Topological network alignment uncovers biological function and phylogeny

Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments. Topology-based alignments have the potential to provide a completely new, independent source of phylogenetic information. Our alignment of the protein-protein interaction networks of two very different species--yeast and human--indicate that even distant species share a surprising amount of network topology with each other, suggesting broad similarities in internal cellular wiring across all life on Earth.Comment: Algorithm explained in more details. Additional analysis adde

Gene/Environment Interaction in Atherosclerosis: An Example of Clinical Medicine as Seen from the Evolutionary Perspective

Evolutionary medicine is the application of evolution theory to understanding health and disease. It provides a complementary scientific approach to the present mechanistic explanations that dominate medical science, and particularly medical education. The chronic multifactorial disease of atherosclerosis clearly illustrates the Darwinian paradigm. Recent research, combining the effects of genes and environment, has provided surprising clues to the pathogenesis of this major public health problem. This example makes a strong case for recognizing evolution biology as a basic science for medicine

Queen control of a key life-history event in a eusocial insect

In eusocial insects, inclusive fitness theory predicts potential queen–worker conflict over the timing of events in colony life history. Whether queens or workers control the timing of these events is poorly understood. In the bumble-bee Bombus terrestris, queens exhibit a ‘switch point’ in which they switch from laying diploid eggs yielding females (workers and new queens) to laying haploid eggs yielding males. By rearing foundress queens whose worker offspring were removed as pupae and sexing their eggs using microsatellite genotyping, we found that queens kept in the complete absence of adult workers still exhibit a switch point. Moreover, the timing of their switch points relative to the start of egg-laying did not differ significantly from that of queens allowed to produce normal colonies. The finding that bumble-bee queens can express the switch point in the absence of workers experimentally demonstrates queen control of a key life-history event in eusocial insects. In addition, we found no evidence that workers affect the timing of the switch point either directly or indirectly via providing cues to queens, suggesting that workers do not fully express their interests in queen–worker conflicts over colony life history

Acceptance of Evolution Increases with Student Academic Level: A Comparison Between a Secular and a Religious College

Acceptance of evolution among the general public, high schools, teachers, and scientists has been documented in the USA; little is known about college students’ views on evolution; this population is relevant since it transits from a high-school/parent-protective environment to an independent role in societal decisions. Here we compare perspectives about evolution, creationism, and intelligent design (ID) between a secular (S) and a religious (R) college in the Northeastern USA. Interinstitutional comparisons showed that 64% (mean S + R) biology majors vs. 42/62% (S/R) nonmajors supported the exclusive teaching of evolution in science classes; 24/29% (S/R) biology majors vs. 26/38% (S/R) nonmajors perceived ID as both alternative to evolution and/or scientific theory about the origin of life; 76% (mean S + R) biology majors and nonmajors accepted evolutionary explanations about the origin of life; 86% (mean S + R) biology majors vs. 79% (mean S + R) nonmajors preferred science courses where human evolution is discussed; 76% (mean S+R) biology majors vs. 79% (mean S + R) nonmajors welcomed questions about evolution in exams and/or thought that such questions should always be in exams; and 66% (mean S + R) biology majors vs. 46% (mean S + R) nonmajors admitted they accept evolution openly and/or privately. Intrainstitutional comparisons showed that overall acceptance of evolution among biologists (S or R) increased gradually from the freshman to the senior year, due to exposure to upper-division courses with evolutionary content. College curricular/pedagogical reform should fortify evolution literacy at all education levels, particularly among nonbiologists

Selective disappearance of individuals with high levels of glycated haemoglobin in a free-living bird

This work was supported by the ANR (ANR-06-JCJC0082 to B.D.), the CNRS (PEPS INEE and PICS France–Switzerland to B.D.), the French Ministe`re de l’Enseignement Supe´rieur et de la Recherche (PhD fellowship to C.R.), the Re´gion Rhoˆne-Alpes (Explora’doc mobility grant to C.R.), the University of Aberdeen (stipend to C.R.), the L’Ore´al Foundation-UNESCO ‘For Women in Science’ program (fellowship to C.R.) and the Rectors’ Conference of the Swiss Universities (grant to C.R. and P.B.).Peer reviewedPostprin

Special Issue on Stingless bees: Integrating basic biology and conservation

It is easy to see why stingless bees (Meliponini) were chosen for this special issue, entitled Stingless bees: Integrating basic biology and conservation. Interest in these bees is increasing each day, with their role as ecosystemservices providers in the pollination of wild and cultivated plants, and their fascinating biology and social behavior. Yet, despite having been kept by the Native Americans for hundreds of years for their honey, they remain much understudied compared to their better known relatives, the bumblebees and honeybees. This is in part due to their massive biodiversity, with known species now numbering over 500 – all with a tropical distribution. The diversity and rich social behavior of the stingless bees has often been compared to the knowledge of the other group of eusocial bees, including the bumblebees (Bombini) and honeybees (Apini). Yet, the development of new scientific techniques and research methods, and progress in deciphering their phylogeny, now allows for an updated interpretation of the evolution, biology and conservation of Meliponini bees

How endo- is endo-?: surface sterilization of delicate samples: a Bryopsis (Bryopsidales, Chlorophyta) case study

In the search for endosymbiotic bacteria, elimination of ectosymbionts is a key point of attention. Commonly, the surface of the host itself or the symbiotic structures are sterilized with aggressive substances such as chlorine or mercury derivatives. Although these disinfectants are adequate to treat many species, they are not suitable for surface sterilization of delicate samples. In order to study the bacterial endosymbionts in the marine green alga Bryopsis, the host plant's cell wall was mechanically, chemically and enzymatically cleaned. Merely a chemical and enzymatical approach proved to be highly effective. Bryopsis thalli treated with cetyltrimethylammonium bromide (CTAB) lysis buffer, proteinase K and bactericidal cleanser Umonium Master showed no bacterial growth on agar plates or bacterial fluorescence when stained with a DNA fluorochrome. Moreover, the algal cells were intact after sterilization, suggesting endophytic DNA is still present within these algae. This new surface sterilization procedure opens the way to explore endosymbiotic microbial communities of other, even difficult to handle, samples