bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural history of ABC systems: not only transporters
Authors: Dassa Elie
Published: September 2011

In recent years, our understanding of the functioning of ABC (ATP-binding cassette) systems has been boosted by the combination of biochemical and structural approaches. However, the origin and the distribution of ABC proteins among living organisms are difficult to understand in a phylogenetic perspective, because it is hard to discriminate orthology and paralogy, due to the existence of horizontal gene transfer. In this chapter, I present an update of the classification of ABC systems and discuss a hypothetical scenario of their evolution. The hypothetical presence of ABC ATPases in the last common ancestor of modern organisms is discussed, as well as the additional possibility that ABC systems might have been transmitted to eukaryotes, after the two endosymbiosis events that led to the constitution of eukaryotic organelles. I update the functional information of selected ABC systems and introduce new families of ABC proteins that have been included recently into this vast superfamily, thanks to the availability of high-resolution three-dimensional structures.
Structure of ABC transporters
Authors: Zolnerciks Joseph K. , Andress Edward J. , Nicolaou Michael , Linton Kenneth J.
Published: September 2011

ABC (ATP-binding cassette) transporters are primary active membrane proteins that translocate solutes (allocrites) across lipid bilayers. The prototypical ABC transporter consists of four domains: two cytoplasmic NBDs (nucleotide-binding domains) and two TMDs (transmembrane domains). The NBDs, whose primary sequence is highly conserved throughout the superfamily, bind and hydrolyse ATP to power the transport cycle. The TMDs, whose primary sequence and protein fold can be quite disparate, form the translocation pathway across the membrane and generally (but not always) determine allocrite specificity. Structure determination of ABC proteins initially took advantage of the relative ease of expression and crystallization of the hydrophilic bacterial NBDs in isolation from the transporter complex, and revealed detailed information on the structural fold of these domains, the amino acids involved in the binding and hydrolysis of nucleotide, and the head-to-tail arrangement of the NBD–NBD dimer interface. More recently, several intact transporters have been crystallized and three types have, so far, been characterized: type I and II ABC importers, and ABC exporters. All three are present in prokaryotes, but only the ABC exporters appear to be present in eukaryotes. Their structural determination has provided insight into the mechanisms of energy and signal transduction between the NBDs and TMDs (i.e. between the ATP- and allocrite-binding sites) and, for some, the nature of the allocrite-binding site(s) within the TMDs. In this chapter, we focus primarily on the ABC exporters and describe the structural, biochemical and biophysical evidence for and against the controversial bellows-like mechanism proposed for allocrite efflux.
Mammalian multidrug-resistance proteins (MRPs)
Authors: Slot Andrew J. , Molinski Steven V. , Cole Susan P.C.
Published: September 2011

Subfamily C of the human ABC (ATP-binding cassette) superfamily contains nine proteins that are often referred to as the MRPs (multidrug-resistance proteins). The ‘short’ MRP/ABCC transporters (MRP4, MRP5, MRP8 and ABCC12) have a typical ABC structure with four domains comprising two membrane-spanning domains (MSD1 and MSD2) each followed by a nucleotide-binding domain (NBD1 and NBD2). The ‘long’ MRP/ABCCs (MRP1, MRP2, MRP3, ABCC6 and MRP7) have five domains with the extra domain, MSD0, at the N-terminus. The proteins encoded by the ABCC6 and ABCC12 genes are not known to transport drugs and are therefore referred to as ABCC6 and ABCC12 (rather than MRP6 and MRP9) respectively. A large number of molecules are transported across the plasma membrane by the MRPs. Many are organic anions derived from exogenous sources such as conjugated drug metabolites. Others are endogenous metabolites such as the cysteinyl leukotrienes and prostaglandins which have important signalling functions in the cell. Some MRPs share a degree of overlap in substrate specificity (at least in vitro), but differences in transport kinetics are often substantial. In some cases, the in vivo substrates for some MRPs have been discovered aided by studies in gene-knockout mice. However, the molecules that are transported in vivo by others, including MRP5, MRP7, ABCC6 and ABCC12, still remain unknown. Important differences in the tissue distribution of the MRPs and their membrane localization (apical in contrast with basolateral) in polarized cells also exist. Together, these differences are responsible for the unique pharmacological and physiological functions of each of the nine ABCC transporters known as the MRPs.
The controversial role of ABC transporters in clinical oncology
Authors: Tamaki Akina , Ierano Caterina , Szakacs Gergely , Robey Robert W. , Bates Susan E.
Published: September 2011

The phenomenon of multidrug resistance in cancer is often associated with the overexpression of the ABC (ATP-binding cassette) transporters Pgp (P-glycoprotein) (ABCB1), MRP1 (multidrug resistance-associated protein 1) (ABCC1) and ABCG2 [BCRP (breast cancer resistance protein)]. Since the discovery of Pgp over 35 years ago, studies have convincingly linked ABC transporter expression to poor outcome in several cancer types, leading to the development of transporter inhibitors. Three generations of inhibitors later, we are still no closer to validating the ‘Pgp hypothesis’, the idea that increased chemotherapy efficacy can be achieved by inhibition of transporter-mediated efflux. In this chapter, we highlight the difficulties and past failures encountered in the development of clinical inhibitors of ABC transporters. We discuss the challenges that remain in our effort to exploit decades of work on ABC transporters in oncology. In learning from past mistakes, it is hoped that ABC transporters can be developed as targets for clinical intervention.
Directional solvent for membrane-free water desalination—A molecular level study
Authors: Luo Tengfei , Bajpayee Anurag , Chen Gang
Published: September 2011

