Estimating fat and protein fuel from fat and muscle scores in passerines

Fat is the prime energy source for birds during prolonged exercise, but protein is also catabolized. Estimates of the amount of catabolizable fat and protein (termed fat and protein fuel) are therefore important for studying energetics of birds. As fat and protein fuel can only be measured by sacrificing individuals or by use of technically complex methods, scoring systems were invented to estimate fat and protein fuel of birds in the field. The visible subcutaneous fat deposits and the thickness of the flight muscles are each scored on an ordinal scale but these scales do not correspond linearly to fat and protein fuel within species, which is needed for analyses such as flight range estimates. We developed an anova ‐type model to estimate fat and protein fuel from fat scores (FS) and muscle scores (MS) along with total mass and a size measurement. Using data from 11 337 individuals of eight passerine species (Common Nightingale Luscinia megarhynchos, Eurasian Reed Warbler Acrocephalus scirpaceus, Melodious Warbler Hippolais polyglotta, Willow Warbler Phylloscopus trochilus, Orphean Warbler Sylvia hortensis, Garden Warbler Sylvia borin, Common Whitethroat Sylvia communis, Subalpine Warbler Sylvia cantillans) mist‐netted in Mauritania, West Africa, we tested for independence of FS and MS and for variation in the relationship between scores and associated mass in response to physiological state. FS, MS and third primary length (size) explained variation in body mass of all eight species analysed (R²: 0.56–0.77). The parameter estimates of the model showed that fat and protein fuel increased monotonically with increasing fat and muscle scores. In two species we found small differences in the estimates between physiological states (seasons). We evaluated our model by comparing the predicted body mass of birds with both FS and MS equal to 0 with the mean body mass of individuals mist‐netted with both scores equal to zero. The values were very close. The amount of fat extracted from dead Garden and Willow Warblers was within the range of predicted fat fuel derived from the model. We conclude that our model is a useful non‐invasive method to estimate simultaneously mean fat and protein fuel of small passerines and we provide recommendations on its use.     

Tazarotene-induced gene 1 interacts with Polo-like kinase 2 and inhibits cell proliferation in HCT116 colorectal cancer cells

Tazarotene-induced gene 1 (TIG1) is considered to be a tumor suppressor gene that is highly expressed in normal or well-differentiated colon tissues, while downregulation of TIG1 expression occurs in poorly differentiated colorectal cancer (CRC) tissues. However, it is still unclear how TIG1 regulates the tumorigenesis of CRC. Polo-like kinases (Plks) are believed to play an important role in regulating the cell cycle. The performance of PLK2 in CRC is negatively correlated with the differentiation status of CRC tissues. Here, we found that PLK2 can induce the growth of CRC cells and that TIG1 can prevent PLK2 from promoting the proliferation of CRC cells. We also found that the expression of PLK2 in CRC cells was associated with low levels of Fbxw7 protein and increased expression of cyclin E1. When TIG1 was coexpressed with PLK2, the changes in Fbxw7/cyclin E1 levels induced by PLK2 were reversed. In contrast, silencing TIG1 promoted the proliferation of CRC, and when PLK2 was also silenced, the proliferation of CRC cells induced by TIG1 silencing was significantly inhibited. The above research results suggest that TIG1 can regulate the tumorigenesis of CRC by regulating the activity of PLK2.     

Outcomes of Anterolateral Thigh Flap Reconstruction for Salvage Laryngopharyngectomy for Hypopharyngeal Cancer after Concurrent Chemoradiotherapy

Objective

To evaluate the functional and oncological outcomes of anterolateral thigh flap reconstruction for salvage laryngopharyngectomy after concurrent chemoradiotherapy for patients with hypopharyngeal carcinoma.

Materials/Methods

A retrospective review was conducted on patients who underwent pharyngoesophageal reconstruction using anterolateral thigh flap after salvage laryngopharyngectomy for recurrent hypopharyngeal carcinoma between June 2003 and May 2010 at Chang Gung Memorial Hospital. The perioperative morbidity, mortality, functional outcomes, and oncological outcomes were evaluated.

Results

33 patients were entered into the study. The mean follow-up time was 19.5±12.3 months. Recurrent pathological TNM stages included 3 (9.1%), 2 (6.1%), and 28 (84.8%) patients with stage II, III, and IV disease, respectively. Mean ICU stay was 10.3 days and the mean hospital stay was 39.9 days. Peri-operative mortality occurred in one patient (3%). 16 patients (48.5%) developed recipient site complications. Among them, 14 patients (42.4%) developed fistulas and 9 patients (27.3%) developed strictures. Except for 4 patients (12.1%), all achieved varying degree of oral intake with 29 patients (60.6%) being completely independent from tube feeding. The mean interval to start oral intake was 15.1 days. The 5-year overall survival and disease–free survival rates were 51.8% and 53.7%, respectively. The pN status is an independent predictor of overall survival and disease–free survival (P = 0.027 and 0.038, respectively).

Conclusion

Pharyngoesophageal reconstruction after salvage laryngopharyngectomy remains challenging even in the experienced hands. Reconstructive microsurgeons who are prepared to take on these cases should be equally well prepared to manage the potential postoperative complications.     

