Showing papers by "Florida State University published in 2009"

Wind-Driven Upwelling in the Southern Ocean and the Deglacial Rise in Atmospheric CO2

Abstract: Wind-driven upwelling in the ocean around Antarctica helps regulate the exchange of carbon dioxide (CO2) between the deep sea and the atmosphere, as well as the supply of dissolved silicon to the euphotic zone of the Southern Ocean. Diatom productivity south of the Antarctic Polar Front and the subsequent burial of biogenic opal in underlying sediments are limited by this silicon supply. We show that opal burial rates, and thus upwelling, were enhanced during the termination of the last ice age in each sector of the Southern Ocean. In the record with the greatest temporal resolution, we find evidence for two intervals of enhanced upwelling concurrent with the two intervals of rising atmospheric CO2 during deglaciation. These results directly link increased ventilation of deep water to the deglacial rise in atmospheric CO2.

Circadian Clock Feedback Cycle Through NAMPT-Mediated NAD+ Biosynthesis

Abstract: The circadian clock is encoded by a transcription-translation feedback loop that synchronizes behavior and metabolism with the light-dark cycle. Here we report that both the rate-limiting enzyme in mammalian nicotinamide adenine dinucleotide (NAD+) biosynthesis, nicotinamide phosphoribosyltransferase (NAMPT), and levels of NAD+ display circadian oscillations that are regulated by the core clock machinery in mice. Inhibition of NAMPT promotes oscillation of the clock gene Per2 by releasing CLOCK:BMAL1 from suppression by SIRT1. In turn, the circadian transcription factor CLOCK binds to and up-regulates Nampt, thus completing a feedback loop involving NAMPT/NAD+ and SIRT1/CLOCK:BMAL1.

Interferometric fluorescent super-resolution microscopy resolves 3D cellular ultrastructure

Abstract: Understanding molecular-scale architecture of cells requires determination of 3D locations of specific proteins with accuracy matching their nanometer-length scale. Existing electron and light microscopy techniques are limited either in molecular specificity or resolution. Here, we introduce interferometric photoactivated localization microscopy (iPALM), the combination of photoactivated localization microscopy with single-photon, simultaneous multiphase interferometry that provides sub-20-nm 3D protein localization with optimal molecular specificity. We demonstrate measurement of the 25-nm microtubule diameter, resolve the dorsal and ventral plasma membranes, and visualize the arrangement of integrin receptors within endoplasmic reticulum and adhesion complexes, 3D protein organization previously resolved only by electron microscopy. iPALM thus closes the gap between electron tomography and light microscopy, enabling both molecular specification and resolution of cellular nanoarchitecture.

The fluorescent protein palette: tools for cellular imaging

Abstract: This critical review provides an overview of the continually expanding family of fluorescent proteins (FPs) that have become essential tools for studies of cell biology and physiology. Here, we describe the characteristics of the genetically encoded fluorescent markers that now span the visible spectrum from deep blue to deep red. We identify some of the novel FPs that have unusual characteristics that make them useful reporters of the dynamic behaviors of proteins inside cells, and describe how many different optical methods can be combined with the FPs to provide quantitative measurements in living systems (227 references). “If wood is rubbed with the Pulmo marinus, it will have all the appearance of being on fire; so much so, indeed, that a walking-stick, thus treated, will light the way like a torch” (translation of Pliny the Elder from John Bostock, 1855).

Multiferroic Behavior Associated with an Order−Disorder Hydrogen Bonding Transition in Metal−Organic Frameworks (MOFs) with the Perovskite ABX3 Architecture

Abstract: Multiferroic behavior in perovskite-related metal−organic frameworks of general formula [(CH3)2NH2]M(HCOO)3, where M = Mn, Fe, Co, and Ni, is reported. All four compounds exhibit paraelectric−antiferroelectric phase transition behavior in the temperature range 160−185 K (Mn: 185 K, Fe: 160 K; Co: 165 K; Ni: 180 K); this is associated with an order−disorder transition involving the hydrogen bonded dimethylammonium cations. On further cooling, the compounds become canted weak ferromagnets below 40 K. This research opens up a new class of multiferroics in which the electrical ordering is achieved by means of hydrogen bonding.

Main predictions of the interpersonal-psychological theory of suicidal behavior: empirical tests in two samples of young adults.

