bluuebunny/crossref_metadata_2025 huggingface dataset:
The Benguela upwelling related to the Miocene cooling events and the development of the Antarctic Circumpolar Current: Evidence from calcareous dinoflagellate cysts
Authors: Heinrich Sonja , Zonneveld Karin A. F. , Bickert Torsten , Willems Helmut
Published: August 2011

Sediment samples from ODP Site 1085 were investigated in order to obtain more information on the initiation and development of the Benguela upwelling system during the middle and upper Miocene. In particular, our intent was to establish the causes of the upwelling as well as the response of the upwelling regime to the development of the Antarctic Circumpolar Current. Based on changes in the calcareous dinoflagellate cyst association, we found an initial increase of the dinoflagellate cyst productivity, probably related to the initiation of upwelling about 11.8 Ma ago. Two distinct increases in cyst productivity in conjunction with temperature decreases of the upper water masses reflect upwelling pulses off Namibia and occur at the end of the Miocene cooling events Mi5 (about 11.5 Ma) and Mi6 (about 10.5 Ma). Both cooling events are associated with an ice volume increase in Antarctica and are thought to have led to an increase in southeasterly winds, possibly causing these two upwelling pulses. We demonstrate a decrease in dinoflagellate cyst productivity and enhanced terrigenous input via the Orange River after the Mi5 event. At about 11.1 Ma, the dinoflagellate cyst productivity increases again. The polar cyst species Caracomia arctica occurs here for the first time. This implies an influence of subantarctic mode water and therefore a change in the quality of the upwelling water which allowed the Benguela upwelling to develop into modern conditions. From about 10.4 Ma, C. arctica forms a permanent part of the association, pointing to an establishment of the upwelling regime.
AEOLIAN PROCESSES AND THE BIOSPHERE
Authors: Ravi Sujith , D'Odorico Paolo , Breshears David D. , Field Jason P. , Goudie Andrew S. , Huxman Travis E. , Li Junran , Okin Gregory S. , Swap Robert J. , Thomas Andrew D. , Van Pelt Scott , Whicker Jeffrey J. , Zobeck Ted M.
Published: August 2011

Aeolian processes affect the biosphere in a wide variety of contexts, including landform evolution, biogeochemical cycles, regional climate, human health, and desertification. Collectively, research on aeolian processes and the biosphere is developing rapidly in many diverse and specialized areas, but integration of these recent advances is needed to better address management issues and to set future research priorities. Here we review recent literature on aeolian processes and their interactions with the biosphere, focusing on (1) geography of dust emissions, (2) impacts, interactions, and feedbacks, (3) drivers of dust emissions, and (4) methodological approaches. Geographically, dust emissions are highly spatially variable but also provide connectivity at global scales between sources and effects, with “hot spots” being of particular concern. Recent research reveals that aeolian processes have impacts, interactions, and feedbacks at a variety of scales, including large‐scale dust transport and global biogeochemical cycles, climate mediated interactions between atmospheric dust and ecosystems, impacts on human health, impacts on agriculture, and interactions between aeolian processes and dryland vegetation. Aeolian dust emissions are driven largely by, in addition to climate, a combination of soil properties, soil moisture, vegetation and roughness, biological and physical crusts, and disturbances. Aeolian research methods span laboratory and field techniques, modeling, and remote sensing. Together these integrated perspectives on aeolian processes and the biosphere provide insights into management options and aid in identifying research priorities, both of which are increasingly important given that global climate models predict an increase in aridity in many dryland systems of the world.
Long‐lived orogenic construction along the paleo‐Pacific margin of Gondwana (Deep Freeze Range, North Victoria Land, Antarctica)
Authors: Rossetti Federico , Vignaroli Gianluca , Di Vincenzo Gianfranco , Gerdes Axel , Ghezzo Claudio , Theye Thomas , Balsamo Fabrizio
Published: August 2011

The paleo‐Pacific margin of Gondwana records a prolonged history of convergence during the Cambrian–Early Ordovician Ross‐Delamerian and the Middle Ordovician–Early Silurian Lachlan orogenies. This study describes structure, petrology, and geochronology of a set of NW‐SE striking ductile shear zones that crosscut the Ross age, Early Cambrian granitoid rocks of the Wilson Terrane in the Deep Freeze Range (North Victoria Land, Antarctica). The shear zones developed under amphibolite facies metamorphic conditions (650–700°C and 0.5–0.7 GPa) and show a systematic top‐to‐the‐NE sense of shear. The shear zone activity interferes with emplacement of late, subhorizontal leucocratic dikes and combined U‐(Th)‐Pb (zircon and monazite) and 40Ar‐39Ar (biotite and phengite) geochronology constrains the shearing event at ∼470 Ma, with the sheared granite yielding U‐Pb zircon crystallization ages of ∼508 Ma. The reconstructed P‐T path followed by the granite protoliths indicates an anticlockwise trajectory, suggesting the synshearing amphibolite metamorphism was associated with the burial of an early formed, Ross continental crustal section. These new findings are interpreted as evidence of a renewed, Ordovician episode of orogenic construction at the paleo‐Pacific margin of Gondwana that predated the onset of the Lachlan orogeny in the region. A polycyclic reactivation of the Ross age Wilson Terrane of North Victoria Land is suggested, which is used to propose a unitary framework for the space‐time transition from the Ross‐Delamerian to the Lachlan orogeny along the proto‐Pacific active margin of Gondwana.
Rotational motions for teleseismic surface waves
Authors: Lin Chin‐Jen , Huang Han‐Pang , Pham Nguyen Dinh , Liu Chun‐Chi , Chi Wu‐Cheng , Lee William H. K.
Published: August 2011

