Mutations in the Arabidopsis Peroxisomal ABC Transporter COMATOSE Allow Differentiation between Multiple Functions In Planta: Insights from an Allelic Series

COMATOSE (CTS), the Arabidopsis homologue of human Adrenoleukodystrophy protein (ALDP), is required for import of substrates for peroxisomal β-oxidation. A new allelic series and a homology model based on the bacterial ABC transporter, Sav1866, provide novel insights into structure-function relations of ABC subfamily D proteins. In contrast to ALDP, where the majority of mutations result in protein absence from the peroxisomal membrane, all CTS mutants produced stable protein. Mutation of conserved residues in the Walker A and B motifs in CTS nucleotide-binding domain (NBD) 1 resulted in a null phenotype but had little effect in NBD2, indicating that the NBDs are functionally distinct in vivo. Two alleles containing mutations in NBD1 outside the Walker motifs (E617K and C631Y) exhibited resistance to auxin precursors 2,4-dichlorophenoxybutyric acid (2,4-DB) and indole butyric acid (IBA) but were wild type in all other tests. The homology model predicted that the transmission interfaces are domain-swapped in CTS, and the differential effects of mutations in the conserved "EAA motif" of coupling helix 2 supported this prediction, consistent with distinct roles for each NBD. Our findings demonstrate that CTS functions can be separated by mutagenesis and the structural model provides a framework for interpretation of phenotypic data

Microarray analyses demonstrate the involvement of type i interferons in psoriasiform pathology development in D6-deficient mice

The inflammatory response is normally limited by mechanisms regulating its resolution. In the absence of resolution, inflammatory pathologies can emerge, resulting in substantial morbidity and mortality. We have been studying the D6 chemokine scavenging receptor, which played an indispensable role in the resolution phase of inflammatory responses and does so by facilitating removal of inflammatory CC chemokines. In D6-deficient mice, otherwise innocuous cutaneous inflammatory stimuli induce a grossly exaggerated inflammatory response that bears many similarities to human psoriasis. In the present study, we have used transcriptomic approaches to define the molecular make up of this response. The data presented highlight potential roles for a number of cytokines in initiating and maintaining the psoriasis-like pathology. Most compellingly, we provide data indicating a key role for the type I interferon pathway in the emergence of this pathology. Neutralizing antibodies to type I interferons are able to ameliorate the psoriasis-like pathology, confirming a role in its development. Comparison of transcriptional data generated from this mouse model with equivalent data obtained from human psoriasis further demonstrates the strong similarities between the experimental and clinical systems. As such, the transcriptional data obtained in this preclinical model provide insights into the cytokine network active in exaggerated inflammatory responses and offer an excellent tool to evaluate the efficacy of compounds designed to therapeutically interfere with inflammatory processes

Genetic Assimilation and Canalisation in the Baldwin Effect

The Baldwin Effect indicates that individually learned behaviours acquired during an organism’s lifetime can influence the evolutionary path taken by a population, without any direct Lamarckian transfer of traits from phenotype to genotype. Several computational studies modelling this effect have included complications that restrict its applicability. Here we present a simplified model that is used to reveal the essential mechanisms and highlight several conceptual issues that have not been clearly defined in prior literature. In particular, we suggest that canalisation and genetic assimilation, often conflated in previous studies, are separate concepts and the former is actually not required for non-heritable phenotypic variation to guide genetic variation. Additionally, learning, often considered to be essential for the Baldwin Effect, can be replaced with a more general phenotypic plasticity model. These simplifications potentially permit the Baldwin Effect to operate in much more general circumstances

