Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose
Aaron M. Socha, Ramakrishnan Parthasarathi, Jian Shi, Sivakumar Pattathil, Dorian Whyte, Maxime Bergeron, Anthe George, Kim Tran, Vitalie Stavila, Sivasankari Venkatachalam, Michael G. Hahn, Blake A. Simmons, and Seema Singh
Ionic liquids (ILs) have unique properties applicable to a variety of industrial processes. Nearly universal solvating capabilities, low vapor pressures, and high thermal stabilities make these compounds ideal substitutes for a wide range of organic solvents. To date, the best performing ILs are derived from nonrenewable sources such as petroleum or natural gas. Due to their potential for large-scale deployment, ILs derived from inexpensive, renewable reagents are highly desirable. Herein (pp. E3587–E3595), we describe a process for synthesizing ILs from materials derived from lignin and hemicellulose, major components of terrestrial plant biomass. With respect to overall sugar yield, experimental evaluation of these compounds showed that they perform comparably to traditional ILs in biomass pretreatment.
Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers
George H. Perry, Matthieu Foll, Jean-Christophe Grenier, Etienne Patin, Yohann Nédélec, Alain Pacis, Maxime Barakatt, Simon Gravel, Xiang Zhou, Sam L. Nsobya, Laurent Excoffier, Lluis Quintana-Murci, Nathaniel J. Dominy, and Luis B. Barreiro
Tropical rainforest hunter-gatherer populations worldwide share the pygmy phenotype, or small human body size. The evolutionary history of this phenotype is largely unknown. Here (pp. E3596–E3603) we studied DNA from the Batwa, a rainforest hunter-gatherer population from east central Africa, to identify regions of the Batwa genome that underlie the pygmy phenotype. We then performed population genomic analyses to study the evolution of these regions, including comparisons with the Baka, a west central African rainforest hunter-gatherer population. We conclude that the pygmy phenotype likely arose due to positive natural selection and that it arose possibly multiple times within Africa. These results support longstanding anthropological hypotheses that small body size confers an important selective advantage for human rainforest hunter-gatherers.
A unique PDZ domain and arrestin-like fold interaction reveals mechanistic details of endocytic recycling by SNX27-retromer
Matthew Gallon, Thomas Clairfeuille, Florian Steinberg, Caroline Mas, Rajesh Ghai, Richard B. Sessions, Rohan D. Teasdale, Brett M. Collins, and Peter J. Cullen
Cell surface proteins are regulated by a constant cycle of internalization and recycling from intracellular compartments called endosomes. From these organelles, two protein sorting platforms, sorting nexin 27 (SNX27) and the retromer complex, play a critical role in the retrieval of various proteins responsible for ion transport, glucose metabolism, neurotransmission, and other cell functions. Based on the three-dimensional structure of SNX27 in complex with the retromer subunit VPS26, we define the mechanism by which these proteins cooperate to drive endosomal cargo sorting. Retromer and SNX27 dysfunction is implicated in various disorders, including diabetes, Down syndrome, Parkinson disease, and Alzheimer’s disease, and this work (pp. E3604–E3613) provides important insights into the assembly of this essential endosomal sorting machinery.
Molecular architecture of mammalian nitric oxide synthases
Melody G. Campbell, Brian C. Smith, Clinton S. Potter, Bridget Carragher, and Michael A. Marletta
In mammals, NO produced by NOS acts as a signaling molecule in the nervous and cardiovascular systems and as a cytotoxin in the immune system’s response to infection. Although structures of smaller portions of NOS have been solved, the structures of the entire NOS homodimer have remained elusive. In this study, we use single-particle EM to directly visualize the 3D structures, domain organization, and conformations accessed by all three mammalian NOSs. The observed conformational changes (pp. E3614–E3623) provide insight into the mechanisms through which calmodulin binding results in efficient NO formation.
Direct measurement of the dielectric polarization properties of DNA
Ana Cuervo, Pablo D. Dans, José L. Carrascosa, Modesto Orozco, Gabriel Gomila, and Laura Fumagalli
The strength of DNA–DNA and DNA–ligand electrostatic interactions crucially depends on the electric polarizability of DNA, represented by its dielectric constant. This has remained unknown owing to the lack of experimental techniques able to measure it. Here (pp. E3624–E3630), we experimentally determined the dielectric constant of double-stranded DNA in a native condensed state inside a single bacteriophage as well as the dielectric constants of the protein shell and tail that compose the viral capsid using scanning force microscopy. We supported the experimental data by theoretically determining the DNA dielectric constant using atomistic simulations. Both approaches yield a dielectric constant of DNA around 8, sensibly higher than commonly assumed, thus revealing a DNA intrinsic property essential for realistic computational description of DNA.
