A panorama of mammalian gene expression evolution

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102623/1/msb201186.pd

Fly wing evolution explained by a neutral model with mutational pleiotropy

To what extent the speed of mutational production of phenotypic variation determines the rate of long‐term phenotypic evolution is a central question. Houle et al. recently addressed this question by studying the mutational variances, additive genetic variances, and macroevolution of locations of vein intersections on fly wings, reporting very slow phenotypic evolution relative to the rates of mutational input, high phylogenetic signals, and a strong, linear relationship between the mutational variance of a trait and its rate of evolution. Houle et al. found no existing model of phenotypic evolution to be consistent with all these observations, and proposed the improbable scenario of equal influence of mutational pleiotropy on all traits. Here, we demonstrate that the purported linear relationship between mutational variance and evolutionary divergence is artifactual. We further show that the data are explainable by a simple model in which the wing traits are effectively neutral at least within a range of phenotypic values but their evolutionary rates are differentially reduced because mutations affecting these traits are purged owing to their different pleiotropic effects on other traits that are under stabilizing selection. Thus, the evolutionary patterns of fly wing morphologies are explainable under the existing theoretical framework of phenotypic evolution.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/162712/3/evo14076.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162712/2/evo14076-sup-0001-SuppMat.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/162712/1/evo14076_am.pd

Zinc ferrite based gas sensors: A review

Flammable, explosive and toxic gases, such as hydrogen, hydrogen sulfide and volatile organic compounds vapor, are major threats to the ecological environment safety and human health. Among the available technologies, gas sensing is a vital component, and has been widely studied in literature for early detection and warning. As a metal oxide semiconductor, zinc ferrite (ZnFe2O4) represents a kind of promising gas sensing material with a spinel structure, which also shows a fine gas sensing performance to reducing gases. Due to its great potentials and widespread applications, this article is intended to provide a review on the latest development in zinc ferrite based gas sensors. We first discuss the general gas sensing mechanism of ZnFe2O4 sensor. This is followed by a review of the recent progress about zinc ferrite based gas sensors from several aspects: different micro-morphology, element doping and heterostructure materials. In the end, we propose that combining ZnFe2O4 which provides unique microstructure (such as the multi-layer porous shells hollow structure), with the semiconductors such as graphene, which provide excellent physical properties. It is expected that the mentioned composites contribute to improving selectivity, long-term stability, and other sensing performance of sensors at room or low temperature

Why Do Hubs Tend to Be Essential in Protein Networks?

The protein–protein interaction (PPI) network has a small number of highly connected protein nodes (known as hubs) and many poorly connected nodes. Genome-wide studies show that deletion of a hub protein is more likely to be lethal than deletion of a non-hub protein, a phenomenon known as the centrality-lethality rule. This rule is widely believed to reflect the special importance of hubs in organizing the network, which in turn suggests the biological significance of network architectures, a key notion of systems biology. Despite the popularity of this explanation, the underlying cause of the centrality-lethality rule has never been critically examined. We here propose the concept of essential PPIs, which are PPIs that are indispensable for the survival or reproduction of an organism. Our network analysis suggests that the centrality-lethality rule is unrelated to the network architecture, but is explained by the simple fact that hubs have large numbers of PPIs, therefore high probabilities of engaging in essential PPIs. We estimate that ~ 3% of PPIs are essential in the yeast, accounting for ~ 43% of essential genes. As expected, essential PPIs are evolutionarily more conserved than nonessential PPIs. Considering the role of essential PPIs in determining gene essentiality, we find the yeast PPI network functionally more robust than random networks, yet far less robust than the potential optimum. These and other findings provide new perspectives on the biological relevance of network structure and robustness

Determinative developmental cell lineages are robust to cell deaths

All forms of life are confronted with environmental and genetic perturbations, making phenotypic robustness an important characteristic of life. Although development has long been viewed as a key component of phenotypic robustness, the underlying mechanism is unclear. Here we report that the determinative developmental cell lineages of two protostomes and one deuterostome are structured such that the resulting cellular compositions of the organisms are only modestly affected by cell deaths. Several features of the cell lineages, including their shallowness, topology, early ontogenic appearances of rare cells, and non-clonality of most cell types, underlie the robustness. Simple simulations of cell lineage evolution demonstrate the possibility that the observed robustness arose as an adaptation in the face of random cell deaths in development. These results reveal general organizing principles of determinative developmental cell lineages and a conceptually new mechanism of phenotypic robustness, both of which have important implications for development and evolution

