Structural Observation of the Primary Isomerization in Vision with Femtosecond-Stimulated Raman

the substrate surface (27) with DOS of polymers could occur, or there could be charge transfer (28) based on the interaction between the polymers and the I-Au(111). These electronic interactions between the polymers and the surface might reduce the HOMO-LUMO gaps compared with those in solution. Chem. Soc. 124, 11862 (2002). 11. H. Sakaguchi, H. Matsumura, H. Gong, Nat. Mater. 3, 551 (2004 Science 271, 1705Science 271, (1996. Adv. Mater. 4, 282 (1992 The primary event that initiates vision is the light-induced 11-cis to all-trans isomerization of retinal in the visual pigment rhodopsin. Despite decades of study with the traditional tools of chemical reaction dynamics, both the timing and nature of the atomic motions that lead to photoproduct production remain unknown. We used femtosecond-stimulated Raman spectroscopy to obtain time-resolved vibrational spectra of the molecular structures formed along the reaction coordinate. The spectral evolution of the vibrational features from 200 femtoseconds to 1 picosecond after photon absorption reveals the temporal sequencing of the geometric changes in the retinal backbone that activate this receptor. Understanding the mechanism of a chemical reaction requires measuring the structure of the reactant as it evolves into product. Many of the most intriguing and efficient photochemical and photobiological reactions take place on ultrafast time scales and their kinetics have been well characterized by femtosecond absorption and fluorescence spectroscopies (1-5). Although x-ray diffraction is being developed for timeresolved structural studies of reactions, this approach is challenging to apply in the condensed phase and currently limited to processes slower than È100 ps (6). Ultrafast vibrational spectroscopy is advantageous in this quest because it offers both excellent temporal and structural information (7). The traditional picosecond timeresolution limitation (8) is being transcended through the use of femtosecond pulses in the infrared (IR) in multidimensional as well as direct time-resolved experiments of ultrafast chemical and biological processes (9-11). The complementary Raman vibrational techniques have also advanced with the recent development of stimulated Raman in the femtosecond time domain (12, 13), which is valuable because of its ability to interrogate biological processes in aqueous media. Here, we demonstrate the capabilities of femtosecond-stimulated Raman spectroscopy (FSRS) in studies of reaction dynamics by elucidating the molecular mechanism of the primary photochemical events in vision. In FSRS, two laser pulses drive the Raman transition: a picosecond BRaman pulse[ and a femtosecond broadband continuum Bprobe pulse[ that stimulates the scattering of any vibrational modes with frequencies between 600 and 2000 cm j1 . The use of the additional probe pulse to induce the Raman scattering offers a number of notable improvements over traditional timeresolved spontaneous Raman spectroscopy (14), such as greatly enhanced cross sections and an order-of-magnitude improvement in time resolution (G100 fs) while maintaining excellent energy resolution (G15 cm j1 ) (15, 16). The impulsive creation of vibrational coherence by the Raman and probe pulses reveals highly time-resolved vibrational structural information that is not accessible by incoherent processes such as spontaneous Raman. The primary step in vision is the photochemical cis-trans isomerization of the 11-cis retinal chromophore in rhodopsin We address these questions by acquiring femtosecond time-resolved vibrational spectra of retinal in rhodopsin throughout the reaction. Modeling of the vibrational structural features after rapid internal conversion to the ground state reveals the highly distorted structure of photorhodopsin. Surprisingly, a large fraction of the atomic rearrangement leading to the formation of fully isomerized bathorhodopsin is shown to occur in the ground electronic state. Vivid details of thi

