bluuebunny/crossref_metadata_2025 huggingface dataset:
Present‐day and future contributions of glacier runoff to summertime flows in a Pacific Northwest watershed: Implications for water resources
Authors: Nolin Anne W. , Phillippe Jeff , Jefferson Anne , Lewis Sarah L.
Published: December 2010

While the impacts of long‐term climate change trends on glacier hydrology have received much attention, little has been done to quantify direct glacier runoff contributions to streamflow. This paper presents an approach for determining glacier runoff contributions to streamflow and estimating the effects of increased temperature and decreased glacier area on future runoff. We focus on late summer streamflow (when flow is lowest and nonglacier contributions to flow are minimal) of a small glacierized watershed on the flanks of Mount Hood, Oregon, United States. Field and lab measurements and satellite imagery were used in conjunction with a temperature‐index model of glacier runoff to simulate potential effects of increased temperature and reduction in glacier area on late summer runoff in the watershed. Discharge and stable isotope data show that 41–73% of late summer streamflow is presently derived directly from glacier melt. Model simulations indicate that while increased temperature leads to rapid glacier melt and therefore increased streamflow, the consequences of glacier recession overcomes this effect, ultimately leading to substantial declines in streamflow. Model sensitivity analyses show that simulation results are most sensitive to degree day factor and less sensitive to uncertainties in debris‐covered area and accumulation area ratio. This case study demonstrates that the effects of glacier recession on streamflow are a concern for water resource management at the local scale. This approach could also be extended to larger scales such as the upper Columbia River basin where glacier contributions to late summer flows are also thought to be substantial.
Organochlorine turnover in forest ecosystems: The missing link in the terrestrial chlorine cycle
Authors: Leri Alessandra C. , Myneni Satish C. B.
Published: December 2010

Research in the last 20 years has shown that chlorine undergoes transformations between inorganic and organic forms as part of a complex biogeochemical cycle in terrestrial systems. Natural organochlorine production appears to be associated with the decomposition of plant material on the soil surface, though the chlorine cycle budget implies that a proportion of natural organochlorine enters soil through plant litter and atmospheric deposition as well. Organochlorine compounds may form through biotic and abiotic pathways, but the rates and magnitude of production in the field remain undefined. We have performed a time‐dependent trace of chlorine concentration through forest ecosystems, revealing distinct fractions of naturally produced organochlorine in plant biomass. Aliphatic organochlorine constitutes an intrinsic component of healthy leaves that persists through senescence and humification of the plant material, making a substantial contribution to the pool of soil organochlorine. Plant leaves also contain soluble aromatic organochlorine compounds that leach from leaf litter during early decay stages. As decay progresses, high concentrations of insoluble aromatic organochlorine accrue in the humus, through de novo production as well as adsorption. The rates of aromatic organochlorine production and degradation vary seasonally and conversely. This study presents the first unambiguous evidence that there exist multiple pools of chlorinated organic matter in the soil environment and that leaf litter deposition makes a significant and refractory contribution to the soil organochlorine pool, providing key insights into the biogeochemical chlorine cycle.
The 7–8 August 2008 eruption of Kasatochi Volcano, central Aleutian Islands, Alaska
Authors: Waythomas Christopher F. , Scott William E. , Prejean Stephanie G. , Schneider David J. , Izbekov Pavel , Nye Christopher J.
Published: December 2010

Kasatochi volcano in the central Aleutian Islands erupted unexpectedly on 7–8 August 2008. Kasatochi has received little study by volcanologists and has had no confirmed historical eruptions. The island is an important nesting area for seabirds and a long‐term biological study site of the U.S. Fish and Wildlife Service. After a notably energetic preeruptive earthquake swarm, the volcano erupted violently in a series of explosive events beginning in the early afternoon of 7 August. Each event produced ash‐gas plumes that reached 14–18 km above sea level. The volcanic plume contained large amounts of SO2 and was tracked around the globe by satellite observations. The cumulative volcanic cloud interfered with air travel across the North Pacific, causing many flight cancelations that affected thousands of travelers. Visits to the volcano in 2008–2009 indicated that the eruption generated pyroclastic flows and surges that swept all flanks of the island, accumulated several tens of meters of pyroclastic debris, and increased the diameter of the island by about 800 m. Pyroclastic flow deposits contain abundant accidental lithic debris derived from the inner walls of the Kasatochi crater. Juvenile material is crystal‐rich silicic andesite that ranges from slightly pumiceous to frothy pumice. Fine‐grained pyroclastic surge and fall deposits with accretionary lapilli cover the lithic‐rich pyroclastic flow deposits and mark a change in eruptive style from episodic explosive activity to more continuous ash emission with smaller intermittent explosions. Pyroclastic deposits completely cover the island, but wave erosion and gully development on the flanks have begun to modify the surface mantle of volcanic deposits.
Thermomechanical models for the dynamics and melting processes in the Mariana subduction system
Authors: Lin Shu‐Chuan , Kuo Ban‐Yuan , Chung Sun‐Lin
Published: December 2010