Abstract: The interpersonal-psychological theory of suicidal behavior (Joiner, 2005) makes two overarching predictions: 1) that perceptions of burdening others and of social alienation combine to instill the desire for death; and 2) that individuals will not act on the desire for death unless they have developed the capability to do so – a capability that develops through exposure and thus habituation to painful and/or fearsome experiences, and which is posited by the theory to be necessary to overcome powerful self-preservation pressures. Two studies test these predictions. In Study 1, the interaction of (low) family social support (cf. social alienation or low belonging) and feeling like one does not matter (cf. perceived burdensomeness) predicted current suicidal ideation, beyond depression indices. In Study 2, the three-way interaction between a measure of low belonging, a measure of perceived burdensomeness, and lifetime number of suicide attempts (viewed as a strong predictor of the level of acquired capability for suicide) predicted current suicide attempt (vs. ideation) among a clinical sample of suicidal young adults, again beyond depression indices and other key covariates. Implications for the understanding, treatment, and prevention of suicidal behavior are discussed.

On instantaneous frequency

Abstract: Instantaneous frequency (IF) is necessary for understanding the detailed mechanisms for nonlinear and nonstationary processes. Historically, IF was computed from analytic signal (AS) through the Hilbert transform. This paper offers an overview of the difficulties involved in using AS, and two new methods to overcome the difficulties for computing IF. The first approach is to compute the quadrature (defined here as a simple 90° shift of phase angle) directly. The second approach is designated as the normalized Hilbert transform (NHT), which consists of applying the Hilbert transform to the empirically determined FM signals. Additionally, we have also introduced alternative methods to compute local frequency, the generalized zero-crossing (GZC), and the teager energy operator (TEO) methods. Through careful comparisons, we found that the NHT and direct quadrature gave the best overall performance. While the TEO method is the most localized, it is limited to data from linear processes, the GZC method is the m...

Fundamental aspects of protein-protein association kinetics.

