Osteological correlates and phylogenetic analysis of deep diving in living and extinct pinnipeds: What good are big eyes?

Marine tetrapods have evolved different sensory solutions to meet the ecological challenges of foraging at depth. It has been proposed that pinipeds, like ichthyosaurs, evolved large eyeballs for such demands. Here, we test this hypothesis using morphological and diving data from a comprehensive data set (n= 54 species; 435 individual specimens), including living and extinct pinnipeds and other select carnivorans as outgroup taxa. We used bony orbit size as a proxy for eyeball size, and recorded associated skull measurements to control for relative changes in orbit size; for diving depth, we used the deepest dive depth reported in the literature. Our analyses included both standard regressions and those corrected for phylogeny (i.e., independent contrasts). Standard regression statistics showed orbit size was a significantly good predictor of diving depth for phocids and for pinnipeds overall, although there was no correlation for otariids. In contrast, independent contrasts showed little support for a relationship between orbit size and diving depth for any group broader than family level, although this approach did demonstrate deep diving has evolved multiple times in crown Pinnipedia. Lastly, using select fossil taxa, we highlight the need to test adaptive hypotheses using comparative data in an evolutionary context.     

How good are articles on adverse drug reactions?

A study was carried out of the quality and completeness of articles on adverse drug reactions: 5737 articles from 80 countries published between 1972 and 1979 were studied. Only 61% of the articles included information on the number of patients treated and the number with adverse drug reactions, yet these are essential for calculating the incidence of adverse reactions. In only 55% could the incidence of a particular adverse reaction be calculated. Great importance is placed on articles on adverse reactions, particularly those that report on many patients. Authors and editors should ensure that articles include the following information: drug regimens, numbers of patients treated, numbers of patients developing adverse reactions, and nature and incidence of adverse reactions.     

What are decision trees?

Decision trees have been applied to problems such as assigning protein function and predicting splice sites. How do these classifiers work, what types of problems can they solve and what are their advantages over alternatives?     

Do most human populations descend from phylogenetic trees?

Molecular biologists and some population geneticists have recently claimed to be able to reconstruct modern human populations remote history by means of phylogenetic trees. Many objections to this method are discussed in the present paper. The most important are

1. Inter-populations migrations are likely to have been important, even in the remote past. So the “treeness” of this evolution is disputable.
2. There is no reason to believe that actual molecular phylogenies would be convergent between different molecules and would therefore represent populations history.

The various kind of genetic data, their relations to other data and the limits of their possible use in the analysis of our past are then discussed, together with the ideological background of the most common theories and of their publication. It is very likely that the history of different populations was heterogeneous. Small and isolated hunter-gatherers frequently evolving close to a phylogenetic model, while dense and increasing populations, since the Neolithic, were closer to a dynamic network model, structured by isolation by distance. In any case, our present knowledge is obviously insufficient to reconstruct our genetic past, especially on the long term, and we can only hope that the development of the HUGO Genome Diversity project is going to yield the significant information presently lacking.     

How good are comparative models in the understanding of protein dynamics?

The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effectiveness of comparative models, compared to experimental structures, in inferring dynamics is not clear. To address this, we compared dynamics features of ~800 comparative models with their crystal structures using normal mode analysis. Average similarity in magnitude, direction, and correlation of residue motions is >0.8 (where value 1 is identical) indicating that the dynamics of models and crystal structures are highly similar. Accuracy of 3D structure and dynamics is significantly higher for models built on multiple and/or high sequence identity templates (>40%). Three-dimensional (3D) structure and residue fluctuations of models are closer to that of crystal structures than to templates (TM score 0.9 vs 0.7 and square inner product 0.92 vs 0.88). Furthermore, long-range molecular dynamics simulations on comparative models of RNase 1 and Angiogenin showed significant differences in the conformational sampling of conserved active-site residues that characterize differences in their activity levels. Similar analyses on two EGFR kinase variant models highlight the effect of mutations on the functional state-specific αC helix motions and these results corroborate with the previous experimental observations. Thus, our study adds confidence to the use of comparative models in understanding protein dynamics.     

Why are so many trees hollow?

