bluuebunny/crossref_metadata_2025 huggingface dataset:
Roundtable: Physics in Transition
Authors: Bostock Judith L. , Bromley D. Allan , Gomory Ralph E. , Kleppner Daniel , Libchaber Albert J. , Massey Walter E. , Schriesheim Alan , Zare Richard N. , Lubkin Gloria B. , Goodwin Irwin
Published: January 2008

The question before us can be stated simply: Where do we go from here? The “we” is the physics community, though it's our hope that the discussion will range more widely into science and technology, so we'll be able to comment on the changes likely to take place in research universities, national laboratories and private industry. Our subject is physics in transition to the 21st century. Some say physics has been in a state of transition for well over a century—certainly since James Clerk Maxwell in the 19th century. In every decade of the 20th century, physics has experienced momentous turning points. In this last decade of the century we seem to have reached another turning point with the end of nuclear weapons rivalry that was given the name of cold war and the increase of global industrial competitiveness. In the past year, pressures by the Federal government and by commercial companies have increased to make physics and the rest of science more relevant to business and to society. We are already witnessing the reduction of physics research at some major corporate laboratories and sensing a shakeup for physics facilities at some national labs. So this discussion of the future of physics is timely.
Physical Review Records the Birth of the Laser Era
Authors: Bloembergen Nicolaas
Published: January 2008

The historical development of masers and lasers has been well documented in several books. It is not my purpose here to recapitulate or improve on those accounts, which focus on the roles individual scientists, industry and funding agencies played in the evolution of the laser.
Fiber Optics
Authors: Glass Alastair M.
Published: January 2008

On looking back to the beginnings of Physical Review it is interesting to find that the very first paper in volume 1, number 1, 1893, addressed the “transmission spectra of certain substances in the infrared.” The article, authored by Ernest Nichols, included quartz and glass as materials of interest. The same volume offers a review of Nikola Tesla's book Light and Other High-Frequency Phenomena. It is therefore fitting that this celebration of the 100th anniversary of Physical Review includes a discussion of a technology that is based on fundamental principles of physics addressed in the journal's first issue and countless numbers of later issues and that has profoundly transformed the telecommunications infrastructure of our society.
Nuclear Magnetic Resonance in Bulk Matter
Authors: Pake George E.
Published: January 2008

In early 1946 the Physical Review published letters from the two discoverers of nuclear magnetic resonance describing their independent detections of nmr in bulk matter. In recognition of their pioneering research, which they carried out simultaneously, albeit in different places and with different conceptual bases, Felix Bloch and Edward Purcell were awarded the 1952 Nobel Prize for Physics.
Superconductivity: From Physics to Technology
Authors: Geballe Theodore H.
Published: January 2008

Superconductivity was discovered in 1911 by Heike Kamerlingh Onnes in Leiden. That discovery can be traced to the steady advance in laboratory techniques for obtaining ever lower temperatures that began when Louis Cailletet in France and Raoul Pictet in Switzerland succeeded in liquefying trace amounts of the “permanent gases,” nitrogen, air and hydrogen. These gases were so named because previous attempts to liquefy them, by Michael Faraday among others, had been unsuccessful.
High-Performance Computing and Plasma Physics
Authors: Dawson John M. , Decyk Viktor , Sydora Richard , Liewer Paulett
Published: January 2008

The physics of ionized gases is a relatively new science. Not until the development of the electrical industry were controlled experiments on ionized gases possible, and so plasma physics is only about 100 years old. The early part of this century saw some pioneering studies of gas discharges and radio propagation in the ionosphere. However, the real impetus came with the initiation of the controlled thermonuclear reaction programs in the 1950s and with the discoveries of the Van Allen belts and the solar wind in the 1960s. Studies in these areas showed that plasma behavior is much more complex than had been anticipated.
Goals for the Federal Role in Science and Technology
Authors: Gomory Ralph E.
Published: January 2008

The arrival of a new Administration in Washington raises once more the question of setting priorities for science and technology. However, this may not be quite the right question. Setting priorities can be difficult without goals. If we don't have goals, if we don't know where we are going, it's hard to have a sensible discussion about the best way of getting there.
Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells
Authors: Bar-Joseph Ziv , Siegfried Zahava , Brandeis Michael , Brors Benedikt , Lu Yong , Eils Roland , Dynlacht Brian D. , Simon Itamar
Published: January 2008

Characterization of the transcriptional regulatory network of the normal cell cycle is essential for understanding the perturbations that lead to cancer. However, the complete set of cycling genes in primary cells has not yet been identified. Here, we report the results of genome-wide expression profiling experiments on synchronized primary human foreskin fibroblasts across the cell cycle. Using a combined experimental and computational approach to deconvolve measured expression values into “single-cell” expression profiles, we were able to overcome the limitations inherent in synchronizing nontransformed mammalian cells. This allowed us to identify 480 periodically expressed genes in primary human foreskin fibroblasts. Analysis of the reconstructed primary cell profiles and comparison with published expression datasets from synchronized transformed cells reveals a large number of genes that cycle exclusively in primary cells. This conclusion was supported by both bioinformatic analysis and experiments performed on other cell types. We suggest that this approach will help pinpoint genetic elements contributing to normal cell growth and cellular transformation.
The elongation factor RfaH and the initiation factor σ bind to the same site on the transcription elongation complex
Authors: Sevostyanova Anastasiya , Svetlov Vladimir , Vassylyev Dmitry G. , Artsimovitch Irina
Published: January 2008