Abstract: The structure of a protein complex, together with information about its affinity and other thermodynamic characteristics, provide a “frozen” view of the complex. This picture ignores the kinetic nature of protein-protein association and dissociation, which are of major biological and biophysical interest. This review focuses on recent advances in deciphering the kinetic pathway of protein complex formation, the nature of the pre-complex formed through diffusion (which we have termed the “transient complex”1), the transition state, and other intermediates (such as the so-called encounter complex) along the association pathway. Protein-protein association is at the center of diverse biological processes ranging from enzyme catalysis/inhibition to regulation of immune response by cytokines. The association rates often play a critical role in such processes, as in situations where speed is of essence.2 For example, the purple cone snail and other venomous animals capture prey with remarkable efficiency and speed by releasing toxins that rapidly bind to ion channels;3 the green mamba achieves a similar feat by targeting acetylcholinesterase (AChE), an enzyme essential for the integrity of neural transmission.4 Bacteria such as Escherichia coli and Bacillus amyloliquefaciens excrete nucleases as weapons against competitors or predators. Defense of the producing cells from damage to their own DNA or RNA by such nucleases requires rapid association with cognate inhibitors.5,6 Indeed, in the last example rapid association is such a priority that the inhibitor barstar has a cluster of acidic residues that facilitate association with the nuclease barnase, even though the clustered charges reduce folding stability.7 In the ruminant gut, RNase A is required for degrading accumulated RNA; potential toxicity of leaked nuclease is prevented by rapid association with a ribonuclease inhibitor.8,9 Reorganization of the actin cytoskeleton provides yet another illustration of the importance of rapid protein association. Reorganization is attained through actin polymerization, which is nucleated by the Arp2/3 complex. The latter is activated by the Wiskott-Aldrich Syndrome protein (WASp), which in turn is released from the auto-inhibited state by the Rho GTPase Cdc42.10 As actin polymerization is initiated with a nucleation process, the speed of upstream signaling has a critical impact on the rate of polymer formation. It is thus not surprising that high association rate constants have been observed between partners along the signaling pathway.11,12 The high association rate constant between Cdc42 and WASp has been found to be essential for the latter to stimulate actin polymerization, as another Rho GTPase sharing 70% sequence identity, TC10, with an identical dissociation rate constant but a 1000-fold lower association rate constant, failed to stimulate actin polymerization.11 The failure to stimulate actin polymerization in patients carrying mutant WAS genes is the root cause of the Wiskott-Aldrich Syndrome. Several other compelling arguments can be made for the biological roles of rapid protein association.13 (a) Fast association may enhance binding affinity. High affinity can also be achieved through slow dissociation; however, for proteins involved in signaling, slow dissociation is not an option, since it implies a long-lasting bound state, which effectively corresponds to a permanent off- or on-switch. A good example for this is the binding of Ras to its natural affector Raf. This protein dissociates within a fraction of a second, but maintains an affinity in the nM range through fast association. Moreover, the difference between the natural effector, Raf, and the non-natural effector, Ral, lies in their rates of association with Ras.14 Therefore, even if not for a direct reason (such as in stimulation of actin polymerization), the affinity requirement alone may call for fast association. (b) Enzyme-substrate binding is a determining factor for the overall turnover rate and becomes the rate-limiting step for catalytically “perfect” enzymes. Substrate-binding rate constants of such enzymes reach 108 M−1s−1 and beyond, as found for the ribotoxin restrictocin and RNase A.15,16 (c) When several proteins compete for the same receptor or when one protein is faced with alternative pathways, kinetic control, not thermodynamic control, dominates in many cases; this is especially true when dissociation is slow. For example, during protein synthesis cognate and noncognate aminoacyl-tRNA synthetases can potentially compete for the same tRNA. As an additional example, consider newly synthesized proteins, which potentially face aggregation if not isolated by a chaperone. From the point of view of kinetic control, it is easy to see why rapid binding of denatured proteins to the chaperonin GroEL has been observed.17 (d) Differences in binding rate between related proteins may serve as an additional mechanism for specificity, as can be suggested for Rho GTPases Cdc42 and TC10 and for Ras effectors Raf and Ral. The examples and arguments presented above suggest that rapid binding is as important as high affinity in the proper functioning of proteins. It is now increasingly recognized that proteins function in the context of multi-component complexes. Manipulating association rate constants of various components presents unique opportunities for the control of protein functions. Many interactions between proteins are also targeted for drug development; in designing such drugs, both high affinity and rapid binding should be taken into consideration. 1.1. Overview of Protein Association Kinetics The observed rate constants of protein association span a wide range, from 109 M−1s−1 (Figure 1). In comprehending these values, a basic fact is that, for two proteins to recognize each other, their interfaces have to be oriented with high specificity. A relative rotation of as little as a few degrees or a relative translation by a few Angstroms is sufficient to break all specific interactions between the two proteins.18 The rate of association of a protein complex is limited by diffusion and geometric constraints of the binding sites, and may be further reduced by subsequent chemical processes.19 Open in a separate window Figure 1 The wide spectrum of association rate constants. The red vertical line marks the start of the diffusion-controlled regime. The shaded range marks the absence of long-range forces. Adapted with permission from Ref. 1. Copyright 2008 Wiley Interscience..

Men, masculinity, and manhood acts.

Abstract: In the 1980s research on men shifted from studying the “male sex role” and masculinity as a singular trait to studying how men enact diverse masculinities. This research has examined men's behavior as gendered beings in many contexts, from intimate relationships to the workplace to global politics. We consider the strengths and weaknesses of the multiple masculinities approach, proposing that further insights into the social construction of gender and the dynamics of male domination can be gained by focusing analytic attention on manhood acts and how they elicit deference from others. We interpret the literature in terms of what it tells us about how males learn to perform manhood acts, about how and why such acts vary, and about how manhood acts reproduce gender inequality. We end with suggestions for further research on the practices and processes through which males construct the category “men” and themselves as its members.

A bright and photostable photoconvertible fluorescent protein

Abstract: Photoconvertible fluorescent proteins are potential tools for investigating dynamic processes in living cells and for emerging super-resolution microscopy techniques. Unfortunately, most probes in this class are hampered by oligomerization, small photon budgets or poor photostability. Here we report an EosFP variant that functions well in a broad range of protein fusions for dynamic investigations, exhibits high photostability and preserves the approximately 10-nm localization precision of its parent.

Far-red fluorescent tags for protein imaging in living tissues.

Abstract: A vast colour palette of monomeric fluorescent proteins has been developed to investigate protein localization, motility and interactions. However, low brightness has remained a problem in far-red variants, which hampers multicolour labelling and whole-body imaging techniques. In the present paper, we report mKate2, a monomeric far-red fluorescent protein that is almost 3-fold brighter than the previously reported mKate and is 10-fold brighter than mPlum. The high-brightness, far-red emission spectrum, excellent pH resistance and photostability, coupled with low toxicity demonstrated in transgenic Xenopus laevis embryos, make mKate2 a superior fluorescent tag for imaging in living tissues. We also report tdKatushka2, a tandem far-red tag that performs well in fusions, provides 4-fold brighter near-IR fluorescence compared with mRaspberry or mCherry, and is 20-fold brighter than mPlum. Together, monomeric mKate2 and pseudo-monomeric tdKatushka2 represent the next generation of extra-bright far-red fluorescent probes offering novel possibilities for fluorescent imaging of proteins in living cells and animals.