Melt generation in the arc‐basin system of the subduction zones depends not only on fluid distribution and detailed temperature and pressure conditions, but also on melting mechanism and melting history. These factors are closely linked to the lithospheric extension, the proximity of the back‐arc basin to the arc, and the migration of the spreading center. In this study the evolution of the back‐arc basin is incorporated to explore the first‐order features of the dynamics and melting processes in the Mariana subduction zone, using coupled thermomechanical numerical experiments. In the models continuous stretching thins the lithosphere, ultimately resulting in breakup of the lithosphere. The spreading center develops and migrates subsequently to form the new ocean basin in the back‐arc region. Potential flux melting and decompression melting regimes are delineated based on the resultant thermal models, experimentally determined solidi, and phase diagrams. The results predict an overlap between the two regimes for several million years, suggesting that both melting mechanisms contribute to arc magma and back‐arc basin basalts during the rifting phases and the earlier stages of spreading. The decompression melting regime progressively separates from the flux melting regime as the ridge migrates along. The mantle flow field driven by subduction and spreading, together with the ridge migration, generate intricate particle paths. This could lead to multiphase melt extraction for both the arc magma and the back‐arc basin basalts and thus cause complex geochemical signatures. These processes may explain the first‐order geochemical characteristics observed in most of the Mariana arc‐basin system.
Development of crystallographic preferred orientation and microstructure during plastic deformation of natural coarse‐grained quartz veins
Authors: Pennacchioni Giorgio , Menegon Luca , Leiss Bernd , Nestola Fabrizio , Bromiley Geoffrey
Published: December 2010

The microstructure and crystallographic preferred orientation (CPO) of quartz were quantified in 17 samples of natural monomineralic tabular veins. The veins opened and were deformed, up to shear strain γ > 15, in a small temperature window (about 25°C) above 500°C, as established by Ti‐in‐quartz thermometry. The veins filled a set of fractures within the Adamello tonalite (southern Alps, Italy) and localized homogeneous simple shear during postmagmatic cooling. The local (square millimeter scale) and bulk (square centimeter) CPO were investigated by computer‐integrated polarization microscopy (CIP) and X‐ray texture goniometry. Weakly deformed veins (WDV: γ < 1) consist of millimeter‐ to centimeter‐sized crystals with a strong CPO showing a c‐axis girdle slightly inclined, mostly with the shear sense, to the foliation (XY) plane and a strong maximum close to the lineation (X). Moderately deformed veins (MDV: 2 < γ < 3) consist of elongated nonrecrystallized ribbon grains and most have a CPO showing a strong Y maximum of c axes some with weak extension into a YZ girdle. Strongly deformed veins (SDV: γ = 4 to 15) are pervasively to completely recrystallized to fine (34–40 μm grain size) aggregates with a strong CPO similar to that of MDV. The slip systems during plastic deformation were dominantly prism 〈a〉 with subordinate rhomb and basal 〈a〉 slip. Recrystallization occurred rather abruptly for 3 < γ < 4. In contrast to dislocation creep experiments in quartz (and other minerals), a steady‐state recrystallized fabric is achieved at early stages of deformation (γ ≈ 4) as there is no evidence, with increasing strain, of strengthening of the CPO, of rotation of the fabric skeleton, or of change in grain size. WDV represent weakly deformed relicts of veins with an initial CPO believed to have developed during crystal growth but unsuitably oriented for prism 〈a〉 slip during subsequent shear. MDV and SDV appear to derive from veins different from WDV, where the vein crystals grew with orientation favorable for prism 〈a〉 slip. The relationship between the initial growth CPO and the kinematic framework suggests that veins opened at a temperature close to that at which there is a switch between the activity of prism 〈c〉 and prism 〈a〉 slip, with the temperature of growth causing growth of crystals well oriented for slip. The initial CPO of veins, from which quartz mylonites are commonly derived, plays a critical role in the fabric evolution. The strong growth‐ and strain‐induced CPOs of these sheared veins inhibited significant reworking during lower temperature stages of pluton cooling when basal 〈a〉 slip would have been dominant.
Diverse slow slip behavior at the Hikurangi subduction margin, New Zealand
Authors: Wallace Laura M. , Beavan John
Published: December 2010

The installation of a continuous GPS (cGPS) network in New Zealand since 2002 has enabled the discovery of 15 slow slip events at the Hikurangi subduction margin. Our analysis and interpretation of the cGPS data reveal a marked diversity in characteristics of slow slip events (SSEs) in the North Island, with durations varying from 6 days to 1.5 years, equivalent moment release between Mw 6.3–7.2, and recurrence intervals of repeating SSEs on the order of 2 years to more than 5 years. The duration and magnitude characteristics of Hikurangi SSEs appear to be related to the depth where they occur. The deepest, longest duration, and largest SSEs occur at the southern Hikurangi margin, near the downdip limit of deep (down to ∼40 km depth), strong interseismic coupling. The shallowest, shortest duration, smallest, and most frequent SSEs occur at the northern and central Hikurangi margin near the downdip limit of unusually shallow (<10–15 km depth) interseismic coupling. The direction of slip on the interface in the Hikurangi SSEs is consistent with slip partitioning at the Hikurangi subduction margin. We also show that moment accumulation rates on the interface for the time periods between SSEs are ∼40% higher than for the period of more than a decade averaging through the SSEs, indicating that SSEs compose a major portion of the overall moment release budget of the Hikurangi subduction interface.
Simulating the one‐dimensional structure of Titan's upper atmosphere: 1. Formulation of the Titan Global Ionosphere‐Thermosphere Model and benchmark simulations
Authors: Bell Jared M. , Bougher Stephen W. , Waite J. Hunter , Ridley Aaron J. , Magee Brian A. , Mandt Kathleen E. , Westlake Joseph , DeJong Anna D. , Bar–Nun Akiva , Jacovi Ronen , Toth Gabor , De La Haye Virginie
Published: December 2010