RNA polymerase is a target for numerous regulatory events in all living cells. Recent studies identified a few “hot spots” on the surface of bacterial RNA polymerase that mediate its interactions with diverse accessory proteins. Prominent among these hot spots, the β′ subunit clamp helices serve as a major binding site for the initiation factor σ and for the elongation factor RfaH. Furthermore, the two proteins interact with the nontemplate DNA strand in transcription complexes and thus may interfere with each other's activity. We show that RfaH does not inhibit transcription initiation but, once recruited to RNA polymerase, abolishes σ-dependent pausing. We argue that this apparent competition is due to a steric exclusion of σ by RfaH that is stably bound to the nontemplate DNA and clamp helices, both of which are necessary for the σ recruitment to the transcription complex. Our findings highlight the key regulatory role played by the clamp helices during both initiation and elongation stages of transcription.
Agonist-directed signaling of the serotonin 2A receptor depends on β-arrestin-2 interactions
in vivo
Authors: Schmid Cullen L. , Raehal Kirsten M. , Bohn Laura M.
Published: January 2008

Visual and auditory hallucinations accompany certain neuropsychiatric disorders, such as schizophrenia, and they also can be induced by the use or abuse of certain drugs. The heptahelical serotonin 2A receptors (5-HT2ARs) are molecular targets for drug-induced hallucinations. However, the cellular mechanisms by which the 5-HT2AR mediates these effects are not well understood. Drugs acting at the 5-HT2AR can trigger diverse signaling pathways that may be directed by the chemical properties of the drug. β-arrestins are intracellular proteins that bind to heptahelical receptors and represent a point where such divergences in ligand-directed functional signaling could occur. Here we compare the endogenous agonist, serotonin, to a synthetic 5-HT2AR hallucinogenic agonist, 2,5-dimethoxy-4-iodoamphetamine (DOI), in mice lacking β-arrestin-2, as well as in cells lacking β-arrestins. In mice, we find that serotonin induces a head twitch response by a β-arrestin-2-dependent mechanism. However, DOI invokes the behavior independent of β-arrestin-2. The two structurally distinct agonists elicit different signal transduction and trafficking patterns upon activation of 5-HT2AR, which hinge on the presence of β-arrestins. Our study suggests that the 5-HT2AR–β-arrestin interaction may be particularly important in receptor function in response to endogenous serotonin levels, which could have major implications in drug development for treating neuropsychiatric disorders such as depression and schizophrenia.
Sexual maturity in growing dinosaurs does not fit reptilian growth models
Authors: Lee Andrew H. , Werning Sarah
Published: January 2008

Recent histological studies suggest relatively rapid growth in dinosaurs. However, the timing of reproductive maturity (RM) in dinosaurs is poorly known because unambiguous indicators of RM are rare. One exception is medullary bone (MB), which is an ephemeral bony tissue that forms before ovulation in the marrow cavities of birds as a calcium source for eggshelling. Recently, MB also was described in a single specimen of the saurischian dinosaurTyrannosaurus rex. Here, we report two other occurrences of MB: in another saurischian dinosaur,Allosaurus, and in the ornithischian dinosaurTenontosaurus. We show by counting lines of arrested growth and performing growth curve reconstructions thatTenontosaurus,Allosaurus, andTyrannosauruswere reproductively mature by 8, 10, and 18 years, respectively. RM in these dinosaurs coincided with a transition from growth acceleration to deceleration. It also far precedes predictions based on the growth rates of living reptiles scaled to similar size. Despite relatively rapid growth, dinosaurs were similar to reptiles in that RM developed before reaching asymptotic size. However, this reproductive strategy also occurs in medium- to large-sized mammals and correlates with a strategy of prolonged multiyear growth. RM in actively growing individuals suggests that these dinosaurs were born relatively precocial and experienced high adult mortality. The origin of the modern avian reproductive strategy in ornithuran birds likely coincided with their extreme elevations in growth rate and truncations to growth duration.
Bacillus subtilis
glutamine synthetase regulates its own synthesis by acting as a chaperone to stabilize GlnR–DNA complexes
Authors: Fisher Susan H. , Wray Lewis V.
Published: January 2008