In many living trees, much of the interior of the trunk can be rotten or even hollowed out. Previously, this has been suggested to be adaptive, with microbial or animal consumption of interior wood producing a rain of nutrients to the soil beneath the tree that allows recycling of those nutrients into new growth via the trees roots. Here I propose an alternative (non-exclusive) explanation: such loss of wood comes at very little cost to the tree and so investment in costly chemical defence of this wood is not economic. I discuss how this theory can be tested empirically.     

How good is our genome?

Our genome has evolved to perpetuate itself through the maintenance of the species via an uninterrupted chain of reproductive somas. Accordingly, evolution is not concerned with diseases occurring after the soma's reproductive stage. Following Richard Dawkins, we would like to reassert that we indeed live as disposable somas, slaves of our germline genome, but could soon start rebelling against such slavery. Cancer and its relation to the TP53 gene may offer a paradigmatic example. The observation that the latency period in cancer can be prolonged in mice by increasing the number of TP53 genes in their genome, suggests that sooner or later we will have to address the question of heritable disease avoidance via the manipulation of the human germline.     

How Tough are Sclerophylls?

Fracture toughness was estimated for a 'least tough' path inthe leaves of woody species from three sclerophyllous plantcommunities. Most of the species from Mediterranean, tropicalheath forest and lowland tropical rain forest habitats had verytough leaves, with toughness generally 600-1300 J m^-2, whichis two to four times higher than soft-leaved tropical pioneertrees. The toughest leaf (2032 J m^-2), Parishia insignis, camefrom the canopy of the lowland rain forest. Leaves from theshaded understorey of the rain forest did not appear any lesstough than those from the canopy.Copyright 1993, 1999 AcademicPress Leaf fracture toughness, sclerophylly, Mediterranean vegetation, tropical forest     

How reticulated are species?

Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree‐like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.     

How repetitive are genomes?

Background  

Genome sequences vary strongly in their repetitiveness and the causes for this are still debated. Here we propose a novel measure of genome repetitiveness, the index of repetitiveness, I _r, which can be computed in time proportional to the length of the sequences analyzed. We apply it to 336 genomes from all three domains of life.     

What are oligomerization domains good for?

Collagen triple helices, coiled coils and other oligomerization domains mediate the subunit assembly of a large number of proteins. Oligomerization leads to functional advantages of multivalency and high binding strength, increased structure stabilization and combined functions of different domains. These features seen in naturally occurring proteins can be engineered by protein design by combining oligomerization domains with functional domains.     

How good is your screening library?

Efficient library design is an ongoing challenge for investigators seeking novel ligands for proteins, whether for drug discovery or chemical biology. Strategies that add neglected chemistry or exclude unproductive compounds are two dominant recent themes, as is a growing awareness of molecular complexity and its implications. The choice of how complex molecules in screening libraries should be often amounts to how big they should be. Small, simple molecules have lower affinities and must be screened at high concentration, but they will also have higher hit rates. Larger compounds, on the other hand, will often more closely resemble final drugs, but because they are more highly functionalized and specific, they will have much lower hit rates. The best general-purpose screening libraries may well be those of intermediate complexity that are free of artifact-causing nuisance compounds.     

Biomarkers of neurodegenerative disorders： How good are they？

Biomarkers are very important indicators of normal and abnormal biological processes. Specific changes in pathologies,biochemistries and genetics can give us comprehensive information regarding the nature of any particular disease. A good biomarker should be precise and reliable, distinguishable between normal and interested disease, and differentiable between different diseases. It is believed that biomarkers have great potential in predicting chances for diseases, aiding in early diagnosis, and setting standards for the development of new remedies to treat diseases. New technologies have enabled scientists to identify biomarkers of several different neurodegenerative diseases. The followings, for instance,are only a few of the many new biomarkers that have been recently identified: the phosphorylated tau protein and aggregated β-amyloid peptide for Alzheimer‘s disease (AD), α-synuclein contained Lewy bodies and altered dopamine transporter (DAT) imaging for Parkinson‘s disease (PD), SOD mutations for familial amyotrophic lateral sclerosis (ALS), and CAG repeats resulted from Huntington‘s gene mutations in Huntington‘s disease (HD). This article will focus on the most-recent findings of biomarkers belonging to the four mentioned neurodegenerative diseases.