Fabrication of Diamond Nanowires for Quantum Information Processing Applications

We present a design and a top-down fabrication method for realizing diamond nanowires in both bulk single crystal and polycrystalline diamond. Numerical modeling was used to study coupling between a Nitrogen Vacancy (NV) color center and optical modes of a nanowire, and to find an optimal range of nanowire diameters that allows for large collection efficiency of emitted photons. Inductively coupled plasma (ICP) reactive ion etching (RIE) with oxygen is used to fabricate the nanowires. Drop-casted nanoparticles (including $\mathrm{Au}$, $\mathrm{SiO_{2}}$ and $\mathrm{Al_2O_3}$) as well as electron beam lithography defined spin-on glass and evaporated $\mathrm{Au}$ have been used as an etch mask. We found $\mathrm{Al_2O_3}$ nanoparticles to be the most etch resistant. At the same time FOx e-beam resist (spin-on glass) proved to be a suitable etch mask for fabrication of ordered arrays of diamond nanowires. We were able to obtain nanowires with near vertical sidewalls in both polycrystalline and single crystal diamond. The heights and diameters of the polycrystalline nanowires presented in this paper are \unit[\approx1]{\mu m} and \unit[120-340]{nm}, respectively, having a \unit[200]{nm/min} etch rate. In the case of single crystal diamond (types Ib and IIa) nanowires the height and diameter for different diamonds and masks shown in this paper were \unit[1-2.4]{\mu m} and \unit[120-490]{nm} with etch rates between \unit[190-240]{nm/min}.Comment: 11 pages, 26 figures, submitted to Diamond and related Materials; http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TWV-4Y7MM1M-1&_user=10&_coverDate=01%2F25%2F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=6dc58b30f4773a710c667306fc541cc

Production of Gas-Solid Structures in Aluminum and Nickel Alloys by Gasar Processing

Experimental data on directional and bulk solidification of hydrogen-charged samples of aluminum alloy A356 and nickel alloy Inconel 718 are discussed. The solidification structure of the porous zone is shown to be dependent on many process variables. Of these variables, hydrogen content in the melt prior to solidification, and furnace atmospheric pressure during solidification play the decisive role. Also important are the furnace atmosphere composition, the solidification velocity, and the temperature distribution of the liquid metal inside the mold

Activation and repression of mammalian gene expression by the c-myc protein.

One mechanism by which nuclear-localized oncogenes might transform cells is through an ability to regulate gene expression. We show that the c-myc protein stimulates the level of appropriately initiated expression from the human heat shock protein 70 (hsp70) promoter. Sequences required for full activation lie upstream of the transcription initiation site and are distinct from sequences necessary for basal expression. These sequences also appear distinct from promoter sequences necessary for heat induction, serum induction, and induction by the papovavirus T antigens. The c-myc protein inhibits appropriately initiated expression from the mouse metallothionein I (MT-I) promoter. A mutation that removes 138 amino acids of exon 2 produces a c-myc gene product that is capable of activating the hsp70 promoter but is no longer capable of inhibiting MT-I expression, suggesting that these two properties reside in different domains of the c-myc protein. Expression from the adenovirus EII promoter is slightly inhibited, while expression from the SV40 early promoter is minimally affected by the c-myc protein. Both the spectrum of promoters regulated by the c-myc protein and the sequence requirements for that regulation differ from those of previously characterized viral trans-activating proteins. The data suggest that the c-myc protein can both stimulate and inhibit transcription from mammalian promoters in a novel manner

Targeting the Canonical Nuclear Factor-κB Pathway with a High-Potency IKK2 Inhibitor Improves Outcomes in a Mouse Model of Idiopathic Pneumonia Syndrome

Idiopathic pneumonia syndrome (IPS) is a noninfectious inflammatory disorder of the lungs that occurs most often after fully myeloablative allogeneic hematopoietic stem cell transplantation (HSCT). IPS can be severe and is associated with high 1-year mortality rates despite existing therapies. The canonical nuclear factor-(NF) κB signaling pathway has previously been linked to several inflammatory disorders of the lung, including asthma and lung allograft rejection. It has never been specifically targeted as a novel IPS treatment approach, however. Here, we report that the IκB kinase 2 (IKK2) antagonist BAY 65-5811 or “compound A,” a highly potent and specific inhibitor of the NF-κB pathway, was able to improve median survival times and recipient oxygenation in a well-described mouse model of IPS. Compound A impaired the production of the proinflammatory chemokines CCL2 and CCL5 within the host lung after transplantation. This resulted in significantly lower numbers of donor lung infiltrating CD4+ and CD8+ T cells and reduced pulmonary inflammatory cytokine production after allograft. Compound A's beneficial effects appeared to be specific for limiting pulmonary injury, as the drug was unable to improve outcomes in a B6 into B6D2 haplotype-matched murine HSCT model in which recipient mice succumb to lethal acute graft-versus-host disease of the gastrointestinal tract. Collectively, our data suggest that the targeting of the canonical NF-κB pathway with a small molecule IKK2 antagonist may represent an effective and novel therapy for the specific management of acute lung injury that can occur after allogeneic HSCT