The
Bacillus subtilis
GlnR repressor controls gene expression in response to nitrogen availability. Because all GlnR-regulated genes are expressed constitutively in mutants lacking glutamine synthetase (GS), GS is required for repression by GlnR. Feedback-inhibited GS (FBI-GS) was shown to activate GlnR DNA binding with an
in vitro
electophoretic mobility shift assay (EMSA). The activation of GlnR DNA binding by GS in these experiments depended on the feedback inhibitor glutamine and did not occur with mutant GS proteins defective in regulating GlnR activity
in vivo
. Although stable GS–GlnR–DNA ternary complexes were not observed in the EMSA experiments, cross-linking experiments showed that a protein–protein interaction occurs between GlnR and FBI-GS. This interaction was reduced in the absence of the feedback inhibitor glutamine and with mutant GS proteins. Because FBI-GS significantly reduced the dissociation rate of the GlnR–DNA complexes, the stability of these complexes is enhanced by FBI-GS. These results argue that FBI-GS acts as a chaperone that activates GlnR DNA binding through a transient protein–protein interaction that stabilizes GlnR–DNA complexes. GS was shown to control the activity of the
B. subtilis
nitrogen transcription factor TnrA by forming a stable complex between FBI-GS and TnrA that inhibits TnrA DNA binding. Thus,
B. subtilis
GS is an enzyme with dual catalytic and regulatory functions that uses distinct mechanisms to control the activity of two different transcription factors.
CD133
+
neural stem cells in the ependyma of mammalian postnatal forebrain
Authors: Coskun Volkan , Wu Hao , Blanchi Bruno , Tsao Sean , Kim Kevin , Zhao Jing , Biancotti Juan Carlos , Hutnick Leah , Krueger Richard C. , Fan Guoping , de Vellis Jean , Sun Yi E.
Published: January 2008

The postnatal forebrain subventricular zone (SVZ) harbors stem cells that give rise to olfactory bulb interneurons throughout life. The identity of stem cells in the adult SVZ has been extensively debated. Although, ependymal cells were once suggested to have stem cell characteristics, subsequent studies have challenged the initial report and postulated that subependymal GFAP
+
cells were the stem cells. Here, we report that, in the adult mouse forebrain, immunoreactivity for a neural stem cell marker, prominin-1/CD133, is exclusively localized to the ependyma, although not all ependymal cells are CD133
+
. Using transplantation and genetic lineage tracing approaches, we demonstrate that CD133
+
ependymal cells continuously produce new neurons destined to olfactory bulb. Collectively, our data indicate that, compared with GFAP expressing adult neural stem cells, CD133
+
ependymal cells represent an additional—perhaps more quiescent—stem cell population in the mammalian forebrain.
Development of JFH1-based cell culture systems for hepatitis C virus genotype 4a and evidence for cross-genotype neutralization
Authors: Scheel Troels K. H. , Gottwein Judith M. , Jensen Tanja B. , Prentoe Jannick C. , Hoegh Anne M. , Alter Harvey J. , Eugen-Olsen Jesper , Bukh Jens
Published: January 2008

Efficient
in vitro
systems to study the life cycle of hepatitis C virus (HCV) were recently developed for JFH1 (genotype 2a), which has unique replication capacity in Huh7 cells. We developed 4a/JFH1 intergenotypic recombinants containing the structural genes (Core, E1, and E2), p7, and all or part of NS2 of the 4a prototype strain ED43 that, after transfection of Huh7.5 cells with RNA transcripts, produced infectious viruses. Compared with the J6/JFH control virus, production of viruses was delayed. However, efficient spread of infection and high HCV RNA and infectivity titers were obtained in serial passages. Sequence analysis of recovered viruses and subsequent reverse genetic studies revealed a vital dependence on one or two NS2 mutations, depending on the 4a/2a junction. Infectivity of ED43/JFH1 viruses was CD81 dependent. The genotype 4 cell culture systems permit functional analyses as well as drug and vaccine research on an increasingly important genotype in the Middle East, Africa, and Europe. We also developed genotype 1a intergenotypic recombinants from H77C with vital mutations in NS3. Using H77C/JFH1 and ED43/JFH1 viruses, we demonstrated high homologous neutralizing antibody titers in 1a and 4a patient sera, respectively. Furthermore, availability of JFH1 viruses with envelope proteins of the six major HCV genotypes permitted cross-neutralization studies; 1a and 4a serum cross-neutralized 1a, 4a, 5a, and 6a but not 2a and 3a viruses. Thus, the JFH1 intergenotypic recombinants will be of importance for future studies of HCV neutralization and accelerate the development of passive and active immunoprophylaxis.
Identification of Plet-1 as a specific marker of early thymic epithelial progenitor cells
Authors: Depreter Marianne G. L. , Blair Natalie F. , Gaskell Terri L. , Nowell Craig S. , Davern Kathleen , Pagliocca Adelina , Stenhouse Frances H. , Farley Alison M. , Fraser Adrian , Vrana Jan , Robertson Kevin , Morahan Grant , Tomlinson Simon R. , Blackburn C. Clare
Published: January 2008

