bluuebunny/crossref_metadata_2025 huggingface dataset:
Chronic indeterminate phase of Chagas’ disease: mitochondrial involvement in infection with two strains
Authors: BÁEZ ALEJANDRA LIDIA , LO PRESTI MARÍA SILVINA , FRETES RICARDO , DÍAZ CINTIA , PONS PATRICIA , BAZÁN PAOLA CAROLINA , STRAUSS MARIANA , RIVAROLA HÉCTOR WALTER , PAGLINI-OLIVA PATRICIA
Published: November 2012

Chagasic cardiopathy has become one of the most frequent causes of heart failure and sudden death, as well as one of the most common causes of cardio-embolic stroke in Latin America. The myocyte response to oxidative stress involves the progression of cellular changes, primarily targeting the mitochondria and modifying therefore the energy supply. In this paper we analysed the effect of the infection of mice with 2 different strains of Trypanosoma cruzi (Tulahuen and SGO Z12) in the chronic indeterminate stage (75 days post-infection), upon the structure and function of cardiac mitochondria. The structural results showed that 83% of the mitochondria from the Tulahuen-infected mice presented an increase in their matrix and 91% of the mitochondria from the SGO Z12-infected group showed a reduction in their diameter (P < 0·05). When the Krebs cycle and mitochondrial respiratory chain functionality was analysed through the measurement of the citrate synthase and complexes I to IV activity, it showed that their activity was altered in all cases in a similar manner in both infected groups. In this paper we have demonstrated that the chronic indeterminate phase is not ‘silent’ and that cardiac mitochondria are clearly involved in the genesis and progression to the chronic chagasic cardiopathy when different factors alter the host-parasite equilibrium.
The No-Minimum argument, satisficing, and no-best-world: a reply to Jeff Jordan
Authors: DRAGOS CHRIS
Published: November 2012

Peter van Inwagen's ‘No-Minimum’ argument boldly rejects a proposition widely accepted by theists and atheists alike: God and gratuitous evil are incompatible. Jeff Jordan (2003) criticizes van Inwagen's argument and (Jordan 2011) defends his position against Michael Schrynemakers (2007). I present two criticisms of Jordan. Concerning his first paper, I argue that if it is plausible to suppose that there exist undetectable evils, Jordan's argument is incomplete. Concerning his second paper, I show how Jordan fails to engage adequately with Schrynemakers's reply and, more seriously, with the notion of satisficing implicit in van Inwagen's No-Minimum argument. To draw out this second criticism, I make use of another debate in the philosophy of religion: the problem of no-best-world.
Outbreak of measles in Central and Eastern Cheshire, UK, October 2008–February 2009
Authors: GHEBREHEWET S. , HAYHURST G. , KEENAN A. , MOORE H.
Published: November 2012

We describe the largest outbreak of measles in Central and Eastern Cheshire (North West England) since the MMR vaccine was introduced in 1988, the majority of cases were not vaccinated and more than 20% of the cases belonged to the travelling community. Over 4 months, 147 clinical cases of measles were notified locally to the Cheshire & Merseyside Health Protection Unit (CMHPU). Of these, 67 (45·6%) were laboratory confirmed, 42 (28·6%) were negative, and one was equivocal, leaving 23 probable and 14 possible cases. The primary case was probably an 8-year-old unvaccinated travelling child, symptomatic on 1 October 2008. Measles spread locally and within school-aged children until early February 2009. Most of Central and Eastern Cheshire, including 23 educational institutions (playgroups, nurseries, primary schools, secondary schools, colleges), were affected, showing that there were enough susceptible/unvaccinated children to sustain an outbreak. Nearly a quarter of the confirmed cases (15/67, 22·4%) were aged <13 months and too young to be vaccinated under the UK immunization schedule. This outbreak is a reminder of the importance of achieving herd immunity to prevent spread and protect those at risk of severe illness or complications. There were no fatalities in this outbreak and no significant complications were reported.
A new description of orthogonal bases
Authors: COECKE BOB , PAVLOVIC DUSKO , VICARY JAMIE
Published: November 2012

We show that an orthogonal basis for a finite-dimensional Hilbert space can be equivalently characterised as a commutative †-Frobenius monoid in the category FdHilb, which has finite-dimensional Hilbert spaces as objects and continuous linear maps as morphisms, and tensor product for the monoidal structure. The basis is normalised exactly when the corresponding commutative †-Frobenius monoid is special. Hence, both orthogonal and orthonormal bases are characterised without mentioning vectors, but just in terms of the categorical structure: composition of operations, tensor product and the †-functor. Moreover, this characterisation can be interpreted operationally, since the †-Frobenius structure allows the cloning and deletion of basis vectors. That is, we capture the basis vectors by relying on their ability to be cloned and deleted. Since this ability distinguishes classical data from quantum data, our result has important implications for categorical quantum mechanics.
A temperate rhamnaceous species with a non-enclosing stone and without physical dormancy
Authors: Walck Jeffrey L. , Shea Cofer M. , Gehan Jayasuriya K.M.G. , Fernando M. Thilina R. , Hidayati Siti N.
Published: November 2012