We employ a newly developed Navier‐Stokes model, the Titan Global Ionosphere‐Thermosphere Model (T‐GITM) to address the one dimensional (1‐D) coupled composition, dynamics, and energetics of Titan's upper atmosphere. Our main goals are to delineate the details of this new theoretical tool and to present benchmark calibration simulations compared against the Ion‐Neutral Mass Spectrometer (INMS) neutral density measurements. First, we outline the key physical routines contained in T‐GITM and their computational formulation. Then, we compare a series of model simulations against recent 1‐D work by Cui et al. (2008), Strobel (2008, 2009), and Yelle et al. (2008) in order to provide a fiducial for calibrating this new model. In paper 2 and a future paper, we explore the uncertainties in our knowledge of Titan's atmosphere between ∼500 km and 1000 km in order to determine how the present measurements constrain our theoretical understanding of atmospheric structures and processes.
Effects of wave forcing on a subterranean estuary
Authors: Xin Pei , Robinson Clare , Li Ling , Barry D. A. , Bakhtyar R.
Published: December 2010

Wave and tide are important forcing factors that typically coexist in coastal environments. A numerical study was conducted to investigate individual and combined effects of these forces on flow and mixing processes in a nearshore subterranean estuary. A hydrodynamic model based on the shallow water equations was used to simulate dynamic sea level oscillations driven by wave and tide. The oscillating sea levels determined the seaward boundary condition of the coastal aquifer, where variably saturated, variable density flow was modeled. The simulation results showed that waves induced an onshore upward tilt in the phase‐averaged sea level (wave setup). The resulting hydraulic gradient generated pore water circulations in the nearshore zone of the coastal aquifer, which led to formation of an upper saline plume (USP) similar to that formed due to tides. However, mixing of recirculating seawater in the USP with underlying fresh groundwater was less intensive under the high‐frequency wave oscillations. In the case of combined forcing, wave‐induced circulations coupled with the intratidal flows strengthened the averaged, circulating pore water flows in the nearshore zone over the tidal period. The circulating flows increased exchange between the subterranean estuary and ocean, contributing 61% of the total submarine groundwater discharge for the simulated condition in comparison with the 40% and 49% proportions caused by the same but separate tidal and wave forcing, respectively. The combined forces also created a more extensive USP with the freshwater discharge zone shifted farther seaward. The freshwater flow paths in the intertidal subterranean estuary were modified with a significant increase in the associated transit times. The interplay of wave and tide led to increased mixing between discharging fresh groundwater and recirculating seawater. These results further demonstrate the complexity of nearshore groundwater systems and have implications for future investigations on the fate of land‐sourced chemicals in the subterranean estuary prior to discharge to the ocean.
Mucolipidosis type IV and the mucolipins
Authors: Bach Gideon , Zeevi David A. , Frumkin Ayala , Kogot-Levin Aviram
Published: December 2010

MLIV (mucolipidosis type IV) is a neurodegenerative lysosomal storage disorder caused by mutations in MCOLN1, a gene that encodes TRPML1 (mucolipin-1), a member of the TRPML (transient receptor potential mucolipin) cation channels. Two additional homologues are TRPML2 and TRPML3 comprising the TRPML subgroup in the TRP superfamily. The three proteins play apparently key roles along the endocytosis process, and thus their cellular localization varies among the different group members. Thus TRPML1 is localized exclusively to late endosomes and lysosomes, TRPML2 is primarily located in the recycling clathrin-independent GPI (glycosylphosphatidylinositol)-anchored proteins and early endosomes, and TRPML3 is primarily located in early endosomes. Apparently, all three proteins' main physiological function underlies Ca2+ channelling, regulating the endocytosis process. Recent findings also indicate that the three TRPML proteins form heteromeric complexes at least in some of their cellular content. The physiological role of these complexes in lysosomal function remains to be elucidated, as well as their effect on the pathophysiology of MLIV. Another open question is whether any one of the TRPMLs bears additional function in channel activity
Storage problems in lysosomal diseases
Authors: Heard Jean Michel , Bruyère Julie , Roy Elise , Bigou Stéphanie , Ausseil Jérôme , Vitry Sandrine
Published: December 2010

Biochemical disorders in lysosomal storage diseases consist of the interruption of metabolic pathways involved in the recycling of the degradation products of one or several types of macromolecules. The progressive accumulation of these primary storage products is the direct consequence of the genetic defect and represents the initial pathogenic event. Downstream consequences for the affected cells include the accumulation of secondary storage products and the formation of histological storage lesions, which appear as intracellular vacuoles that represent the pathological hallmark of lysosomal storage diseases. Relationships between storage products and storage lesions are not simple and are still largely not understood. Primary storage products induce malfunction of the organelles where they accumulate, these being primarily, but not only, lysosomes. Consequences for cell metabolism and intracellular trafficking combine the effects of primary storage product toxicity and the compensatory mechanisms activated to protect the cell. Induced disorders extend far beyond the primarily interrupted metabolic pathway.
Molecular mechanisms of pathogenesis in a glycosphingolipid and a glycoprotein storage disease
Authors: d'Azzo Alessandra , Bonten Erik
Published: December 2010

