The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants

We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.     

A well-preserved Archaeopteryx specimen with theropod features

A nearly complete skeleton of Archaeopteryx with excellent bone preservation shows that the osteology of the urvogel is similar to that of nonavian theropod dinosaurs. The new specimen confirms the presence of a hyperextendible second toe as in dromaeosaurs and troodontids. Archaeopteryx had a plesiomorphic tetraradiate palatine bone and no fully reversed first toe. These observations provide further evidence for the theropod ancestry of birds. In addition, the presence of a hyperextendible second toe blurs the distinction of archaeopterygids from basal deinonychosaurs (troodontids and dromaeosaurs) and challenges the monophyly of Aves.     

Structure of PTB bound to RNA: specific binding and implications for splicing regulation

The polypyrimidine tract binding protein (PTB) is a 58-kilodalton RNA binding protein involved in multiple aspects of messenger RNA metabolism, including the repression of alternative exons. We have determined the solution structures of the four RNA binding domains (RBDs) of PTB, each bound to a CUCUCU oligonucleotide. Each RBD binds RNA with a different binding specificity. RBD3 and RBD4 interact, resulting in an antiparallel orientation of their bound RNAs. Thus, PTB will induce RNA looping when bound to two separated pyrimidine tracts within the same RNA. This leads to structural models for how PTB functions as an alternative-splicing repressor.     

Deciphering the reaction dynamics underlying optimal control laser fields

Femtosecond high-resolution pump-probe experiments have been used together with theoretical ab initio quantum calculations and wave packet dynamics simulations to decode an optimal femtosecond pulse that is generated from adaptive learning algorithms. This pulse is designed to maximize the yield of the organometallic ion CpMn(CO)3 while hindering the competing fragmentation. The sequential excitation and ionization of the target ion are accomplished by an optimized field consisting of two dominant subpulses with optimal frequencies and time delays.     

Shocks in ion sputtering sharpen steep surface features

We report a regime of ion beam sputtering that occurs for sufficiently steep slopes. High slopes propagate over large distances without dissipating the steepest features. Both the propagation velocity and the dynamically selected slope are universal, independent of the details of the initial shape of the surface. The resulting behavior can be understood as the propagation of a shock front that self-selects a stable slope, as has been previously observed in thin-film fluid flows. Experiments confirm predictions of the theory. An important implication of the propagative behavior at high surface slopes is that a pattern can be fabricated at a large length scale and, through uniform ion irradiation, reduced to a smaller length scale while preserving, or even sharpening, the sharpest features.     

Mutations in dynein link motor neuron degeneration to defects in retrograde transport

Degenerative disorders of motor neurons include a range of progressive fatal diseases such as amyotrophic lateral sclerosis (ALS), spinal-bulbar muscular atrophy (SBMA), and spinal muscular atrophy (SMA). Although the causative genetic alterations are known for some cases, the molecular basis of many SMA and SBMA-like syndromes and most ALS cases is unknown. Here we show that missense point mutations in the cytoplasmic dynein heavy chain result in progressive motor neuron degeneration in heterozygous mice, and in homozygotes this is accompanied by the formation of Lewy-like inclusion bodies, thus resembling key features of human pathology. These mutations exclusively perturb neuron-specific functions of dynein.     

Multi-university research teams: shifting impact, geography, and stratification in science

This paper demonstrates that teamwork in science increasingly spans university boundaries, a dramatic shift in knowledge production that generalizes across virtually all fields of science, engineering, and social science. Moreover, elite universities play a dominant role in this shift. By examining 4.2 million papers published over three decades, we found that multi-university collaborations (i) are the fastest growing type of authorship structure, (ii) produce the highest-impact papers when they include a top-tier university, and (iii) are increasingly stratified by in-group university rank. Despite the rising frequency of research that crosses university boundaries, the intensification of social stratification in multi-university collaborations suggests a concentration of the production of scientific knowledge in fewer rather than more centers of high-impact science.     

Fossilized nuclei and germination structures identify Ediacaran "animal embryos" as encysting protists

Globular fossils showing palintomic cell cleavage in the Ediacaran Doushantuo Formation, China, are widely regarded as embryos of early metazoans, although metazoan synapomorphies, tissue differentiation, and associated juveniles or adults are lacking. We demonstrate using synchrotron-based x-ray tomographic microscopy that the fossils have features incompatible with multicellular metazoan embryos. The developmental pattern is comparable with nonmetazoan holozoans, including germination stages that preclude postcleavage embryology characteristic of metazoans. We conclude that these fossils are neither animals nor embryos. They belong outside crown-group Metazoa, within total-group Holozoa (the sister clade to Fungi that includes Metazoa, Choanoflagellata, and Mesomycetozoea) or perhaps on even more distant branches in the eukaryote tree. They represent an evolutionary grade in which palintomic cleavage served the function of producing propagules for dispersion.