The purpose of the present study was to investigate the dormancy break and germination requirements of seeds from the rhamnaceous vineBerchemia scandens. The fleshy fruit contains a two-locular stone with an endocarp described as ‘bony, thickish’. Scarified and non-scarified stones increased by about 30–50% in mass during imbibition over a 24-h period. The endocarp of the stone does not completely enclose the seeds and a soft tissue region is present. This region is the primary area of water entrance to the seed, as shown by dye-tracking and by sealing it. Freshly matured and overwintered seeds ofB. scandensgerminated to low percentages at all temperatures during 2 weeks of incubation in light, and they germinated from moderate to high percentages during 12–14 weeks of incubation in light. While cold stratification had a relatively modest effect on the promotion of total germination across most temperatures assessed (if seeds were left for long enough), it had a somewhat stronger effect on germination rate. Cold-stratified seeds germinated equally well in light and darkness. The class of dormancy found in seeds ofB. scandenswould be physiological. The anatomy of the stones readily allows water imbibition, showing that seeds ofB. scandenslack physical dormancy, an uncommon trait in Rhamnaceae.
The Swedish Twin Registry: Establishment of a Biobank and Other Recent Developments
Authors: Magnusson Patrik K. E. , Almqvist Catarina , Rahman Iffat , Ganna Andrea , Viktorin Alexander , Walum Hasse , Halldner Linda , Lundström Sebastian , Ullén Fredrik , Långström Niklas , Larsson Henrik , Nyman Anastasia , Gumpert Clara Hellner , Råstam Maria , Anckarsäter Henrik , Cnattingius Sven , Johannesson Magnus , Ingelsson Erik , Klareskog Lars , de Faire Ulf , Pedersen Nancy L. , Lichtenstein Paul
Published: November 2012

The Swedish Twin Registry (STR) today contains more than 194,000 twins and more than 75,000 pairs have zygosity determined by an intra-pair similarity algorithm, DNA, or by being of opposite sex. Of these, approximately 20,000, 25,000, and 30,000 pairs are monozygotic, same-sex dizygotic, and opposite-sex dizygotic pairs, respectively. Since its establishment in the late 1950s, the STR has been an important epidemiological resource for the study of genetic and environmental influences on a multitude of traits, behaviors, and diseases. Following large investments in the collection of biological specimens in the past 10 years we have now established a Swedish twin biobank with DNA from 45,000 twins and blood serum from 15,000 twins, which effectively has also transformed the registry into a powerful resource for molecular studies. We here describe the main projects within which the new collections of both biological samples as well as phenotypic measures have been collected. Coverage by year of birth, zygosity determination, ethnic heterogeneity, and influences of in vitro fertilization are also described.
Turbulent viscosity in natural surf zones
Authors: Grasso F. , Ruessink B. G.
Published: November 2012

Waves breaking in the shallow surf zone near the shoreline inject turbulence into the water column that may reach the bed to suspend sediment. Breaking‐wave turbulence in the surf zone is, however, poorly understood, which is one of the reasons why many process‐based coastal‐evolution models predict coastal change during severe storms inadequately. Here, we use data collected in two natural surf zones to derive a new parameterization for the stability functionCμ that determines the magnitude of the eddy viscosity νtin two‐equation turbulent‐viscosity models,νt = Cμk2/ε, where k is turbulent kinetic energy and ε is the turbulence dissipation rate. In both data sets, the ratio of turbulence production to dissipation is small (≈0.15), while vertical turbulence diffusion is significant. This differs from assumptions underlying existing Cμ parameterizations, which we show to severely overpredict observed Cμ for most conditions. Additionally, we rewrite our new Cμparameterization into a formulation that accurately reproduces our Reynolds‐stress based estimates of turbulence production. This formulation is linear with strain, consistent with earlier theoritical work for large strain rates. Also, it does not depend onεand can, therefore, also be applied in one‐equation turbulent‐viscosity models. We anticipate our work to improve turbulence modeling in natural surf zones and to eventually lead to more reliable predictions of coastal evolution in response to severe storms.
The effect of windstress change on future sea level change in the Southern Ocean
Authors: Bouttes N. , Gregory J. M. , Kuhlbrodt T. , Suzuki T.
Published: November 2012

AOGCMs of the two latest phases (CMIP3 and CMIP5) of the Coupled Model Intercomparison Project, like earlier AOGCMs, predict large regional variations in future sea level change. The model‐mean pattern of change in CMIP3 and CMIP5 is very similar, and its most prominent feature is a zonal dipole in the Southern Ocean: sea level rise is larger than the global mean north of 50°S and smaller than the global mean south of 50°S in most models. The individual models show widely varying patterns, although the inter‐model spread in local sea level change is smaller in CMIP5 than in CMIP3. Here we investigate whether changes in windstress can explain the different patterns of projected sea level change, especially the Southern Ocean feature, using two AOGCMs forced by the changes in windstress from the CMIP3 and CMIP5 AOGCMs. We show that the strengthening and poleward shift of westerly windstress accounts for the most of the large spread among models in magnitude of this feature. In the Indian, North Pacific and Arctic Oceans, the windstress change is influential, but does not completely account for the projected sea level change.
Source directionality of ambient seismic noise inferred from three‐component beamforming
Authors: Behr Y. , Townend J. , Bowen M. , Carter L. , Gorman R. , Brooks L. , Bannister S.
Published: November 2012

