Structural switch of lysyl-tRNA synthetase between translation and transcription.

Lysyl-tRNA synthetase (LysRS), a component of the translation apparatus, is released from the cytoplasmic multi-tRNA synthetase complex (MSC) to activate the transcription factor MITF in stimulated mast cells through undefined mechanisms. Here we show that Ser207 phosphorylation provokes a new conformer of LysRS that inactivates its translational function but activates its transcriptional function. The crystal structure of an MSC subcomplex established that LysRS is held in the MSC by binding to the N terminus of the scaffold protein p38/AIMP2. Phosphorylation-created steric clashes at the LysRS domain interface disrupt its binding grooves for p38/AIMP2, releasing LysRS and provoking its nuclear translocation. This alteration also exposes the C-terminal domain of LysRS to bind to MITF and triggers LysRS-directed production of the second messenger Ap(4)A that activates MITF. Thus our results establish that a single conformational change triggered by phosphorylation leads to multiple effects driving an exclusive switch of LysRS function from translation to transcription.

Role of RanBP9 on amyloidogenic processing of APP and synaptic protein levels in the mouse brain.

We previously reported that RanBP9 binds low-density lipoprotein receptor-related protein (LRP), amyloid precursor protein (APP), and BACE1 and robustly increased Aß generation in a variety of cell lines and primary neuronal cultures. To confirm the physiological/ pathological significance of this phenotype in vivo, we successfully generated transgenic mice overexpressing RanBP9 as well as RanBP9-null mice. Here we show that RanBP9 overexpression resulted in >2-fold increase in Aß40 levels as early as 4 mo of age. A sustained increase in Aß40 levels was seen at 12 mo of age in both CHAPS-soluble and formic acid (FA)-soluble brain fractions. In addition, Aß42 levels were also significantly increased in FA-soluble fractions at 12 mo of age. More important, increased Aß levels were translated to increased deposition of amyloid plaques. In addition, RanBP9 overexpression significantly decreased the levels of synaptophysin and PSD-95 proteins. Conversely, RanBP9-null mice showed increased levels of synaptophysin, PSD-95, and drebrin A protein levels. Given that loss of synapses is the best pathological correlate of cognitive deficits in Alzheimer's disease (AD), increased Aß levels by RanBP9 observed in the present study provides compelling evidence that RanBP9 may indeed play a key role in the etiology of AD. If so, RanBP9 provides a great opportunity to develop novel therapy for AD.

A unique hyperdynamic dimer interface permits small molecule perturbation of the melanoma oncoprotein MITF for melanoma therapy.

Microphthalmia transcription factor (MITF) regulates melanocyte development and is the "lineage-specific survival" oncogene of melanoma. MITF is essential for melanoma initiation, progression, and relapse and has been considered an important therapeutic target; however, direct inhibition of MITF through small molecules is considered impossible, due to the absence of a ligand-binding pocket for drug design. Here, our structural analyses show that the structure of MITF is hyperdynamic because of its out-of-register leucine zipper with a 3-residue insertion. The dynamic MITF is highly vulnerable to dimer-disrupting mutations, as we observed that MITF loss-of-function mutations in human Waardenburg syndrome type 2 A are frequently located on the dimer interface and disrupt the dimer forming ability accordingly. These observations suggest a unique opportunity to inhibit MITF with small molecules capable of disrupting the MITF dimer. From a high throughput screening against 654,650 compounds, we discovered compound TT-012, which specifically binds to dynamic MITF and destroys the latter's dimer formation and DNA-binding ability. Using chromatin immunoprecipitation assay and RNA sequencing, we showed that TT-012 inhibits the transcriptional activity of MITF in B16F10 melanoma cells. In addition, TT-012 inhibits the growth of high-MITF melanoma cells, and inhibits the tumor growth and metastasis with tolerable toxicity to liver and immune cells in animal models. Together, this study demonstrates a unique hyperdynamic dimer interface in melanoma oncoprotein MITF, and reveals a novel approach to therapeutically suppress MITF activity.

High-speed metamagnetic switching of FeRh through Joule heating.