Loss of Miro1-directed mitochondrial movement results in a novel murine model for neuron disease
Tammy T. Nguyen, Sang S. Oh, David Weaver, Agnieszka Lewandowska, Dane Maxfield, Max-Hinderk Schuler, Nathan K. Smith, Jane Macfarlane, Gerald Saunders, Cheryl A. Palmer, Valentina Debattisti, Takumi Koshiba, Stefan Pulst, Eva L. Feldman, György Hajnóczky, and Janet M. Shaw
This report (pp. E3631–E3640) probes the physiological roles of mammalian mitochondrial Rho 1 (Miro1), a calcium-binding, membrane-anchored GTPase necessary for mitochondrial motility on microtubules. Using two new mouse models and primary cells, the study demonstrates a specific role for Miro1 in upper motor neuron development and retrograde transport of axonal mitochondria. Unexpectedly, Miro1 is not essential for calcium-regulated mitochondrial movement, mitochondrial-mediated calcium buffering, or maintenance of mitochondrial respiratory activity. Nevertheless, a neuron-specific Miro1 KO mouse model displays physical hallmarks of neurological disease in the brainstem and spinal cord and develops rapidly progressing upper motor neuron disease symptoms culminating in death after approximately 4 wk. These studies demonstrate that defects in mitochondrial motility and distribution alone are sufficient to cause neurological disease.
IL-6/STAT3 promotes regeneration of airway ciliated cells from basal stem cells
Tomomi Tadokoro, Yang Wang, Larry S. Barak, Yushi Bai, Scott H. Randell, and Brigid L. M. Hogan
The airways of the lungs are lined by ciliated and secretory epithelial cells important for mucociliary clearance. When these cells are damaged or lost, they are replaced by the differentiation of basal stem cells. Little is known about how this repair is orchestrated by signaling pathways in the epithelium and underlying stroma. We present evidence (pp. E3641–E3649) using cultured airway cells and genetic manipulation of a mouse model of airway repair that the cytokine IL-6 promotes the differentiation of ciliated vs. secretory cells. This process involves direct Stat3 regulation of genes controlling both cell fate (Notch1) and the differentiation of multiciliated cells (Multicilin and forkhead box protein J1). Moreover, the major producer of IL-6 appears to be mesenchymal cells in the stroma rather than immune cells.
Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria
Joakim Palovaara, Neelam Akram, Federico Baltar, Carina Bunse, Jeremy Forsberg, Carlos Pedrós-Alió, José M. González, and Jarone Pinhassi
Bacteria control biogeochemical cycles of elements and fluxes of energy in the ocean. Discovery of a membrane photoprotein widespread in marine bacteria—proteorhodopsin—expanded their potential importance for global energy budgets, providing a novel mechanism to harness light energy. Yet, how proteorhodopsin-derived energy is used for cell metabolism remains largely unexplored. We combined experiments in a model marine bacterium with gene expression analyses (pp. E3650–E3658). Light-stimulated growth coincided with a shift in carbon acquisition pathways, with anaplerotic CO2 fixation providing up to one-third of the cell carbon. Exposure to light resulted in the up-regulation of several central metabolism genes, including the glyoxylate shunt. Thus, light provides proteorhodopsin-containing bacteria with wider means to adapt to environmental variability than previously recognized.
A critical appraisal of the use of microRNA data in phylogenetics
Robert C. Thomson, David C. Plachetzki, D. Luke Mahler, and Brian R. Moore
As progress toward a highly resolved tree of life continues, evolutionary relationships that defy resolution continue to be identified. Recently, the presence/absence of microRNA families has emerged as a potentially ideal source of information to resolve these difficult phylogenetic problems, and these data have been used to address several long-standing problems in the metazoan phylogeny. To our knowledge, this study (pp. E3659–E3668) performs the first rigorous statistical assessment of the phylogenetic utility of microRNAs and finds that a high incidence of homoplasy and sampling error renders published phylogenies based on microRNA data highly biased or uncertain. This study casts serious doubt on the central phylogenetic conclusions of several previous analyses of microRNA datasets.