The increased use of ambient seismic noise for seismic imaging requires better understanding of the ambient seismic noise wavefield and its source locations and mechanisms. Although the source regions and mechanisms of Rayleigh waves have been studied extensively, characterization of Love wave source processes are sparse or absent. We present here the first systematic comparison of ambient seismic noise source directions within the primary (~10–20 s period) and secondary (~5–10 s period) microseism bands for both Rayleigh and Love waves in the Southern Hemisphere using vertical‐ and horizontal‐component ambient seismic noise recordings from a dense temporary network of 68 broadband seismometers in New Zealand. Our analysis indicates that Rayleigh and Love waves within the primary microseism band appear to be mostly generated in different areas, whereas in the secondary microseism band they arrive from similar backazimuths. Furthermore, the source areas of surface waves within the secondary microseism band correlate well with modeled deep‐water and near‐coastal source regions.
Frictional properties of olivine at high temperature with applications to the strength and dynamics of the oceanic lithosphere
Authors: King D. S. H. , Marone C.
Published: November 2012

Faulting and brittle deformation of mantle rocks occurs in many tectonic settings such as oceanic transform faults, oceanic detachment faults, subduction zones, and continental rifts. However, few data exist that directly explore the frictional properties of peridotite rocks. Improved constraints on the brittle deformation of peridotite is important for a more complete understanding of the rheological properties of the lithosphere. Furthermore, our comparatively detailed understanding of plastic deformation in olivine allows us to explore the possible role of thermally activated intracrystalline deformation mechanisms in macroscopically brittle processes. It has been hypothesized, and some experimental data indicate, that plastic yielding by dislocation glide (low temperature plasticity) determines the direct effect in the rate and state frictional constitutive formulation. Plastic flow may also have important implications for the blunting or necking at asperity contacts that influences the time and/or displacement dependent friction evolution effect and frictional healing. We present results from saw cut experiments on fine grained synthetic olivine fault gouge conducted in a gas‐medium deformation apparatus in the temperature range of 400–1000°C with 100 MPa confining pressure. We conducted velocity stepping tests to explore the rate and temperature dependence of sliding stability. We also conducted slide‐hold‐slide experiments to investigate the time and temperature dependence of fault zone restrengthening (frictional healing). The mechanical data and microstructural observations allow us to explore the role of thermally activated processes in frictional sliding. The data indicate systematic temperature dependenceof rate and state variables that can be attributed to plastic yielding at grain to grain contacts. We explore the implications of such temperature dependent behavior for controlling the base of the seismogenic zone in the oceanic lithosphere, and we seek insight into possible mechanistic models for the interactions between fracture and flow that could lead to improved constraints on the strength of the lithosphere.
Fractional seismic velocity change related to magma intrusions during earthquake swarms in the eastern Izu peninsula, central Japan
Authors: Ueno Tomotake , Saito Tatsuhiko , Shiomi Katsuhiko , Enescu Bogdan , Hirose Hitoshi , Obara Kazushige
Published: November 2012

We investigated temporal changes in seismic velocity associated with active seismic swarms and crustal deformations that occurred in 2006 and 2009 in the eastern Izu peninsula of Japan. To detect changes in seismic velocity during and after these swarm episodes, we used a passive image interferometry technique, by estimating the phase shift of auto‐correlation functions of continuous seismic waveforms in a frequency band of 1–3 Hz. During the 2006 and 2009 swarm episodes, a significant velocity decrease (>0.3%) was detected at the station nearest the swarm area. This velocity decrease occurred when the volumetric strain change at the surface due to magma intrusion was larger than 10−6. We could not, however, find a clear correlation between the velocity decrease and the peak ground acceleration caused by moderate earthquakes (M ∼ 5) that occurred during the swarms. We also found that during the interseismic period the velocity decrease gradually recovered, and appears to be proportional to displacement at the surface measured by GPS stations. These results suggest that the change in the subsurface velocity structure in the eastern Izu peninsula strongly reflects strain changes caused by magma intrusion into the crust.
Local and remote forcing of decadal sea level and thermocline depth variability in the South Indian Ocean
Authors: Trenary Laurie L. , Han Weiqing
Published: November 2012

Analysis is performed on a set of diagnostic numerical experiments designed to isolate local Indian Ocean forcing versus remote forcing from the Pacific via the Indonesian throughflow on decadal variability of subsurface temperature, sea level, and thermocline depth of the South Indian Ocean. It is found that the vertical structure of decadal temperature variability varies from decade‐to‐decade, with maximum variation peaking in the vicinity of the thermocline. The decadal‐scale temperature variations in the tropical southwestern Indian Ocean between 5°S and 17°S are primarily associated with the vertical displacements of the thermocline. Prior to the early 1990s, decadal variations in sea level and thermocline depth can be described in terms of a baroclinic Sverdrup balance, forced by Ekman pumping velocity associated with windstress curl acting on the Indian Ocean. Beginning in the early 1990s, decadal variability of the equatorial Pacific trades forces thermocline variations that modify the sea level and thermocline depth across the tropical South Indian Ocean basin. Farther south, between 20°S and 30°S, oceanic internal variability makes significant contributions to decadal variability of the thermocline. The anomalies along the western coast of Australia are primarily driven by regional forcing acting on the Indian Ocean prior to the 1990s, and signals originating from the equatorial Pacific make a greater contribution thereafter.
Global investigation of olivine on Mars: Insights into crust and mantle compositions
Authors: Ody A. , Poulet F. , Bibring J.‐P. , Loizeau D. , Carter J. , Gondet B. , Langevin Y.
Published: November 2012