The lysosomal system comprises a specialized network of organelles crucial for the sorting, digestion, recycling and secretion of cellular components. With their content of hydrolytic enzymes, lysosomes regulate the degradation of a multitude of substrates that reach these organelles via the biosynthetic or the endocytic route. Gene defects that affect one or more of these hydrolases lead to LSDs (lysosomal storage diseases). This underscores the apparent lack of redundancy of these enzymes and the importance of the lysosomal system in cell and tissue homoeostasis. Some of the lysosomal enzymes may form multiprotein complexes, which usually work synergistically on substrates and, in this configuration, may respond more efficiently to changes in substrate load and composition. A well-characterized lysosomal multienzyme complex is the one comprising the glycosidases β-gal (β-galactosidase) and NEU1 (neuramidase-1), and of the serine carboxypeptidase PPCA (protective protein/cathepsin A). Three neurodegenerative LSDs are caused by either single or combined deficiency of these lysosomal enzymes. Sialidosis (NEU1 deficiency) and galactosialidosis (combined NEU1 and β-gal deficiency, secondary to a primary defect of PPCA) belong to the glycoprotein storage diseases, whereas GM1-gangliosidosis (β-gal deficiency) is a glycosphingolipid storage disease. Identification of novel molecular pathways that are deregulated because of loss of enzyme activity and/or accumulation of specific metabolites in various cell types has shed light on mechanisms of disease pathogenesis and may pave the way for future development of new therapies for these LSDs.
Treatments for lysosomal storage disorders
Authors: Lachmann Robin
Published: December 2010

There are over 70 human diseases that are caused by defects in various aspects of lysosomal function. Until 20 years ago, the only specific therapy available for lysosomal storage disorders was allogeneic haemopoietic stem cell transplantation. Over the last two decades, there has been remarkable progress and there are now licensed treatments for seven of these diseases. In some cases, a choice of agents is available. For selected enzyme-deficiency disordes, ERT (enzyme-replacement therapy) has proved to be highly effective. In other cases, ERT has been less impressive, and it seems that it is not possible to efficiently deliver recombinant enzyme to all tissues. These difficulties have led to the development of other small-molecule-based therapies, and a drug for SRT (substrate-reduction therapy) is now licensed and potential chaperone molecules for ERT are in the late stages of clinical development. Nonetheless, there is still significant unmet clinical need, particularly when it comes to treating LSDs which affect the brain. LSDs have led the way in the development of treatment for genetic disorders, and it seems likely that there will be further therapeutic innovations in the future.
Presenilins: how much more than γ-secretase?!
Authors: Coen Katrijn , Annaert Wim
Published: December 2010

AD (Alzheimer's disease) is a neurodegenerative disease characterized by a gradual loss of neurons and the accumulation of neurotoxic Aβ (amyloid β-peptide) and hyperphosphorylated tau. The discovery of mutations in three genes, PSEN1 (presenilin 1), PSEN2 (presenilin 2) and APP (amyloid precursor protein), in patients with FAD (familial AD) has made an important contribution towards an understanding of the disease aetiology; however, a complete molecular mechanism is still lacking. Both presenilins belong to the γ-secretase complex, and serve as the catalytic entity needed for the final cleavage of APP into Aβ. PSEN only functions within the γ-secretase complex through intra- and inter-molecular interactions with three other membrane components, including nicastrin, Aph-1 (anterior pharynx defective-1) and Pen-2 (PSEN enhancer-2). However, although the list of γ-secretase substrates is still expanding, other non-catalytic activities of presenilins are also increasing the complexity behind its molecular contribution towards AD. These γ-secretase-independent roles are so far mainly attributed to PSEN1, including the transport of membrane proteins, cell adhesion, ER (endoplasmic reticulum) Ca2+ regulation and cell signalling. In the present minireview, we discuss the current understanding of the γ-secretase-independent roles of PSENs and their possible implications in respect of AD.
Nonsense-mediated mRNA decay and development: shoot the messenger to survive?
Authors: Vicente-Crespo Marta , Palacios Isabel M.
Published: December 2010

NMD (nonsense-mediated mRNA decay) is a surveillance mechanism that degrades transcripts containing nonsense mutations, preventing the translation of potentially harmful truncated proteins. Although the mechanistic details of NMD are gradually being understood, the physiological role of this RNA surveillance pathway still remains largely unknown. The core NMD genes Upf1 (up-frameshift suppressor 1) and Upf2 are essential for animal viability in the fruitfly, mouse and zebrafish. These findings may reflect an important role for NMD during animal development. Alternatively, the lethal phenotypes of upf1 and upf2 mutants might be due to their function in NMD-independent processes. In the present paper, we describe the phenotypes observed when the NMD factors are mutated in various organisms, and discuss findings that might shed light on the function of NMD in cellular growth and development of an organism.
Manipulation of the host translation initiation complex eIF4F by DNA viruses
Authors: Walsh Derek
Published: December 2010