The thymus is essential for a functional immune system, because the thymic stroma uniquely supports T lymphocyte development. We have previously identified the epithelial progenitor population from which the thymus arises and demonstrated its ability to generate an organized functional thymus upon transplantation. These thymic epithelial progenitor cells (TEPC) are defined by surface determinants recognized by the mAbs MTS20 and MTS24, which were also recently shown to identify keratinocyte progenitor cells in the skin. However, the biochemical nature of the MTS20 and MTS24 determinants has remained unknown. Here we show, via expression profiling of fetal mouse TEPC and their differentiated progeny and subsequent analyses, that both MTS20 and MTS24 specifically bind an orphan protein of unknown function, Placenta-expressed transcript (Plet)-1. In the postgastrulation embryo,Plet-1expression is highly restricted to the developing pharyngeal endoderm and mesonephros until day 11.5 of embryogenesis, consistent with the MTS20 and MTS24 staining pattern; both MTS20 and MTS24 specifically bind cell lines transfected withPlet-1; and antibodies to Plet-1 recapitulate MTS20/24 staining. In adult tissues, we demonstrate expression in a number of sites, including mammary and prostate epithelia and in the pancreas, where Plet-1 is specifically expressed by the major duct epithelium, providing a specific cell surface marker for this putative reservoir of pancreatic progenitor/stem cells.Plet-1will thus provide an invaluable tool for genetic analysis of the lineage relationships and molecular mechanisms operating in the development, homeostasis, and injury in several organ/tissue systems.
Risperidone and ritanserin but not haloperidol block effect of dizocilpine on the active allothetic place avoidance task
Authors: Bubenikova-Valesova Vera , Stuchlik Ales , Svoboda Jan , Bures Jan , Vales Karel
Published: January 2008

Spatial working memory or short-term place memory is impaired in schizophrenia. The efficiency of antipsychotic drugs, particularly of typical antipsychotics, on cognitive deficit in schizophrenia remains disputable. Inhibition of serotonin (5-HT) 2A/2C receptors is important for cognitive improvement in schizophrenic patients treated with antipsychotics. The aim of the present work was to establish the effect of the 5-HT2A/2C receptor antagonist ritanserin (2.5 or 5 mg/kg), the dopamine D2 antagonist haloperidol (0.1 or 1 mg/kg), and the atypical antipsychotic risperidone (0.1 mg/kg or 1 mg/kg), which is an antagonist of both 5-HT2A/2C and D2 receptors, on cognitive deficit induced by subchronic administration of dizocilpine (MK-801, 0.1 mg/kg). We used the active allothetic place avoidance (AAPA) task, requiring the rat to differentiate between relevant and irrelevant stimuli, in a way similar to disruption of information processing disturbed in schizophrenic patients. Our results show that treatment with 5-HT2A/2C receptor antagonists, regardless of their effect on D2 receptors, blocked the cognitive impairment produced by MK-801. Haloperidol did not sufficiently reduce the deficit in AAPA induced by MK-801. Interestingly, administration of risperidone and haloperidol alone, but not ritanserin, impaired the AAPA performance in intact rats. Ritanserin and risperidone actually improve cognition independently of their effect on locomotor activity in an animal model of schizophrenia-like behavior. This finding is in accordance with the assumption that some antipsychotics are primarily effective against cognitive dysfunction in schizophrenia.
Synaptic AMPA receptor subunit trafficking is independent of the C terminus in the GluR2-lacking mouse
Authors: Panicker Sandip , Brown Keith , Nicoll Roger A.
Published: January 2008

Glutamate is the primary excitatory neurotransmitter in the brain, and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) type glutamate receptors mediate most fast synaptic transmission. AMPA receptors are tetrameric assemblies composed from four possible subunits (GluR1–4). In hippocampal pyramidal cells, AMPA receptors are heteromeric receptors containing the GluR2 subunit and either GluR1 or GluR3. It is generally accepted that the trafficking of GluR1/GluR2 receptors to synapses requires activity, whereas GluR2/GluR3 receptors traffic constitutively. It has been suggested that the trafficking is governed by the cytoplasmic C termini of the subunits. Because the basis for this theory relied on the introduction of unnatural, homomeric, calcium-permeable AMPA receptors, we have used the GluR2−/−knock out mouse to determine whether the expression of mutated forms of GluR2 can rescue WT synaptic responses. We find that GluR2, lacking its entire C terminus, or a GluR2 chimera containing the C terminus of GluR1, is capable of trafficking to the synapse in the absence of activity. These findings suggest that the GluR2 C terminus is not required for GluR2 synaptic insertion.
Temperature Dependence of Fusion Kinetics and Fusion Pores in Ca2+-triggered Exocytosis from PC12 Cells
Authors: Zhang Zhen , Jackson Meyer B.
Published: January 2008

The temperature dependence of Ca2+-triggered exocytosis was studied using carbon fiber amperometry to record the release of norepinephrine from PC12 cells. Single-vesicle fusion events were examined at temperatures varying from 12 to 28°C, and with release elicited by depolarization. Measurements were made of the initial and maximum frequencies of exocytotic events, of fusion pore lifetime, flux through the open fusion pore, kiss-and-run versus full-fusion probability, and parameters associated with the shapes of amperometric spikes. The fusion pore open-state flux, and all parameters associated with spike shape, including area, rise time, and decay time, had weak temperature dependences and activation energies in the range expected for bulk diffusion in an aqueous solution. Kiss-and-run events also varied with temperature, with lower temperatures increasing the relative probability of kiss-and-run events by ∼50%. By contrast, kinetic parameters relating to the frequency of exocytotic events and fusion pore transitions depended much more strongly on temperature, suggesting that these processes entail structural rearrangements of proteins or lipids or both. The weak temperature dependence of spike shape suggests that after the fusion pore has started to expand, structural transitions of membrane components are no longer kinetically limiting. This indicates that the content of a vesicle is expelled completely after fusion pore expansion.
Pinnacle: a fast, automatic and accurate method for detecting and quantifying protein spots in 2-dimensional gel electrophoresis data
Authors: Morris Jeffrey S. , Clark Brittan N. , Gutstein Howard B.
Published: January 2008