We present the distribution of olivine on Mars, derived from spectral parameters based on the 1 µm olivine absorption band. The olivine can be defined with respect to two spectral end‐members: type 1 corresponds to olivine with low iron content and/or small grain size and/or small abundance, and type 2, which corresponds to olivine with higher iron content and/or larger grain size and/or larger abundance. The spatial and statistical analysis of the global olivine distribution points out five major geological settings where olivine is detected: (1) Early Hesperian olivine‐bearing smooth crater floors and flat intercrater plains throughout the southern highlands; (2) olivine deposits around the three main basins Argyre, Hellas, and Isidis; (3) olivine in intercrater dunes, crater ejecta, or extended deposits in the northern plains; (4) olivine associated with outcrops and sand in the floor of Valles Marineris; and (5) olivine‐bearing butte outcrops in the vicinity of Hellas. The geological context, the age, and the composition of the olivine detections associated with these five major geological settings are detailed. Their origin and the implication of their occurrence on the composition of the Martian mantle and crust, as well as on the evolution of Mars volcanism are discussed.
Craters hosting radar‐bright deposits in Mercury's north polar region: Areas of persistent shadow determined from MESSENGER images
Authors: Chabot Nancy L. , Ernst Carolyn M. , Harmon John K. , Murchie Scott L. , Solomon Sean C. , Blewett David T. , Denevi Brett W.
Published: November 2012

Radar‐bright features near Mercury's poles were discovered in Earth‐based radar images and proposed to be water ice present in permanently shadowed areas. Images from MESSENGER's one‐year primary orbital mission provide the first nearly complete view of Mercury's north polar region, as well as multiple images of the surface under a range of illumination conditions. We find that radar‐bright features near Mercury's north pole are associated with locations persistently shadowed in MESSENGER images. Within 10° of the pole, almost all craters larger than 10 km in diameter host radar‐bright deposits. There are several craters located near Mercury's north pole with sufficiently large diameters to enable long‐lived water ice to be thermally stable at the surface within regions of permanent shadow. Craters located farther south also host radar‐bright deposits and show a preference for cold‐pole longitudes; thermal models suggest that a thin insulating layer is required to cover these deposits if the radar‐bright material consists predominantly of long‐lived water ice. Many small (<10 km diameter) and low‐latitude (extending southward to 66°N) craters host radar‐bright material, and water ice may not be thermally stable in these craters for  ~1 Gy, even beneath an insulating layer. The correlation of radar‐bright features with persistently shadowed areas is consistent with the deposits being composed of water ice, and future thermal modeling of small and low‐latitude craters has the potential to further constrain the nature, source, and timing of emplacement of the radar‐bright material.
Role of LRRK2 kinase activity in the pathogenesis of Parkinson's disease
Authors: Greggio Elisa
Published: November 2012

Interest in studying the biology of LRRK2 (leucine-rich repeat kinase 2) started in 2004 when missense mutations in the LRRK2 gene were linked to an inherited form of Parkinson's disease with clinical and pathological presentation resembling the sporadic syndrome. LRRK2 is a complex molecule containing domains implicated in protein interactions, as well as kinase and GTPase activities. The observation that the common G2019S mutation increases kinase activity in vitro suggests that altered phosphorylation of LRRK2 targets may have pathological outcomes. Given that protein kinases are ideal targets for drug therapies, much effort has been directed at understanding the role of LRRK2 kinase activity on disease onset. However, no clear physiological substrates have been identified to date, indicating that much research is still needed to fully understand the signalling pathways orchestrated by LRRK2 and deregulated under pathological conditions.
Mechanisms of small-molecule binding to intrinsically disordered proteins
Authors: Cuchillo Rémi , Michel Julien
Published: November 2012

IDPs (intrinsically disordered proteins) play crucial roles in many important cellular processes such as signalling or transcription and are attractive therapeutic targets for several diseases. The considerable structural flexibility of IDPs poses a challenge for rational drug discovery approaches. Consequently, structure-based drug design efforts to date have mostly focused on inhibiting interactions of IDPs with other proteins whose structure can be solved by conventional biophysical methods. Yet, in recent years, several examples of small molecules that bind to monomeric IDPs in their disordered states have been reported, suggesting that this approach may offer new opportunities for therapeutic interventions. Further developments of this strategy will greatly benefit from an improved understanding of molecular recognition mechanisms between small molecules and IDPs. The present article summarizes findings from experimental and computational studies of the mechanisms of interaction between small molecules and three IDPs in their disordered states: c-Myc, Aβ (amyloid β-peptide) and α-synuclein.
Analysis of LRRK2 accessory repeat domains: prediction of repeat length, number and sites of Parkinson's disease mutations
Authors: Mills Ryan D. , Mulhern Terrence D. , Cheng Heung-Chin , Culvenor Janetta G.
Published: November 2012