Due to its proximity to room temperature and demonstrated high degree of temperature tunability, FeRh's metamagnetic ordering transition is attractive for novel high-performance computing devices seeking to use magnetism as the state variable. We demonstrate electrical control of the antiferromagnetic-to-ferromagnetic transition via Joule heating in FeRh wires. The magnetic transition of FeRh is accompanied by a change in resistivity, which can be probed electrically and allows for integration into switching devices. Finite element simulations based on abrupt state transition within each domain result in a globally smooth transition that agrees with the experimental findings and provides insight into the thermodynamics involved. We measure a 150 K decrease in transition temperature with currents up to 60 mA, limited only by the dimensions of the device. The sizeable shift in transition temperature scales with current density and wire length, suggesting the absolute resistance and heat dissipation of the substrate are also important. The FeRh phase change is evaluated by pulsed I-V using a variety of bias conditions. We demonstrate high speed (~ ns) memristor-like behavior and report device performance parameters such as switching speed and power consumption that compare favorably with state-of-the-art phase change memristive technologies.

Idiopathic Constrictive Bronchiolitis in an Active Duty Soldier.

Constrictive bronchiolitis is characterized by fibroproliferative thickening of the bronchiolar walls causing narrowing of the bronchiolar lumen, which may progress to the complete obliteration of bronchioles, resulting in progressive dyspnea and ultimately respiratory failure. Active duty service members returning from deployment with toxic exposures such as "burn pits" are known to be at risk for this condition. Other proposed etiologies for this condition include inhalation (nitrogen oxides, ammonia, welding fumes, aerosols [nicotine, diacetyl, and vitamin E acetate]), infection (respiratory syncytial virus, adenovirus, or Mycoplasma pneumoniae), rheumatic diseases, and graft-versus-host disease (lung or hematopoietic cell transplantation). Uncommonly, constrictive bronchiolitis can also be idiopathic. Here we present a case of a young active duty soldier with idiopathic constrictive bronchiolitis without any known risk factors for this disease. The goal of this case presentation is to help the military physician better understand this condition, including identification of this disease process, underlying etiologies, risk factors, and treatments available.

Direct-Write of Nanoscale Domains with Tunable Metamagnetic Order in FeRh Thin Films.

We have directly written nanoscale patterns of magnetic ordering in FeRh films using focused helium-ion beam irradiation. By varying the dose, we pattern arrays with metamagnetic transition temperatures that range from the as-grown film temperature to below room temperature. We employ transmission electron microscopy, X-ray diffraction, and temperature-dependent transport measurements to characterize the as-grown film, and magneto-optic Kerr effect imaging to quantify the He+ irradiation-induced changes to the magnetic order. Moreover, we demonstrate temperature-dependent optical microscopy and conductive atomic force microscopy as indirect probes of the metamagnetic transition that are sensitive to the differences in dielectric properties and electrical conductivity, respectively, of FeRh in the antiferromagnetic (AF) and ferromagnetic (FM) states. Using density functional theory, we quantify strain- and defect-induced changes in spin-flip energy to understand their influence on the metamagnetic transition temperature. This work holds promise for in-plane AF-FM spintronic devices, by reducing the need for multiple patterning steps or different materials, and potentially eliminating interfacial polarization losses due to cross material interfacial spin scattering.

Probabilistic risk analysis and terrorism risk.

Since the terrorist attacks of September 11, 2001, and the subsequent establishment of the U.S. Department of Homeland Security (DHS), considerable efforts have been made to estimate the risks of terrorism and the cost effectiveness of security policies to reduce these risks. DHS, industry, and the academic risk analysis communities have all invested heavily in the development of tools and approaches that can assist decisionmakers in effectively allocating limited resources across the vast array of potential investments that could mitigate risks from terrorism and other threats to the homeland. Decisionmakers demand models, analyses, and decision support that are useful for this task and based on the state of the art. Since terrorism risk analysis is new, no single method is likely to meet this challenge. In this article we explore a number of existing and potential approaches for terrorism risk analysis, focusing particularly on recent discussions regarding the applicability of probabilistic and decision analytic approaches to bioterrorism risks and the Bioterrorism Risk Assessment methodology used by the DHS and criticized by the National Academies and others.

Hydrostatic pressure mapping of barium titanate phase transitions with quenched FeRh.