Motivation: One of the key limitations for proteomic studies using 2-dimensional gel electrophoresis (2DE) is the lack of rapid, robust and reproducible methods for detecting, matching and quantifying protein spots. The most commonly used approaches involve first detecting spots and drawing spot boundaries on individual gels, then matching spots across gels and finally quantifying each spot by calculating normalized spot volumes. This approach is time consuming, error-prone and frequently requires extensive manual editing, which can unintentionally introduce bias into the results.

Results: We introduce a new method for spot detection and quantification called Pinnacle that is automatic, quick, sensitive and specific and yields spot quantifications that are reliable and precise. This method incorporates a spot definition that is based on simple, straightforward criteria rather than complex arbitrary definitions, and results in no missing data. Using dilution series for validation, we demonstrate Pinnacle outperformed two well-established 2DE analysis packages, proving to be more accurate and yielding smaller coefficiant of variations (CVs). More accurate quantifications may lead to increased power for detecting differentially expressed spots, an idea supported by the results of our group comparison experiment. Our fast, automatic analysis method makes it feasible to conduct very large 2DE-based proteomic studies that are adequately powered to find important protein expression differences.

Availability: Matlab code to implement Pinnacle is available from the authors upon request for non-commercial use.

Contact:  jefmorris@mdanderson.org

Supplementary information: Supplementary data are available at Bioinformatics online.
Site-specific gene transfer with high efficiency onto a carbon nanotube-loaded electrode
Authors: Inoue Y , Fujimoto H , Ogino T , Iwata H
Published: January 2008

A transfection array, which is specifically developed for use in high-throughput analyses of genome functions by the over-expression or suppression of genes on a chip, is expected to become an important method for post-genome research. High efficiency of gene expression or suppression is indispensable for high-throughput analyses because the adherent cell number on a single spot decreases as the density of spots increases in the transfection array. We have studied an electro-stimulated pore formation on the cell membrane for gene delivery. Fine pores should be formed on the cell membrane to increase the efficiency of gene transfection without cell damage. Herein, we examined the electrode carrying chemically functionalized carbon nanotubes (CNTs) on the surface. The CNTs were loaded on a gold electrode with a self-assembled monolayer membrane by electrostatic interaction. Adsorbed plasmid DNA was transfected with higher efficiency into adherent cells on the CNT-loaded electrode than on an electrode without CNTs. This result may be due to the strong but fine field emission formed from the tips of the CNTs.
Non-adhesive lotus and other hydrophobic materials
Authors: Quéré David , Reyssat Mathilde
Published: January 2008

Superhydrophobic materials recently attracted a lot of attention, owing to the potential practical applications of such surfaces—they literally repel water, which hardly sticks to them, bounces off after an impact and slips on them. In this short review, we describe how water repellency arises from the presence of hydrophobic microstructures at the solid surface. A drop deposited on such a substrate can float above the textures, mimicking at room temperature what happens on very hot plates; then, a vapour layer comes between the solid and the volatile liquid, as described long ago by Leidenfrost. We present several examples of superhydrophobic materials (either natural or synthetic), and stress more particularly the stability of the air cushion—the liquid could also penetrate the textures, inducing a very different wetting state, much more sticky, due to the possibility of pinning on the numerous defects. This description allows us to discuss (in quite a preliminary way) the optimal design to be given to a solid surface to make it robustly water repellent.
Gecko adhesion: evolutionary nanotechnology
Authors: Autumn Kellar , Gravish Nick
Published: January 2008

If geckos had not evolved, it is possible that humans would never have invented adhesive nanostructures. Geckos use millions of adhesive setae on their toes to climb vertical surfaces at speeds of over 1 m s−1. Climbing presents a significant challenge for an adhesive in requiring both strong attachment and easy rapid removal. Conventional pressure-sensitive adhesives (PSAs) are either strong and difficult to remove (e.g. duct tape) or weak and easy to remove (e.g. sticky notes). The gecko adhesive differs dramatically from conventional adhesives. Conventional PSAs are soft viscoelastic polymers that degrade, foul, self-adhere and attach accidentally to inappropriate surfaces. In contrast, gecko toes bear angled arrays of branched, hair-like setae formed from stiff, hydrophobic keratin that act as a bed of angled springs with similar effective elastic modulus to that of PSAs. Setae are self-cleaning and maintain function for months during repeated use in dirty conditions. Setae are an anisotropic ‘frictional adhesive’ in that adhesion requires maintenance of a proximally directed shear load, enabling either a tough bond or spontaneous detachment. Gecko-like synthetic adhesives may become the glue of the future—and perhaps the screw of the future as well.
Nanomechanics of carbon nanotubes
Authors: Kis Andras , Zettl Alex
Published: January 2008