Development of desalination technologies has been identified as vital to fulfilling future water demand. In this paper, we use molecular simulation to demonstrate that decanoic acid can dissolve water but reject salt, and itself is insoluble in water. We have recently demonstrated that the directional properties of decanoic acid together with the temperature dependence of water solubility in decanoic acid can be utilized to design a desalination process which extracts water molecules, using the decanoic acid as a directional solvent, from saline source at a higher-than-ambient temperature, and precipitate out the water from the solvent at a lower temperature to recover pure water. Such a desalination process is membrane-free and can make use of low temperature heat sources. Solubility properties between water and decanoic acid are characterized through free energy calculations, and water-decanoic acid interdiffusion processes are studied by molecular dynamics simulations. This work also exemplifies an approach to characterize other possible directional solvents.
Continuum modes in rotating plasmas: General equations and continuous spectra for large aspect ratio tokamaks
Authors: Lakhin V. P. , Ilgisonis V. I.
Published: September 2011

A theory for localized low-frequency ideal magnetohydrodynamical (MHD) modes in axisymmetric toroidal systems is generalized to take into account both toroidal and poloidal equilibrium plasma flows. The general set of equations describing the coupling of shear Alfvén and slow (sound) modes and defining the continuous spectrum of rotating plasmas in axisymmetric toroidal systems is derived. The equations are applied to study the continuous spectra in large aspect ratio tokamaks. The unstable continuous modes in the case of predominantly poloidal plasma rotation with the angular velocity exceeding the sound frequency are found. Their stabilization by the shear Alfvén coupling effect is studied.
Chemical and structural investigation of the role of both Mn and Mn oxide in the formation of manganese silicate barrier layers on SiO2
Authors: Casey P. , Bogan J. , Lozano J. G. , Nellist P. D. , Hughes G.
Published: September 2011

In this study, Mn silicate (MnSiO3) barrier layers were formed on thermally grown SiO2 using both metallic Mn and oxidized Mn films, in order to investigate the role of oxygen in determining the extent of the interaction between the deposited Mn and the SiO2 substrate. Using x-ray photoelectron spectroscopy, it has been shown that a metallic Mn film with an approximate thickness of 1 nm cannot be fully converted to Mn silicate following vacuum annealing to 500 °C. Transmission electron microscopy (TEM) analysis suggests the maximum MnSiO3 layer thickness obtainable using metallic Mn is ∼1.7 nm. In contrast, a ∼1 nm partially oxidized Mn film can be fully converted to Mn silicate following thermal annealing to 400 °C, forming a MnSiO3 layer with a measured thickness of 2.6 nm. TEM analysis also clearly shows that MnSiO3 growth results in a corresponding reduction in the SiO2 layer thickness. It has also been shown that a fully oxidized Mn oxide thin film can be converted to Mn silicate, in the absence of metallic Mn. Based on these results it is suggested that the presence of Mn oxide species at the Mn/SiO2 interface facilitates the conversion of SiO2 to MnSiO3, in agreement with previously published studies.
Kinetic simulations of stimulated Raman backscattering and related processes for the shock-ignition approach to inertial confinement fusion
Authors: Riconda C. , Weber S. , Tikhonchuk V. T. , Héron A.
Published: September 2011

A detailed description of stimulated Raman backscattering and related processes for the purpose of inertial confinement fusion requires multi-dimensional kinetic simulations of a full speckle in a high-temperature, large-scale, inhomogeneous plasma. In particular for the shock-ignition scheme operating at high laser intensities, kinetic aspects are predominant. High- (Iλo2~5×1015Wμm2/cm2) as well as low-intensity (Iλo2~1015Wμm2/cm2) cases show the predominance of collisionless, collective processes for the interaction. While the two-plasmon decay instability and the cavitation scenario are hardly affected by intensity variation, inflationary Raman backscattering proves to be very sensitive. Brillouin backscattering evolves on longer time scales and dominates the reflectivities, although it is sensitive to the intensity. Filamentation and self-focusing do occur for all cases but on time scales too long to affect Raman backscattering.
Damping dependence in microwave assisted magnetization reversal
Authors: Chen Y. P. , Fan X. , Lu Q. , Xiao John Q.
Published: September 2011

This letter reports a demonstration of microwave assisted magnetization reversal (MAMR) in a CoFeB film and the damping dependence in MAMR through the measurement of ferromagnetic resonance (FMR). Spin-pumping in non-ferromagnetic/ferromagnetic films provides a large range variation of Gilbert damping constants in magnetic samples when changing the thickness of non-ferromagnetic layers without changing the ferromagnetic film. An evident dependence of switching fields on the damping constant is observed in the presence of microwaves. The trend of the experimental data is well reproduced by a numerical simulation based on the Landau–Lifshitz–Gilbert equation. The result indicates that the large damping decreases the efficiency of microwaves in reducing the magnetization switching field.
Local structure analysis of boron-doped graphite by soft x-ray emission and absorption spectroscopy using synchrotron radiation
Authors: Hanafusa Atsushi , Muramatsu Yasuji , Kaburagi Yutaka , Yoshida Akira , Hishiyama Yoshihiro , Yang Wanli , Denlinger Jonathan D. , Gullikson Eric M.
Published: September 2011