Biochemical Oscillations and Cellular Rhythms: The Molecular Bases of Periodic and Chaotic Behavior

the threads of complexity in chemical systems. The promise of this new activity is particularly rich for macromolecules (including biologically relevant macromolecules), in which opportunities for the existence of many different molecular conformations, each with different properties, are high. At the core of chemical interest in complexity are the two fundamental problems concerning life, that is, trying to understand (i) how collections of molecules can give rise to the varieties of behaviors that characterize cells and organisms and (ii) how individual molecules might have originally assembled into collections that had the characteristics of life (energy dissipation, self-replication, and adaptation). Whether the understanding of complexity at the molecular level will reveal important elements of the structure of life is unclear. We do not know if it is conceptually possible to connect molecular-level processes to organismic behavior deterministically. Certainly, knowing everything about the electronic properties of Si and the operating characteristics of transistors tells very little about the higher level characteristics of computers. Fortunately, there is also the inverse opportunity: learning from biological complexity as a method of stimulating new chemistry. With this opportunity, there is great reason for optimism. Biological systems display such a large number of remarkable capabilities (and capabilities that are so clearly complex) that their analysis will unquestionably be a rich source of models for new areas of chemistry. ANNs are one example of a successful transfer of information about a complex biological system to nonbiological applications. ANNs were developed, in part, as a tool with which to model the brain. To what extent current ANNs do so is a continuing subject of discussion, but the effort to make the connection between ANNs and brains (and to learn from the brain) has unquestionably expanded the capabilities of computation. In this same sense, biology (and perhaps also complex materials) offers examples of complex systems that show types of behavior that are now uncommon in molecular chemistry. One of the opportunities in fundamental chemical research is to learn from biology and to use what is learned to design nonbiological systems that dissipate energy, replicate, and adapt. Whether such systems would model life is moot; they would unquestionably be very interesting and probably very important

Optically measuring force near the standard quantum limit

0.1, consistent with a small finite microwave occupation factor (n c ≈ 0.6 T 0.1) in addition to the quantum fluctuations. In contrast, we do not observe a large increase in the mechanical fluctuations in BAE as the imprecision decreases (red dots in Quantum fluctuations of a single mode in a microwave field can be sensed with a mechanical system, and, with the proper pump field, these fluctuations can be steered into an unobserved aspect of the motion. These results lead the way toward measuring and manipulating the quantum noise of a mechanical resonator. As described i

These data will be reported in full elsewhere

where, as here, faithful recapitulation of molecular and pathological phenotypes is possible, our findings argue that primary human BSE prion infection, as well as secondary infection with vCJD prions by iatrogenic routes, may not be restricted to a single disease phenotype. These data, together with the recent recognition of probable iatrogenic transmission of vCJD prions to recipients of blood (21, 22), including a PRNP codon 129 Met/Val heterozygous individua

18. See supporting on Science Online for detailed methods. 19

particles have substantially more of them. If these low coordination number corner and/or edge positions are implicated as active sites for toluene oxidation, then their relatively higher occurrence in the Au-Pd/C sample could account for the superior performance displayed by this catalyst. Another possible explanation could lie in the difference in the distribution of Au-Pd particle morphologies found in the two catalyst samples. The Au-Pd/C catalyst predominantly has multiply twinned (icosahedral and decahedral) particles, which tend to have {111} facet terminations. In comparison, the Au-Pd/TiO 2 materials show an increased fraction of cuboctahedral and singly/doubly twinned particles, which exhibit mixed {100}/{111} facet terminations. Hence, the increasing proportion of {100}-type facets in the Au-Pd/TiO 2 sample correlates with a lowering of the catalytic activity, and preparation strategies need to avoid them. In a final set of experiments, we investigated the stability of the catalysts, because it is crucial to confirm that high-activity catalysts can be reused. With the Au-Pd/TiO 2 catalyst, the reaction was stopped after 7 hours, and the catalyst was recovered by decantation. Identical conversion was obtained on reuse of the Au-Pd/TiO 2 catalyst A critical design rule is that the range of interparticle interactions (hydrophobic attraction and electrostatic repulsion) must be short relative to particle size and that the interactions must be reversible. Clustering then favors densely packed structures with at most six nearest neighbors per particle, in contrast to the more open and less ordered structures formed by particles whose interaction range is larger (13). At very low salt concentrations, particles repel one another electrostatically, whereas at high salt concentrations, van der Waals forces cause the particles to aggregate irreversibly (19). Therefore, we consider intermediate concentrations of monovalent salt at which amphiphilic clusters self-assemble (20). If the hydrophobic patch is too small, assembly admits clusters composed of at most four particles. However, increase in patch size allows such clusters to grow into larger assemblies, with two constraints: First, particles must approach closely enough to experience hydrophobic attrac