In the absence of their own translational machinery, all viruses must gain access to host cell ribosomes to synthesize viral proteins and replicate. Ribosome recruitment and scanning of capped host mRNAs is facilitated by the multisubunit eIF (eukaryotic initiation factor) 4F, which consists of a cap-binding protein, eIF4E and an RNA helicase, eIF4A, assembled on a large scaffolding protein, eIF4G. Although inactivated by many viruses to inhibit host translation, a growing number of DNA viruses are being found to employ diverse strategies to stimulate eIF4F activity in infected cells and maximize viral protein synthesis. These strategies include stimulation of cellular mTOR (mammalian target of rapamycin) signalling to inactivate 4E-BPs (eIF4E-binding proteins), a family of translational repressors that limit eIF4E availability and eIF4F complex formation, together with modulating the activity of the eIF4E kinase Mnk (mitogen-activated protein kinase signal-integrating kinase) in a variety of manners to regulate both host and viral mRNA translation. In some cases, specific viral proteins that mediate these signalling events have been identified, whereas others have been shown to interact with host translation initiation factors or complexes and modify their activity and/or subcellular localization. The present review outlines current understanding of the role of eIF4F in the life cycle of various DNA viruses and discusses its potential as a therapeutic target to suppress viral infection.
Translational control of synaptic plasticity
Authors: Richter Joel D.
Published: December 2010

Synapses, points of contact between axons and dendrites, are conduits for the flow of information in the circuitry of the central nervous system. The strength of synaptic transmission reflects the interconnectedness of the axons and dendrites at synapses; synaptic strength in turn is modified by the frequency with which the synapses are stimulated. This modulation of synaptic strength, or synaptic plasticity, probably forms the cellular basis for learning and memory. RNA metabolism, particularly translational control at or near the synapse, is one process that controls long-lasting synaptic plasticity and, by extension, memory formation and consolidation. In the present paper, I review some salient features of translational control of synaptic plasticity.
The different pathways of HIV genomic RNA translation
Authors: Chamond Nathalie , Locker Nicolas , Sargueil Bruno
Published: December 2010

Lentiviruses, the prototype of which is HIV-1, can initiate translation either by the classical cap-dependent mechanism or by internal recruitment of the ribosome through RNA domains called IRESs (internal ribosome entry sites). Depending on the virus considered, the mechanism of IRES-dependent translation differs widely. It can occur by direct binding of the 40S subunit to the mRNA, necessitating a subset or most of the canonical initiation factors and/or ITAF (IRES trans-acting factors). Nonetheless, a common feature of IRESs is that ribosomal recruitment relies, at least in part, on IRES structural determinants. Lentiviral genomic RNAs present an additional level of complexity, as, in addition to the 5′-UTR (untranslated region) IRES, the presence of a new type of IRES, embedded within Gag coding region was described recently. This IRES, conserved in all three lentiviruses examined, presents conserved structural motifs that are crucial for its activity, thus reinforcing the link between RNA structure and function. However, there are still important gaps in our understanding of the molecular mechanism underlying IRES-dependent translation initiation of HIV, including the determination of the initiation factors required, the dynamics of initiation complex assembly and the dynamics of the RNA structure during initiation complex formation. Finally, the ability of HIV genomic RNA to initiate translation through different pathways questions the possible mechanisms of regulation and their correlation to the viral paradigm, i.e. translation versus encapsidation of its genomic RNA.
Regulation and biological function of the liver-specific miR-122
Authors: Lewis Andrew P. , Jopling Catherine L.
Published: December 2010

miRNAs (microRNAs) are important regulators of gene expression. In higher eukaryotes, the tightly controlled expression of different miRNAs, each of which regulates multiple target mRNAs, is crucial for the maintenance of tissue type and the control of differentiation. miR-122 is a highly liver-specific miRNA that is important in hepatitis C virus infection, cholesterol metabolism and hepatocellular carcinoma. In the present review, we discuss the effects of miR-122 on liver physiology and pathology. Recent evidence of pathways involved in the regulation of miR-122 expression is also considered.
The involvement of microRNAs in Type 2 diabetes
Authors: Ferland-McCollough David , Ozanne Susan E. , Siddle Kenneth , Willis Anne E. , Bushell Martin
Published: December 2010

T2D (Type 2 diabetes mellitus) is a major health issue that has reached epidemic status worldwide. T2D is a progressive metabolic disorder characterized by reduced insulin sensitivity, insulin resistance and pancreatic β-cell dysfunction. Improper treatment of TD2 can lead to severe complications such as heart disease, stroke, kidney failure, blindness and nerve damage. The aetiology and molecular mechanisms of T2D are not fully understood, but compelling evidence points to a link between T2D, obesity, dyslipidaemia and insulin resistance. Although T2D seems to be strongly linked to environmental factors such as nutrition and lifestyle, studies have shown that genetic factors, such as polymorphisms associated with metabolic genes, imprinting, fetal programming and miRNA (microRNA) expression, could also contribute to the development of this disease. miRNAs are small 22–25-nt-long untranslated RNAs that negatively regulate the translation of mRNAs. miRNAs are involved in a large number of biological functions such as development, metabolism, immunity and diseases such as cancer, cardiovascular diseases and diabetes. The present review examines the various miRNAs that have been identified as being potentially involved in T2D, focusing on the insulin-sensitive organs: white adipose tissue, liver, skeletal muscle and the insulin-producing pancreatic β-cells.
Elucidating mechanistic principles underpinning eukaryotic translation initiation using quantitative fluorescence methods
Authors: Stevenson Abigail L. , Juanes Pedro P. , McCarthy John E.G.
Published: December 2010