The local structure of boron-doped highly oriented graphite films was determined via soft x-ray emission and absorption spectroscopy using synchrotron radiation. Analysis of the BK and CK x-ray emission spectra using the discrete variational-Xα molecular orbital method clarified that boron atoms are chemisorbed onto graphite by substituting for carbon atoms in the carbon hexagonal rings. Compared to graphite, boron-doped graphite exhibits spectral differences in the higher edge of the CK x-ray emission spectrum and the CK x-ray absorption edge. Such a spectral profile of boron-doped graphite, which reflects the band structure, is well explained by the chemisorbed boron structure.
A self-sustaining micro thermomechanic-pyroelectric generator
Authors: Ravindran S. K. T. , Huesgen T. , Kroener M. , Woias P.
Published: September 2011

Pyroelectric generators (PEGs) can be used for thermal energy harvesting and present a potential alternative to thermoelectric generators. However, in contrary to thermoelectric generators, the PEG principle requires thermal transients to stimulate the conversion process. Such suitable thermal transients are rare in nature, hindering the deployment. In this paper, we present a micro thermomechanic-pyroelectric energy generator (μTMPG) that converts a stationary spatial thermal gradient into the required transient temperature profile across the PEG. The measured power output of the μTMPG is 3 μW from a temperature difference of 79.5 K. However, with an optimized design, a power output of 39.4 mW is estimated for the same temperature difference.
Enhancement of channel conductivity in AlGaN/GaN heterostructure field effect transistors by AlGaN:Si back barrier
Authors: Cho E. , Brunner F. , Zhytnytska R. , Kotara P. , Würfl J. , Weyers M.
Published: September 2011

Heterostructure field effect transistors with three AlGaN/GaN interfaces were designed and investigated. A Si-doped AlGaN back barrier was used to compensate for the reduction of channel conductivity due to a carbon doped semi-insulating GaN buffer layer. Simulation using a one dimensional Poisson-Schrödinger solver showed an enhancement of the charge carrier density which was then confirmed experimentally. Hall and magnetic field dependent mobility measurements proved the Si-doped AlGaN back barrier layer causes neither degradation of electron mobility nor a parasitic conduction channel. Id,max of the transistors was enhanced by a factor of 1.5–2 without decreasing the off-state breakdown voltage.
Magnetic resonance on core-shell nanowires with notches
Authors: Xu Lina , Zhang Zhi-Jian , Jae Lee Bong
Published: September 2011

In this paper, a two-dimensional core-shell nanowire made of a dielectric core and metallic cladding is proposed for exciting the magnetic resonance on an isolated nanostructure. The key idea is to remove a small portion of the metallic cladding on the nanowire so that the incident magnetic field can be localized in the dielectric core. It is also found that the core-shell nanowire can support the localized surface plasmon, whose resonance frequency mainly depends on the thickness of the metallic cladding. The finite-difference time-domain method is employed to calculate the scattering cross-section of the proposed structure and the near-field distribution of the magnetic field at resonance conditions. The results obtained from this study will advance our fundamental understanding of the light-matter interaction at nanometer scales and facilitate the development of multi-dimensional metamaterials for subwavelength imaging.
Effect of aluminum addition on the optical, morphology and electrical behavior of spin coated zinc oxide thin films
Authors: Srivastava Amit Kumar , Kumar Jitendra
Published: September 2011

Aluminum-doped ZnO thin films of high optical transmittance (∼ 84-100%) and low resistivity (∼ 2.3x10-2 Ωcm) have been prepared on glass substrate by the spin coating and subsequent annealing at 500°C for 1h in air or vacuum. Effect of aluminum doping and annealing environment on morphology, optical transmittance and electrical resistivity of ZnO thin films has been studied with possible application as a transparent electrode in photovoltaic. The changes occurring due to aluminum addition include reduction in grain size, root mean square roughness, peak-valley separation, and sheet resistance with improvement in the optical transmittance to 84-100% in the visible range. The origin of low electrical resistivity lies in increase in i) electron concentration following aluminum doping (being trivalent), formation of oxygen vacancies due to vacuum annealing, filling of cation site with additional zinc at solution stage itself and ii) carrier mobility.
Dopamine neurons learn to encode the long-term value of multiple future rewards
Authors: Enomoto Kazuki , Matsumoto Naoyuki , Nakai Sadamu , Satoh Takemasa , Sato Tatsuo K. , Ueda Yasumasa , Inokawa Hitoshi , Haruno Masahiko , Kimura Minoru
Published: September 2011

Midbrain dopamine neurons signal reward value, their prediction error, and the salience of events. If they play a critical role in achieving specific distant goals, long-term future rewards should also be encoded as suggested in reinforcement learning theories. Here, we address this experimentally untested issue. We recorded 185 dopamine neurons in three monkeys that performed a multistep choice task in which they explored a reward target among alternatives and then exploited that knowledge to receive one or two additional rewards by choosing the same target in a set of subsequent trials. An analysis of anticipatory licking for reward water indicated that the monkeys did not anticipate an immediately expected reward in individual trials; rather, they anticipated the sum of immediate and multiple future rewards. In accordance with this behavioral observation, the dopamine responses to the start cues and reinforcer beeps reflected the expected values of the multiple future rewards and their errors, respectively. More specifically, when monkeys learned the multistep choice task over the course of several weeks, the responses of dopamine neurons encoded the sum of the immediate and expected multiple future rewards. The dopamine responses were quantitatively predicted by theoretical descriptions of the value function with time discounting in reinforcement learning. These findings demonstrate that dopamine neurons learn to encode the long-term value of multiple future rewards with distant rewards discounted.
Neurofibromatosis-1 regulates mTOR-mediated astrocyte growth and glioma formation in a TSC/Rheb-independent manner
Authors: Banerjee Sutapa , Crouse Nikkilina R. , Emnett Ryan J. , Gianino Scott M. , Gutmann David H.
Published: September 2011