Some of the most important potential applications of carbon nanotubes are related to their mechanical properties. Stiff sp
2
bonds result in a Young’s modulus close to that of diamond, while the relatively weak van der Waals interaction between the graphitic shells acts as a form of lubrication. Previous characterization of the mechanical properties of nanotubes includes a rich variety of experiments involving mechanical deformation of nanotubes using scanning probe microscopes. These results have led to promising prototypes of nanoelectromechanical devices such as high-performance nanomotors, switches and oscillators based on carbon nanotubes.
Effective reinforcement in carbon nanotube–polymer composites
Authors: Wang W , Ciselli P , Kuznetsov E , Peijs T , Barber A.H
Published: January 2008

Carbon nanotubes have mechanical properties that are far in excess of conventional fibrous materials used in engineering polymer composites. Effective reinforcement of polymers using carbon nanotubes is difficult due to poor dispersion and alignment of the nanotubes along the same axis as the applied force during composite loading. This paper reviews the mechanical properties of carbon nanotubes and their polymer composites to highlight how many previously prepared composites do not effectively use the excellent mechanical behaviour of the reinforcement. Nanomechanical tests using atomic force microscopy are carried out on simple uniaxially aligned carbon nanotube-reinforced polyvinyl alcohol (PVA) fibres prepared using electrospinning processes. Dispersion of the carbon nanotubes within the polymer is achieved using a surfactant. Young's modulus of these simple composites is shown to approach theoretically predicted values, indicating that the carbon nanotubes are effective reinforcements. However, the use of dispersant is also shown to lower Young's modulus of the electrospun PVA fibres.
The evolution of the animals: introduction to a Linnean tercentenary celebration
Authors: Telford Maximilian J , Littlewood D. Timothy J
Published: January 2008

Celebrating 300 years since the birth of Carl Linnaeus (1707–1778), a meeting was held in June 2007 to review recent progress made in understanding the origins and evolutionary radiation of the animals. The year 2008 celebrates the 250th anniversary of the publication of the 10th edition of Linnaeus'
Systema Naturae
, generally considered to be the starting point of zoological nomenclature. With subsequent advances in comparative taxonomic and systematic studies, Darwin's discovery of evolution by natural selection, the birth of phylogenetic systematics, and the wider interest in biodiversity, it is salutary to consider that many of the major advances in our understanding of animal evolution have been made in recent years. Phylogenetic systematics, drawing from evidence provided by genotype, phenotype and an understanding of the link between them through comparative embryological and evolutionary developmental studies, has provided a wide consensus of the major branching patterns of the tree of life. More importantly, the integrated approaches discussed in the 16 contributions to this volume highlight the identity and nature of problematic taxa, the missing data, errors in existing analytical procedures and the promise of a wealth of additional characters from genomes that need to be accumulated and assessed in providing a definitive
Systema Naturae
.
The earliest fossil record of the animals and its significance
Authors: Budd Graham E
Published: January 2008

The fossil record of the earliest animals has been enlivened in recent years by a series of spectacular discoveries, including embryos, from the Ediacaran to the Cambrian, but many issues, not least of dating and interpretation, remain controversial. In particular, aspects of taphonomy of the earliest fossils require careful consideration before pronouncements about their affinities. Nevertheless, a reasonable case can now be made for the extension of the fossil record of at least basal animals (sponges and perhaps cnidarians) to a period of time significantly before the beginning of the Cambrian. The Cambrian explosion itself still seems to represent the arrival of the bilaterians, and many new fossils in recent years have added significant data on the origin of the three major bilaterian clades. Why animals appear so late in the fossil record is still unclear, but the recent trend to embrace rising oxygen levels as being the proximate cause remains unproven and may even involve a degree of circularity.
Origins of the other metazoan body plans: the evolution of larval forms
Authors: Raff Rudolf A
Published: January 2008

Bilaterian animal body plan origins are not solely about adult forms. Most animals have larvae with body plans, ontogenies and ecologies distinct from adults. There are two primary hypotheses for larval origins. The first hypothesis suggests that the first animals were small pelagic forms similar to modern larvae, with adult bilaterian body plans evolved subsequently. The second hypothesis suggests that adult bilaterian body plans evolved first and that larval body plans arose by interpolation of features into direct-developing ontogenies. The two hypotheses have different consequences for understanding parsimony in evolution of larvae and of developmental genetic mechanisms. If primitive metazoans were like modern larvae and distinct adult forms evolved independently, there should be little commonality of patterning genes among adult body plans. However, sharing of patterning genes is observed. If larvae arose by co-option of adult bilaterian-expressed genes into independently evolved larval forms, larvae may show morphological convergence, but with distinct patterning genes, and this is observed. Thus, comparative studies of gene expression support independent origins of larval features. Precambrian and Cambrian embryonic fossils are also consistent with direct development of the adult as being primitive, with planktonic larvae arising during the Cambrian. Larvae have continued to co-opt genes and evolve new features, allowing study of developmental evolution.
Acoel development supports a simple planula-like urbilaterian
Authors: Hejnol Andreas , Martindale Mark Q
Published: January 2008

