Structural and functional analysis of Nup133 domains reveals modular building blocks of the nuclear pore complex

Nucleocytoplasmic transport occurs through nuclear pore complexes (NPCs) whose complex architecture is generated from a set of only ∼30 proteins, termed nucleoporins. Here, we explore the domain structure of Nup133, a nucleoporin in a conserved NPC subcomplex that is crucial for NPC biogenesis and is believed to form part of the NPC scaffold. We show that human Nup133 contains two domains: a COOH-terminal domain responsible for its interaction with its subcomplex through Nup107; and an NH2-terminal domain whose crystal structure reveals a seven-bladed β-propeller. The surface properties and conservation of the Nup133 β-propeller suggest it may mediate multiple interactions with other proteins. Other β-propellers are predicted in a third of all nucleoporins. These and several other repeat-based motifs appear to be major elements of nucleoporins, indicating a level of structural repetition that may conceptually simplify the assembly and disassembly of this huge protein complex

Mechanism of arginine sensing by CASTOR1 upstream of mTORC1

The mechanistic Target of Rapamycin Complex 1 (mTORC1) is a major regulator of eukaryotic growth that coordinates anabolic and catabolic cellular processes with inputs such as growth factors and nutrients, including amino acids. In mammals arginine is particularly important, promoting diverse physiological effects such as immune cell activation, insulin secretion, and muscle growth, largely mediated through activation of mTORC1 (refs 4, 5, 6, 7).Arginine activates mTORC1 upstream of the Rag family of GTPases, through either the lysosomal amino acid transporter SLC38A9 or the GATOR2-interacting Cellular Arginine Sensor for mTORC1 (CASTOR1). However, the mechanism by which the mTORC1 pathway detects and transmits this arginine signal has been elusive. Here, we present the 1.8 Å crystal structure of arginine-bound CASTOR1. Homodimeric CASTOR1 binds arginine at the interface of two Aspartate kinase, Chorismate mutase, TyrA (ACT) domains, enabling allosteric control of the adjacent GATOR2-binding site to trigger dissociation from GATOR2 and downstream activation of mTORC1. Our data reveal that CASTOR1 shares substantial structural homology with the lysine-binding regulatory domain of prokaryotic aspartate kinases, suggesting that the mTORC1 pathway exploited an ancient, amino-acid-dependent allosteric mechanism to acquire arginine sensitivity. Together, these results establish a structural basis for arginine sensing by the mTORC1 pathway and provide insights into the evolution of a mammalian nutrient sensor.National Institutes of Health (U.S.) (Grant R01CA103866)National Institutes of Health (U.S.) (Grant AI47389)United States. Department of Defense (Award W81XWH-07-0448)National Institutes of Health (U.S.) (Grant F31 CA180271

Presence of suicidality as a prognostic indicator

Background: Suicidal symptoms in depression are often thought to predict a higher severity of illness and a worse prognosis. Aims: To determine if suicidal ideation at the time of treatment for major depression can predict response to antidepressant medication in primary care. Settings and Design: A retrospective analysis of subjects receiving anti-depressant drugs in a primary care setting Methods and Material: Nine depressed patients (14%) who acknowledged suicidality on the PHQ-9 depression scale were followed up for and compared to a group of 54 (86%) depressed patients (controls) who did not have suicidal thoughts for four months. All were given treatment with antidepressants and followed with a disease management protocol where the PHQ-9 was used as a systematic outcome measure. Statistical Analysis: Descriptive measures and t-tests were utilized to show statistical significance. Results: There were no statistical differences in remission from depressive symptoms based on the PHQ-9 scale after antidepressant treatment, between patients with suicidal thoughts (56%) and those without (44%). Conclusion: The presence of suicidality as a depressive symptom did not predict poorer clinical outcome when treating depression in the primary care setting in the patients studied