Converging evidence from the analysis of human brain tumors and genetically engineered mice has revealed that the mammalian target of rapamycin (mTOR) pathway is a central regulator of glial and glioma cell growth. In this regard, mutational inactivation of neurofibromatosis-1 (NF1), tuberous sclerosis complex (TSC), and PTEN genes is associated with glioma formation, such that pharmacologic inhibition of mTOR signaling results in attenuated tumor growth. This shared dependence on mTOR suggests that PTEN and NF1 (neurofibromin) glial growth regulation requires TSC/Rheb (Ras homolog enriched in brain) control of mTOR function. In this report, we use a combination of genetic silencing in vitro and conditional mouse transgenesis approaches in vivo to demonstrate that neurofibromin regulates astrocyte cell growth and glioma formation in a TSC/Rheb-independent fashion. First, we show that
Nf1
or
Pten
inactivation, but not
Tsc1
loss or Rheb overexpression, increases astrocyte cell growth in vitro. Second,
Nf1
-deficient increased mTOR signaling and astrocyte hyperproliferation is unaffected by Rheb shRNA silencing. Third, conditional
Tsc1
inactivation or Rheb overexpression in glial progenitors of
Nf1
+/−
mice does not lead to glioma formation. Collectively, these findings establish TSC/Rheb-independent mechanisms for mTOR-dependent glial cell growth control and gliomagenesis relevant to the design of therapies for individuals with glioma.
Medial prefrontal cortex and striatum mediate the influence of social comparison on the decision process
Authors: Bault Nadège , Joffily Mateus , Rustichini Aldo , Coricelli Giorgio
Published: September 2011

We compared private and social decision making to investigate the neural underpinnings of the effect of social comparison on risky choices. We measured brain activity using functional MRI while participants chose between two lotteries: in the private condition, they observed the outcome of the unchosen lottery, and in the social condition, the outcome of the lottery chosen by another person. The striatum, a reward-related brain structure, showed higher activity when participants won more than their counterpart (social gains) compared with winning in isolation and lower activity when they won less than their counterpart (social loss) compared with private loss. The medial prefrontal cortex, implicated in social reasoning, was more activated by social gains than all other events. Sensitivity to social gains influenced both brain activity and behavior during subsequent choices. Specifically, striatal activity associated with social gains predicted medial prefrontal cortex activity during social choices, and experienced social gains induced more risky and competitive behavior in later trials. These results show that interplay between reward and social reasoning networks mediates the influence of social comparison on the decision process.
Structural basis for the broad specificity to host-cell ligands by the pathogenic fungus
Candida albicans
Authors: Salgado Paula S. , Yan Robert , Taylor Jonathan D. , Burchell Lynn , Jones Rhian , Hoyer Lois L. , Matthews Steve J. , Simpson Peter J. , Cota Ernesto
Published: September 2011

Candida albicans
is the most prevalent fungal pathogen in humans and a major source of life-threatening nosocomial infections. The Als (
a
gglutinin-
l
ike
s
equence) glycoproteins are an important virulence factor for this fungus and have been associated with binding of host-cell surface proteins and small peptides of random sequence, the formation of biofilms and amyloid fibers. High-resolution structures of N-terminal Als adhesins (NT-Als; up to 314 amino acids) show that ligand recognition relies on a motif capable of binding flexible C termini of peptides in extended conformation. Central to this mechanism is an invariant lysine that recognizes the C-terminal carboxylate of ligands at the end of a deep-binding cavity. In addition to several protein–peptide interactions, a network of water molecules runs parallel to one side of the ligand and contributes to the recognition of diverse peptide sequences. These data establish NT-Als adhesins as a separate family of peptide-binding proteins and an unexpected adhesion system for primary, widespread protein–protein interactions at the
Candida
/host-cell interface.
Misfolded human tRNA isodecoder binds and neutralizes a 3′ UTR-embedded Alu element
Authors: Rudinger-Thirion Joëlle , Lescure Alain , Paulus Caroline , Frugier Magali
Published: September 2011

Several classes of small noncoding RNAs are key players in cellular metabolism including mRNA decoding, RNA processing, and mRNA stability. Here we show that a tRNA
Asp
isodecoder, corresponding to a human tRNA-derived sequence, binds to an embedded Alu RNA element contained in the 3′ UTR of the human aspartyl-tRNA synthetase mRNA. This interaction between two well-known classes of RNA molecules, tRNA and Alu RNA, is driven by an unexpected structural motif and induces a global rearrangement of the 3′ UTR. Besides, this 3′ UTR contains two functional polyadenylation signals. We propose a model where the tRNA/Alu interaction would modulate the accessibility of the two alternative polyadenylation sites and regulate the stability of the mRNA. This unique regulation mechanism would link gene expression to RNA polymerase III transcription and may have implications in a primate-specific signal pathway.
Restraint of angiogenesis by zinc finger transcription factor CTCF-dependent chromatin insulation
Authors: Tang Ming , Chen Bo , Lin Tong , Li Zhaozhong , Pardo Carolina , Pampo Christine , Chen Jing , Lien Ching-Ling , Wu Lizi , Ai Lingbao , Wang Heiman , Yao Kai , Oh S. Paul , Seto Edward , Smith Lois E. H. , Siemann Dietmar W. , Kladde Michael P. , Cepko Constance L. , Lu Jianrong
Published: September 2011