Eukaryotic translation initiation is an intricate process involving at least 11 formally classified eIFs (eukaryotic initiation factors), which, together with the ribosome, comprise one of the largest molecular machines in the cell. Studying such huge macromolecular complexes presents many challenges which cannot readily be overcome by traditional molecular and structural methods. Increasingly, novel quantitative techniques are being used to further dissect such complex assembly pathways. One area of methodology involves the labelling of ribosomal subunits and/or eIFs with fluorophores and the use of techniques such as FRET (Förster resonance energy transfer) and FA (fluorescence anisotropy). The applicability of such techniques in such a complex system has been greatly enhanced by recent methodological developments. In the present mini-review, we introduce these quantitative fluorescence methods and discuss the impact they are beginning to have on the field.
Translation deregulation in B-cell lymphomas
Authors: Horvilleur Emilie , Wilson Lindsay A. , Willis Anne E.
Published: December 2010

B-cell lymphomas are a heterogeneous group of diseases that can arise at different stages of B-cell development, often as a result of errors in the cells' unique ontogeny. Common oncogenic features are often observed, including chromosomal rearrangements, somatic mutations and transcriptional change. Disruption of translation regulation is also frequently implicated in both B-cell lymphoma development and progression. Deregulation of translation in lymphomagenesis can arise through changes to the proteins constituting the translational machinery or to their regulators, and to changes in miRNA (microRNA) expression.
Pat1 proteins: a life in translation, translation repression and mRNA decay
Authors: Marnef Aline , Standart Nancy
Published: December 2010

Pat1 proteins are conserved across eukaryotes. Vertebrates have evolved two Pat1 proteins paralogues, whereas invertebrates and yeast only possess one such protein. Despite their lack of known domains or motifs, Pat1 proteins are involved in several key post-transcriptional mechanisms of gene expression control. In yeast, Pat1p interacts with translating mRNPs (messenger ribonucleoproteins), and is responsible for translational repression and decapping activation, ultimately leading to mRNP degradation. Drosophila HPat and human Pat1b (PatL1) proteins also have conserved roles in the 5′→3′ mRNA decay pathway. Consistent with their functions in silencing gene expression, Pat1 proteins localize to P-bodies (processing bodies) in yeast, Drosophila, Caenorhabditis elegans and human cells. Altogether, Pat1 proteins may act as scaffold proteins allowing the sequential binding of repression and decay factors on mRNPs, eventually leading to their degradation. In the present mini-review, we present the current knowledge on Pat1 proteins in the context of their multiple functions in post-transcriptional control.
Analysis of post-transcriptional regulation using the FunREG method
Authors: Laloo Benoît , Maurel Marion , Jalvy-Delvaille Sandra , Sagliocco Francis , Grosset Christophe F.
Published: December 2010

An increasing number of arguments, including altered microRNA expression, support the idea that post-transcriptional deregulation participates in gene disturbances found in diseased tissues. To evaluate this hypothesis, we developed a method which facilitates post-transcriptional investigations in a wide range of human cells and experimental conditions. This method, called FunREG (functional, integrated and quantitative method to measure post-transcriptional regulation), connects lentiviral transduction with a fluorescent reporter system and quantitative PCR. Using FunREG, we efficiently measured post-transcriptional regulation mediated either by selected RNA sequences or regulatory factors (microRNAs), and then evaluated the contribution of mRNA decay and translation efficiency in the observed regulation. We demonstrated the existence of gene-specific post-transcriptional deregulation in liver tumour cells, and also reported a molecular link between a transcript variant abrogating HDAC6 (histone deacetylase 6) regulation by miR-433 and a rare familial genetic disease. Because FunREG is sensitive, quantitative and easy to use, many applications can be envisioned in fundamental and pathophysiological research.
Aneuploidy as an early mechanistic event in metal carcinogenesis
Authors: Wise Sandra S. , Wise John Pierce
Published: December 2010

Aneuploidy has recently been proposed as an initiating event for carcinogenesis. There is significant evidence that carcinogenic metals induce aneuploidy. Here we review the mechanisms for how carcinogenic metals may induce aneuploidy and the evidence that carcinogenic metals induce an aneugenic effect which can destabilize the genome leading to genomic instability and cancer.
Use of DT40 conditional-knockout cell lines to study chromosomal passenger protein function
Authors: Fant Xavier , Samejima Kumiko , Carvalho Ana , Ogawa Hiromi , Xu Zhenjie , Yue Zuojun , Earnshaw William C. , Ruchaud Sandrine
Published: December 2010