Multimodal signals in male European treefrog (Hyla arborea) and the influence of population isolation on signal expression

In nocturnal treefrogs, mate choice implies the use of acoustic and visual signals. Multimodality is suspected to have evolved for either information redundancy or information complementariness. It is essential to explore multimodality in a natural context to understand the selection pressures operating on the signals. In the present study, we investigated calling and coloration in relation to male biometry and condition in four populations of European treefrog (Hyla arborea) varying in size and genetic isolation. We compared the signal intensity between core and satellite populations to estimate the impact of genetic diversity on male secondary sexual traits. The results obtained show important regional variations in both traits, likely as a result of local adaptations. Call and coloration are weakly correlated within an individual, implying that these traits likely convey different information about the signaller's identity or quality, thus supporting the hypothesis of complementariness of multiple messages. By contrast to the experimental evidence, we find that call and coloration are not related to male condition (as estimated by the residual of mass over size), suggesting that the condition‐dependence of these traits may be mediated by complex mechanisms not accurately reflected by the chosen estimator. Finally, male call and colour phenotypes present no robust pattern of variation with isolation status, probably because of variation in local selective pressures and in history of population dynamics. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 633–647.     

Charged residues at protein interaction interfaces: unexpected conservation and orchestrated divergence

Protein-protein interactions play an essential role in the functioning of cell. The importance of charged residues and their diverse role in protein-protein interactions have been well studied using experimental and computational methods. Often, charged residues located in protein interaction interfaces are conserved across the families of homologous proteins and protein complexes. However, on a large scale, it has been recently shown that charged residues are significantly less conserved than other residue types in protein interaction interfaces. The goal of this work is to understand the role of charged residues in the protein interaction interfaces through their conservation patterns. Here, we propose a simple approach where the structural conservation of the charged residue pairs is analyzed among the pairs of homologous binary complexes. Specifically, we determine a large set of homologous interactions using an interaction interface similarity measure and catalog the basic types of conservation patterns among the charged residue pairs. We find an unexpected conservation pattern, which we call the correlated reappearance, occurring among the pairs of homologous interfaces more frequently than the fully conserved pairs of charged residues. Furthermore, the analysis of the conservation patterns across different superkingdoms as well as structural classes of proteins has revealed that the correlated reappearance of charged residues is by far the most prevalent conservation pattern, often occurring more frequently than the unconserved charged residues. We discuss a possible role that the new conservation pattern may play in the long-range electrostatic steering effect.     

Species richness estimation and determinants of species detectability in butterfly monitoring programmes

Abstract 1. Species richness is the most widely used biodiversity index, but can be hard to measure. Many species remain undetected, hence raw species counts will often underestimate true species richness. In contrast, capture–recapture methods estimate true species richness and correct for imperfect and varying detectability. 2. Detectability is a crucial quantity that provides the link between a species count and true species richness. For insects, it has hardly ever been estimated, although this is required for the interpretation of species counts. 3. In the Swiss butterfly monitoring programme about 100 transect routes are surveyed seven times a year using a highly standardised protocol. In July 2003, control observers made two additional surveys on 38 transects. Data from these 38 quadrats were analysed to see whether currently available capture–recapture models can provide quadrat‐specific estimates of species richness, and to estimate species detectability in relation to transect, observer, survey, region, and abundance. 4. Species richness over the entire season cannot be estimated using current capture–recapture methods. The species pool was open, preventing use of closed population models, and detectability varied by species, preventing use of current open population models. Assuming a closed species pool during two mid‐season (July) surveys, a Jackknife capture–recapture method was used that accounts for heterogeneity to estimate mean detectability and species richness. 5. In every case, more species were present than were counted. Mean species detectability was 0.61 (SE 0.01) with significant differences between observers (range 0.37–0.83). Species‐specific detection at time t+ 1 was then modelled for those species seen at t for three mid‐season surveys. Detectability averaged 0.50 (range 0.17–0.81) for individual species and 0.65, 0.44, and 0.42 for surveys. Abundant species were detected more easily, although this relationship explained only 5% of variation in species detectability. 6. These are important, although not entirely unexpected, results for species richness estimation of short‐lived animals. Raw counts of species may be misleading species richness indicators unless many surveys are conducted. Monitoring programmes should be calibrated, i.e. the assumption of constant detectability over dimensions of interest needs to be tested. The development of capture–recapture or similar models that can cope with both open populations and heterogeneous species detectability to estimate species richness should be a research priority.     

Feature-based classification of native and non-native protein-protein interactions: Comparing supervised and semi-supervised learning approaches

Structural knowledge about protein-protein interactions can provide insights to the basic processes underlying cell function. Recent progress in experimental and computational structural biology has led to a rapid growth of experimentally resolved structures and computationally determined near-native models of protein-protein interactions. However, determining whether a protein-protein interaction is physiological or it is the artifact of an experimental or computational method remains a challenging problem. In this work, we have addressed two related problems. The first problem is distinguishing between the experimentally obtained physiological and crystal-packing protein-protein interactions. The second problem is concerned with the classification of near-native and inaccurate docking models. We first defined a universal set of interface features and employed a support vector machines (SVM)-based approach to classify the interactions for both problems, with the accuracy, precision, and recall for the first problem classifier reaching 93%. To improve the classification, we next developed a semi-supervised learning approach for the second problem, using transductive SVM (TSVM). We applied both classifiers to a commonly used protein docking benchmark of 124 complexes. We found that while we reached the classification accuracies of 78.9% for the SVM classifier and 80.3% for the TSVM classifier, improving protein-docking methods by model re-ranking remains a challenging problem.