Angiogenesis is meticulously controlled by a fine balance between positive and negative regulatory activities. Vascular endothelial growth factor (VEGF) is a predominant angiogenic factor and its dosage is precisely regulated during normal vascular formation. In cancer, VEGF is commonly overproduced, resulting in abnormal neovascularization. VEGF is induced in response to various stimuli including hypoxia; however, very little is known about the mechanisms that confine its induction to ensure proper angiogenesis. Chromatin insulation is a key transcription mechanism that prevents promiscuous gene activation by interfering with the action of enhancers. Here we show that the chromatin insulator-binding factor CTCF binds to the proximal promoter of
VEGF
. Consistent with the enhancer-blocking mode of chromatin insulators, CTCF has little effect on basal expression of VEGF but specifically affects its activation by enhancers. CTCF knockdown cells are sensitized for induction of VEGF and exhibit elevated proangiogenic potential. Cancer-derived CTCF missense mutants are mostly defective in blocking enhancers at the
VEGF
locus. Moreover, during mouse retinal development, depletion of CTCF causes excess angiogenesis. Therefore, CTCF-mediated chromatin insulation acts as a crucial safeguard against hyperactivation of angiogenesis.
AMP-activated protein kinase (AMPK) β1β2 muscle null mice reveal an essential role for AMPK in maintaining mitochondrial content and glucose uptake during exercise
Authors: O'Neill Hayley M. , Maarbjerg Stine J. , Crane Justin D. , Jeppesen Jacob , Jørgensen Sebastian B. , Schertzer Jonathan D. , Shyroka Olga , Kiens Bente , van Denderen Bryce J. , Tarnopolsky Mark A. , Kemp Bruce E. , Richter Erik A. , Steinberg Gregory R.
Published: September 2011

AMP-activated protein kinase (AMPK) β1 or β2 subunits are required for assembling of AMPK heterotrimers and are important for regulating enzyme activity and cellular localization. In skeletal muscle, α2β2γ3-containing heterotrimers predominate. However, compensatory up-regulation and redundancy of AMPK subunits in whole-body AMPK α2, β2, and γ3 null mice has made it difficult to determine the physiological importance of AMPK in regulating muscle metabolism, because these models have normal mitochondrial content, contraction-stimulated glucose uptake, and insulin sensitivity. In the current study, we generated mice lacking both AMPK β1 and β2 isoforms in skeletal muscle (β1β2M-KO). β1β2M-KO mice are physically inactive and have a drastically impaired capacity for treadmill running that is associated with reductions in skeletal muscle mitochondrial content but not a fiber-type switch. Interestingly, young β1β2M-KO mice fed a control chow diet are not obese or insulin resistant but do have impaired contraction-stimulated glucose uptake. These data demonstrate an obligatory role for skeletal muscle AMPK in maintaining mitochondrial capacity and contraction-stimulated glucose uptake, findings that were not apparent in mice with single mutations or deletions in muscle α, β, or γ subunits.
MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda
Authors: Campbell Lahcen I. , Rota-Stabelli Omar , Edgecombe Gregory D. , Marchioro Trevor , Longhorn Stuart J. , Telford Maximilian J. , Philippe Hervé , Rebecchi Lorena , Peterson Kevin J. , Pisani Davide
Published: September 2011

Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the inclusion of tardigrades within the Panarthropoda, but instead place them closer to Nematoda (roundworms). Here we present results from the analyses of two independent genomic datasets, expressed sequence tags (ESTs) and microRNAs (miRNAs), which congruently resolve the phylogenetic relationships of Tardigrada. Our EST analyses, based on 49,023 amino acid sites from 255 proteins, significantly support a monophyletic Panarthropoda including Tardigrada and suggest a sister group relationship between Arthropoda and Onychophora. Using careful experimental manipulations—comparisons of model fit, signal dissection, and taxonomic pruning—we show that support for a Tardigrada + Nematoda group derives from the phylogenetic artifact of long-branch attraction. Our small RNA libraries fully support our EST results; no miRNAs were found to link Tardigrada and Nematoda, whereas all panarthropods were found to share one unique miRNA (miR-276). In addition, Onychophora and Arthropoda were found to share a second miRNA (miR-305). Our study confirms the monophyly of the legged ecdysozoans, shows that past support for a Tardigrada + Nematoda group was due to long-branch attraction, and suggests that the velvet worms are the sister group to the arthropods.
Modulatory profiling identifies mechanisms of small molecule-induced cell death
Authors: Wolpaw Adam J. , Shimada Kenichi , Skouta Rachid , Welsch Matthew E. , Akavia Uri David , Pe'er Dana , Shaik Fatima , Bulinski J. Chloe , Stockwell Brent R.
Published: September 2011