Molecular approaches to the study of development and evolution have had profound effects on our understanding of the nature of the evolutionary process. Developmental biologists became intoxicated with fanciful notions of reconstructing genetic pathways of morphogenesis while evolutionary biologists were sobered by the fallacy of reconstructing organismal relationships along increasing grades of morphological complexity. Increased taxon sampling and improvements in analytical techniques are providing a new approach and are forcing biologists to move past historical biases to allow more accurate mapping of morphological and developmental characters through evolutionary time. Here, we discuss the possible developmental and morphological features of the ‘urbilaterian’, the triploblastic animal with anterior-posterior and dorsoventral axes and predecessor of the protostome–deuterostome ancestor. We argue that this animal, with features resembling acoelomorph flatworms, was far simpler morphologically than the protostome–deuterostome ancestor despite possessing a nearly complete eubilaterian genome. We show that the deployment of some genes expected to pattern the protostome–deuterostome ancestor is not deployed in acoels in the predicted manner and thus might have been co-opted after the evolution of the urbilaterian. We also identify the developmental changes related to gastrulation that gave rise to the urbilaterian from a simpler cnidarian-like ancestor.
Problematica old and new
Authors: Jenner Ronald A , Littlewood D.Timothy J
Published: January 2008

Problematica are taxa that defy robust phylogenetic placement. Traditionally the term was restricted to fossil forms, but it is clear that extant taxa may be just as difficult to place, whether using morphological or molecular (nucleotide, gene or genomic) markers for phylogeny reconstruction. We discuss the kinds and causes of Problematica within the Metazoa, as well as criteria for their recognition and possible solutions. The inclusive set of Problematica changes depending upon the nature and quality of (homologous) data available, the methods of phylogeny reconstruction and the sister taxa inferred by their placement or displacement. We address Problematica in the context of pre-cladistic phylogenetics, numerical morphological cladistics and molecular phylogenetics, and focus on general biological and methodological implications of Problematica, rather than presenting a review of individual taxa. Rather than excluding Problematica from phylogeny reconstruction, as has often been preferred, we conclude that the study of Problematica is crucial for both the resolution of metazoan phylogeny and the proper inference of body plan evolution.
Assembling the lophotrochozoan (=spiralian) tree of life
Authors: Giribet Gonzalo
Published: January 2008

The advent of numerical methods for analysing phylogenetic relationships, along with the study of morphology and molecular data, has driven our understanding of animal relationships for the past three decades. Within the protostome branch of the animal tree of life, these data have sufficed to establish its two main side branches, the moulting Ecdysozoa and the non-moulting Lophotrochozoa. In this review, I explore our current knowledge of protostome relationships and discuss progress and future perspectives and strategies to increase resolution within the main lophotrochozoan clades. Novel approaches to coding morphological characters are needed by scoring real observations on species selected as terminals. Still, methodological issues, for example, how to deal with inapplicable characters or the coding of absences, may require novel algorithmic developments. Taxon sampling is another key issue, as phyla should include enough species so as to represent their span of anatomical disparity. On the molecular side, phylogenomics is playing an increasingly important role in elucidating animal relationships, but genomic sampling is still fairly limited within the lophotrochozoan protostomes, for which only three phyla are represented in currently available phylogenies. Future work should therefore concentrate on generating novel morphological observations and on producing genomic data for the lophotrochozoan side of the animal tree of life.
The evolution of developmental gene networks: lessons from comparative studies on holometabolous insects
Authors: Peel Andrew D
Published: January 2008

Recent comparative studies have revealed significant differences in the developmental gene networks operating in three holometabolous insects: the beetleTribolium castaneum, the parasitic waspNasonia vitripennisand the fruitflyDrosophila melanogaster. I discuss these differences in relation to divergent and convergent changes in cellular embryology. I speculate on how segmentation gene networks have evolved to operate in divergent embryological contexts, and highlight the role that co-option might have played in this process. I argue that insects represent an important example of how diversification in life-history strategies between lineages can lead to divergence in the genetic and cellular mechanisms controlling the development of homologous adult structures.
Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives
Authors: Swalla Billie J , Smith Andrew B
Published: January 2008

Deuterostomes are a monophyletic group of animals that include the vertebrates, invertebrate chordates, ambulacrarians and xenoturbellids. Fossil representatives from most major deuterostome groups, including some phylum-level crown groups, are found in the Lower Cambrian, suggesting that evolutionary divergence occurred in the Late Precambrian, in agreement with some molecular clock estimates. Molecular phylogenies, larval morphology and the adult heart/kidney complex all support echinoderms and hemichordates as a sister grouping (Ambulacraria). Xenoturbellids are a relatively newly discovered phylum of worm-like deuterostomes that lacks a fossil record, but molecular evidence suggests that these animals are a sister group to the Ambulacraria. Within the chordates, cephalochordates share large stretches of chromosomal synteny with the vertebrates, have a completeHoxcomplex and are sister group to the vertebrates based on ribosomal and mitochondrial gene evidence. In contrast, tunicates have a highly derived adult body plan and are sister group to the vertebrates based on the analyses of concatenated genomic sequences. Cephalochordates and hemichordates share gill slits and an acellular cartilage, suggesting that the ancestral deuterostome also shared these features. Gene network data suggest that the deuterostome ancestor had an anterior–posterior body axis specified byHoxandWntgenes, a dorsoventral axis specified by aBMP/chordingradient, and was bilaterally symmetrical with left–right asymmetry determined by expression ofnodal.
Calcium waves
Authors: Jaffe Lionel F
Published: January 2008