Various investigators have identified the major domain organization of LRRK2 (leucine-rich repeat kinase 2), which includes a GTPase ROC (Ras of complex proteins) domain followed by a COR (C-terminal of ROC) domain and a protein kinase domain. In addition, there are four domains composed of structural repeat motifs likely to be involved in regulation and localization of this complex protein. In the present paper, we report our bioinformatic analyses of the human LRRK2 amino acid sequence to predict the repeat size, number and likely boundaries for the armadillo repeat, ankyrin repeat, the leucine-rich repeat and WD40 repeat regions of LRRK2. Homology modelling using known protein structures with similar domains was used to predict structures, exposed residues and location of mutations for these repeat regions. We predict that the armadillo repeats, ankyrin repeats and leucine-rich repeats together form an extended N-terminal flexible ‘solenoid’-like structure composed of tandem repeat modules likely to be important in anchoring to the membrane and cytoskeletal structures as well as binding to other protein ligands. Near the C-terminus of LRRK2, the WD40 repeat region is predicted to form a closed propeller structure that is important for protein complex formation.
LRRK2 GTPase dysfunction in the pathogenesis of Parkinson's disease
Authors: Xiong Yulan , Dawson Valina L. , Dawson Ted M.
Published: November 2012

Mutations in the LRRK2 (leucine-rich repeat kinase 2) gene are the most frequent genetic cause of PD (Parkinson's disease), and these mutations play important roles in sporadic PD. The LRRK2 protein contains GTPase and kinase domains and several protein–protein interaction domains. The kinase and GTPase activity of LRRK2 seem to be important in regulating LRRK2-dependent cellular signalling pathways. LRRK2's GTPase and kinase domains may reciprocally regulate each other to direct LRRK2's ultimate function. Although most LRRK2 investigations are centred on LRRK2's kinase activity, the present review focuses on the function of LRRK2's GTPase activity in LRRK2 physiology and pathophysiology.
Bacterial in-cell NMR of human α-synuclein: a disordered monomer by nature?
Authors: Binolfi Andres , Theillet Francois-Xavier , Selenko Philipp
Published: November 2012

The notion that human α-synuclein is an intrinsically disordered monomeric protein was recently challenged by a postulated α-helical tetramer as the physiologically relevant protein structure. The fact that this alleged conformation had evaded detection for so many years was primarily attributed to a widely used denaturation protocol to purify recombinant α-synuclein. In the present paper, we provide in-cell NMR evidence obtained directly in intact Escherichia coli cells that challenges a tetrameric conformation under native in vivo conditions. Although our data cannot rule out the existence of other intracellular protein states, especially in cells of higher organisms, they indicate clearly that inside E. coli α-synuclein is mostly monomeric and disordered.
An intrinsically disordered protein, CP12: jack of all trades and master of the Calvin cycle
Authors: Gontero Brigitte , Maberly Stephen C.
Published: November 2012

Many proteins contain disordered regions under physiological conditions and lack specific three-dimensional structure. These are referred to as IDPs (intrinsically disordered proteins). CP12 is a chloroplast protein of approximately 80 amino acids and has a molecular mass of approximately 8.2–8.5 kDa. It is enriched in charged amino acids and has a small number of hydrophobic residues. It has a high proportion of disorder-promoting residues, but has at least two (often four) cysteine residues forming one (or two) disulfide bridge(s) under oxidizing conditions that confers some order. However, CP12 behaves like an IDP. It appears to be universally distributed in oxygenic photosynthetic organisms and has recently been detected in a cyanophage. The best studied role of CP12 is its regulation of the Calvin cycle responsible for CO2 assimilation. Oxidized CP12 forms a supramolecular complex with two key Calvin cycle enzymes, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and PRK (phosphoribulokinase), down-regulating their activity. Association–dissociation of this complex, induced by the redox state of CP12, allows the Calvin cycle to be inactive in the dark and active in the light. CP12 is promiscuous and interacts with other enzymes such as aldolase and malate dehydrogenase. It also plays other roles in plant metabolism such as protecting GAPDH from inactivation and scavenging metal ions such as copper and nickel, and it is also linked to stress responses. Thus CP12 seems to be involved in many functions in photosynthetic cells and behaves like a jack of all trades as well as being a master of the Calvin cycle.
Structures and interactions in ‘bottlebrush’ neurofilaments: the role of charged disordered proteins in forming hydrogel networks
Authors: Beck Roy , Deek Joanna , Safinya Cyrus R.
Published: November 2012

NFs (neurofilaments), the major cytoskeletal constituent of myelinated axons in vertebrates, consist of three different molecular-mass subunit proteins, NF-L (low), NF-M (medium) and NF-H (high), assembled to form mature filaments with protruding intrinsically disordered C-terminal side-arms. Liquid crystal gel networks of side-arm-mediated NF assemblies play a key role in the mechanical stability of neuronal processes. Disruptions of the NF network, due to NF overaccumulation or incorrect side-arm interactions, are a hallmark of motor neuron diseases including amyotrophic lateral sclerosis. Using synchrotron small-angle X-ray scattering and various microscopy techniques, we have investigated the role of the peptide charges in the subunit side-arms on the structure and interaction of NFs. Our findings, which delineate the distinct roles of NF-M and NF-H in regulating NF interactions, shed light on possible mechanisms of disruption of optimal mechanical network properties.
Diverse functional manifestations of intrinsic structural disorder in molecular chaperones
Authors: Kovacs Denes , Tompa Peter
Published: November 2012