Cell death is a complex process that plays a vital role in development, homeostasis, and disease. Our understanding of and ability to control cell death is impeded by an incomplete characterization of the full range of cell death processes that occur in mammalian systems, especially in response to exogenous perturbations. We present here a general approach to address this problem, which we call modulatory profiling. Modulatory profiles are composed of the changes in potency and efficacy of lethal compounds produced by a second cell death-modulating agent in human cell lines. We show that compounds with the same characterized mechanism of action have similar modulatory profiles. Furthermore, clustering of modulatory profiles revealed relationships not evident when clustering lethal compounds based on gene expression profiles alone. Finally, modulatory profiling of compounds correctly predicted three previously uncharacterized compounds to be microtubule-destabilizing agents, classified numerous compounds that act nonspecifically, and identified compounds that cause cell death through a mechanism that is morphologically and biochemically distinct from previously established ones.
Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil
Authors: Lehtovirta-Morley Laura E. , Stoecker Kilian , Vilcinskas Andreas , Prosser James I. , Nicol Graeme W.
Published: September 2011

Nitrification is a fundamental component of the global nitrogen cycle and leads to significant fertilizer loss and atmospheric and groundwater pollution. Nitrification rates in acidic soils (pH < 5.5), which comprise 30% of the world's soils, equal or exceed those of neutral soils. Paradoxically, autotrophic ammonia oxidizing bacteria and archaea, which perform the first stage in nitrification, demonstrate little or no growth in suspended liquid culture below pH 6.5, at which ammonia availability is reduced by ionization. Here we report the discovery and cultivation of a chemolithotrophic, obligately acidophilic thaumarchaeal ammonia oxidizer, “
Candidatus
Nitrosotalea devanaterra,” from an acidic agricultural soil. Phylogenetic analysis places the organism within a previously uncultivated thaumarchaeal lineage that has been observed in acidic soils. Growth of the organism is optimal in the pH range 4 to 5 and is restricted to the pH range 4 to 5.5, unlike all previously cultivated ammonia oxidizers. Growth of this organism and associated ammonia oxidation and autotrophy also occur during nitrification in soil at pH 4.5. The discovery of
Nitrosotalea devanaterra
provides a previously unsuspected explanation for high rates of nitrification in acidic soils, and confirms the vital role that thaumarchaea play in terrestrial nitrogen cycling. Growth at extremely low ammonia concentration (0.18 nM) also challenges accepted views on ammonia uptake and metabolism and indicates novel mechanisms for ammonia oxidation at low pH.
Expression of the metabotropic glutamate receptor 5 (mGluR5) induces melanoma in transgenic mice
Authors: Choi Kyu Yeong , Chang Kai , Pickel James M. , Badger John D. , Roche Katherine W.
Published: September 2011

Glutamate is the major excitatory neurotransmitter in the mammalian CNS and mediates fast synaptic transmission upon activation of glutamate-gated ion channels. In addition, glutamate modulates a variety of other synaptic responses and intracellular signaling by activating metabotropic glutamate receptors (mGluRs), which are G protein-coupled receptors. The mGluRs are also expressed in nonneuronal tissues and are implicated in a variety of normal biological functions as well as diseases. To study mGluR-activated calcium signaling in neurons, we generated mGluR5 transgenic animals using a Thy1 promoter to drive expression in the forebrain, and one founder unexpectedly developed melanoma. To directly investigate the role of mGluR5 in melanoma formation, we generated mGluR5 transgenic lines under a melanocyte-specific promoter, tyrosinase-related protein 1. A majority of the founders showed a severe phenotype with early onset. Hyperpigmentation of the pinnae and tail could be detected as early as 3–5 d after birth for most of the mGluR5 transgene-positive mice. There was 100% penetrance in the progeny from the tyrosinase-related protein 1-mGluR5 lines generated from founders that developed melanoma. Expression of mGluR5 was detected in melanoma samples by RT-PCR, immunoblotting, and immunohistochemistry. We evaluated the expression of several cancer-related proteins in tumor samples and observed a dramatic increase in the phosphorylation of ERK, implicating ERK as a downstream effector of mGluR5 signaling in tumors. Our findings show that mGluR5-mediated glutamatergic signaling can trigger melanoma in vivo. The aggressive growth and severe phenotype make these mouse lines unique and a potentially powerful tool for therapeutic studies.
Prostaglandin E
2
release from astrocytes triggers gonadotropin-releasing hormone (GnRH) neuron firing via EP2 receptor activation
Authors: Clasadonte Jerome , Poulain Pierre , Hanchate Naresh K. , Corfas Gabriel , Ojeda Sergio R. , Prevot Vincent
Published: September 2011

Astrocytes in the hypothalamus release prostaglandin E
2
(PGE
2
) in response to cell–cell signaling initiated by neurons and glial cells. Upon release, PGE
2
stimulates the secretion of gonadotropin-releasing hormone (GnRH), the neuropeptide that controls reproduction, from hypothalamic neuroendocrine neurons. Whether this effect on GnRH secretion is accompanied by changes in the firing behavior of these neurons is unknown. Using patch-clamp recording we demonstrate that PGE
2
exerts a dose-dependent postsynaptic excitatory effect on GnRH neurons. These effects are mimicked by an EP2 receptor agonist and attenuated by protein kinase A (PKA) inhibitors. The acute blockade of prostaglandin synthesis by indomethacin (INDO) or the selective inhibition of astrocyte metabolism by fluoroacetate (FA) suppresses the spontaneous firing activity of GnRH neurons in brain slices. Similarly, GnRH neuronal activity is reduced in mice with impaired astrocytic PGE
2
release due to defective erbB signaling in astrocytes. These results indicate that astrocyte-to-neuron communication in the hypothalamus is essential for the activity of GnRH neurons and suggest that PGE
2
acts as a gliotransmitter within the GnRH neurosecretory system.
Second-generation high-throughput forward genetic screen in mice to isolate subtle behavioral mutants
Authors: Kumar Vivek , Kim Kyungin , Joseph Chryshanthi , Thomas Lisa C. , Hong Heekyung , Takahashi Joseph S.
Published: September 2011