We report the findings for the first teleseismic six degree‐of‐freedom (6‐DOF) measurements including three components of rotational motions recorded by a sensitive rotation‐rate sensor (model R‐1, made by eentec) and three components of translational motions recorded by a traditional seismometer (STS‐2) at the NACB station in Taiwan. The consistent observations in waveforms of rotational motions and translational motions in sections of Rayleigh and Love waves are presented in reference to the analytical solution for these waves in a half space of Poisson solid. We show that additional information (e.g., Rayleigh wave phase velocity, shear wave velocity of the surface layer) might be exploited from six degree‐of‐freedom recordings of teleseismic events at only one station. We also find significant errors in the translational records of these teleseismic surface waves due to the sensitivity of inertial translation sensors (seismometers) to rotational motions. The result suggests that the effects of such errors need to be counted in surface wave inversions commonly used to derive earthquake source parameters and Earth structure.
Chlorophyll anomalies along the critical latitude at 30°N in the NE Pacific
Authors: Wilson Cara
Published: August 2011

The dissipation of surface tidal energy into internal tides plays a critical role in ocean mixing. However, quantifying the spatial distribution of this energy flux, which is required for ocean and climate modeling, has been largely based on modeling efforts and there is a need for validating observations. The summer development of large blooms of chlorophyll along 30°N in the E. Pacific is presented as evidence of enhanced tidal mixing. The region near 30° is a “double” critical latitude, with a transformation of internal waves occurring at both diurnal and semidiurnal frequencies. The breakdown at the critical latitude of internal waves generated at Hawaii could provide the physical mechanism to explain these blooms. The blooms develop in a region characterized by a weak summer surface stratification, which is therefore more susceptible to mixing.
The ‘Impossible’ Community of the Citizens: Past and Present Problems
Authors: Balibar Etienne
Published: August 2011

In the wake of previous reflections on the antinomies of citizenship—which derive both from the tension between an ‘insurrectional’ logic of equal liberty and a ‘constitutional’ project of building a community of citizens, and more recently from the conflict between (national) social citizenship and neoliberal forms of global governance—this paper focuses on problems of ‘representation’ and ‘agency’ linked to the idea of democratizing democracy itself. It will try in this sense to propose a more specific determination to the idea of an unfinished, although contingent, history of citizenship in the modern world.
Geddes in India: Town Planning, Plant Sentience, and Cooperative Evolution
Authors: Khan Naveeda
Published: August 2011

In this paper I focus on the ideas and efforts of Patrick Geddes, which are well known but not often discussed, by which he attempted to elevate the status of Indian sweepers and sewage collectors into gardeners by transforming sewage into fertilizer for gardens. Geddes transmitted his vision by means of religious performances, and through these efforts he attempted to produce change in Indian society in the register of human evolution. In this paper I take seriously the triangulation of waste, gardens, and performance as a reasoned means by which Geddes attempted to aid evolution. I suggest that by ‘evolution’ Geddes had in mind less an abstract process and more a state of awareness of one's capacities for self-transformation and relationship with one's environment. Furthermore, this awareness would largely be inculcated by taking into consideration the environment from the plant's point of view. In other words, expanding one's consciousness to be able to sense plant presence would not so much ready one for evolution as it would indicate that one had already evolved. This was town planning toward evolution. To make my arguments, I draw on Geddes's 1918 town planning reports for the Princely State of Indore, India, and draw out his intellectual engagements with William James, Henri Bergson, and Jagadis Chandra Bose implicit in these reports and elsewhere in his writings.
Reference Frame Preferences in Haptics Differ for the Blind and Sighted in the Horizontal but Not in the Vertical Plane
Authors: Struiksma Marijn E , Noordzij Matthijs L , Postma Albert
Published: August 2011

We investigated which reference frames are preferred when matching spatial language to the haptic domain. Sighted, low-vision, and blind participants were tested on a haptic-sentence-verification task where participants had to haptically explore different configurations of a ball and a shoe and judge the relation between them. Results from the spatial relation “above”, in the vertical plane, showed that various reference frames are available after haptic inspection of a configuration. Moreover, the pattern of results was similar for all three groups and resembled patterns found for the sighted on visual sentence-verification tasks. In contrast, when judging the spatial relation “in front”, in the horizontal plane, the blind showed a markedly different response pattern. The sighted and low-vision participants did not show a clear preference for either the absolute/relative or the intrinsic reference frame when these frames were dissociated. The blind, on the other hand, showed a clear preference for the intrinsic reference frame. In the absence of a dominant cue, such as gravity in the vertical plane, the blind might emphasise the functional relationship between the objects owing to enhanced experience with haptic exploration of objects.
The Effect of Body Posture on Long-Range Time-to-Contact Estimation
Authors: Baurès Robin , Hecht Heiko
Published: August 2011

