In vivo selective cancer-tracking gadolinium eradicator as new-generation photodynamic therapy agent
Tao Zhang, Rongfeng Lan, Chi-Fai Chan, Ga-Lai Law, Wai-Kwok Wong, and Ka-Leung Wong
Next-generation photodynamic therapy (NG-PDT) for the treatment of tumors preponderates over conventional practices in that it is a kind of effective precision medicine with minimal invasive procedures and side effects. Herein (pp. E5492–E5497), a newly developed NG-PDT paradigm agent of gadolinium-porphyrin complex, Gd-N, is introduced, which can successfully trace and recognize tumor tissues via simple injection into the blood vessel of the mouse models, selectively accumulate within them, and superiorly exert the therapeutic effect via cytotoxic singlet oxygen generation (∼51% quantum yield) to eradicate the solid tumor by one-half within a short period of time only upon due two-photon excitation. Its characteristic two-photon–induced near-infrared emission is also always available for direct monitoring for transportation and effectiveness in vitro and in vivo.
Structural basis and dynamics of multidrug recognition in a minimal bacterial multidrug resistance system
Judith Habazettl, Martin Allan, Pernille Rose Jensen, Hans-Jürgen Sass, Charles J. Thompson, and Stephan Grzesiek
Multidrug recognition is an important phenomenon that is not well understood. TipA, a bacterial transcriptional regulator, constitutes a minimal multidrug resistance system against numerous thiopeptide antibiotics. We show (pp. E5498–E5507) that motions in the millisecond to microsecond time range form the basis of the TipA multidrug recognition mechanism. This may be common to many multidrug recognition systems. The discovery that the structural antibiotic motifs essential for binding to TipA and to the ribosome are identical makes the multidrug recognition mechanism of TipA a useful model for ribosomal thiopeptide binding and current antibiotic drug development.
Analogs of natural aminoacyl-tRNA synthetase inhibitors clear malaria in vivo
Eva Maria Novoa, Noelia Camacho, Anna Tor, Barrie Wilkinson, Steven Moss, Patricia Marín-García, Isabel G. Azcárate, José M. Bautista, Adam C. Mirando, Christopher S. Francklyn, Sònia Varon, Miriam Royo, Alfred Cortés, and Lluís Ribas de Pouplana
Malaria remains one of the main health threats in the developing world, with staggering social and economic costs. Resistance to artemisins, the main pharmacological tool currently available against malaria, has been widely reported. Borrelidin, a natural compound that inhibits threonyl-tRNA synthetase, has long been studied for its antibacterial and antiparasitic properties, but undesirable toxic effects prevented its further clinical development. Here (pp. E5508–E5517) we present a group of borrelidin derivatives that retain their ability to inhibit Plasmodium threonyl-tRNA synthetase but not its human homolog. Furthermore, we demonstrate, for the first time to our knowledge, that these compounds are capable of effectively clearing a Plasmodium infection in animals, curing malaria with a potency equivalent to reference drugs such as chloroquine.
Structural and functional studies of Bud23–Trm112 reveal 18S rRNA N7-G1575 methylation occurs on late 40S precursor ribosomes
Juliette Létoquart, Emmeline Huvelle, Ludivine Wacheul, Gabrielle Bourgeois, Christiane Zorbas, Marc Graille, Valérie Heurgué-Hamard, and Denis L. J. Lafontaine
Ribosomes are essential cellular nanomachines responsible for all protein synthesis in vivo. Efficient and faithful ribosome biogenesis requires a plethora of assembly factors whose precise role and timing of action remains to be established. Here (pp. E5518–E5526) we determined the crystal structure of Bud23–Trm112, which is required for efficient pre-rRNA processing steps leading to 18S rRNA synthesis and methylation of 18S rRNA at position G1575. For the first time, to our knowledge, we identified where on Bud23–Trm112 the contacts with precursor ribosomes occur. We further report that the essential helicase Dhr1 interacts directly with Bud23–Trm112, proposing a concerted action of these proteins in ribosome assembly. Finally, we reveal that the methyltransferase activity of Bud23–Trm112 and its requirement for pre-rRNA processing are disconnected in time.