We thank X. Liu and B. Roth for sharing reagents; X Unlearning implicit social biases during sleep

However, direct activation of DG engram cells of the ANI group elicited as much freezing behavior as did the activation of these cells of the SAL group. This unexpected finding is supported by a set of additional cellular and behavioral experiments. Whereas amygdala engram cell reactivation upon exposure to the conditioned context is significantly lower in the ANI group as compared with the SAL group, optogenetic activation of DG engram cells results in normal reactivation of downstream CA3 and BLA engram cells These findings suggest that although a rapid increase of synaptic strength is likely to be crucial during the encoding phase, the augmented synaptic strength is not a crucial component of the stored memory The integrative memory engram-based approach used here for parsing memory and amnesia into encoding, consolidation, and retrieval aspects may be of wider use to other experimental and clinical cases of amnesia, such as Alzheimer's disease (40). REFERENCES AND NOTES 1. G. E. Müller, A. Pilzecker, Z. Psychol. 1, 1-288 (1900). 2. C. P. Duncan, J. Comp. Physiol. Psychol. 42, 32-44 (1949 11. M. Krug, B. Lössner, T. Ott, Brain Res. Bull. 13, 39-42 (1984). 12. U. Frey, M. Krug, K. G. Reymann, H. Matthies, Brain Res. 452, 57-65 (1988 Corresponding bias reductions were fortified in comparison with the social bias not externally reactivated during sleep. This advantage remained 1 week later, the magnitude of which was associated with time in slow-wave and rapid-eye-movement sleep after training. We conclude that memory reactivation during sleep enhances counterstereotype training and that maintaining a bias reduction is sleep-dependent. S ocial interactions are often fraught with bias. Our preconceptions about other people can influence many types of behavior. For example, documented policing errors have repeatedly shown the potential harm of racial profiling (1). In experiments that used a first-person-shooter videogame, both White and Black participants were more likely to shoot Black than White individuals, even when they held a harmless object rather than a gun (2). When hiring potential research assistants, both male and female faculty members were more likely to hire male than equally qualified female candidates (3). Although the tendency for people to endorse racist or sexist attitudes explicitly has decreased in recent years (4), social biases may nevertheless influence people's behavior in an implicit or unconscious manner, regardless of their intentions or efforts to avoid bias (5). Ample evidence indicates that implicit biases can drive discriminatory behaviors and exacerbate intergroup conflict (5-8). For instance, implicit racial biases decrease investments given to racial out-group members in a trust game (6). At a broader level, the gender gap in science achievement in a nation is correlated with the level of implicit stereotyping of females as not having an aptitude for science (8). Whereas discriminatory behaviors can be detrimental to individuals and society, implicit social bias can be difficult to correct because of a range of affective, cognitive, motivational, and social factors, as follows (9, 10). First, out-group members can be perceived as threatening, and the fear response to those individuals can resist extinction (11). Second, biases are acquired over many years of exposure to stereotypes, and they can efficiently operate without occupying cognitive resources (5, 10). Third, motivation to seek higher status or self-enhancement commonly results in out-group derogation (9, 10). Last, perceived social norms can prescribe people's expression of stereotyping and prejudice (12). Despite such challenges, implicit biases can be reduced by learning about counterstereotype cases (13). However, benefits of this counterbias training can be fragile, subject to reversal when the original stereotypes are again reinforced in typical circumstances, such as through the media (14). Longer-term reductions in implicit social biases may necessitate that counterbias training be followed by further memory consolidation, as is the case for many other types of learning (15). Recent findings suggest that memory consolidation during sleep may be essential for preserving newly acquired information, such as declarative and procedural memories (15-19). During sleep, information recently stored in the brain can be integrated with other information and transformed into stable representations through a process known as systems-level consolidation (15). The mechanisms of this transformation are thought to involve repeated reactivation of information, particularly during sleep, leading to subsequent improvement in postsleep memory performance (19)(20)(21)(22)(23)(24). Taking into consideration the role of sleep in memory consolidation, we adapted procedures for (i) reducing implicit social biases and (ii) reactivating this training during sleep. We were particularly interested in factors that can influence whether such training procedures produce transient or persistent effects. Because pervasive stereotypes in the media and broader culture could function to regenerate a bias that is momentarily reduced (14), maintaining the benefits of