On Earth, gravity accelerates freely moving objects downward, whereas upward-moving objects are being decelerated. Do humans take internalised knowledge of gravity into account when estimating time-to-contact (TTC, the time remaining before the moving object reaches the observer)? To answer this question, we created a motion-prediction task in which participants saw the initial part of an object's trajectory moving on a collision course prior to an occlusion. Observers had to judge when the object would make contact with them. The visual scene was presented with a head-mounted display. Participants lay either supine (looking up) or prone (looking down), suggestive of the ball either rising up or falling down toward them. Results showed that body posture had a significant effect on time-to-contact estimation, but only when occlusion times were long (2.5 s). The effect was also rather small. This lack of immediacy in the posture effect suggests that TTC estimation is initially robust toward the effect of gravity, which comes to bear only as more time is allowed for post-processing of the visual information.
Supramolecular nanostructures that mimic VEGF as a strategy for ischemic tissue repair
Authors: Webber Matthew J. , Tongers Jörn , Newcomb Christina J. , Marquardt Katja-Theres , Bauersachs Johann , Losordo Douglas W. , Stupp Samuel I.
Published: August 2011

There is great demand for the development of novel therapies for ischemic cardiovascular disease, a leading cause of morbidity and mortality worldwide. We report here on the development of a completely synthetic cell-free therapy based on peptide amphiphile nanostructures designed to mimic the activity of VEGF, one of the most potent angiogenic signaling proteins. Following self-assembly of peptide amphiphiles, nanoscale filaments form that display on their surfaces a VEGF-mimetic peptide at high density. The VEGF-mimetic filaments were found to induce phosphorylation of VEGF receptors and promote proangiogenic behavior in endothelial cells, indicated by an enhancement in proliferation, survival, and migration in vitro. In a chicken embryo assay, these nanostructures elicited an angiogenic response in the host vasculature. When evaluated in a mouse hind-limb ischemia model, the nanofibers increased tissue perfusion, functional recovery, limb salvage, and treadmill endurance compared to controls, which included the VEGF-mimetic peptide alone. Immunohistological evidence also demonstrated an increase in the density of microcirculation in the ischemic hind limb, suggesting the mechanism of efficacy of this promising potential therapy is linked to the enhanced microcirculatory angiogenesis that results from treatment with these polyvalent VEGF-mimetic nanofibers.
Role for the actomyosin complex in regulated exocytosis revealed by intravital microscopy
Authors: Masedunskas Andrius , Sramkova Monika , Parente Laura , Sales Katiuchia Uzzun , Amornphimoltham Panomwat , Bugge Thomas H. , Weigert Roberto
Published: August 2011

The regulation and the dynamics of membrane trafficking events have been studied primarily in in vitro models that often do not fully reflect the functional complexity found in a living multicellular organism. Here we used intravital microscopy in the salivary glands of live rodents to investigate regulated exocytosis, a fundamental process in all of the secretory organs. We found that β-adrenergic stimulation elicits exocytosis of large secretory granules, which gradually collapse with the apical plasma membrane without any evidence of compound exocytosis, as was previously described. Furthermore, we show that the driving force required to complete the collapse of the granules is provided by the recruitment of F-actin and nonmuscle myosin II on the granule membranes that is triggered upon fusion with the plasma membrane. Our results provide information on the machinery controlling regulated secretion and show that intravital microscopy provides unique opportunities to address fundamental questions in cell biology under physiological conditions.
Satellite methods underestimate indirect climate forcing by aerosols
Authors: Penner Joyce E. , Xu Li , Wang Minghuai
Published: August 2011

Satellite-based estimates of the aerosol indirect effect (AIE) are consistently smaller than the estimates from global aerosol models, and, partly as a result of these differences, the assessment of this climate forcing includes large uncertainties. Satellite estimates typically use the present-day (PD) relationship between observed cloud drop number concentrations (
N

c

) and aerosol optical depths (AODs) to determine the preindustrial (PI) values of
N

c

. These values are then used to determine the PD and PI cloud albedos and, thus, the effect of anthropogenic aerosols on top of the atmosphere radiative fluxes. Here, we use a model with realistic aerosol and cloud processes to show that empirical relationships for ln(
N

c

) versus ln(AOD) derived from PD results do not represent the atmospheric perturbation caused by the addition of anthropogenic aerosols to the preindustrial atmosphere. As a result, the model estimates based on satellite methods of the AIE are between a factor of 3 to more than a factor of 6 smaller than model estimates based on actual PD and PI values for
N

c

. Using ln(
N

c

) versus ln(AI) (Aerosol Index, or the optical depth times angstrom exponent) to estimate preindustrial values for
N

c

provides estimates for
N

c

and forcing that are closer to the values predicted by the model. Nevertheless, the AIE using ln(
N

c

) versus ln(AI) may be substantially incorrect on a regional basis and may underestimate or overestimate the global average forcing by 25 to 35%.
High-throughput microfluidic single-cell RT-qPCR
Authors: White Adam K. , VanInsberghe Michael , Petriv Oleh I. , Hamidi Mani , Sikorski Darek , Marra Marco A. , Piret James , Aparicio Samuel , Hansen Carl L.
Published: August 2011