We report a pressure study of the metamagnetic/ferroelectric hybrid heterostructure of a quenched FeRh thin film (25 nm) grown on single crystal barium titanate (BTO). It has been previously reported that when the BTO undergoes a crystal transition a massive magnetization and coercivity change is triggered in the highly strain sensitive quenched FeRh thin film. Therefore quenched FeRh makes for an ideal probe for mapping a materials structural phase transitions. In this work we demonstrate this effect as a function of both temperature and hydrostatic pressure. As a result, we present the pressure dependence of the hybrid material which aligns identically with the BTO substrates pressure dependence reported in literature. The concept of combining a structural phase transitional (SPT) material with a magnetostrictive magnetic metal has been shown with vanadium oxides and our findings here prove that this methodology can be extended to strain sensitive metamagnetic materials systems in thin film, and possibly in bulk, heterostructures.

Lymphopenia and spontaneous autorosette formation in SOD1 mouse model of ALS.

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder characterized by motoneuron degeneration. Increasing evidence suggests immune system involvement in ALS pathogenesis but information about peripheral blood characteristics has been lacking. We evaluated hematological and morphological parameters in peripheral blood of G93A SOD1 mice. A significant decrease in white blood cells was found at the end stage of disease. The lymphocyte reduction may suggest immunodeficiency in ALS. Spontaneously forming rosettes with autologous erythrocytes were noted in approximately 28% of lymphocytes in SOD1 mice. To our knowledge, this is the first study characterizing hematology and revealing autorosettes in the SOD1 mouse model of ALS at the terminal phase of disease.

3MATRIX and 3MOTIF: a protein structure visualization system for conserved sequence motifs.

Computational methods such as sequence alignment and motif construction are useful in grouping related proteins into families, as well as helping to annotate new proteins of unknown function. These methods identify conserved amino acids in protein sequences, but cannot determine the specific functional or structural roles of conserved amino acids without additional study. In this work, we present 3MATRIX (http://3matrix.stanford.edu) and 3MOTIF (http://3motif.stanford.edu), a web-based sequence motif visualization system that displays sequence motif information in its appropriate three-dimensional (3D) context. This system is flexible in that users can enter sequences, keywords, structures or sequence motifs to generate visualizations. In 3MOTIF, users can search using discrete sequence motifs such as PROSITE patterns, eMOTIFs, or any other regular expression-like motif. Similarly, 3MATRIX accepts an eMATRIX position-specific scoring matrix, or will convert a multiple sequence alignment block into an eMATRIX for visualization. Each query motif is used to search the protein structure database for matches, in which the motif is then visually highlighted in three dimensions. Important properties of motifs such as sequence conservation and solvent accessible surface area are also displayed in the visualizations, using carefully chosen color shading schemes.

GM-CSF upregulated in rheumatoid arthritis reverses cognitive impairment and amyloidosis in Alzheimer mice.

Rheumatoid arthritis (RA) is a negative risk factor for the development of Alzheimer's disease (AD). While it has been commonly assumed that RA patients' usage of non-steroidal anti-inflammatory drugs (NSAIDs) helped prevent onset and progression of AD, NSAID clinical trials have proven unsuccessful in AD patients. To determine whether intrinsic factors within RA pathogenesis itself may underlie RA's protective effect, we investigated the activity of colony-stimulating factors, upregulated in RA, on the pathology and behavior of transgenic AD mice. 5 microg bolus injections of macrophage, granulocyte, and granulocyte-macrophage colony-stimulating factors (M-CSF, G-CSF, or GM-CSF) were administered unilaterally into the hippocampus of aged cognitively-impaired AD mice and the resulting amyloid load reductions determined one week later, using the artificial cerebrospinal fluid-injected contralateral sides as controls. G-CSF and more significantly, GM-CSF reduced amyloidosis throughout the treated brain hemisphere one week following bolus administration to AD mice. 20 daily subcutaneous injections of 5 microg of GM-CSF (the most amyloid-reducing CSF in the bolus experiment) were administered to balanced cohorts of AD mice after assessment in a battery of cognitive tests. Reductions in amyloid load and improvements in cognitive function were assessed. Subcutaneous GM-CSF administration significantly reduced brain amyloidosis and completely reversed the cognitive impairment, while increasing hippocampal synaptic area and microglial density. These findings, along with two decades of accrued safety data using Leukine, recombinant human GMCSF, in elderly leukopenic patients, suggest that Leukine should be tested as a treatment to reverse cerebral amyloid pathology and cognitive impairment in AD.