FHODs: Nuclear tethered formins for nuclear mechanotransduction

In this review, we discuss FHOD formins with a focus on recent studies that reveal a new role for them as critical links for nuclear mechanotransduction. The FHOD family in vertebrates comprises two structurally related proteins, FHOD1 and FHOD3. Their similar biochemical properties suggest overlapping and redundant functions. FHOD1 is widely expressed, FHOD3 less so, with highest expression in skeletal (FHOD1) and cardiac (FHOD3) muscle where specific splice isoforms are expressed. Unlike other formins, FHODs have strong F-actin bundling activity and relatively weak actin polymerization activity. These activities are regulated by phosphorylation by ROCK and Src kinases; bundling is additionally regulated by ERK1/2 kinases. FHODs are unique among formins in their association with the nuclear envelope through direct, high affinity binding to the outer nuclear membrane proteins nesprin-1G and nesprin-2G. Recent crystallographic structures reveal an interaction between a conserved motif in one of the spectrin repeats (SRs) of nesprin-1G/2G and a site adjacent to the regulatory domain in the amino terminus of FHODs. Nesprins are components of the LINC (linker of nucleoskeleton and cytoskeleton) complex that spans both nuclear membranes and mediates bidirectional transmission of mechanical forces between the nucleus and the cytoskeleton. FHODs interact near the actin-binding calponin homology (CH) domains of nesprin-1G/2G enabling a branched connection to actin filaments that presumably strengthens the interaction. At the cellular level, the tethering of FHODs to the outer nuclear membrane mechanically couples perinuclear actin arrays to the nucleus to move and position it in fibroblasts, cardiomyocytes, and potentially other cells. FHODs also function in adhesion maturation during cell migration and in the generation of sarcomeres, activities distant from the nucleus but that are still influenced by it. Human genetic studies have identified multiple FHOD3 variants linked to dilated and hypertrophic cardiomyopathies, with many mutations mapping to “hot spots” in FHOD3 domains. We discuss how FHOD1/3’s role in reinforcing the LINC complex and connecting to perinuclear actin contributes to functions of mechanically active tissues such as striated muscle

Antibiotic residues in final effluents of European wastewater treatment plants and their impact on the aquatic environment

A comprehensive monitoring of a broad set of antibiotics in the final effluent of wastewater treatment plants (WWTPs) of 7 European countries (Portugal, Spain, Ireland, Cyprus, Germany, Finland, and Norway) was carried out in two consecutive years (2015 and 2016). This is the first study of this kind performed at an international level. Within the 53 antibiotics monitored 17 were detected at least once in the final effluent of the WWTPs, i.e.: ciprofloxacin, ofloxacin, enrofloxacin, orbifloxacin, azithromycin, clarithromycin, sulfapyridine, sulfamethoxazole, trimethoprim, nalidixic acid, pipemidic acid, oxolinic acid, cefalexin, clindamycin, metronidazole, ampicillin, and tetracycline. The countries exhibiting the highest effluent average concentrations of antibiotics were Ireland and the southern countries Portugal and Spain, whereas the northern countries (Norway, Finland and Germany) and Cyprus exhibited lower total concentration. The antibiotic occurrence data in the final effluents were used for the assessment of their impact on the aquatic environment. Both, environmental predicted no effect concentration (PNEC-ENVs) and the PNECs based on minimal inhibitory concentrations (PNEC-MICs) were considered for the evaluation of the impact on microbial communities in aquatic systems and on the evolution of antibiotic resistance, respectively. Based on this analysis, three compounds, ciprofloxacin, azithromycin and cefalexin are proposed as markers of antibiotic pollution, as they could occasionally pose a risk to the environment. Integrated studies like this are crucial to map the impact of antibiotic pollution and to provide the basis for designing water quality and environmental risk in regular water monitoring programs.Peer reviewe

Performance confirmation of the Belle II imaging Time Of Propogation (iTOP) prototype counter

The Bell Detector at the KEKB asymmetric-energy e{sup +}e{sup -} collider performed extremely well, logging an integrated luminosity an order of magnitude higher than the design baseline. With this inverse attobarn of integrated luminosity, time-dependent CP-violation inn the 3rd generation beauty quarks was firmly established, and is now a precision measurement. Going beyond this to explore if the Kobayashi-Maskawa mechanism is the only contributor to quark-mixing, and to interrogate the flavor sector for non-standard model enhancements, requires a detector and accelerator capable of topping this world-record luminosity by more than an order of magnitude. The Belle II detector at the upgraded Super-KEKB accelerator has been designed to meet this highly ambitious goal of operating at a luminosity approaching 10{sup 36} cm{sup -2} s{sup -1}. Such higher event rates and backgrounds require upgrade of essentially all detector subsystems, as well as their readout. Comparing the Belle composite (threshold Aerogel + Time of Flight) particle identification (PID) system with the DIRC employed by BaBar, quartz radiator internal Cherenkov photon detection proved to have higher kaon efficiency and lower pion fake rates. However, because the detector structure and CsI calorimeter will be retained, an improved barrel PID must fit within a very narrow envelope, as indicated in Figure 1. To effectively utilize this space, a more compact detector concept based on the same quartz radiators, but primarily using photon arrival time was proposed. This Time Of Propagation (TOP) counter was studied in a number of earlier prototype tests. Key to the necessary 10's of picosecond single-photon timing has been the development of the so-called SL-10 Micro-Channel Plate Photo-Multiplier Tube (MCP-PMT), which has demonstrated sub-40 ps single photon Transit Time Spread TTS. Further simulation study of this detector concept indicated that a focusing mirror in the forward direction, as well as a modest image expansion volume and more highly pixelated image plane improve the theoretical detector performance, since timing alone is limited by chromatic dispersion of the Cherenkov photons. This imaging-TOP (or iTOP) counter is the basis of Belle II barrel PID upgrade. However, a number of critical performance parameters must be demonstrated prior to releasing this prototype design for production manufacture