A long-sought milestone in microfluidics research has been the development of integrated technology for scalable analysis of transcription in single cells. Here we present a fully integrated microfluidic device capable of performing high-precision RT-qPCR measurements of gene expression from hundreds of single cells per run. Our device executes all steps of single-cell processing, including cell capture, cell lysis, reverse transcription, and quantitative PCR. In addition to higher throughput and reduced cost, we show that nanoliter volume processing reduced measurement noise, increased sensitivity, and provided single nucleotide specificity. We apply this technology to 3,300 single-cell measurements of (
i
) miRNA expression in K562 cells, (
ii
) coregulation of a miRNA and one of its target transcripts during differentiation in embryonic stem cells, and (
iii
) single nucleotide variant detection in primary lobular breast cancer cells. The core functionality established here provides the foundation from which a variety of on-chip single-cell transcription analyses will be developed.
Mechanistic insight into Myc stabilization in breast cancer involving aberrant Axin1 expression
Authors: Zhang Xiaoli , Farrell Amy S. , Daniel Colin J. , Arnold Hugh , Scanlan Charles , Laraway Bryan J. , Janghorban Mahnaz , Lum Lawrence , Chen Dexi , Troxell Megan , Sears Rosalie
Published: August 2011

High expression of the oncoprotein Myc has been linked to poor outcome in human tumors. Although
MYC
gene amplification and translocations have been observed, this can explain Myc overexpression in only a subset of human tumors. Myc expression is in part controlled by its protein stability, which can be regulated by phosphorylation at threonine 58 (T58) and serine 62 (S62). We now report that Myc protein stability is increased in a number of breast cancer cell lines and this correlates with increased phosphorylation at S62 and decreased phosphorylation at T58. Moreover, we find this same shift in phosphorylation in primary breast cancers. The signaling cascade that controls phosphorylation at T58 and S62 is coordinated by the scaffold protein Axin1. We therefore examined Axin1 in breast cancer and report decreased
AXIN1
expression and a shift in the ratio of expression of two naturally occurring
AXIN1
splice variants. We demonstrate that this contributes to increased Myc protein stability, altered phosphorylation at S62 and T58, and increased oncogenic activity of Myc in breast cancer. Thus, our results reveal an important mode of Myc activation in human breast cancer and a mechanism contributing to Myc deregulation involving unique insight into inactivation of the Axin1 tumor suppressor in breast cancer.
In vivo expression profile of the antiviral restriction factor and tumor-targeting antigen CD317/BST-2/HM1.24/tetherin in humans
Authors: Erikson Elina , Adam Tarek , Schmidt Sarah , Lehmann-Koch Judith , Over Benjamin , Goffinet Christine , Harter Christoph , Bekeredjian-Ding Isabelle , Sertel Serkan , Lasitschka Felix , Keppler Oliver T.
Published: August 2011

Human CD317 is an intrinsic immunity factor that restricts the release of enveloped viruses, including the major pathogens HIV and Lassa virus, from infected cells in culture. Its importance for infection control in humans is unclear, due in part to its incompletely defined in vivo expression pattern. CD317 also has been proposed as a selective target for immunotherapy of multiple myeloma. To provide a framework for studies of the biological functions, regulation, and therapeutic potential of CD317, we performed microarray-based expression profiling in 468 tissue samples from 25 healthy organs from more than 210 patients. We found that CD317 protein was expressed to varying degrees in all organs tested and detected in a number of specialized cell types, including hepatocytes, pneumocytes, ducts of major salivary glands, pancreas and kidney, Paneth cells, epithelia, Leydig cells, plasma cells, bone marrow stromal cells, monocytes, and vascular endothelium. Although many of these cell types are in vivo targets for pathogenic viruses, restriction by CD317 or virus-encoded antagonists has been documented in only some of them. Limited cell type–dependent coexpression of CD317 with the IFN biomarker MxA in vivo and lack of responsive stimulation in organ explants suggest that interferons may only partially regulate CD317. This in vivo expression profiling sheds light on the biology and species-specificity of CD317, identifies multiple thus far unknown interaction sites of viruses with this restriction factor, and refutes the concept of its restricted constitutive expression and primary IFN inducibility. CD317's widespread expression calls into question its suitability as a target for immunotherapy.
Structural conservation of druggable hot spots in protein–protein interfaces
Authors: Kozakov Dima , Hall David R. , Chuang Gwo-Yu , Cencic Regina , Brenke Ryan , Grove Laurie E. , Beglov Dmitri , Pelletier Jerry , Whitty Adrian , Vajda Sandor
Published: August 2011

Despite the growing number of examples of small-molecule inhibitors that disrupt protein–protein interactions (PPIs), the origin of druggability of such targets is poorly understood. To identify druggable sites in protein–protein interfaces we combine computational solvent mapping, which explores the protein surface using a variety of small “probe” molecules, with a conformer generator to account for side-chain flexibility. Applications to unliganded structures of 15 PPI target proteins show that the druggable sites comprise a cluster of binding hot spots, distinguishable from other regions of the protein due to their concave topology combined with a pattern of hydrophobic and polar functionality. This combination of properties confers on the hot spots a tendency to bind organic species possessing some polar groups decorating largely hydrophobic scaffolds. Thus, druggable sites at PPI are not simply sites that are complementary to particular organic functionality, but rather possess a general tendency to bind organic compounds with a variety of structures, including key side chains of the partner protein. Results also highlight the importance of conformational adaptivity at the binding site to allow the hot spots to expand to accommodate a ligand of drug-like dimensions. The critical components of this adaptivity are largely local, involving primarily low energy side-chain motions within 6 Å of a hot spot. The structural and physicochemical signature of druggable sites at PPI interfaces is sufficiently robust to be detectable from the structure of the unliganded protein, even when substantial conformational adaptation is required for optimal ligand binding.
The Cdc48 ATPase modulates the interaction between two proteolytic factors Ufd2 and Rad23
Authors: Baek Guem Hee , Kim Ikjin , Rao Hai
Published: August 2011