Forward genetic screens have been highly successful in revealing roles of genes and pathways in complex biological events. Traditionally these screens have focused on isolating mutants with the greatest phenotypic deviance, with the hopes of discovering genes that are central to the biological event being investigated. Behavioral screens in mice typically use simple activity-based assays as endophenotypes for more complex emotional states of the animal. They generally set the selection threshold for a putative mutant at 3 SDs (
z
score of 3) from the average behavior of normal animals to minimize false-positive results. Behavioral screens using a high threshold for detection have generally had limited success, with high false-positive rates and subtle phenotypic differences that have made mapping and cloning difficult. In addition, targeted reverse genetic approaches have shown that when genes central to behaviors such as open field behavior, psychostimulant response, and learning and memory tasks are mutated, they produce subtle phenotypes that differ from wild-type animals by 1 to 2 SDs (
z
scores of 1 to 2). We have conducted a second-generation (G2) dominant
N
-ethyl-
N
-nitrosourea (ENU) screen especially designed to detect subtle behavioral mutants for open field activity and psychostimulant response behaviors. We successfully detect mutant lines with only 1 to 2 SD shifts in mean response compared with wild-type control animals and present a robust statistical and methodological framework for conducting such forward genetic screens. Using this methodology we have screened 229 ENU mutant lines and have identified 15 heritable mutant lines. We conclude that for screens in mice that use activity-based endophenotypic measurements for complex behavioral states, this G2 screening approach yields better results.
Finding the ciliary beating pattern with optimal efficiency
Authors: Osterman Natan , Vilfan Andrej
Published: September 2011

We introduce a measure for energetic efficiency of biological cilia acting individually or collectively and numerically determine the optimal beating patterns according to this criterion. Maximizing the efficiency of a single cilium leads to curly, often symmetric, and somewhat counterintuitive patterns. However, when looking at a densely ciliated surface, the optimal patterns become remarkably similar to what is observed in microorganisms like Paramecium. The optimal beating pattern then consists of a fast effective stroke and a slow sweeping recovery stroke. Metachronal coordination is essential for efficient pumping and the highest efficiency is achieved with antiplectic waves. Efficiency also increases with an increasing density of cilia up to the point where crowding becomes a problem. We finally relate the pumping efficiency of cilia to the swimming efficiency of a spherical microorganism and show that the experimentally estimated efficiency of Paramecium is surprisingly close to the theoretically possible optimum.
Genetic evidence for archaic admixture in Africa
Authors: Hammer Michael F. , Woerner August E. , Mendez Fernando L. , Watkins Joseph C. , Wall Jeffrey D.
Published: September 2011

A long-debated question concerns the fate of archaic forms of the genus
Homo
: did they go extinct without interbreeding with anatomically modern humans, or are their genes present in contemporary populations? This question is typically focused on the genetic contribution of archaic forms outside of Africa. Here we use DNA sequence data gathered from 61 noncoding autosomal regions in a sample of three sub-Saharan African populations (Mandenka, Biaka, and San) to test models of African archaic admixture. We use two complementary approximate-likelihood approaches and a model of human evolution that involves recent population structure, with and without gene flow from an archaic population. Extensive simulation results reject the null model of no admixture and allow us to infer that contemporary African populations contain a small proportion of genetic material (≈2%) that introgressed ≈35 kya from an archaic population that split from the ancestors of anatomically modern humans ≈700 kya. Three candidate regions showing deep haplotype divergence, unusual patterns of linkage disequilibrium, and small basal clade size are identified and the distributions of introgressive haplotypes surveyed in a sample of populations from across sub-Saharan Africa. One candidate locus with an unusual segment of DNA that extends for >31 kb on chromosome 4 seems to have introgressed into modern Africans from a now-extinct taxon that may have lived in central Africa. Taken together our results suggest that polymorphisms present in extant populations introgressed via relatively recent interbreeding with hominin forms that diverged from the ancestors of modern humans in the Lower-Middle Pleistocene.
Surface architecture of endospores of the
Bacillus cereus/anthracis/thuringiensis
family at the subnanometer scale
Authors: Kailas Lekshmi , Terry Cassandra , Abbott Nicholas , Taylor Robert , Mullin Nic , Tzokov Svetomir B. , Todd Sarah J. , Wallace B. A. , Hobbs Jamie K. , Moir Anne , Bullough Per A.
Published: September 2011