IDPs (intrinsically disordered proteins) represent a unique class of proteins which show diverse molecular mechanisms in key biological functions. The aim of the present mini-review is to summarize IDP chaperones that have increasingly been studied in the last few years, by focusing on the role of intrinsic disorder in their molecular mechanism. Disordered regions in both globular and disordered chaperones are often involved directly in chaperone action, either by modulating activity or through direct involvement in substrate identification and binding. They might also be responsible for the subcellular localization of the protein. In outlining the state of the art, we survey known IDP chaperones discussing the following points: (i) globular chaperones that have an experimentally proven functional disordered region(s), (ii) chaperones that are completely disordered along their entire length, and (iii) the possible mechanisms of action of disordered chaperones. Through all of these details, we chart out how far the field has progressed, only to emphasize the long road ahead before the chaperone function can be firmly established as part of the physiological mechanistic arsenal of the emerging group of IDPs.
Genetic analysis of Parkinson's disease-linked leucine-rich repeat kinase 2
Authors: Tong Youren , Shen Jie
Published: November 2012

Mutations in LRRK2 (leucine-rich repeat kinase 2) are the most common genetic cause of PD (Parkinson's disease). To investigate how mutations in LRRK2 cause PD, we generated LRRK2 mutant mice either lacking its expression or expressing the R1441C mutant form. Homozygous R1441C knockin mice exhibit no dopaminergic neurodegeneration or alterations in steady-state levels of striatal dopamine, but they show impaired dopamine neurotransmission, as was evident from reductions in amphetamine-induced locomotor activity and stimulated catecholamine release in cultured chromaffin cells as well as impaired dopamine D2 receptor-mediated functions. Whereas LRRK2−/− brains are normal, LRRK2−/− kidneys at 20 months of age develop striking accumulation and aggregation of α-synuclein and ubiquitinated proteins, impairment of the autophagy–lysosomal pathway, and increases in apoptotic cell death, inflammatory responses and oxidative damage. Our further analysis of LRRK2−/− kidneys at multiple ages revealed unique age-dependent biphasic alterations of the autophagic activity, which is unchanged at 1 month of age, enhanced at 7 months, but reduced at 20 months. Levels of α-synuclein and protein carbonyls, a general oxidative damage marker, are also decreased in LRRK2−/− kidneys at 7 months of age. Interestingly, this biphasic alteration is associated with increased levels of lysosomal proteins and proteases as well as progressive accumulation of autolysosomes and lipofuscin granules. We conclude that pathogenic mutations in LRRK2 impair the nigrostriatal dopaminergic pathway, and LRRK2 plays an essential role in the dynamic regulation of autophagy function in vivo.
LRRK2 and vesicle trafficking
Authors: Sanna Giovanna , Del Giudice Maria Grazia , Crosio Claudia , Iaccarino Ciro
Published: November 2012

Mutations in LRRK2 (leucine-rich repeat kinase 2) (also known as PARK8 or dardarin) are responsible for the autosomal-dominant form of PD (Parkinson's disease). LRRK2 mutations were found in approximately 3–5% of familial and 1–3% of sporadic PD cases with the highest prevalence (up to 40%) in North Africans and Ashkenazi Jews. To date, mutations in LRRK2 are a major genetic risk factor for familial and sporadic PD. Despite the fact that 8 years have passed from the establishment of the first link between PD and dardarin in 2004, the pathophysiological role of LRRK2 in PD onset and progression is far from clearly defined. Also the generation of different LRRK2 transgenic or knockout animals has not provided new hints on the function of LRRK2 in the brain. The present paper reviews recent evidence regarding a potential role of LRRK2 in the regulation of membrane trafficking from vesicle generation to the movement along cytoskeleton and finally to vesicle fusion with cell membrane.
The importance of Wnt signalling for neurodegeneration in Parkinson's disease
Authors: Berwick Daniel C. , Harvey Kirsten
Published: November 2012

PD (Parkinson's disease) is a devastating progressive motor disorder with no available cure. Over the last two decades, an increasing number of genetic defects have been found that cause familial and idiopathic forms of PD. In parallel, the importance of Wnt signalling pathways for the healthy functioning of the adult brain and the dysregulation of these pathways in neurodegenerative disease has become apparent. Cell biological functions disrupted in PD are partially controlled by Wnt signalling pathways and proteins encoded by PARK genes have been shown to modify Wnt signalling. This suggests the prospect of targeting Wnt signalling pathways to modify PD progression.
Presynaptic dysfunction in Parkinson's disease: a focus on LRRK2
Authors: Belluzzi Elisa , Greggio Elisa , Piccoli Giovanni
Published: November 2012

PD (Parkinson's disease) is a common neurodegenerative disease clinically characterized by bradykinesia, rigidity and resting tremor. Recent studies have proposed that synaptic dysfunction, implicated in numerous studies of animal models of PD, might be a key factor in PD. The molecular defects that lead to PD progression might be hidden at the presynaptic neuron: in fact accumulating evidence has shown that the majority of the genes linked to PD play a critical role at the presynaptic site. In the present paper, we focus on the presynaptic function of LRRK2 (leucine-rich repeat kinase 2), a protein that mutated represents the main genetic cause of familial PD described to date. Neurotransmission relies on proper presynaptic vesicle trafficking; defects in this process, variation in dopamine flow and alteration of presynaptic plasticity have been reported in several animal models of LRRK2 mutations. Furthermore, impaired dopamine turnover has been described in presymptomatic LRRK2 PD patients. Thus, given the pathological events occurring at the synapses of PD patients, the presynaptic site may represent a promising target for early diagnostic therapeutic intervention.
Intrinsic disorder in proteins: a challenge for (un)structural biology met by ion mobility–mass spectrometry
Authors: Jurneczko Ewa , Cruickshank Faye , Porrini Massimiliano , Nikolova Penka , Campuzano Iain D.G. , Morris Michael , Barran Perdita E.
Published: November 2012