Waves through living systems are best characterized by their speeds at 20°C. These speeds vary from those of calcium action potentials to those of ultraslow ones which move at 1–10 and/or 10–20 nm s−1. All such waves are known or inferred to be calcium waves. The two classes of calcium waves which include ones with important morphogenetic effects are slow waves that move at 0.2–2 μm s−1and ultraslow ones. Both may be propagated by cycles in which the entry of calcium through the plasma membrane induces subsurface contraction. This contraction opens nearby stretch-sensitive calcium channels. Calcium entry through these channels propagates the calcium wave. Many slow waves are seen as waves of indentation. Some are considered to act via cellular peristalsis; for example, those which seem to drive the germ plasm to the vegetal pole of theXenopusegg. Other good examples of morphogenetic slow waves are ones through fertilizing maize eggs, through developing barnacle eggs and through axolotl embryos during neural induction. Good examples of ultraslow morphogenetic waves are ones during inversion in developingVolvoxembryos and across developingDrosophilaeye discs. Morphogenetic waves may be best pursued by imaging their calcium with aequorins.
Hypoxia regulates TSC1/2–mTOR signaling and tumor suppression through REDD1-mediated 14–3–3 shuttling
Authors: DeYoung Maurice Phillip , Horak Peter , Sofer Avi , Sgroi Dennis , Ellisen Leif W.
Published: January 2008

Hypoxia induces rapid and dramatic changes in cellular metabolism, in part through inhibition of target of rapamycin (TOR) kinase complex 1 (TORC1) activity. Genetic studies have shown the tuberous sclerosis tumor suppressors TSC1/2 and the REDD1 protein to be essential for hypoxia regulation of TORC1 activity in Drosophila and in mammalian cells. The molecular mechanism and physiologic significance of this effect of hypoxia remain unknown. Here, we demonstrate that hypoxia and REDD1 suppress mammalian TORC1 (mTORC1) activity by releasing TSC2 from its growth factor-induced association with inhibitory 14–3–3 proteins. Endogenous REDD1 is required for both dissociation of endogenous TSC2/14–3–3 and inhibition of mTORC1 in response to hypoxia. REDD1 mutants that fail to bind 14–3–3 are defective in eliciting TSC2/14–3–3 dissociation and mTORC1 inhibition, while TSC2 mutants that do not bind 14-3-3 are inactive in hypoxia signaling to mTORC1. In vitro, loss of REDD1 signaling promotes proliferation and anchorage-independent growth under hypoxia through mTORC1 dysregulation. In vivo, REDD1 loss elicits tumorigenesis in a mouse model, and down-regulation of REDD1 is observed in a subset of human cancers. Together, these findings define a molecular mechanism of signal integration by TSC1/2 that provides insight into the ability of REDD1 to function in a hypoxia-dependent tumor suppressor pathway.
Regulatory divergence modifies limb length between mammals
Authors: Cretekos Chris J. , Wang Ying , Green Eric D. ,   NISC Comparative Sequencing Program, Martin James F. , Rasweiler John J. , Behringer Richard R.
Published: January 2008

Natural selection acts on variation within populations, resulting in modified organ morphology, physiology, and ultimately the formation of new species. Although variation in orthologous proteins can contribute to these modifications, differences in DNA sequences regulating gene expression may be a primary source of variation. We replaced a limb-specific transcriptional enhancer of the mouse Prx1 locus with the orthologous sequence from a bat. Prx1 expression directed by the bat enhancer results in elevated transcript levels in developing forelimb bones and forelimbs that are significantly longer than controls because of endochondral bone formation alterations. Surprisingly, deletion of the mouse Prx1 limb enhancer results in normal forelimb length and Prx1 expression, revealing regulatory redundancy. These findings suggest that mutations accumulating in pre-existing noncoding regulatory sequences within a population are a source of variation for the evolution of morphological differences between species and that cis-regulatory redundancy may facilitate accumulation of such mutations.
DNA damage response at functional and dysfunctional telomeres
Authors: Longhese Maria Pia
Published: January 2008

The ends of eukaryotic chromosomes have long been defined as structures that must avoid being detected as DNA breaks. They are protected from checkpoints, homologous recombination, end-to-end fusions, or other events that normally promote repair of intrachromosomal DNA breaks. This differentiation is thought to be the consequence of a unique organization of chromosomal ends into specialized nucleoprotein complexes called telomeres. However, it is becoming increasingly clear that proteins governing the DNA damage response are intimately involved in the regulation of telomeres, which undergo processing and structural changes that elicit a transient DNA damage response. This suggests that functional telomeres can be recognized as DNA breaks during a temporally limited window, indicating that the difference between a break and a telomere is less defined than previously assumed.