Mannan induces ROS-regulated, IL-17A–dependent psoriasis arthritis-like disease in mice
Ia Khmaladze, Tiina Kelkka, Simon Guerard, Kajsa Wing, Angela Pizzolla, Amit Saxena, Katarina Lundqvist, Meirav Holmdahl, Kutty Selva Nandakumar, and Rikard Holmdahl
We identified a previously undescribed disease mechanism for psoriasis (Ps) and psoriasis arthritis (PsA)-like disease by developing a new mouse model having characteristic features similar to those of Ps and PsA in human patients (pp. E3669–E3678). Mannan-induced activation of tissue macrophages triggers IL-17A secretion from γδ T cells, causing Ps-like inflammation. Such inflammation was significantly increased under a reduced oxidative environment. Increased frequency of monocytes/macrophages, depletion experiments, and the disease suppressor function of macrophage-derived reactive oxygen species clearly argue in favor of a role for monocytes/macrophages in this disease model, which is in accordance with the findings in patients with the psoriatic form of skin lesions and arthritis. This novel PsA model could be immensely useful to test new therapeutics for patients with Ps and PsA.
A sharp T-cell antigen receptor signaling threshold for T-cell proliferation
Byron B. Au-Yeung, Julie Zikherman, James L. Mueller, Judith F. Ashouri, Mehrdad Matloubian, Debra A. Cheng, Yiling Chen, Kevan M. Shokat, and Arthur Weiss
Biochemical signals triggered by the T-cell receptor (TCR) are required for stimulating T cells and can be initiated within seconds. However, a hallmark of T-cell activation, cell division, occurs hours after TCR signaling has begun, implying that T cells require a minimum duration and/or accumulate TCR signaling events to drive proliferation. To visualize the accumulated signaling experienced by T cells, we used a fluorescent reporter gene that is activated by TCR stimulation. This technique (pp. E3679–E3688) showed a threshold between dividing and nondividing T cells for TCR signaling that does not change with stronger or weaker TCR signaling or the presence of growth factor. Together these data may have implications for the development of T-cell–targeted therapies for autoimmunity.
The role of PI3K/AKT-related PIP5K1α and the discovery of its selective inhibitor for treatment of advanced prostate cancer
Julius Semenas, Andreas Hedblom, Regina R. Miftakhova, Martuza Sarwar, Rikard Larsson, Liliya Shcherbina, Martin E. Johansson, Pirkko Härkönen, Olov Sterner, and Jenny L. Persson
Prostate cancer is the most common malignancy and the third leading cancer-related cause of death among men of the Western world. Treatment options at advanced stages of the disease are scarce, and better therapies are in urgent need. In our study (pp. E3689–E3698), we show that the clinically relevant lipid kinase phosphatidylinositol-4-phosphate 5-kinase-α (PIP5Kα) plays an important role in cancer cell invasion and survival by regulating the PI3K/AKT/androgen receptor pathways. Elevated levels of PIP5K1α contribute to cancer cell proliferation, survival, and invasion. In this context we introduce a newly developed compound, ISA-2011B, with promising anticancer effects by inhibiting the PIP5K1α-associated AKT pathways. Conclusively, we propose that PIP5K1α may be used as a potential therapeutic target for treatment of advanced prostate cancer.
TIM-family proteins inhibit HIV-1 release
Minghua Li, Sherimay D. Ablan, Chunhui Miao, Yi-Min Zheng, Matthew S. Fuller, Paul D. Rennert, Wendy Maury, Marc C. Johnson, Eric O. Freed, and Shan-Lu Liu
TIM-family proteins have been recently shown to promote viral entry into host cells. Unexpectedly, we discovered that human TIM-1, along with TIM-3 and TIM-4, potently inhibits HIV-1 release. We showed that TIM-1 is incorporated into HIV-1 virions and retains HIV-1 particles on the plasma membrane via phosphatidylserine (PS), a phospholipid that is exposed on the cellular plasma membrane and the viral envelope. Expression of TIM-1 inhibits HIV-1 replication in CD4+ T cells, and knockdown of TIM-3 in monocyte-derived macrophages enhances HIV-1 production. We extended this function of TIMs to other PS receptors, and demonstrated (pp. E3699–E3707) that they also inhibited release of additional viruses, including murine leukemia virus and Ebola virus. The novel role of TIMs in blocking viral release provides new insights into viral replication and AIDS pathogenesis.
Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes
Meiling Zhang, Jonathan R. Chekan, Dylan Dodd, Pei-Ying Hong, Lauren Radlinski, Vanessa Revindran, Satish K. Nair, Roderick I. Mackie, and Isaac Cann
Fermentation of dietary fiber in the lower gut of humans is a critical process for the function and integrity of both the bacterial community and host cells. Here we demonstrate (pp. E3708–E3717) that two human gut commensal Bacteroides are equipped with unique enzymes that allow degradation of xylan, a common hemicellulose in human diets. Furthermore, we identify a novel carbohydrate-binding module (CBM) family that disrupts the catalytic domain of a glycoside hydrolase 10 (GH10) endoxylanase and facilitates the hydrolytic activity of the enzyme. The conservation of the unique modular architecture of the GH10 endoxylanase in the genomes of diverse Bacteroidetes suggests a critical role in fiber digestion in this phylum.