Gene Losses during Human Origins

Pseudogenization is a widespread phenomenon in genome evolution, and it has been proposed to serve as an engine of evolutionary change, especially during human origins (the “less-is-more” hypothesis). However, there has been no comprehensive analysis of human-specific pseudogenes. Furthermore, it is unclear whether pseudogenization itself can be selectively favored and thus play an active role in human evolution. Here we conduct a comparative genomic analysis and a literature survey to identify 80 nonprocessed pseudogenes that were inactivated in the human lineage after its separation from the chimpanzee lineage. Many functions are involved among these genes, with chemoreception and immune response being outstandingly overrepresented, suggesting potential species-specific features in these aspects of human physiology. To explore the possibility of adaptive pseudogenization, we focus on CASPASE12, a cysteinyl aspartate proteinase participating in inflammatory and innate immune response to endotoxins. We provide population genetic evidence that the nearly complete fixation of a null allele at CASPASE12 has been driven by positive selection, probably because the null allele confers protection from severe sepsis. We estimate that the selective advantage of the null allele is about 0.9% and the pseudogenization started shortly before the out-of-Africa migration of modern humans. Interestingly, two other genes related to sepsis were also pseudogenized in humans, possibly by selection. These adaptive gene losses might have occurred because of changes in our environment or genetic background that altered the threat from or response to sepsis. The identification and analysis of human-specific pseudogenes open the door for understanding the roles of gene losses in human origins, and the demonstration that gene loss itself can be adaptive supports and extends the “less-is-more” hypothesis

In Search of the Biological Significance of Modular Structures in Protein Networks

Many complex networks such as computer and social networks exhibit modular structures, where links between nodes are much denser within modules than between modules. It is widely believed that cellular networks are also modular, reflecting the relative independence and coherence of different functional units in a cell. While many authors have claimed that observations from the yeast protein–protein interaction (PPI) network support the above hypothesis, the observed structural modularity may be an artifact because the current PPI data include interactions inferred from protein complexes through approaches that create modules (e.g., assigning pairwise interactions among all proteins in a complex). Here we analyze the yeast PPI network including protein complexes (PIC network) and excluding complexes (PEC network). We find that both PIC and PEC networks show a significantly greater structural modularity than that of randomly rewired networks. Nonetheless, there is little evidence that the structural modules correspond to functional units, particularly in the PEC network. More disturbingly, there is no evolutionary conservation among yeast, fly, and nematode modules at either the whole-module or protein-pair level. Neither is there a correlation between the evolutionary or phylogenetic conservation of a protein and the extent of its participation in various modules. Using computer simulation, we demonstrate that a higher-than-expected modularity can arise during network growth through a simple model of gene duplication, without natural selection for modularity. Taken together, our results suggest the intriguing possibility that the structural modules in the PPI network originated as an evolutionary byproduct without biological significance

Molecular Dynamic Simulation of Diffusion in the Melt Pool in Laser Additive Alloying Process of Co-Ni-Cr-Mn-Fe High Entropy Alloy

High entropy alloys (HEAs) can be manufactured in many conventional ways, but it becomes difficult of fabricating heterogeneous materials and structures. Selective Laser Melting (SLM) method generally melts pure elemental powders or prefabricated alloy powders without alloying process. In-situ alloying in SLM, which is also called Laser Additive Alloying (LAA), using pure elemental powders becomes a promising method for creating HEA with heterogeneous structures. However, the effect of the diffusion of elements in the molten pool on the formation of HEA remains unclear. In this paper, the well-discussed Cantor HEA was studied in an in-situ alloying situation, where pure elemental powders (Co, Cr, Mn, Ni, Fe) distributed on a powder bed were irradiated by laser and were subsequently allowed to cool back to room temperature. The diffusion of specific elements, with respect to their original clusters, was tracked via Mean Square Displacement (MSD) as well as the final composition of key locations. Our model was verified by showing a good agreement with the overall average diffusion rates of each element in the Cantor HEA qualitatively in other works from literature. Results initially showed that as the energy density increases, better diffusion was observed through a pixel overlay analysis about the mixing of different elements. The best-case scenario of diffusion from the pixel overlay map indicated a strong presence of 3 to 4 elements after the laser scanning. Given the conditions in the MD simulation, there was no apparent segregation of elements during the alloying process. In addition, we also conducted a simulation by implementing a 0.03 nm/ps laser scanning in a meander 2-track scan in order to completely melt the powder bed. After cooling and equilibration, Polyhedral Template Analysis was applied to analyze the crystal structure of the solidified powder bed in the presence of increasing components. When the powders of Cantor HEA were alloyed using LAA approach, all elements experienced a complex diffusion behavior, elements like Cr also experienced a relatively rapid diffusion compared to other elements. Despite this, Cr only diffused for a short period and diffused minimally during the in-situ alloying process. The analysis of element-specific behavior, such as diffusion, can provide a framework for the LAA production of HEA. This MD study provides a detailed analysis about the effect of diffusion on the formation of HEA system if in-situ alloying is adopted, the findings of this study can be used to guide the material design and the appropriate parameters for manufacturing process of new HEAs. This study can also be extended to analyze the effect of diffusion on the thermomechanical properties of HEAs

Genomic evidence for elevated mutation rates in highly expressed genes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102069/1/embr2012165.reviewer_comments.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102069/2/embr2012165-sup-0001.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/102069/3/embr2012165.pd