Attention training for generalized social anxiety disorder.

Abstract: Attentional bias toward negative social cues is thought to serve an etiological and/or maintaining role in social anxiety disorder (SAD). The current study tested whether training patients to disengage from negative social cues may ameliorate social anxiety in patients (N = 36) with a primary diagnosis of generalized SAD. Patients were randomly assigned to either an attention training condition (n = 18), in which patients completed a modified dot-probe task designed to facilitate attentional disengagement from disgusted faces, or a control dot-probe task condition (n = 18). As predicted, patients in the attention training condition exhibited significantly greater reductions in social anxiety and trait anxiety, compared with patients in the control condition. At termination, 72% of patients in the active treatment condition, relative to 11% of patients in the control condition, no longer met Diagnostic and Statistical Manual of Mental Disorders (4th ed.) criteria for SAD. At 4-month follow-up, patients in the attention training condition continued to maintain their clinical improvement, and diagnostic differences across conditions were also maintained. Results support attention-based models of anxiety and suggest that attention training is a promising alternative or complementary intervention.

Password Cracking Using Probabilistic Context-Free Grammars

Abstract: Choosing the most effective word-mangling rules to use when performing a dictionary-based password cracking attack can be a difficult task In this paper we discuss a new method that generates password structures in highest probability order We first automatically create a probabilistic context-free grammar based upon a training set of previously disclosed passwords This grammar then allows us to generate word-mangling rules, and from them, password guesses to be used in password cracking We will also show that this approach seems to provide a more effective way to crack passwords as compared to traditional methods by testing our tools and techniques on real password sets In one series of experiments, training on a set of disclosed passwords, our approach was able to crack 28% to 129% more passwords than John the Ripper, a publicly available standard password cracking program

The spatial turn : interdisciplinary perspectives

Abstract: 1. Introduction (Barney Warf and Santa Arias) 2. Taking Space Personally (Edward W. Soja) 3. Spacing Movements (Sebastian Cobarrubias and John Pickles) 4. From Surfaces to Networks (Barney Warf) 5. Geography, Postcommunism, and Comparative Politics (Jeffrey Kopstein) 6. Retheorizing Global Space in Sociology (Harry Dahms) 7. Sex and the Modern City (Pamela K. Gilbert) 8. The Geopolitics of Historiography from Europe to the Americas (Santa Arias) 9. "To See a World in a Grain of Sand": Space and Place on an Ethnographical Journey in Colombia (Margarita Serje) 10. Spatiality and Religion (John Corrigan) 11. The Cultural Production of Space in Colonial Latin America (Mariselle Melendez) 12. Documentary as a Space of Intuition (Joan Ramon Resina)

Aging and Information Technology Use Potential and Barriers

Abstract: Why are older adults reluctant to adopt new technology, such as the Internet, given its potential to improve the quality of their lives? We review evidence indicating that attitudes and abilities are among the most powerful predictors of technology use. We conclude that normative age-related changes in ability must be taken into account when designing products and training programs for aging adults, and we discuss new tools to support designers. The most promising emerging technologies likely lie in training cognitive abilities and augmenting or substituting for impaired abilities. We discuss reasons to expect that the lag in technology adoption between younger and older adults may lessen but will not disappear in future generations.

Cognitive abilities and superior decision making under risk : A protocol analysis and process model evaluation

Abstract: Individual differences in cognitive abilities and skills can predict normatively superior and logically consistent judgments and decisions. The current experiment investigates the processes that mediate individual differences in risky choices. We assessed working memory span, numeracy, and cognitive impulsivity and conducted a protocol analysis to trace variations in conscious deliberative processes. People higher in cognitive abilities made more choices consistent with expected values; however, expected-value choices rarely resulted from expected-value calculations. Instead, the cognitive ability and choice relationship was mediated by the number of simple considerations made during decision making — e.g., transforming probabilities and considering the relative size of gains. Results imply that, even in simple lotteries, superior risky decisions associated with cognitive abilities and controlled cognition can reflect metacognitive dynamics and elaborative heuristic search processes, rather than normative calculations. Modes of cognitive control (e.g., dual process dynamics) and implications for process models of risky decision-making (e.g., priority heuristic) are discussed.

