Black-eared Fairy (Heliothryx aurita, Trochilidae) using a gliding flight like falling leaves when leaving nest

Summary In forest of the Brasilian Amazon, the Black-eared Fairy (Heliothryx aurita) uses a gliding fall, similar to that movement presented by the fall of a dead leaf, when leaving the nest. This behaviour may protect adult or nest against forest hawk predators.

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Zusammenfassung Der KolibriHeliothryx aurita zeigt beim Verlassen des Nestes eine Flugweise, die einem herabfallenden Blatt sehr ähnlich ist. Wie beiH. barroti ist zu vermuten, daß die Imitation fallenden Laubes als Schutz vor Nesträubern zu interpretieren ist.

     

POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes

Background

Detection of genes evolving under positive Darwinian evolution in genome-scale data is nowadays a prevailing strategy in comparative genomics studies to identify genes potentially involved in adaptation processes. Despite the large number of studies aiming to detect and contextualize such gene sets, there is virtually no software available to perform this task in a general, automatic, large-scale and reliable manner. This certainly occurs due to the computational challenges involved in this task, such as the appropriate modeling of data under analysis, the computation time to perform several of the required steps when dealing with genome-scale data and the highly error-prone nature of the sequence and alignment data structures needed for genome-wide positive selection detection.

Results

We present POTION, an open source, modular and end-to-end software for genome-scale detection of positive Darwinian selection in groups of homologous coding sequences. Our software represents a key step towards genome-scale, automated detection of positive selection, from predicted coding sequences and their homology relationships to high-quality groups of positively selected genes. POTION reduces false positives through several sophisticated sequence and group filters based on numeric, phylogenetic, quality and conservation criteria to remove spurious data and through multiple hypothesis corrections, and considerably reduces computation time thanks to a parallelized design. Our software achieved a high classification performance when used to evaluate a curated dataset of Trypanosoma brucei paralogs previously surveyed for positive selection. When used to analyze predicted groups of homologous genes of 19 strains of Mycobacterium tuberculosis as a case study we demonstrated the filters implemented in POTION to remove sources of errors that commonly inflate errors in positive selection detection. A thorough literature review found no other software similar to POTION in terms of customization, scale and automation.

Conclusion

To the best of our knowledge, POTION is the first tool to allow users to construct and check hypotheses regarding the occurrence of site-based evidence of positive selection in non-curated, genome-scale data within a feasible time frame and with no human intervention after initial configuration. POTION is available at http://www.lmb.cnptia.embrapa.br/share/POTION/.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1765-0) contains supplementary material, which is available to authorized users.     

Downhill Running-Based Overtraining Protocol Improves Hepatic Insulin Signaling Pathway without Concomitant Decrease of Inflammatory Proteins

The purpose of this study was to verify the effects of overtraining (OT) on insulin, inflammatory and gluconeogenesis signaling pathways in the livers of mice. Rodents were divided into control (CT), overtrained by downhill running (OTR/down), overtrained by uphill running (OTR/up) and overtrained by running without inclination (OTR). Rotarod, incremental load, exhaustive and grip force tests were used to evaluate performance. Thirty-six hours after a grip force test, the livers were extracted for subsequent protein analyses. The phosphorylation of insulin receptor beta (pIRbeta), glycogen synthase kinase 3 beta (pGSK3beta) and forkhead box O1 (pFoxo1) increased in OTR/down versus CT. pGSK3beta was higher in OTR/up versus CT, and pFoxo1 was higher in OTR/up and OTR versus CT. Phosphorylation of protein kinase B (pAkt) and insulin receptor substrate 1 (pIRS–1) were higher in OTR/up versus CT and OTR/down. The phosphorylation of IκB kinase alpha and beta (pIKKalpha/beta) was higher in all OT protocols versus CT, and the phosphorylation of stress-activated protein kinases/Jun amino-terminal kinases (pSAPK-JNK) was higher in OTR/down versus CT. Protein levels of peroxisome proliferator-activated receptor-gamma coactivator 1alpha (PGC-1alpha) and hepatocyte nuclear factor 4alpha (HNF-4alpha) were higher in OTR versus CT. In summary, OTR/down improved the major proteins of insulin signaling pathway but up-regulated TRB3, an Akt inhibitor, and its association with Akt.     

Experimental stress in inflammatory rheumatic diseases: a review of psychophysiological stress responses

Introduction  

Stressful events are thought to contribute to the aetiology, maintenance and exacerbation of rheumatic diseases. Given the growing interest in acute stress responses and disease, this review investigates the impact of real-life experimental psychosocial, cognitive, exercise and sensory stressors on autonomic, neuroendocrine and immune function in patients with inflammatory rheumatic diseases.     

A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on 13C mass isotopologue profiles under non-steady-state conditions

This article is a response to Wang and Luo. See correspondence article http://www.biomedcentral.com/1741-7007/10/30/ [WEBCITE] and the original research article http://www.biomedcentral.com/1741-7007/9/24 [WEBCITE].     

Limbs vs. Jaws: Can They Be Compared?

Current experimental research on mammalian limb muscle structureand function is compared to that on mammalian jaw muscles. Twomajor areas of comparison are stressed: structural and functional.Comparisons of limbs and jaws are made from the point of viewof the impact of recent studies on simple mechanical modelsof limb/jaw muscle function. Limb muscle structure is comparedto jaw muscles at the level of muscle architecture, muscle histochemicaland motor unit properties, and the organization of motor unitsinto neuromuscular compartments. Such comparisons reveal thatalthough limb muscles and jaw muscles might be organized insimilar ways, fundamental differences exist, both in terms ofmuscle structure and the functional conclusions which have beenbased on studies of muscle structure. The comparisons also demonstratethat much recent evidence from structural studies have had littledirect impact on simple models of muscle function but a muchlarger influence on the assumptions of the models. Comparisonsof limb/jaw muscle function from kinematic and EMG studies,indicate that many masticatory strategies are used by differentmammals but the basic problems of posture and locomotion havebeen met with essentially similar solutions, even among diversemammalian groups. The results of such comparisons demonstratethat both limb and jaw muscle function are sufficiently complexthat new or re-vitalized models are needed if the relationshipbetween structure and function are ever to be understood.