Coupled/decoupled spray simulation comparison of the ECN spray a condition with the Sigma-Y Eulerian atomization model

This work evaluates the performance of the Σ-Y Eulerian atomization model at reproducing the internal structure of a diesel spray in the near- field. In the study, three different computational domains have been used in order to perform 3D and 2D coupled simulations, where the internal nozzle flow and external spray are modeled in one continuous domain, and 2D decoupled simulations, where only the external spray is modeled. While the 3D simulation did the best job of capturing the dense zone of the spray, the 2D simulations also performed well, with the coupled 2D simulation slightly outperforming the decoupled simulation. The similarity in results between the coupled and the decoupled simulation show that internal and external flow calculations can be performed independently. In addition, the use of spatially averaged nozzle outlet conditions, in the case of an axisymmetric (single-hole) convergent nozzle, leads to a slightly worse near-field spray predictions but to an accurate far-field ones. Finally, a novel constraint on turbulent driven mixing multiphase flows is introduced which prevents the slip velocity from exceeding the magnitude of the turbulent fluctuations through a realizable Schmidt number. This constraint increased model stability, allowing for a 4x increase in Courant number.Authors acknowledge that part of this work was possible thanks to the Programa de Ayudas de Investigacion y Desarrollo (PAID-2013 3198) of the Universitat Politecnica de Valencia. Also this study was partially funded by the Spanish Ministry of Economy and Competitiveness in the frame of the COMEFF(TRA2014-59483-R) project.Desantes Fernández, JM.; García Oliver, JM.; Pastor Enguídanos, JM.; Pandal-Blanco, A.; Baldwin, E.; Schmidt, DP. (2016). Coupled/decoupled spray simulation comparison of the ECN spray a condition with the Sigma-Y Eulerian atomization model. International Journal of Multiphase Flow. 80:89-99. https://doi.org/10.1016/j.ijmultiphaseflow.2015.12.002S89998

USP37 promotes deubiquitination of HIF2α in kidney cancer

Clear cell renal cell carcinoma (ccRCC) is characterized by loss of tumor suppressor Von Hippel Lindau (VHL) function, which leads to accumulation of hypoxia inducible factor α (including HIF1α and HIF2α). HIF2α was previously reported to be one of the major oncogenic drivers in ccRCC, however, its therapeutic targets remain challenging. Here we performed a deubiquitinase (DUB) complementary DNA (cDNA) library binding screen and discovered that ubiquitin-specific peptidase 37 (USP37) is a DUB that binds HIF2α and promotes HIF2α deubiquitination. As a result, USP37 promotes HIF2α protein stability in an enzymatically dependent manner, and depletion of USP37 leads to HIF2α down-regulation in ccRCC. Functionally, USP37 depletion causes decreased cell proliferation measured by MTS, two-dimensional (2D) colony formation as well as three-dimensional (3D) anchorage- independent growth. USP37 is also essential for maintaining kidney tumorigenesis in an orthotopic xenograft model and its depletion leads to both decreased primary kidney tumorigenesis and spontaneous lung metastasis. Our results suggest that USP37 is a potential therapeutic target in ccRCC

Performance of a Neutron Polarimeter to Measure the Electric Form Factor of the Neutron

This research was sponsored by the National Science Foundation Grant NSF PHY-931478