Reconstruction and minimal gene requirements for the alternative iron-only nitrogenase in Escherichia coli
Jianguo Yang, Xiaqing Xie, Xia Wang, Ray Dixon, and Yi-Ping Wang
To date, three different nitrogenase systems [molybdenum (MoFe), vanadium (VFe), and iron-only (FeFe)] have been found in nature. The MoFe nitrogenase has been studied extensively, but the alternative vanadium-dependent (Vnf) and iron-only (Anf) systems are less well characterized, particularly with respect to components required for their biosynthesis and activity. We have engineered an artificial FeFe nitrogenase system in Escherichia coli that combines anf structural genes with accessory nitrogen fixation genes (nif) to provide a minimal 10-gene cluster that supports the biosynthesis and activity of the FeFe nitrogenase. Our findings (pp. E3718–E3725) underscore the potential for the future engineering of nitrogen fixation in eukaryotes because the Anf system can bypass limitations in molybdenum availability in plant organelles.
The human dynamic clamp as a paradigm for social interaction
Guillaume Dumas, Gonzalo C. de Guzman, Emmanuelle Tognoli, and J. A. Scott Kelso
The human dynamic clamp (HDC) is proposed as a general paradigm for studies of elementary forms of social behavior in complex biological systems. HDC enables parametric control of real-time bidirectional interaction between humans and empirically grounded theoretical models of coordination dynamics. It thus provides necessary experimental access for laboratory investigations, while preserving the reciprocity and open boundary conditions inherent in daily life social interactions. As proof of concept, different implementations are illustrated (pp. E3726–E3734), ranging from coordination of rhythmic and discrete movements to adaptive and directed behaviors. The HDC may be a powerful tool for blending theory and experiment at different levels of description, from neuronal populations to cognition and social behavior.
Narcolepsy patients have antibodies that stain distinct cell populations in rat brain and influence sleep patterns
Peter Bergman, Csaba Adori, Szilvia Vas, Ylva Kai-Larsen, Tomi Sarkanen, Andreas Cederlund, Birgitta Agerberth, Ilkka Julkunen, Beata Horvath, Diana Kostyalik, Lajos Kalmár, Gyorgy Bagdy, Anne Huutoniemi, Markku Partinen, and Tomas Hökfelt
Narcolepsy is a chronic sleep disease with autoimmune origin. We explored occurrence of autoantibodies in narcolepsy and other sleep-related disorders (OSRDs) by screening human sera with immunohistochemistry on rat brains (pp. E3735–E3744). Hypocretin/orexinergic neurons were not stained, but a prominent immunostaining pattern of hypothalamic melanin-concentrating hormone (MCH) and proopiomelanocortin (POMC) neurons was overrepresented in cases of narcolepsy and OSRD patients. The autoantigen was identified as the common C-terminal epitope of neuropeptide glutamic acid-isoleucine/α–melanocyte-stimulating hormone (NEI/αMSH). Purified IgGs from a patient with MCH/POMC staining injected intracerebroventricularly to rats caused disturbed sleep patterns. Also, GABAergic cortical interneurons were stained with other narcolepsy and OSRD sera. Thus, autoantibodies are frequent in patients with sleep disorders, and NEI/αMSH may be a previously unidentified autoantigen involved in pathomechanism(s). These findings indicate possible diagnostic/therapeutic targets.
Hampered long-term depression and thin spine loss in the nucleus accumbens of ethanol-dependent rats
Saturnino Spiga, Giuseppe Talani, Giovanna Mulas, Valentina Licheri, Giulia R. Fois, Giulia Muggironi, Nicola Masala, Carla Cannizzaro, Giovanni Biggio, Enrico Sanna, and Marco Diana
This paper examines the intimate neuroarchitecture of the nucleus accumbens shell region and how it affects synaptic plasticity in alcohol-dependent rats. To do so, a simultaneous morphometrical/immunofluorescence method was applied to visualize various types of dendritic spines and patch-clamp techniques to detect changes in synaptic currents. Using these tools, we show (pp. E3745–E3754) a selective loss of “long thin” spines accompanied by an impaired long-term depression (LTD) in alcohol-dependent rats. Dopaminergic and glutamatergic signaling are similarly altered. The results highlight the role of long thin dendritic spines in the genesis of LTD in alcohol dependence.