Nanobodies as allosteric modulators of Parkinson's disease-associated LRRK2

Mutations in the gene coding for leucine-rich repeat kinase 2 (LRRK2) are a leading cause of the inherited form of Parkinson’s disease (PD), while LRRK2 overactivation is also associated with the more common idiopathic form of PD. LRRK2 is a large multidomain protein, including a GTPase as well as a Ser/Thr protein kinase domain. Common, disease-causing mutations increase LRRK2 kinase activity, presenting LRRK2 as an attractive target for drug discovery. Currently, drug development has mainly focused on ATP-competitive kinase inhibitors. Here, we report the identification and characterization of a variety of nanobodies that bind to different LRRK2 domains and inhibit or activate LRRK2 in cells and in in vitro. Importantly, nanobodies were identified that inhibit LRRK2 kinase activity while binding to a site that is topographically distinct from the active site and thus act through an allosteric inhibitory mechanism that does not involve binding to the ATP pocket or even to the kinase domain. Moreover, while certain nanobodies completely inhibit the LRRK2 kinase activity, we also identified nanobodies that specifically inhibit the phosphorylation of Rab protein substrates. Finally, in contrast to current type I kinase inhibitors, the studied kinase-inhibitory nanobodies did not induce LRRK2 microtubule association. These comprehensively characterized nanobodies represent versatile tools to study the LRRK2 function and mechanism and can pave the way toward novel diagnostic and therapeutic strategies for PD

Exposure Assessment Approaches for Engineered Nanomaterials

Products based on nanotechnology are rapidly emerging in the marketplace, sometimes with little notice to consumers of their nanotechnology pedigree. This wide variety of nanotechnology products will result (in some cases) in unintentional human exposure to purposely engineered nanoscale materials via the dermal, inhalation, ingestion, and ocular pathways. Occupational, consumer, and environmental exposure to the nanomaterials should be characterized during the entire product lifecycle—manufacture, use, and disposal. Monitoring the fate and transport of engineered nanomaterials is complicated by the lack of detection techniques and the lack of a defined set of standardized metrics to be consistently measured. New exposure metrics may be required for engineered nanomaterials, but progress is possible by building on existing tools. An exposure metric matrix could organize existing data by relating likely exposure pathways (dermal, inhalation, ocular, ingestion) with existing measurements of important characteristics of nanoscale materials (particle number, mass, size distribution, charge). Nanomaterial characteristics not commonly measured, but shown to initiate a biological response during toxicity testing, signal a need for further research, such as the pressing need to develop monitoring devices capable of measuring those aspects of engineered nanomaterials that result in biological responses in humans. Modeling the behavior of nanoparticles may require new types of exposure models that individually track particles through the environment while keeping track of the particle shape, surface area, and other surface characteristics as the nanoparticles are transformed or become reactive. Lifecycle analysis could also be used to develop conceptual models of exposure from engineered nanomaterials.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/79200/1/j.1539-6924.2010.01446.x.pd

The structure of the scaffold nucleoporin Nup120 reveals a new and unexpected domain architecture

Nucleocytoplasmic transport is mediated by nuclear pore complexes (NPCs), enormous protein assemblies residing in circular openings in the nuclear envelope. The NPC is modular, with transient and stable components. The stable core is essentially built from two multiprotein complexes, the Y-shaped heptameric Nup84 complex and the Nic96 complex, arranged around an eightfold axis. We present the crystal structure of Nup120[subscript 1-757], one of the two short arms of the Y-shaped Nup84 complex. The protein adopts a compact oval shape built around a novel bipartite α-helical domain intimately integrated with a β-propeller domain. The domain arrangement is substantially different from the Nup85•Seh1 complex, which forms the other short arm of the Y. With the data presented here, we establish that all three branches of the Y-shaped Nup84 complex are tightly connected by helical interactions and that the β-propellers likely form interaction site(s) to neighboring complexes.National Institutes of Health (U.S.) (Grant GM77537)Pew Charitable Trusts (Scholar Award