The N- and C-terminal autolytic fragments of CAPN3/p94/calpain-3 restore proteolytic activity by intermolecular complementation
Yasuko Ono, Mayumi Shindo, Naoko Doi, Fujiko Kitamura, Carol C. Gregorio, and Hiroyuki Sorimachi
CAPN3/p94/calpain-3, a calpain protease family member, has uniquely rapid and exhaustive autolytic activity. Here (pp. E5527–E5536), we demonstrate that active protease core domain of CAPN3 is reconstituted by de novo intermolecular complementation (iMOC) between its two autolytic fragments. We also show that iMOC between one of the autolytic fragments and an unautolyzed full-length CAPN3 effectively generates autolytic activity. So far, CAPN3 is the only example of calpain that exhibits activity mediated by intermolecular complementation of its autolytic products. Mutations in the human CAPN3 gene cause limb-girdle muscular dystrophy type 2A (LGMD2A or calpainopathy). Understanding the genotype–phenotype links in the pathology of LGMD2A will be accelerated by incorporating iMOC-CAPN3 as one of active CAPN3 entities.
Bnip3 mediates doxorubicin-induced cardiac myocyte necrosis and mortality through changes in mitochondrial signaling
Rimpy Dhingra, Victoria Margulets, Subir Roy Chowdhury, James Thliveris, Davinder Jassal, Paul Fernyhough, Gerald W. Dorn II, and Lorrie A. Kirshenbaum
We provide (pp. E5537–E5544) new, exciting evidence for a previously unidentified signaling pathway that mechanistically links mitochondrial respiratory chain defects to necrosis and heart failure induced by the chemotherapy agent doxorubicin (DOX). We specifically show that DOX disrupts protein complexes between the key respiratory chain proteins, including uncoupling protein 3 and cytochrome c oxidase, resulting in abnormal mitochondrial respiration and necrosis through a mechanism contingent on Bcl-2-like 19kDa-interacting protein 3 (Bnip3). Perhaps most compelling is our finding that inhibiting Bnip3 completely abrogated the cardiotoxic effects of DOX. These exciting findings have important clinical implications not only for preventing heart failure by targeting Bnip3 in cancer patients undergoing chemotherapy, but also for understanding the pathogenesis of other diseases in which mitochondrial function is compromised.
Fire responses to postglacial climate change and human impact in northern Patagonia (41–43°S)
Virginia Iglesias and Cathy Whitlock
Fire is a key ecological process affecting ecosystem dynamics and services. Fire frequency, intensity, and size reflect complex climate–vegetation–human interactions and their evolution through time. The long-term history of these interactions provides insights into the variability of the ecosystem and a context for future environmental change. We use (pp. E5545–E5554) paleoenvironmental data from the Patagonian forest/steppe border and introduce generalized additive models as trend-detection tools in paleoecology to assess the relative influence of climate, vegetation, and humans in shaping the fire regime. Our results suggest that for the last 18,000 y, fires have been predominantly limited by fuel discontinuity rather than by suitable climate conditions. In contrast to extensive present-day anthropogenic impact, Patagonian ecosystems evolved with minimal human influence prior to European settlement.
Mechanisms of NDV-3 vaccine efficacy in MRSA skin versus invasive infection
Michael R. Yeaman, Scott G. Filler, Siyang Chaili, Kevin Barr, Huiyuan Wang, Deborah Kupferwasser, John P. Hennessey Jr., Yue Fu, Clint S. Schmidt, John E. Edwards Jr., Yan Q. Xiong, and Ashraf S. Ibrahim
Staphylococcus aureus is an opportunistic pathogen of the normal human flora. It is among the most frequent causes of cutaneous abscesses, leading to life-threatening invasive infection. Incomplete understanding of host defenses against S. aureus skin or invasive infection has hindered development of effective vaccines to address these issues. NDV-3 is a unique cross-kingdom vaccine targeting S. aureus and Candida albicans. The present studies (pp. E5555–E5563) offer important new evidence: (i) NDV-3 protects against methicillin-resistant S. aureus skin and skin structure infection largely through IL-22– and IL-17A–mediated host defense peptide and neutrophil induction, (ii) vaccine-mediated IL-22 and IL-17A play distinct roles in protection against cutaneous versus invasive infection, and (iii) NDV-3 vaccine efficacy in this model involves a coordinated induction of innate and adaptive immunity.
Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma
Jennifer A. Perry, Adam Kiezun, Peter Tonzi, Eliezer M. Van Allen, Scott L. Carter, Sylvan C. Baca, Glenn S. Cowley, Ami S. Bhatt, Esther Rheinbay, Chandra Sekhar Pedamallu, Elena Helman, Amaro Taylor-Weiner, Aaron McKenna, David S. DeLuca, Michael S. Lawrence, Lauren Ambrogio, Carrie Sougnez, Andrey Sivachenko, Loren D. Walensky, Nikhil Wagle, Jaume Mora, Carmen de Torres, Cinzia Lavarino, Simone Dos Santos Aguiar, Jose Andres Yunes, Silvia Regina Brandalise, Gabriela Elisa Mercado-Celis, Jorge Melendez-Zajgla, Rocío Cárdenas-Cardós, Liliana Velasco-Hidalgo, Charles W. M. Roberts, Levi A. Garraway, Carlos Rodriguez-Galindo, Stacey B. Gabriel, Eric S. Lander, Todd R. Golub, Stuart H. Orkin, Gad Getz, and Katherine A. Janeway
We present (pp. E5564–E5573), to our knowledge, the first comprehensive next-generation sequencing of osteosarcoma in combination with a functional genomic screen in a genetically defined mouse model of osteosarcoma. Our data provide a strong rationale for targeting the phosphatidylinositol 3-kinase/mammalian target of rapamycin pathway in osteosarcoma and a foundation for rational clinical trial design. These findings present an immediate clinical opportunity because multiple inhibitors of this pathway are currently in clinical trials.
Restoration of visual function by expression of a light-gated mammalian ion channel in retinal ganglion cells or ON-bipolar cells
Benjamin M. Gaub, Michael H. Berry, Amy E. Holt, Andreas Reiner, Michael A. Kienzler, Natalia Dolgova, Sergei Nikonov, Gustavo D. Aguirre, William A. Beltran, John G. Flannery, and Ehud Y. Isacoff
We restored (pp. E5574–E5583) visual function to animal models of human blindness using a chemical compound that photosensitizes a mammalian ion channel. Virus-mediated expression of this light sensor in surviving retinal cells of blind mice restored light responses in vitro, reanimated innate light avoidance, and enabled learned visually guided behavior. The treatment also restored light responses to the retina of blind dogs. Patients that might benefit from this treatment would need to have intact ganglion cell and nerve fiber layers. In general, these are patients diagnosed with retinitis pigmentosa and some forms of Leber congenital amaurosis. Patients diagnosed with other types of blindness, for example, age-related macular degeneration or diabetic retinopathy, would not be candidates for this treatment.
Hebbian and neuromodulatory mechanisms interact to trigger associative memory formation
Joshua P. Johansen, Lorenzo Diaz-Mataix, Hiroki Hamanaka, Takaaki Ozawa, Edgar Ycu, Jenny Koivumaa, Ashwani Kumar, Mian Hou, Karl Deisseroth, Edward S. Boyden, and Joseph E. LeDoux
The influential Hebbian plasticity hypothesis suggests that an increase in the strength of connections between neurons whose activity is correlated produces memories. Other theories, however, propose that neuromodulatory systems need to be activated together with Hebbian plasticity mechanisms to engage memory formation. The present work (pp. E5584–E5592) provides direct in vivo evidence supporting the idea that a parallel mechanism involving neuromodulation and Hebbian processes is both necessary and sufficient to trigger synaptic strengthening and behavioral associative memory formation. This parallel process may represent a general mechanism used by many learning systems in the brain.
rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
Shihao Shen, Juw Won Park, Zhi-xiang Lu, Lan Lin, Michael D. Henry, Ying Nian Wu, Qing Zhou, and Yi Xing
Alternative splicing (AS) is an important mechanism of eukaryotic gene regulation. Deep RNA sequencing (RNA-Seq) has become a powerful approach for quantitative profiling of AS. With the increasing capacity of high-throughput sequencers, it has become common for RNA-Seq studies of AS to examine multiple biological replicates. We developed (pp. E5593–E5601) rMATS, a new statistical method for robust and flexible detection of differential AS from replicate RNA-Seq data. Besides the analysis of unpaired replicates, rMATS includes a model specifically designed for paired replicates, such as case–control matched pairs in clinical RNA-Seq datasets. We expect rMATS will be useful for genome-wide studies of AS in diverse research projects. Our data also provide new insights about the experimental design for RNA-Seq studies of AS.