Scientific Reports Biology Table of Contents e-alert: September 2012

03 September 2012      • Visit Scientific Reports • Submit your manuscript to Scientific Reports     Welcome to your Table of Contents e-alert for Scientific Reports             Online-only personal subscriptions now available For only 49 USD/29 GBP/29 EUR to selected journals Subscribe now!                 Biological Sciences               Nonlinear Dependencies of Biochemical Reactions for Context-specific Signaling Dynamics ▶     Myong-Hee Sung, Gordon L. Hager     Mathematical modeling can provide unique insights and predictions about a signaling pathway. Parameter variations allow identification of key reactions that govern signaling …             Evidence for a bacterial mechanism for group-specific social odors among hyenas ▶     Kevin R. Theis, Thomas M. Schmidt, Kay E. Holekamp     Symbiotic microbes can benefit their animal hosts by enhancing the diversity of communication signals available to them. The fermentation hypothesis for chemical recognition …             Pf155/RESA protein influences the dynamic microcirculatory behavior of ring-stage Plasmodium falciparum infected red blood cells ▶     Monica Diez-Silva, YongKeun Park, Sha Huang et al.     Proteins exported by Plasmodium falciparum to the red blood cell (RBC) membrane modify the structural properties of the parasitized RBC (Pf-RBC). Although quasi-static single cell …             Tryptophan-based chromophore in fluorescent proteins can be anionic ▶     Karen S. Sarkisyan, Ilia V. Yampolsky, Kyril M. Solntsev et al.     Cyan fluorescent proteins (CFP) with tryptophan66-based chromophore are widely used for live cell imaging. In contrast to green and red fluorescent proteins, no charged states of …             X-ray imaging of tumor growth in live mice by detecting gold-nanoparticle-loaded cells ▶     Chia-Chi Chien, Hsiang-Hsin Chen, Sheng-Feng Lai et al.     We show that sufficient concentrations of gold nanoparticles produced by an original synthesis method in EMT-6 and CT-26 cancer cells make it possible to detect the presence, …             Predicting effects of structural stress in a genome-reduced model bacterial metabolism ▶     Oriol Güell, Francesc Sagués, M. Ángeles Serrano     Mycoplasma pneumoniae is a human pathogen recently proposed as a genome-reduced model for bacterial systems biology. Here, we study the response of its metabolic network to …             Optical properties of in-vitro biomineralised silica ▶     Alessandro Polini, Stefano Pagliara, Andrea Camposeo et al.     Silicon is the second most common element on the Earth's crust and its oxide (SiO2) the most abundant mineral. Silica and silicates are widely used in medicine and industry as …             Control of Adaptive Immune Responses by Staphylococcus aureus through IL-10, PD-L1, and TLR2 ▶     Jinhai Wang, Gregory Roderiquez, Michael A. Norcross     Microbes induce innate immune responses in hosts. It is critical to know how different microbes control adaptive responses through innate pathways. The impact of gram-positive …             Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain ▶     Boris Rogelj, Laura E. Easton, Gireesh K. Bogu et al.     Fused in sarcoma (FUS) and TAR DNA-binding protein 43 (TDP-43) are RNA-binding proteins pathogenetically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar …             Vertical distribution of microbial communities in a perennially stratified Arctic lake with saline, anoxic bottom waters ▶     André M. Comeau, Tommy Harding, Pierre E. Galand et al.     Meromictic lakes are useful biogeochemical models because of their stratified chemical gradients and separation of redox reactions down the water column. Perennially ice-covered …             Sex determination in beetles: Production of all male progeny by Parental RNAi knockdown of transformer ▶     Jayendra Nath Shukla, Subba Reddy Palli     Sex in insects is determined by a cascade of regulators ultimately controlling sex-specific splicing of a transcription factor, Doublesex (Dsx). We recently identified homolog of …             Why the bigger live longer and travel farther: animals, vehicles, rivers and the winds ▶     Adrian Bejan     Here we show that constructal-law physics unifies the design of animate and inanimate movement by requiring that larger bodies move farther, and their movement on the landscape …             ERRATUM: Phosphatidylinositol 4,5-bisphosphate (PIP2) controls magnesium gatekeeper TRPM6 activity ▶     Jia Xie, Baonan Sun, Jianyang Du et al.                 Human responses to unfairness with primary rewards and their biological limits ▶     Nicholas D. Wright, Karen Hodgson, Stephen M. Fleming et al.     Humans bargaining over money tend to reject unfair offers, whilst chimpanzees bargaining over primary rewards of food do not show this same motivation to reject. Whether such …             Reversal of Aberrant Cancer Methylome and Transcriptome upon Direct Reprogramming of Lung Cancer Cells ▶     Dashayini Mahalingam, Chiou Mee Kong, Jason Lai et al.     Recent reports on direct reprogramming of cancer cells (iPCs) which results in reduced tumorigenic potential has attributed the importance of epigenetics in tumorigenesis, but …             Exploring the Physical Limits of Saturation Contrast in Magnetic Resonance Imaging ▶     M. Lapert, Y. Zhang, M. A. Janich et al.     