training is crucial for the ultimate usefulness of potential bias-reducing interventions. We reactivated counterbias information during sleep using subtle auditory cues that had been associated with counterbias training. Participants were White males and females from a university community (N = 40) and were recruited as two subsamples that allowed for a direct replication (25). First, biases were quantified using two versions of the implicit association test (IAT) (26). The IAT allows for an assessment of the strength of implicit associations between social groups and attributes (26). One test examined the degree to which female faces were preferentially associated with art versus science words-or the reverse for male faces (gender-bias IAT). The other test examined the degree to which Black faces were preferentially associated with bad versus good words-or the reverse for White faces (racialbias IAT). Results were quantified by using a conventional scoring procedure (27), in which zero indicates no bias and larger scores indicate greater bias. Consistent with previous research (7), IAT scores showed that participants held implicit social biases for both gender and race, with both scores significantly greater than zero [mean T SEM, 0.559 T 0.044; gender t(39) = 9.076, P < 0.001; race t(39) = 8.388, P < 0.001]. After this confirmation of baseline levels of implicit bias, participants engaged in training designed to reduce gender and racial bias (13). In both cases, bias reduction was expected because participants intentionally selected counterstereotype information intermixed with other information. Participants viewed several types of face-word pairing but were required to attend and respond only to pairings that countered the typical bias RESEARCH | REPORTS Biases were reduced compared with baseline levels Next, participants were invited to take a 90-min afternoon nap ( Implicit biases were measured again after waking. Bias change from prenap to postnap varied with cueing condition as predicted [substantiated by a two-way interaction (cued or uncued by prenap or postnap), F 1,39 = 14.612, P < 0.001, h p 2 = 0.273]. As shown in Implicit biases were measured again after 1 week, revealing that the differential bias reduction endured ( Neurophysiological activity during sleep-such as sleep spindles, slow waves, and rapid-eyemovement (REM) duration-can predict later memory performance (17). Accordingly, we explored possible relations between cueing-specific bias reduction and measures of sleep physiology. We found that only SWS × REM sleep duration consistently predicted cueing-specific bias reduction at 1 week relative to baseline Past research indicates that by pairing learning episodes with auditory or olfactory stimuli and then presenting these stimuli again during postlearning SWS, learned information can be specifically reactivated and strengthened (19). Benefits of this targeted memory reactivation (TMR) have been documented for declarative, procedural, and emotional memories (19). Such learning typically does not challenge preexisting knowledge nor compete with daily experiences outside the laboratory. In contrast, we examined learning-induced changes in long-standing social biases. We showed that selectively reactivating counterbias learning during sleep weakened preexisting implicit social biases immediately after the nap and facilitated the retention of this learning going forward. Without TMR during sleep, training effects tended to dissipate, and the bias returned to baseline levels. These results thus enlarge our conception of sleep's role in socially relevant learning. Observed relations between sleep neurophysiology and behavior further reinforced the conclusion that bias reduction is sleep-dependent. Current thinking about consolidation emphasizes sets of cortical networks that can become integrated through interactions with hippocampal networks, possibly by means of cyclic SWS-REM periods (15)(16)(17) 28). The correlation with SWS × REM duration implicates a benefit from REM-based processing subsequent to SWS-based reactivation, perhaps to integrate learning within associative knowledge networks. These findings support the notion that both SWS and REM are operative in sleep-dependent memory consolidation (16, 17, 28, 29). Future research is needed to address many outstanding questions in relation to our findings. For example, how much training is needed to make implicit benefits persist for long periods of time and transfer to explicit benefits in interpersonal interactions? To what extent do persistent benefits depend on repeated training, the nature of other waking activities after training, and repeated memory reactivation during sleep? Although IAT measures are imperfect and may sometimes reflect knowledge of cultural stereotypes rather than implicit bias per se (30), prior research has demonstrated consequences for social behavior, such that low implicit bias as measured with the IAT may indeed be linked with egalitarianism (6, 7). Given that training to reduce implicit bias can be conceptualized as a type of habit learning (31), perhaps novel sleep manipulations could be adapted to aid people in changing various unwanted or maladaptive habits, such as smoking, unhealthy eating, catastrophizing, or selfishness (32)