The CPC [chromosomal passenger complex; INCENP (inner centromere protein), Aurora B kinase, survivin and borealin] is implicated in many mitotic processes. In the present paper we describe how we generated DT40 conditional-knockout cell lines for incenp1 and survivin1 to better understand the role of these CPC subunits in the control of Aurora B kinase activity. These lines enabled us to reassess current knowledge of survivin function and to show that INCENP acts as a rheostat for Aurora B activity.
Synapsis and recombination in inversion heterozygotes
Authors: Torgasheva Anna A. , Borodin Pavel M.
Published: December 2010

Inversion heterozygotes are expected to suffer from reduced fertility and a high incidence of chromosomally unbalanced gametes due to recombination within the inverted region. Non-homologous synapsis of the inverted regions can prevent recombination there and diminish the deleterious effects of inversion heterozygosity. The choice between non-homologous and homologous synapsis depends on the size of inversion, its genetic content, its location in relation to the centromere and telomere, and genetic background. In addition, there is a class of inversions in which homologous synapsis is gradually replaced by non-homologous synapsis during meiotic progression. This process is called synaptic adjustment. The degree of synaptic adjustment depends critically on the presence and location of the COs (crossovers) within the inversion loop. Only bivalents without COs within the loop and those with COs in the middle of the inversion can be completely adjusted and became linear.
Induction of chromosome malsegregation by nanomaterials
Authors: Gonzalez Laetitia , Decordier Ilse , Kirsch-Volders Micheline
Published: December 2010

NMs (nanomaterials), defined as materials with at least one dimension smaller than 100 nm, are able to induce genotoxic effects. One of the hypotheses of the mode-of-action in which they exert their genotoxic potential is to mechanically interfere with subcellular structures, in particular the microtubules. In the present paper, we review studies exploring interactions between NMs and tubulin; therefore a PubMed literature search was performed. From this search 12 studies, applying both acellular and cellular assays, were retrieved and are summarized according to endpoint and particle type. These studies show that there are interactions between different types of NMs and tubulins in both acellular and cellular systems. For several types of NMs, the multi-walled carbon nanotubes, amorphous SiO2, TiO2 and CoCr, an induction of aneuploidy was observed in vitro. There is, therefore, a critical need to assess the capacity of NMs to interfere with the cytoskeleton, and in particular the tubulins. This might require definition of relevant dosimetry, adaptations of some testing protocols, possibly development of new methodologies and studies on a larger size-range of NMs.
Group Intervention for Adolescents With Chronic Acquired Brain Injury: The Future Zone
Authors: Hickey Ellen M. , Saunders Jennifer N.
Published: December 2010

Introduction: Acquired brain injury (ABI) is a common cause of social cognition deficits and psychosocial challenges in adolescents. A group intervention program was designed to support teens with chronic ABI.

Method: Quantitative and qualitative analyses were conducted to examine participants' self-knowledge and satisfaction with the program.

Results: Results revealed that participants and parents valued increased self-knowledge and an understanding of brain injuries, the focus on friendships and individual strengths, and feelings of togetherness and not being judged.

Discussion: Support for strength-based, project-oriented, group intervention programs for adolescents with ABI and directions for future research are discussed.
Note: Multivariate system spectroscopic model using Lorentz oscillators and partial least squares regression analysis
Authors: Gad R. S. , Parab J. S. , Naik G. M.
Published: December 2010

Multivariate system spectroscopic model plays important role in understanding chemometrics of ensemble under study. Here in this manuscript we discuss various approaches of modeling of spectroscopic system and demonstrate how Lorentz oscillator can be used to model any general spectroscopic system. Chemometric studies require customized templates design for the corresponding variants participating in ensemble, which generates the characteristic matrix of the ensemble under study. The typical biological system that resembles human blood tissue consisting of five major constituents i.e., alanine, urea, lactate, glucose, ascorbate; has been tested on the model. The model was validated using three approaches, namely, root mean square error (RMSE) analysis in the range of ±5% confidence interval, clerk gird error plot, and RMSE versus percent noise level study. Also the model was tested across various template sizes (consisting of samples ranging from 10 up to 1000) to ascertain the validity of partial least squares regression. The model has potential in understanding the chemometrics of proteomics pathways.
Effect of Cr concentration on resistance switching in Cr-doped SrZrO3 films and surface accumulation of Cr ions
Authors: Cho Suyeon , Park W. G. , Cho Deok-Yong , Berthet P. , Oh S.-J.
Published: December 2010

The role of Cr ions in the resistance switching (RS) of Cr-doped SrZrO3 films has been investigated by x-ray photoelectron spectroscopy and electric current measurements. The results show that the RS behavior depends on the Cr concentration, substrate temperature during film growth, and oxygen pressure during the postannealing process. Migration of Cr3+ ions to the surface makes the surface Cr rich, and thus, appreciable RS is observed. These observations suggest that the RS behavior can be controlled by trapping and releasing Cr carriers in the interface region between the film and the electrode.
Double-pass tapered amplifier diode laser with an output power of 1 W for an injection power of only 200 μW
Authors: Bolpasi V. , von Klitzing W.
Published: December 2010

A 1 W tapered amplifier requiring only 200 μW of injection power at 780 nm is presented in this paper. This is achieved by injecting the seeding light into the amplifier from its tapered side and feeding the amplified light back into the small side. The amplified spontaneous emission of the tapered amplifier is suppressed by 75 dB. The double-passed tapered laser, presented here, is extremely stable and reliable. The output beam remains well coupled to the optical fiber for a timescale of months, whereas the injection of the seed light did not require realignment for over a year of daily operation.
Carrier-depletion in the stripe-length method: Consequences for gain measurement
Authors: Lange C. , Schwalm M. , Metzger B. , Chatterjee S.
Published: December 2010