Magnetic Resonance Imaging has become nowadays an indispensable tool with applications ranging from medicine to material science. However, so far the physical limits of the …             Network Biology of Tumor Stem-like Cells Identified a Regulatory Role of CBX5 in Lung Cancer ▶     Yau-Hua Yu, Guang-Yuh Chiou, Pin-I Huang et al.     Mounting evidence links cancers possessing stem-like properties with worse prognosis. Network biology with signal processing mechanics was explored here using expression profiles …             Light- induced electron transfer and ATP synthesis in a carotene synthesizing insect ▶     Jean Christophe Valmalette, Aviv Dombrovsky, Pierre Brat et al.     A singular adaptive phenotype of a parthenogenetic insect species (Acyrthosiphon pisum) was selected in cold conditions and is characterized by a remarkable apparition of a …             Arachidonic Acid Enhances Caffeine-Induced Cell Death via Caspase-Independent Cell Death ▶     Hidekazu Kuwayama     Caffeine is a globally consumed psychostimulant but can be fatal to cells at overdose exposures. Although caspase-dependent apoptosis plays a role in caffeine-induced cell death, …             Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks ▶     Steven M. Kelk, Brett G. Olivier, Leen Stougie et al.     The metabolism of organisms can be studied with comprehensive stoichiometric models of their metabolic networks. Flux balance analysis (FBA) calculates optimal metabolic …             Plant viruses alter insect behavior to enhance their spread ▶     Laura L. Ingwell, Sanford D. Eigenbrode, Nilsa A. Bosque-Pérez     Pathogens and parasites can induce changes in host or vector behavior that enhance their transmission. In plant systems, such effects are largely restricted to vectors, because …             TLR9 is important for protection against intestinal damage and for intestinal repair ▶     William Alfred Rose II, Kaori Sakamoto, Cynthia Anne Leifer     Toll-like receptors (TLRs) are innate receptors critical for host defense, and play a role in normal biological processes. For example, host DNA, a TLR9 ligand, stimulates …             Nanoscale analysis of the effects of antibiotics and CX1 on a Pseudomonas aeruginosa multidrug-resistant strain ▶     C. Formosa, M. Grare, E. Jauvert et al.     Drug resistance is a challenge that can be addressed using nanotechnology. We focused on the resistance of the bacteria Pseudomonas aeruginosa and investigated, using Atomic Force …             Wisdom of groups promotes cooperation in evolutionary social dilemmas ▶     Attila Szolnoki, Zhen Wang, Matjaž Perc     Whether or not to change strategy depends not only on the personal success of each individual, but also on the success of others. Using this as motivation, we study the evolution …             The potential of GPNMB as novel neuroprotective factor in amyotrophic lateral sclerosis ▶     Hirotaka Tanaka, Masamitsu Shimazawa, Masataka Kimura et al.     Amyotrophic lateral sclerosis (ALS) is an incurable and fatal neurodegenerative disease characterized by the loss of motor neurons. Despite substantial research, the causes of ALS …             Finding low-energy conformations of lattice protein models by quantum annealing ▶     Alejandro Perdomo-Ortiz, Neil Dickson, Marshall Drew-Brook et al.     Lattice protein folding models are a cornerstone of computational biophysics. Although these models are a coarse grained representation, they provide useful insight into the …             Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible 'seed-less' targets ▶     Zhen Xia, Peter Clark, Tien Huynh et al.     To better understand the recognition mechanism of RISC and the repertoire of guide-target interactions we introduced G: wobbles and mismatches at various positions of the microRNA …             Metabolic trajectory of cellular differentiation in small intestine by Phasor Fluorescence Lifetime Microscopy of NADH ▶     Chiara Stringari, Robert A. Edwards, Kira T. Pate et al.     There is a lack of fast and high resolution methods to measure metabolic activity of single cells in their native environment. Here we develop a straightforward, non-invasive and …             The biological impacts of the Fukushima nuclear accident on the pale grass blue butterfly ▶     Atsuki Hiyama, Chiyo Nohara, Seira Kinjo et al.     The collapse of the Fukushima Dai-ichi Nuclear Power Plant caused a massive release of radioactive materials to the environment. A prompt and reliable system for evaluating the …             Mechanisms for redox actions of nicotine and glutathione in cell culture, relevant to periodontitis ▶     Federico Tinti, Mena Soory     The oxidative effect of nicotine was investigated using androgen biomarkers of redox status and wound healing in fibroblasts; using the antioxidant glutathione for confirmation of …             Extinction Risk and Overfishing: Reconciling Conservation and Fisheries Perspectives on the Status of Marine Fishes ▶     Trevor D. Davies, Julia K. Baum     Anthropogenic disturbances are ubiquitous in the ocean, but their impacts on marine species are hotly debated. We evaluated marine fish statuses using conservation (Red List …             Surface engineering of nanoparticles in suspension for particle based bio-sensing ▶     Tapas Sen, Ian J. Bruce     Surface activation of nanoparticles in suspension using amino organosilane has been carried out via strict control of a particle surface ad-layer of water using a simple but …             Akt signaling-associated metabolic effects of dietary gold nanoparticles in Drosophila ▶     Bin Wang, Nan Chen, Yingliang Wei et al.     