14. E. Suss-Toby

Moreover, the binding of the extracellular domains of adhesins to host cell surface receptors remains incompletely characterized, as are the molecular interactions that govern processing by proteases. Judging from their deep branching evolutionary position and present-day success, apicomplexans are likely to be with us for some time. Thus far, our glimpses into parasite motility have revealed a very different process than that used by mammalian cells. Although these differences may explain the tremendous success of apicomplexans, their understanding may also enable selective disruption of parasite motility. If we are to thwart these ancient and mysterious parasites, our attention should be focused on defining their unique biology. The acquisitions of mitochondria and plastids were important events in the evolution of the eukaryotic cell, supplying it with compartmentalized bioenergetic and biosynthetic factories. Ancient invasions by eubacteria through symbiosis more than a billion years ago initiated these processes. Advances in geochemistry, molecular phylogeny, and cell biology have offered insight into complex molecular events that drove the evolution of endosymbionts into contemporary organelles. In losing their autonomy, endosymbionts lost the bulk of their genomes, necessitating the evolution of elaborate mechanisms for organelle biogenesis and metabolite exchange. In the process, symbionts acquired many host-derived properties, lost much of their eubacterial identity, and were transformed into extraordinarily diverse organelles that reveal complex histories that we are only beginning to decipher. Analyses of mitochondrial genes and their genomic organization and distribution indicate that mitochondrial genomes are derived from an ␣-proteobacterium-like ancestor, probably due to a single ancient invasion (Fig

Supporting Online Material Preparation of Poly(diiododiacetylene), an Ordered Conjugated Polymer of Carbon and Iodine

amount of ASODNs delivered using antisense nanoparticles (0.024 nmol ASNP: 2.64 nmol ASODN); however, extreme toxicity was observed in both cases as measured by cell death, so we lowered the amount of ASODN and transfection reagent to the point that one strand of transfected ASODN was equivalent to one antisense particle (0.024 nmol ASNP: 0.024 nmol ASODN). In these cases, ASODNs transfected with either Lipofectamine or Cytofectin resulted in only È6 to 8% knockdown in EGFP expression Although these systems have not yet been optimized for maximum efficacy, the ability to systematically control the oligonucleotide loading on the NP surface has allowed us to identify several features that make them attractive candidates for antisense studies and therapies. The ability to modify the gold nanoparticle surface allows one to realize unusual cooperative properties that lead to enhanced target binding and allows the introduction of a variety of functional groups that have proven to be informative in terms of studying how the structure works within a cell. Moreover, this platform will allow us and others to add functionality (31, 32) that could direct the oligonucleotidemodified nanoparticle agents to specific cell types and different components within the cell, thus opening the door for new possibilities in the study of gene function and nanotherapies