Bering or posterior re-expansions to recolonize northern regions after ice sheets melting-and we suggest that they result from allele surfing processes. Conversely, our results on the entire continent show a northwest-southeast gradient obtained with any scenario, which we interpreted as a consequence of isolation by distance along the long length of the continent. These findings suggest that distinct genetic gradients can be detected at different regions of the Americas and that subcontinent regions present gradients more sensible to evolutionary and environmental factors (such as LDD and the LGM) than the whole continent.

Mutation and recombination in pathogen evolution: Relevance, methods and controversies

Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.

Motor task performance under vibratory feedback early poststroke: single center, randomized, cross-over, controlled clinical trial

Stroke rehabilitation is far from meeting patient needs in terms of timing, intensity and quality. This study evaluates the efficacy and safety of an innovative technological tool, combining 3D motion analysis with targeted vibratory feedback, on upper-limb task performance early poststroke (<4 weeks). The study design was a two-sequence, two-period, randomized, crossover trial (NCT01967290) in 44 patients with upper-limb motor deficit (non-plegic) after medial cerebral artery ischemia. Participants were randomly assigned to receive either the experimental session (repetitive motor task under vibratory feedback and 3D motor characterization) or the active comparator (3D motor characterization only). The primary outcome was the number of correct movements per minute on a hand-to-mouth task measured independently. Vibratory feedback was able to modulate motor training, increasing the number of correct movements by an average of 7.2/min (95%CI [4.9;9.4]; P < 0.001) and reducing the probability of performing an error from 1:3 to 1:9. This strategy may improve the efficacy of training on motor re-learning processes after stroke, and its clinical relevance deserves further study in longer duration trials.

Peroral esophageal segmentectomy and anastomosis with single transthoracic trocar: a step forward in thoracic NOTES

BACKGROUND AND STUDY AIMS

A transesophageal natural orifice transluminal endoscopic surgery (NOTES) approach has been proposed for thoracic and mediastinal access. Similarly to transgastric surgery, serious limitations remain related to creating an esophagotomy and its safe closure. A hybrid approach in thoracic NOTES could work as an intermediate step before pure transesophageal NOTES. We assessed the benefit of hybrid thoracic NOTES for peroral segmental esophagectomy and subsequent complete esophageal anastomosis with a single transthoracic port.

METHODS

Two protocols were used to attempt esophago-esophageal anastomosis: ex vivo using a phantom model (n = 5), and in vivo after esophageal mobilization, and segmental esophagectomy achieved using either a gastroscope (flexible) (n = 5) or thoracoscope (rigid) instruments (n = 5). A forward-viewing double-channel endoscope and a transthoracic operative thoracoscope with a working channel were coordinated in order to create a complete single-layer, end-to-end esophageal anastomosis ex vivo as well as in vivo. Feasibility and anastomosis quality were evaluated by inside and outside assessment of: patency, the incorporation of mucosa in all stitches, and a leak test.

RESULTS

Anastomosis was achieved in all ex vivo experiments and thoracoscopically-led in vivo procedures. All anastomoses were patent, allowing distal passage of the endoscope, with mucosa incorporation. In in vivo experiments, a leak was detected in three animals and corrected with additional stitching.

CONCLUSIONS

Peroral esophageal anastomosis with a single transthoracic trocar is feasible, which may represent a step forward in thoracic NOTES.

Olfactory mucosal autografts and rehabilitation for chronic traumatic spinal cord injury

BACKGROUND/OBJECTIVE

Basic science advances in spinal cord injury (SCI) are leading to novel clinical approaches. The authors report a prospective, uncontrolled pilot study of the safety and outcomes of implanting olfactory mucosal autografts (OMA) in 20 patients with chronic, sensorimotor complete or motor complete SCI.

METHODS

Seven paraplegic and 13 tetraplegic subjects (17 men and 3 women; 19-37 years old) who sustained a traumatic SCI 18 to 189 months previously (mean = 49 months) were enrolled. Preoperative rehabilitation that emphasized lower extremity stepping using either overground walking training or a robotic weight-supported treadmill training was provided for 25 to 39 hours per week for a median of 4 months at 3 sites. No change in ASIA Impairment Scale (AIS) motor scores for the lower extremities or AIS grades of completeness was found. OMAs were transplanted into 1.3- to 4-cm lesions at C4-T12 neurological levels after partial scar removal. Therapy was continued postoperatively. Preoperative and postoperative assessments included AIS scores and classification, electromyography (EMG) of attempted voluntary contractions, somatosensory evoked potentials (SSEP), urodynamic studies with sphincter EMG, spinal cord magnetic resonance imaging (MRI), and otolaryngology and psychology evaluations. The Functional Independence Measure (FIM) and Walking Index for Spinal Cord Injury (WISCI) were obtained in 13 patients.

RESULTS

All patients survived and recovered olfaction. One patient was rehospitalized for aseptic meningitis. Minor adverse events occurred in 4 others. The mean duration of follow-up was 27.7 months (range = 12-45 months). By MRI, the lesion site was filled in all patients with no neoplastic overgrowth or syringomyelia. AIS grades improved in 11 of 20 patients, 6 (A --> C), 3 (B --> C), and 2 (A --> B), and declined in 1 (B --> A). Improvements included new voluntary EMG responses (15 patients) and SSEPs (4 patients). Scores improved in the FIM and WISCI (13/13 tested), and urodynamic responses improved in 5 patients.

CONCLUSION

OMA is feasible, relatively safe, and possibly beneficial in people with chronic SCI when combined with postoperative rehabilitation. Future controlled trials may need to include a lengthy and intensive rehabilitation arm as a control.

Comparison of chickpea rhizobia isolates from diverse Portuguese natural populations based on symbiotic effectiveness and DNA fingerprint

AIMS

To test the hypothesis that differences in chickpea yields obtained in four distinct Portuguese regions (Beja, Elvas-Casas Velhas, Elvas-Estação Nacional de Melhoramento de Plantas (ENMP) and Evora) could be due to variation between the natural rhizobia populations.

METHODS AND RESULTS

Estimation of the size of the different rhizobial populations showed that Elvas-ENMP population was the largest one. Elvas-ENMP population also revealed a higher proportion of isolates carrying more than one plasmid. Assessment of genetic diversity of the native rhizobia populations by a DNA fingerprinting PCR method, here designated as DAPD (Direct Amplified Polymorphic DNA), showed a higher degree of variation in Elvas-ENMP and Beja populations. The symbiotic effectiveness (SE) of 39 isolates was determined and ranged 13-34%. Statistical analysis showed that SE was negatively correlated with plasmid number of the isolate.

CONCLUSIONS

The largest indigenous rhizobia population was found in Elvas-ENMP. DAPD pattern and plasmid profile analysis both suggested a higher genetic diversity among the populations of Elvas-ENMP and Beja. No relationship was found between SE of the isolates and their origin site.

SIGNIFICANCE AND IMPACT OF STUDY

The large native population, rather than the symbiotic performance of individual rhizobia, could contribute to the higher chickpea yields obtained in Elvas-ENMP.

[The application of the endovascular prosthesis (stent)]

We report two cases of symptomatic internal carotid stenosis treated by vasoplasty and stent placement in two male patients aged 57 and 64 years, one who had been suffering from transient ischemic events and the other had had a recent cerebral infarction with hemiparesis. The treatment sessions took place without complications. We discuss the choice of simultaneous vasoplasty and stent placement, some of the current possible indications for the method and the importance of multidisciplinary planning for the patient's evaluation and treatment.