Bacteria of the
Bacillus cereus
family form highly resistant spores, which in the case of the pathogen
B. anthracis
act as the agents of infection. The outermost layer, the exosporium, enveloping spores of the
B. cereus
family as well as a number of
Clostridia
, plays roles in spore adhesion, dissemination, targeting, and germination control. We have analyzed two naturally crystalline layers associated with the exosporium, one representing the “basal” layer to which the outermost spore layer (“hairy nap”) is attached, and the other likely representing a subsurface (“parasporal”) layer. We have used electron cryomicroscopy at a resolution of 0.8–0.6 nm and circular dichroism spectroscopic measurements to reveal a highly α-helical structure for both layers. The helices are assembled into 2D arrays of “cups” or “crowns.” High-resolution atomic force microscopy of the outermost layer showed that the open ends of these cups face the external environment and the highly immunogenic collagen-like fibrils of the hairy nap (BclA) are attached to this surface. Based on our findings, we present a molecular model for the spore surface and propose how this surface can act as a semipermeable barrier and a matrix for binding of molecules involved in defense, germination control, and other interactions of the spore with the environment.
Heparan sulfate binding by natural eastern equine encephalitis viruses promotes neurovirulence
Authors: Gardner Christina L. , Ebel Gregory D. , Ryman Kate D. , Klimstra William B.
Published: September 2011

TheAlphavirusgenus of the family Togaviridae contains mosquito-vectored viruses that primarily cause either arthritogenic disease or acute encephalitis. North American eastern equine encephalitis virus (NA-EEEV) is uniquely neurovirulent among encephalitic alphaviruses, causing mortality in a majority of symptomatic cases and neurological sequelae in many survivors. Unlike many alphaviruses, NA-EEEV infection of mice yields limited signs of febrile illness typically associated with lymphoid tissue replication. Rather, signs of brain infection, including seizures, are prominent. Use of heparan sulfate (HS) as an attachment receptor increases the neurovirulence of cell culture-adapted strains of Sindbis virus, an arthritogenic alphavirus. However, this receptor is not known to be used by naturally circulating alphaviruses. We demonstrate that wild-type NA-EEEV strain FL91-4679 uses HS as an attachment receptor and that the amino acid sequence of its E2 attachment protein is identical to those of natural isolates sequenced by RT-PCR amplification of field samples. This finding unequivocally confirms the use of HS receptors by naturally circulating NA-EEEV strains. Inactivation of the major HS binding domain in NA-EEEV E2 demonstrated that the HS binding increased brain replication and neurologic disease but reduced lymphoid tissue replication, febrile illness signs, and cytokine/chemokine induction in mice. We propose that HS binding by natural NA-EEEV strains alters tropism in vivo to antagonize/evade immune responses, and the extreme neurovirulence of wild-type NA-EEEV may be a consequence. Therefore, reinvestigation of HS binding by this and other arboviruses is warranted.
Arbovirus high fidelity variant loses fitness in mosquitoes and mice
Authors: Coffey Lark L. , Beeharry Yasnee , Bordería Antonio V. , Blanc Hervé , Vignuzzi Marco
Published: September 2011

The error rate of RNA-dependent RNA polymerases (RdRp) affects the mutation frequency in a population of viral RNAs. Using chikungunya virus (CHIKV), we describe a unique arbovirus fidelity variant with a single C483Y amino acid change in the nsP4 RdRp that increases replication fidelity and generates populations with reduced genetic diversity. In mosquitoes, high fidelity CHIKV presents lower infection and dissemination titers than wild type. In newborn mice, high fidelity CHIKV produces truncated viremias and lower organ titers. These results indicate that increased replication fidelity and reduced genetic diversity negatively impact arbovirus fitness in invertebrate and vertebrate hosts.
Pattern of trauma determines the threshold for epileptic activity in a model of cortical deafferentation
Authors: Volman Vladislav , Bazhenov Maxim , Sejnowski Terrence J.
Published: September 2011

Epileptic activity often occurs in the cortex after a latent period after head trauma; this delay has been attributed to the destabilizing influence of homeostatic synaptic scaling and changes in intrinsic properties. However, the impact of the spatial organization of cortical trauma on epileptogenesis is poorly understood. We addressed this question by analyzing the dynamics of a large-scale biophysically realistic cortical network model subjected to different patterns of trauma. Our results suggest that the spatial pattern of trauma can greatly affect the propensity for developing posttraumatic epileptic activity. For the same fraction of lesioned neurons, spatially compact trauma resulted in stronger posttraumatic elevation of paroxysmal activity than spatially diffuse trauma. In the case of very severe trauma, diffuse distribution of a small number of surviving intact neurons alleviated posttraumatic epileptogenesis. We suggest that clinical evaluation of the severity of brain trauma should take into account the spatial pattern of the injured cortex.
Neural-specific elongation of 3′ UTRs during
Drosophila
development
Authors: Hilgers Valérie , Perry Michael W. , Hendrix David , Stark Alexander , Levine Michael , Haley Benjamin
Published: September 2011

The 3′ termini of eukaryotic mRNAs influence transcript stability, translation efficiency, and subcellular localization. Here we report that a subset of developmental regulatory genes, enriched in critical RNA-processing factors, exhibits synchronous lengthening of their 3′ UTRs during embryogenesis. The resulting UTRs are up to 20-fold longer than those found on typical
Drosophila
mRNAs. The large mRNAs emerge shortly after the onset of zygotic transcription, with several of these genes acquiring additional, phased UTR extensions later in embryogenesis. We show that these extended 3′ UTR sequences are selectively expressed in neural tissues and contain putative recognition motifs for the translational repressor, Pumilio, which also exhibits the 3′ lengthening phenomenon documented in this study. These findings suggest a previously unknown mode of posttranscriptional regulation that may contribute to the complexity of neurogenesis or neural function.