The variable stripe-length method is considered a powerful yet easily implemented approach to measure the optical material gain of a semiconductor sample. However, the results obtained with this method are not as straightforward to interpret as originally suggested. Here, we discuss the general validity of the method by calculating the influence of carrier depletion on the emission of the sample—and thus the extracted gain—on the basis of a semiclassical description. We find that the method must only be applied within a narrow parameter window, and that even then, unreliable values may be obtained.
Euler characteristic of coherent sheaves on simplicial torics via the Stanley–Reisner ring
Authors: Schenck Hal
Published: December 2010

We combine work of Cox on the total coordinate ring of a toric variety and results of Eisenbud–Mustaţǎ–Stillman and Mustaţǎ on cohomology of toric and monomial ideals to obtain a formula for computing \documentclass[12pt]{minimal}\begin{document}$\chi (\mathcal {O}_X(D))$\end{document}χ(OX(D)) for a Weil divisor D on a complete simplicial toric variety XΣ. The main point is to use Alexander duality to pass from the toric irrelevant ideal, which appears in the computation of \documentclass[12pt]{minimal}\begin{document}$\chi (\mathcal {O}_X(D))$\end{document}χ(OX(D)), to the Stanley–Reisner ideal of Σ, which is used in defining the Chow ring of XΣ.
Photodissociation dynamics of ionic argon pentamer
Authors: Pukowiecová Pavla , Gadea Florent Xavier , Kalus René
Published: December 2010

Photodissociation of the ionized argon pentamer, Ar5+, is studied using an extended diatomics-in-molecules interaction model with the inclusion of the spin-orbit coupling and various dynamical approaches. A thorough comparison with the experimental data available in the literature is presented, including photofragment abundances and their kinetic and internal energy distributions. New predictions are reported for ultraviolet photoexcitation energies, a range that has not been studied before either experimentally or theoretically.
Crystalline free energies of micelles of diblock copolymer solutions
Authors: D’Adamo Giuseppe , Pierleoni Carlo
Published: December 2010

We report a characterization of the relative stability and structural behavior of various micellar crystals of an athermal model of AB-diblock copolymers in solution. We adopt a previously developed coarse-graining representation of the chains which maps each copolymer on a soft dumbbell. Thanks to this strong reduction of degrees of freedom, we are able to investigate large aggregated systems and for a specific length ratio of the blocks f = MA/(MA + MB) = 0.6, to locate the order–disorder transition of the system of micelles. Above the transition, mechanical and thermal properties are found to depend on the number of particles per lattice site in the simulation box, and the application of a recent methodology for multiple occupancy crystals [B. M. Mladek et al., Phys. Rev. Lett. 99, 235702 (2007)] is necessary to correctly define the equilibrium state. Within this scheme we have performed free energy calculations at two reduced density ρ/ρ* = 4, 5 and for several cubic structures such as fcc, bcc, and A15. At both densities, the bcc symmetry is found to correspond to the minimum of the unconstrained free energy, that is to the stable symmetry among the few considered, while the A15 structure is almost degenerate, indicating that the present system prefers to crystallize in less packed structures. At ρ/ρ* = 4 close to melting, the Lindemann ratio is fairly high (∼0.29) and the concentration of vacancies is roughly 6%. At ρ/ρ* = 5 the mechanical stability of the stable bcc structure increases and the concentration of vacancies accordingly decreases. The ratio of the corona layer thickness to the core radius is found to be in good agreement with experimental data for poly(styrene-b-isoprene)(22-12) in isoprene selective solvent which is also reported to crystallize in the bcc structure.
Collocation method for fractional quantum mechanics
Authors: Amore Paolo , Fernández Francisco M. , Hofmann Christoph P. , Sáenz Ricardo A.
Published: December 2010

We show that it is possible to obtain numerical solutions to quantum mechanical problems involving a fractional Laplacian, using a collocation approach based on little sinc functions, which discretizes the Schrödinger equation on a uniform grid. The different boundary conditions are naturally implemented using sets of functions with the appropriate behavior. Good convergence properties are observed. A comparison with results based on a Wentzel–Kramers–Brillouin analysis is performed.
The martensitic transformation, magnetocaloric effect, and magnetoresistance in high-Mn content Mn47+xNi43−xSn10 ferromagnetic shape memory alloys
Authors: Xuan H. C. , Zheng Y. X. , Ma S. C. , Cao Q. Q. , Wang D. H. , Du Y. W.
Published: December 2010

A series of high-Mn content Mn47+xNi43−xSn10 (x=0, 1, 2, 3, 4, and 5) ferromagnetic shape memory alloys were prepared by arc melting method. The martensitic transformation were observed in these alloys, even the content of Mn is higher than 50 at. %. The phase transition temperature of these alloys can be adjusted by tuning the compositions of Ni and Mn. Large positive magnetic entropy change and negative magnetoresistance which originate from the magnetic-field-induced martensitic transformation are obtained in these alloys.