Rad23 and cell division cycle protein 48 (Cdc48), two key regulators of postubiquitylation events, act on distinct and overlapping sets of substrates. The principle underlying their division of labor and cooperation in proteolysis remains elusive. Both Rad23 and Cdc48 bind a ubiquitin protein ligase ubiquitin fusion degradation-2 (Ufd2), and regulate the degradation of Ufd2 substrates. With its ability to bind ubiquitin chains directly and the proteasome via different domains, Rad23 serves as a bridge linking ubiquitylated substrates to the proteasome. The significance and specific role of the Ufd2–Cdc48 interaction are unclear. Here, we demonstrate that mutations in Ufd2 alter its interaction with Cdc48 and impair its function in substrate proteolysis but not in ubiquitylation. Furthermore, Cdc48 promotes the disassembly of the Ufd2–Rad23 complex in an manner that is dependent on ATP and Ufd2 binding, revealing a biochemical role for Cdc48. Rad23 was shown to bind separately to Ufd2 and to the proteasome subunit Rpn1, which define two distinct steps in proteolysis. The action of Cdc48 could free Rad23 from Ufd2 to allow its subsequent association with Rpn1, which in turn may facilitate the orderly transfer of the substrate from the ubiquitylation apparatus to the proteasome.
Role of olivocerebellar system in timing without awareness
Authors: Wu Xiang , Ashe James , Bushara Khalaf O.
Published: August 2011

The timing of events can be implicit or without awareness yet critical for task performance. However, the neural correlates of implicit timing are unknown. One system that has long been implicated in event timing is the olivocerebellar system, which originates exclusively from the inferior olive. By using event-related functional MRI in human subjects and a specially designed behavioral task, we examined the effect of the subjects’ awareness of changes in stimulus timing on the olivocerebellar system response. Subjects were scanned while observing changes in stimulus timing that were presented near each subject's detection threshold such that subjects were aware of such changes in only approximately half the trials. The inferior olive and multiple areas within the cerebellar cortex showed a robust response to time changes regardless of whether the subjects were aware of these changes. Our findings provide support to the proposed role of the olivocerebellar system in encoding temporal information and further suggest that this system can operate independently of awareness and mediate implicit timing in a multitude of perceptual and motor operations, including classical conditioning and implicit learning.
Myosin Va and myosin VI coordinate their steps while engaged in an in vitro tug of war during cargo transport
Authors: Ali M. Yusuf , Kennedy Guy G. , Safer Daniel , Trybus Kathleen M. , Sweeney H. Lee , Warshaw David M.
Published: August 2011

Myosin Va (myoV) and myosin VI (myoVI) are processive molecular motors that transport cargo in opposite directions on actin tracks. Because these motors may bind to the same cargo in vivo, we developed an in vitro “tug of war” to characterize the stepping dynamics of single quantum-dot-labeled myoV and myoVI motors linked to a common cargo. MyoV dominates its myoVI partner 79% of the time. Regardless of which motor wins, its stepping rate slows due to the resistive load of the losing motor (myoV, 2.1 pN; myoVI, 1.4 pN). Interestingly, the losing motor steps backward in synchrony with the winning motor. With ADP present, myoVI acts as an anchor to prevent myoV from stepping forward. This model system emphasizes the physical communication between opposing motors bound to a common cargo and highlights the potential for modulating this interaction by changes in the cell’s ionic milieu.
Long-lasting behavioral responses to stress involve a direct interaction of glucocorticoid receptors with ERK1/2–MSK1–Elk-1 signaling
Authors: Gutièrrez-Mecinas María , Trollope Alexandra F. , Collins Andrew , Morfett Hazel , Hesketh Shirley A. , Kersanté Flavie , Reul Johannes M. H. M.
Published: August 2011

Stressful events are known to have a long-term impact on future behavioral stress responses. Previous studies suggested that both glucocorticoid hormones and glutamate acting via glucocorticoid receptors (GRs) and
N
-methyl
d
-aspartate (NMDA) receptors, respectively, are of critical importance for the consolidation of these long-lasting behavioral responses at the dentate gyrus, the gateway of the hippocampal formation. We found that an acute psychologically stressful event resulted in ERK1/2 phosphorylation (pERK1/2), which within 15 min led to the activation of the nuclear kinases MSK1 and Elk-1 in granule neurons of the dentate gyrus. Next, MSK1 and Elk-1 activation evoked serine-10 phosphorylation and lysine-14 acetylation in histone H3, resulting in the induction of the neuroplasticity-associated immediate-early genes c-Fos and Egr-1 in these neurons. The pERK1/2-mediated activation of MSK1 and Elk-1 required a rapid protein–protein interaction between pERK1/2 and activated GRs. This is a unique nongenomic mechanism of glucocorticoid hormone action in dentate gyrus granule neurons on long-lasting behavioral responses to stress involving direct cross-talk of GRs with ERK1/2–MSK1–Elk-1 signaling to the nucleus.
Long-term in vivo glucose monitoring using fluorescent hydrogel fibers
Authors: Heo Yun Jung , Shibata Hideaki , Okitsu Teru , Kawanishi Tetsuro , Takeuchi Shoji
Published: August 2011