Advance and prospectus of seasonal prediction: assessment of the APCC/CliPAS 14-model ensemble retrospective seasonal prediction (1980–2004)

Abstract: We assessed current status of multi-model ensemble (MME) deterministic and probabilistic seasonal prediction based on 25-year (1980–2004) retrospective forecasts performed by 14 climate model systems (7 one-tier and 7 two-tier systems) that participate in the Climate Prediction and its Application to Society (CliPAS) project sponsored by the Asian-Pacific Economic Cooperation Climate Center (APCC). We also evaluated seven DEMETER models’ MME for the period of 1981–2001 for comparison. Based on the assessment, future direction for improvement of seasonal prediction is discussed. We found that two measures of probabilistic forecast skill, the Brier Skill Score (BSS) and Area under the Relative Operating Characteristic curve (AROC), display similar spatial patterns as those represented by temporal correlation coefficient (TCC) score of deterministic MME forecast. A TCC score of 0.6 corresponds approximately to a BSS of 0.1 and an AROC of 0.7 and beyond these critical threshold values, they are almost linearly correlated. The MME method is demonstrated to be a valuable approach for reducing errors and quantifying forecast uncertainty due to model formulation. The MME prediction skill is substantially better than the averaged skill of all individual models. For instance, the TCC score of CliPAS one-tier MME forecast of Nino 3.4 index at a 6-month lead initiated from 1 May is 0.77, which is significantly higher than the corresponding averaged skill of seven individual coupled models (0.63). The MME made by using 14 coupled models from both DEMETER and CliPAS shows an even higher TCC score of 0.87. Effectiveness of MME depends on the averaged skill of individual models and their mutual independency. For probabilistic forecast the CliPAS MME gains considerable skill from increased forecast reliability as the number of model being used increases; the forecast resolution also increases for 2 m temperature but slightly decreases for precipitation. Equatorial Sea Surface Temperature (SST) anomalies are primary sources of atmospheric climate variability worldwide. The MME 1-month lead hindcast can predict, with high fidelity, the spatial–temporal structures of the first two leading empirical orthogonal modes of the equatorial SST anomalies for both boreal summer (JJA) and winter (DJF), which account for about 80–90% of the total variance. The major bias is a westward shift of SST anomaly between the dateline and 120°E, which may potentially degrade global teleconnection associated with it. The TCC score for SST predictions over the equatorial eastern Indian Ocean reaches about 0.68 with a 6-month lead forecast. However, the TCC score for Indian Ocean Dipole (IOD) index drops below 0.40 at a 3-month lead for both the May and November initial conditions due to the prediction barriers across July, and January, respectively. The MME prediction skills are well correlated with the amplitude of Nino 3.4 SST variation. The forecasts for 2 m air temperature are better in El Nino years than in La Nina years. The precipitation and circulation are predicted better in ENSO-decaying JJA than in ENSO-developing JJA. There is virtually no skill in ENSO-neutral years. Continuing improvement of the one-tier climate model’s slow coupled dynamics in reproducing realistic amplitude, spatial patterns, and temporal evolution of ENSO cycle is a key for long-lead seasonal forecast. Forecast of monsoon precipitation remains a major challenge. The seasonal rainfall predictions over land and during local summer have little skill, especially over tropical Africa. The differences in forecast skills over land areas between the CliPAS and DEMETER MMEs indicate potentials for further improvement of prediction over land. There is an urgent need to assess impacts of land surface initialization on the skill of seasonal and monthly forecast using a multi-model framework.

Rejection Elicits Emotional Reactions but Neither Causes Immediate Distress nor Lowers Self-Esteem: A Meta-Analytic Review of 192 Studies on Social Exclusion

Abstract: Competing predictions about the effect of social exclusion were tested by meta-analyzing findings from studies of interpersonal rejection, ostracism, and similar procedures. Rejection appears to cause a significant shift toward a more negative emotional state. Typically, however, the result was an emotionally neutral state marked by low levels of both positive and negative affect. Acceptance caused a slight increase in positive mood and a moderate increase in self-esteem. Self-esteem among rejected persons was no different from neutral controls. These findings are discussed in terms of belongingness motivation, sociometer theory, affective numbing, and self-esteem defenses.