Gold nanoparticles (AuNPs) are often used as vehicles to deliver drugs or biomolecules, due to their mild effect on cell survival and proliferation. However, little is known about …             SNP in starch biosynthesis genes associated with nutritional and functional properties of rice ▶     Ardashir Kharabian-Masouleh, Daniel L. E. Waters, Russell F. Reinke et al.     Starch is a major component of human diets. The relative contribution of variation in the genes of starch biosynthesis to the nutritional and functional properties of the rice was …             Actin cap associated focal adhesions and their distinct role in cellular mechanosensing ▶     Dong-Hwee Kim, Shyam B. Khatau, Yunfeng Feng et al.     The ability for cells to sense and adapt to different physical microenvironments plays a critical role in development, immune responses, and cancer metastasis. Here we identify a …             Calcium signaling is gated by a mechanical threshold in three-dimensional environments ▶     Warren C. Ruder, Erica D. Pratt, Nailah Z. D. Brandy et al.     Cells interpret their mechanical environment using diverse signaling pathways that affect complex phenotypes. These pathways often interact with ubiquitous 2nd-messengers such as …             Direct interaction between the Gulf Stream and the shelfbreak south of New England ▶     Glen G. Gawarkiewicz, Robert E. Todd, Albert J. Plueddemann et al.     Sea surface temperature imagery, satellite altimetry, and a surface drifter track reveal an unusual tilt in the Gulf Stream path that brought the Gulf Stream to 39.9°N near the …             A new mechanism of stem cell differentiation through slow binding/unbinding of regulators to genes ▶     Haidong Feng, Jin Wang     Understanding differentiation, a biological process from a multipotent stem or progenitor state to a mature cell is critically important. We developed a theoretical framework to …             Localized outbreak of attached diatoms on the coral Montipora due to low-temperature stress ▶     Hideyuki Yamashiro, Yurika Mikame, Hidekazu Suzuki     A short-term, localized outbreak of diatoms attached to live corals was observed along the coast of Sesoko Island, Okinawa, Japan in February, 2011. Diatoms are recognized as …                         Scientific Reports is accepting submissions from all scientific fields. Submit your manuscript now.               • Careers & Jobs           naturejobs.com Science jobs of the week       Protein Biochemist     Opus Scientific            Faculty Position in the Molecular Biology Department at Princeton University     Princeton University            Associate or Full Professor in Molecular Biology     Princeton University            Assistant Professor     University of Chicago            Predoctoral Positions     Cristina Andres-Lacueva            Postdoc in Regulatory Genomics     Technical University of Denmark, Center for Biological Sequence Analysis            Senior Manager / Associate Director, Global Marketing Emerging Brands     MedImmune UK            Research associate(Magnetic Nanoparticle Mediated gene Delivery)     Keele University            Postdoctoral Scientist     University of Oxford, Weatherall Institute of Molecular Medicine            Research Assistant     Imperial College London - Faculty of Medicine          No matter what your career stage, student, postdoc or senior scientist, you will find articles on naturejobs.com to help guide you in your science career. Keep up-to-date with the latest sector trends, vote in our reader poll and sign-up to receive the monthly Naturejobs newsletter.           • Scientific Reports events featured events           natureevents featured events         1st International Conference on Stem Cells     6-11 September 2012 Crete, Greece         Nature events is the premier resource for scientists looking for the latest scientific conferences, courses, meetings and symposia. Featured across Nature Publishing Group journals and centrally at natureevents.com it is an essential reference guide to scientific events worldwide.                 Your email address is in the Scientific Reports: Biology mailing list. You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/nams/svc/myaccount (You will need to log in to be recognised as a nature.com registrant). For further technical assistance, please contact our registration department For other enquiries, please contact our customer feedback department Nature Publishing Group | 75 Varick Street, 9th floor | New York | NY 10013-1917 | USA Nature Publishing Group's offices: Principal offices: London - New York - Tokyo Worldwide offices: Basingstoke - Boston - Buenos Aires - Delhi - Hong Kong - Madrid - Melbourne - Munich - Paris - San Francisco - Seoul - Washington DC Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. © 2012 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.