The use of fluorescence-based sensors holds great promise for continuous glucose monitoring (CGM) in vivo, allowing wireless transdermal transmission and long-lasting functionality in vivo. The ability to monitor glucose concentrations in vivo over the long term enables the sensors to be implanted and replaced less often, thereby bringing CGM closer to practical implementation. However, the full potential of long-term in vivo glucose monitoring has yet to be realized because current fluorescence-based sensors cannot remain at an implantation site and respond to blood glucose concentrations over an extended period. Here, we present a long-term in vivo glucose monitoring method using glucose-responsive fluorescent hydrogel fibers. We fabricated glucose-responsive fluorescent hydrogels in a fibrous structure because this structure enables the sensors to remain at the implantation site for a long period. Moreover, these fibers allow easy control of the amount of fluorescent sensors implanted, simply by cutting the fibers to the desired length, and facilitate sensor removal from the implantation site after use. We found that the polyethylene glycol (PEG)-bonded polyacrylamide (PAM) hydrogel fibers reduced inflammation compared with PAM hydrogel fibers, transdermally glowed, and continuously responded to blood glucose concentration changes for up to 140 days, showing their potential application for long-term in vivo continuous glucose monitoring.
A bacterial process for selenium nanosphere assembly
Authors: Debieux Charles M. , Dridge Elizabeth J. , Mueller Claudia M. , Splatt Peter , Paszkiewicz Konrad , Knight Iona , Florance Hannah , Love John , Titball Richard W. , Lewis Richard J. , Richardson David J. , Butler Clive S.
Published: August 2011

During selenate respiration by
Thauera selenatis
, the reduction of selenate results in the formation of intracellular selenium (Se) deposits that are ultimately secreted as Se nanospheres of approximately 150 nm in diameter. We report that the Se nanospheres are associated with a protein of approximately 95 kDa. Subsequent experiments to investigate the expression and secretion profile of this protein have demonstrated that it is up-regulated and secreted in response to increasing selenite concentrations. The protein was purified from Se nanospheres, and peptide fragments from a tryptic digest were used to identify the gene in the draft
T. selenatis
genome. A matched open reading frame was located, encoding a protein with a calculated mass of 94.5 kDa. N-terminal sequence analysis of the mature protein revealed no cleavable signal peptide, suggesting that the protein is exported directly from the cytoplasm. The protein has been called Se factor A (SefA), and homologues of known function have not been reported previously. The
sefA
gene was cloned and expressed in
Escherichia coli
, and the recombinant His-tagged SefA purified. In vivo experiments demonstrate that SefA forms larger (approximately 300 nm) Se nanospheres in
E. coli
when treated with selenite, and these are retained within the cell. In vitro assays demonstrate that the formation of Se nanospheres upon the reduction of selenite by glutathione are stabilized by the presence of SefA. The role of SefA in selenium nanosphere assembly has potential for exploitation in bionanomaterial fabrication.
Structural basis for human NADPH-cytochrome P450 oxidoreductase deficiency
Authors: Xia Chuanwu , Panda Satya P. , Marohnic Christopher C. , Martásek Pavel , Masters Bettie Sue , Kim Jung-Ja P.
Published: August 2011

NADPH-cytochrome P450 oxidoreductase (CYPOR) is essential for electron donation to microsomal cytochrome P450-mediated monooxygenation in such diverse physiological processes as drug metabolism (approximately 85–90% of therapeutic drugs), steroid biosynthesis, and bioactive metabolite production (vitamin D and retinoic acid metabolites). Expressed by a single gene, CYPOR’s role with these multiple redox partners renders it a model for understanding protein–protein interactions at the structural level. Polymorphisms in human CYPOR have been shown to lead to defects in bone development and steroidogenesis, resulting in sexual dimorphisms, the severity of which differs significantly depending on the degree of CYPOR impairment. The atomic structure of human CYPOR is presented, with structures of two naturally occurring missense mutations, V492E and R457H. The overall structures of these CYPOR variants are similar to wild type. However, in both variants, local disruption of H bonding and salt bridging, involving the FAD pyrophosphate moiety, leads to weaker FAD binding, unstable protein, and loss of catalytic activity, which can be rescued by cofactor addition. The modes of polypeptide unfolding in these two variants differ significantly, as revealed by limited trypsin digestion: V492E is less stable but unfolds locally and gradually, whereas R457H is more stable but unfolds globally. FAD addition to either variant prevents trypsin digestion, supporting the role of the cofactor in conferring stability to CYPOR structure. Thus, CYPOR dysfunction in patients harboring these particular mutations may possibly be prevented by riboflavin therapy in utero, if predicted prenatally, or rescued postnatally in less severe cases.
Structural basis for the sequence-specific recognition of human ISG15 by the NS1 protein of influenza B virus
Authors: Guan Rongjin , Ma Li-Chung , Leonard Paul G. , Amer Brendan R. , Sridharan Haripriya , Zhao Chen , Krug Robert M. , Montelione Gaetano T.
Published: August 2011