A novel technique for simultaneous bilateral brain infusions in a mouse model of neurodegenerative disease.

A common problem faced by researchers using transgenic models to study disease is the phenotypic variability that exists within a group or colony of animals. Significant pathological analyses thus often require large numbers of mice to perform. Many lines of transgenic mice harboring the gene for human amyloid precursor protein (APP) with different mutations causing familial Alzheimer's disease have been developed over the past decade to study plaque deposition and other aspects of AD. However, variations in size, density, plaque number, and total amyloid load between animals of the same age and genotype have been identified by our lab and others. Therefore, to study the effects of compounds on amyloid pathology, it was imperative to develop a technique that would allow each brain hemisphere to receive different infusions. We have developed catheters that facilitate simultaneous bilateral infusion in mouse brains, thereby using the contralateral hemisphere of the same animal as an internal control while studying, for example, the effect of compounds on amyloid plaques, a pathological hallmark of the progression of Alzheimer's disease (AD). Several molecules have been identified within the plaques including the major component, the Abeta peptide, and two inflammation-related proteins, apolipoprotein E (apoE) and the serine protease inhibitor alpha-1-antichymotrypsin (ACT). In these experiments, ACT was infused unilaterally over a period of 28 days into the parenchyma and lateral ventricles of PS/APP mice and observed to associate with amyloid plaques, with minimal mortality. Utilizing the ACT/Abeta interaction, details of this procedure are discussed here in detail.

Evidence of compromised blood-spinal cord barrier in early and late symptomatic SOD1 mice modeling ALS.

BACKGROUND: The blood-brain barrier (BBB), blood-spinal cord barrier (BSCB), and blood-cerebrospinal fluid barrier (BCSFB) control cerebral/spinal cord homeostasis by selective transport of molecules and cells from the systemic compartment. In the spinal cord and brain of both ALS patients and animal models, infiltration of T-cell lymphocytes, monocyte-derived macrophages and dendritic cells, and IgG deposits have been observed that may have a critical role in motor neuron damage. Additionally, increased levels of albumin and IgG have been found in the cerebrospinal fluid in ALS patients. These findings suggest altered barrier permeability in ALS. Recently, we showed disruption of the BBB and BSCB in areas of motor neuron degeneration in the brain and spinal cord in G93A SOD1 mice modeling ALS at both early and late stages of disease using electron microscopy. Examination of capillary ultrastructure revealed endothelial cell degeneration, which, along with astrocyte alteration, compromised the BBB and BSCB. However, the effect of these alterations upon barrier function in ALS is still unclear. The aim of this study was to determine the functional competence of the BSCB in G93A mice at different stages of disease. METHODOLOGY/PRINCIPAL FINDINGS: Evans Blue (EB) dye was intravenously injected into ALS mice at early or late stage disease. Vascular leakage and the condition of basement membranes, endothelial cells, and astrocytes were investigated in cervical and lumbar spinal cords using immunohistochemistry. Results showed EB leakage in spinal cord microvessels from all G93A mice, indicating dysfunction in endothelia and basement membranes and confirming our previous ultrastructural findings on BSCB disruption. Additionally, downregulation of Glut-1 and CD146 expressions in the endothelial cells of the BSCB were found which may relate to vascular leakage. CONCLUSIONS/SIGNIFICANCE: Results suggest that the BSCB is compromised in areas of motor neuron degeneration in ALS mice at both early and late stages of the disease.

3MOTIF: visualizing conserved protein sequence motifs in the protein structure database.

SUMMARY: 3MOTIF is a web application that visually maps conserved sequence motifs onto three-dimensional protein structures in the Protein Data Bank (PDB; Berman et al., Nucleic Acids Res., 28, 235-242, 2000). Important properties of motifs such as conservation strength and solvent accessible surface area at each position are visually represented on the structure using a variety of color shading schemes. Users can manipulate the displayed motifs using the freely available Chime plugin. AVAILABILITY: http://motif.stanford.edu/3motif/