The link between structure and function of a given protein is a principal tenet of biology. The established approach to understand the function of a protein is to ‘solve’ its structure and subsequently investigate interactions between the protein and its binding partners. However, structure determination via crystallography or NMR is challenging for proteins where localized regions or even their entire structure fail to fold into a three-dimensional form. These so called IDPs (intrinsically disordered proteins) or intrinsically disordered regions constitute up to 40% of all expressed proteins, and a much higher percentage in proteins involved in the proliferation of cancer. For these proteins, there is a need to develop new methods for structural characterization which exploit their biophysical properties. IM (ion mobility)–MS is uniquely able to examine both absolute conformation(s), populations of conformation and also conformational change, and is therefore highly applicable to the study of IDPs. The present article details the technique of IM–MS and illustrates its use in assessing the relative disorder of the wild-type p53 DNA-core-binding domain of cellular tumour antigen p53. The IM data were acquired on a Waters Synapt HDMS instrument following nESI (nanoelectrospray ionization) from ‘native’ and low-pH solution conditions.
Pharmacological inhibition of LRRK2 cellular phosphorylation sites provides insight into LRRK2 biology
Authors: Zhao Jing , Hermanson Spencer B. , Carlson Coby B. , Riddle Steven M. , Vogel Kurt W. , Bi Kun , Nichols R. Jeremy
Published: November 2012

Mutations in LRRK2 (leucine-rich repeat kinase 2) have been linked to inherited forms of PD (Parkinson's disease). Substantial pre-clinical research and drug discovery efforts have focused on LRRK2 with the hope that small-molecule inhibitors of the enzyme may be valuable for the treatment or prevention of the onset of PD. The pathway to develop therapeutic or neuroprotective agents based on LRRK2 function (i.e. kinase activity) has been facilitated by the development of both biochemical and cell-based assays for LRRK2. LRRK2 is phosphorylated on Ser910, Ser935, Ser955 and Ser973 in the N-terminal domain of the enzyme, and these sites of phosphorylation are likely to be regulated by upstream enzymes in an LRRK2 kinase-activity-dependent manner. Knowledge of these phosphorylation sites and their regulation can be adapted to high-throughput-screening-amenable platforms. The present review describes the utilization of LRRK2 phosphorylation as indicators of enzyme inhibition, as well as how such assays can be used to deconvolute the pathways in which LRRK2 plays a role.
A link between LRRK2, autophagy and NAADP-mediated endolysosomal calcium signalling
Authors: Gómez-Suaga Patricia , Churchill Grant C. , Patel Sandip , Hilfiker Sabine
Published: November 2012

Mutations in LRRK2 (leucine-rich repeat kinase 2) represent a significant component of both sporadic and familial PD (Parkinson's disease). Pathogenic mutations cluster in the enzymatic domains of LRRK2, and kinase activity seems to correlate with cytotoxicity, suggesting the possibility of kinase-based therapeutic strategies for LRRK2-associated PD. Apart from cytotoxicity, changes in autophagy have consistently been observed upon overexpression of mutant, or knockdown of endogenous, LRRK2. However, delineating the precise mechanism(s) by which LRRK2 regulates autophagy has been difficult. Recent data suggest a mechanism involving late steps in autophagic–lysosomal clearance in a manner dependent on NAADP (nicotinic acid–adenine dinucleotide phosphate)-sensitive lysosomal Ca2+ channels. In the present paper, we review our current knowledge of the link between LRRK2 and autophagic–lysosomal clearance, including regulation of Ca2+-dependent events involving NAADP.
Synthesis of post-translationally modified proteins
Authors: van Kasteren Sander
Published: November 2012

Post-translational modifications of proteins can have dramatic effect on the function of proteins. Significant research effort has gone into understanding the effect of particular modifications on protein parameters. In the present paper, I review some of the recently developed tools for the synthesis of proteins modified with single post-translational modifications at specific sites in the protein, such as amber codon suppression technologies, tag and modify, and native chemical ligation.
Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS
Authors: Sibille Nathalie , Bernadó Pau
Published: November 2012

In recent years, IDPs (intrinsically disordered proteins) have emerged as pivotal actors in biology. Despite IDPs being present in all kingdoms of life, they are more abundant in eukaryotes where they are involved in the vast majority of regulation and signalling processes. The realization that, in some cases, functional states of proteins were partly or fully disordered was in contradiction to the traditional view where a well defined three-dimensional structure was required for activity. Several experimental evidences indicate, however, that structural features in IDPs such as transient secondary-structural elements and overall dimensions are crucial to their function. NMR has been the main tool to study IDP structure by probing conformational preferences at residue level. Additionally, SAXS (small-angle X-ray scattering) has the capacity to report on the three-dimensional space sampled by disordered states and therefore complements the local information provided by NMR. The present review describes how the synergy between NMR and SAXS can be exploited to obtain more detailed structural and dynamic models of IDPs in solution. These combined strategies, embedded into computational approaches, promise the elucidation of the structure–function properties of this important, but elusive, family of biomolecules.
Cellular reprogramming: a new approach to modelling Parkinson's disease
Authors: Hartfield Elizabeth M. , Fernandes Hugo J.R. , Vowles Jane , Cowley Sally A. , Wade-Martins Richard
Published: November 2012