Interferon-induced ISG15 conjugation plays an important antiviral role against several viruses, including influenza viruses. The NS1 protein of influenza B virus (NS1B) specifically binds only human and nonhuman primate ISG15s and inhibits their conjugation. To elucidate the structural basis for the sequence-specific recognition of human ISG15, we determined the crystal structure of the complex formed between human ISG15 and the N-terminal region of NS1B (NS1B-NTR). The NS1B-NTR homodimer interacts with two ISG15 molecules in the crystal and also in solution. The two ISG15-binding sites on the NS1B-NTR dimer are composed of residues from both chains, namely residues in the RNA-binding domain (RBD) from one chain, and residues in the linker between the RBD and the effector domain from the other chain. The primary contact region of NS1B-NTR on ISG15 is composed of residues at the junction of the N-terminal ubiquitin-like (Ubl) domain and the short linker region between the two Ubl domains, explaining why the sequence of the short linker in human and nonhuman primate ISG15s is essential for the species-specific binding of these ISG15s. In addition, the crystal structure identifies NS1B-NTR binding sites in the N-terminal Ubl domain of ISG15, and shows that there are essentially no contacts with the C-terminal Ubl domain of ISG15. Consequently, NS1B-NTR binding to ISG15 would not occlude access of the C-terminal Ubl domain of ISG15 to its conjugating enzymes. Nonetheless, transfection assays show that NS1B-NTR binding of ISG15 is responsible for the inhibition of interferon-induced ISG15 conjugation in cells.
Tissue-engineered intervertebral discs produce new matrix, maintain disc height, and restore biomechanical function to the rodent spine
Authors: Bowles Robby D. , Gebhard Harry H. , Härtl Roger , Bonassar Lawrence J.
Published: August 2011

Lower back and neck pain are leading physical conditions for which patients see their doctors in the United States. The organ commonly implicated in this condition is the intervertebral disc (IVD), which frequently herniates, ruptures, or tears, often causing pain and limiting spinal mobility. To date, approaches for replacement of diseased IVD have been confined to purely mechanical devices designed to either eliminate or enable flexibility of the diseased motion segment. Here we present the evaluation of a living, tissue-engineered IVD composed of a gelatinous nucleus pulposus surrounded by an aligned collagenous annulus fibrosus in the caudal spine of athymic rats for up to 6 mo. When implanted into the rat caudal spine, tissue-engineered IVD maintained disc space height, produced de novo extracellular matrix, and integrated into the spine, yielding an intact motion segment with dynamic mechanical properties similar to that of native IVD. These studies demonstrate the feasibility of engineering a functional spinal motion segment and represent a critical step in developing biological therapies for degenerative disc disease.
Single methyl group determines prion propagation and protein degradation activities of yeast heat shock protein (Hsp)-70 chaperones Ssa1p and Ssa2p
Authors: Sharma Deepak , Masison Daniel C.
Published: August 2011

Organisms encode multiple homologous heat shock protein (Hsp)-70s, which are essential protein chaperones that play the major role in cellular protein “quality control.” Although Hsp70s are functionally redundant and highly homologous, many possess distinct functions. A regulatory motif underlying such distinctions, however, is unknown. The 98% identical cytoplasmic Hsp70s Ssa1p and Ssa2p function differently with regard to propagation of yeast [URE3] prions and in the vacuolar-mediated degradation of gluconeogenesis enzymes, such as FBPase. Here, we show that the Hsp70 nucleotide binding domain (NBD) regulates these functional specificities. We find little difference in ATPase, protein refolding, and amyloid inhibiting activities of purified Ssa1p and Ssa2p, but show that interchanging NBD residue alanine 83 (Ssa1p) and glycine 83 (Ssa2p) switched functions of Ssa1p and Ssa2p in [URE3] propagation and FBPase degradation. Disrupting the degradation pathway did not affect prion propagation, however, indicating these are two distinct processes where Ssa1/2p chaperones function differently. Our results suggest that the primary evolutionary pressure for Hsp70 functional distinctions is not to specify interactions of Hsp70 with substrate, but to specify the regulation of this activity. Our data suggest a rationale for maintaining multiple Hsp70s and suggest that subtle differences among Hsp70s evolved to provide functional specificity without affecting overall enzymatic activity.
In vitro reconstitution of Bluetongue virus infectious cores
Authors: Lourenco Sofia , Roy Polly
Published: August 2011

Bluetongue virus (BTV) is a vector-borne, nonenveloped icosahedral particle that is organized in two capsids, an outer capsid of two proteins, VP2 and VP5, and an inner capsid (or core) composed of two major proteins, VP7 and VP3, in two layers. The VP3 layer (subcore) encloses viral transcription complex (VP1 polymerase, VP4 capping enzyme, VP6 helicase) and a 10-segmented double-stranded (dsRNA) genome. Although much is known about the BTV capsids, the order of the core assembly and the mechanism of genome packaging remain unclear. Here, we established a cell-free system to reconstitute subcore and core structures with the proteins and ssRNAs, demonstrating that reconstituted cores are infectious in insect cells. Furthermore, we showed that the BTV ssRNAs are essential to drive the assembly reaction and that there is a distinct order of internal protein recruitment during the assembly process. The in vitro engineering of infectious BTV cores is unique for any member of the
Reoviridae
and will facilitate future studies of RNA-protein interactions during BTV core assembly.
Pre-mRNA splicing is a determinant of histone H3K36 methylation
Authors: Kim Soojin , Kim Hyunmin , Fong Nova , Erickson Benjamin , Bentley David L.
Published: August 2011