iPSCs (induced pluripotent stem cells) offer an unparalleled opportunity to generate and study physiologically relevant cell types in culture. iPSCs can be generated by reprogramming almost any somatic cell type using pluripotency factors such as Oct4, SOX2, Nanog and Klf4. By reprogramming cells from patients carrying disease-associated mutations, and subsequent differentiation into the cell type of interest, researchers now have the opportunity to study disease-specific cell types which were previously inaccessible. In the case of PD (Parkinson's disease), reprogramming is advancing rapidly, and cell lines have been generated from patients carrying mutations in several disease-associated genes, including SNCA (α-synuclein), PARK2 (parkin), PINK1 (phosphatase and tensin homologue deleted on chromosome 10-induced putative kinase 1), PARK7 (DJ-1) and LRRK2 (leucine-rich repeat kinase 2), as well as idiopathic cases. Functional dopaminergic neurons have been differentiated from these cells and their physiology has been compared with control neurons. Human dopaminergic neurons had been previously inaccessible until post-mortem, when the disease is generally highly progressed into pathology. In comparison, iPSCs provide a living cell model with the potential to study early molecular changes which accumulate in cells and ultimately result in neurodegeneration. Although clear phenotypes have not yet been unambiguously identified in patient-derived dopaminergic neurons, there are suggested aberrations in cellular pathways involved in neurodegeneration. Overall, these cells offer a unique opportunity to study dopaminergic neurons carrying a ‘Parkinsonian genome’. The present review discusses the advances in cellular reprogramming technologies and studies that have been carried out on PD-derived iPSCs and differentiated dopaminergic neurons.
Evolutionary selection for protein aggregation
Authors: Sanchez de Groot Natalia , Torrent Marc , Villar-Piqué Anna , Lang Benjamin , Ventura Salvador , Gsponer Jörg , Babu M. Madan
Published: November 2012

Protein aggregation is being found to be associated with an increasing number of human diseases. Aggregation can lead to a loss of function (lack of active protein) or to a toxic gain of function (cytotoxicity associated with protein aggregates). Although potentially harmful, protein sequences predisposed to aggregation seem to be ubiquitous in all kingdoms of life, which suggests an evolutionary advantage to having such segments in polypeptide sequences. In fact, aggregation-prone segments are essential for protein folding and for mediating certain protein–protein interactions. Moreover, cells use protein aggregates for a wide range of functions. Against this background, life has adapted to tolerate the presence of potentially dangerous aggregation-prone sequences by constraining and counteracting the aggregation process. In the present review, we summarize the current knowledge of the advantages associated with aggregation-prone stretches in proteomes and the strategies that cellular systems have developed to control the aggregation process.
Interplay between allostery and intrinsic disorder in an ensemble
Authors: Motlagh Hesam N. , Li Jing , Thompson E. Brad , Hilser Vincent J.
Published: November 2012

Allostery is a biological phenomenon of critical importance in metabolic regulation and cell signalling. The fundamental premise of classical models that describe allostery is that structure mediates ‘action at a distance’. Recently, this paradigm has been challenged by the enrichment of IDPs (intrinsically disordered proteins) or ID (intrinsically disordered) segments in transcription factors and signalling pathways of higher organisms, where an allosteric response from external signals is requisite for regulated function. This observation strongly suggests that IDPs elicit the capacity for finely tunable allosteric regulation. Is there a set of transferable ground rules that reconcile these disparate allosteric phenomena? We focus on findings from the human GR (glucocorticoid receptor) which is a nuclear transcription factor in the SHR (steroid hormone receptor) family. GR contains an intrinsically disordered NTD (N-terminal domain) that is obligatory for transcription activity. Different GR translational isoforms have various lengths of NTD and by studying these isoforms we found that the full-length ID NTD consists of two thermodynamically distinct coupled regions. The data are interpreted in the context of an EAM (ensemble allosteric model) that considers only the intrinsic and measurable energetics of allosteric systems. Expansion of the EAM is able to reconcile the paradox that ligands for SHRs can be agonists and antagonists in a cell-context-dependent manner. These findings suggest a mechanism by which SHRs in particular, and IDPs in general, may have evolved to couple thermodynamically distinct ID segments. The ensemble view of allostery that is illuminated provides organizing principles to unify the description of all allosteric systems and insight into ‘how’ allostery works.
Deciphering the function of leucine-rich repeat kinase 2 and targeting its dysfunction in disease
Authors: Lewis Patrick A. , Alessi Dario R.
Published: November 2012

LRRK2 (leucine-rich repeat kinase 2) is a gene of unknown function that has been linked to a number a human diseases, including PD (Parkinson's disease), IBD (inflammatory bowel disease), leprosy and cancer. The papers from the LRRK2: Function and Dysfunction meeting in this issue of Biochemical Society Transactions explore our growing knowledge of LRRK2's normal function, the role that it plays in disease and emerging strategies to exploit LRRK2 as a therapeutic target.