A chromatin code appears to mark introns and exons with distinct patterns of nucleosome enrichment and histone methylation. We investigated whether a causal relationship exists between splicing and chromatin modification by asking whether splice-site mutations affect the methylation of histone H3K36. Deletions of the 3′ splice site in intron 2 or in both introns 1 and 2 of an integrated β-globin reporter gene caused a shift in relative distribution of H3K36 trimethylation away from 5′ ends and toward 3′ ends. The effects of splice-site mutations correlated with enhanced retention of a U5 snRNP subunit on transcription complexes downstream of the gene. In contrast, a poly(A) site mutation did not affect H3K36 methylation. Similarly, global inhibition of splicing by spliceostatin A caused a rapid repositioning of H3K36me3 away from 5′ ends in favor of 3′ ends. These results suggest that the cotranscriptional splicing apparatus influences establishment of normal patterns of histone modification.
Injectable fibroblast growth factor-2 coacervate for persistent angiogenesis
Authors: Chu Hunghao , Gao Jin , Chen Chien-Wen , Huard Johnny , Wang Yadong
Published: August 2011

Enhancing the maturity of the newly formed blood vessels is critical for the success of therapeutic angiogenesis. The maturation of vasculature relies on active participation of mural cells to stabilize endothelium and a basal level of relevant growth factors. We set out to design and successfully achieved robust angiogenesis using an injectable polyvalent coacervate of a polycation, heparin, and fibroblast growth factor-2 (FGF2). FGF2 was loaded into the coacervate at nearly 100% efficiency. In vitro assays demonstrated that the matrix protected FGF2 from proteolytic degradations. FGF2 released from the coacervate was more effective in the differentiation of endothelial cells and chemotaxis of pericytes than free FGF2. One injection of 500 ng of FGF2 in the coacervate elicited comprehensive angiogenesis in vivo. The number of endothelial and mural cells increased significantly, and the local tissue contained more and larger blood vessels with increased circulation. Mural cells actively participated during the whole angiogenic process: Within 7 d of the injection, pericytes were recruited to close proximity of the endothelial cells. Mature vasculature stabilized by vascular smooth muscle cells persisted till at least 4 wk. On the other hand, bolus injection of an identical amount of free FGF2 induced weak angiogenic responses. These results demonstrate the potential of polyvalent coacervate as a new controlled delivery platform.
Developmental factor IRF6 exhibits tumor suppressor activity in squamous cell carcinomas
Authors: Botti Elisabetta , Spallone Giulia , Moretti Francesca , Marinari Barbara , Pinetti Valentina , Galanti Sergio , De Meo Paolo D'Onorio , De Nicola Francesca , Ganci Federica , Castrignanò Tiziana , Pesole Graziano , Chimenti Sergio , Guerrini Luisa , Fanciulli Maurizio , Blandino Giovanni , Karin Michael , Costanzo Antonio
Published: August 2011

The transcription factor interferon regulatory factor 6 (IRF6) regulates craniofacial development and epidermal proliferation. We recently showed that IRF6 is a component of a regulatory feedback loop that controls the proliferative potential of epidermal cells. IRF6 is transcriptionally activated by p63 and induces its proteasome-mediated down-regulation, thereby limiting keratinocyte proliferative potential. We hypothesized that IRF6 may also be involved in skin carcinogenesis. Hence, we analyzed IRF6 expression in a large series of squamous cell carcinomas (SCCs) and found a strong down-regulation of IRF6 that correlated with tumor invasive and differentiation status. IRF6 down-regulation in SCC cell lines and primary tumors correlates with methylation on a CpG dinucleotide island located in its promoter region. To identify the molecular mechanisms regulating IRF6 potential tumor suppressive activity, we performed a genome-wide analysis by combining ChIP sequencing for IRF6 binding sites and gene expression profiling in primary human keratinocytes after siRNA-mediated IRF6 depletion. We observed dysregulation of cell cycle-related genes and genes involved in differentiation, cell adhesion, and cell–cell contact. Many of these genes were direct IRF6 targets. We also performed in vitro invasion assays showing that IRF6 down-regulation promotes invasive behavior and that reintroduction of IRF6 into SCC cells strongly inhibits cell growth. These results indicate a function for IRF6 in suppression of tumorigenesis in stratified epithelia.
Falling Behind: Delayed Growth Explains Life‐History Variation in Snake River Fall Chinook Salmon
Authors: Perkins T. Alex , Jager Henrïette I.
Published: August 2011

Fall Chinook salmon Oncorhynchus tshawytscha typically migrate to the ocean as subyearlings (age 0), but a strategy whereby juveniles overwinter in freshwater and migrate to the ocean as yearlings (age 1) has emerged over the past few decades in Idaho's Snake River population. The recent appearance of the yearling strategy has conservation implications for this threatened population because of survival and reproductive differences between the two life histories. Different proportions of juveniles adopt the yearling life history in different river reaches and years, and temperature differences are thought to play some role in accounting for this variation. The specific circumstances under which juveniles pursue the yearling life history are poorly understood. We advance a hypothesis for the mechanism by which juveniles adopt a life history, formalize it with a model, and present the results of fitting this model to life history data. The model captures patterns of variation in proportions of yearling out‐migrants among reaches and years, and it appears robust to uncertainty in a key unknown parameter. Results from fitting the model to empirical yearling migrant proportions suggest that juveniles commit to a life history earlier in development than the time at which smoltification typically begins. Specifically, juveniles that become yearling migrants do so soon after emergence if they are too far behind a typical growth schedule given temperature and photoperiod cues at that time. Our model also offers those interested in the management and conservation of Snake River fall Chinook salmon a useful tool by which to account for life history variation in population viability analyses and decision making.