Stable Isotope Probing-nanoFTIR for Quantitation of Cellular Metabolism and Observation of Growth-Dependent Spectral Features.

This study utilizes nanoscale Fourier transform infrared spectroscopy (nanoFTIR) to perform stable isotope probing (SIP) on individual bacteria cells cultured in the presence of 13C-labelled glucose. SIP-nanoFTIR simultaneously quantifies single-cell metabolism through infrared spectroscopy and acquires cellular morphological information via atomic force microscopy. The redshift of the amide I peak corresponds to the isotopic enrichment of newly synthesized proteins. These observations of single-cell translational activity are comparable to those of conventional methods, examining bulk cell numbers. Observing cells cultured under conditions of limited carbon, SIP- nanoFTIR is used to identify environmentally-induced changes in metabolic heterogeneity and cellular morphology. Individuals outcompeting their neighboring cells will likely play a disproportionately large role in shaping population dynamics during adverse conditions or environmental fluctuations. Additionally, SIP-nanoFTIR enables the spectroscopic differentiation of specific cellular growth phases. During cellular replication, subcellular isotope distribution becomes more homogenous, which is reflected in the spectroscopic features dependent on the extent of 13C-13C mode coupling or to specific isotopic symmetries within protein secondary structures. As SIP-nanoFTIR captures single-cell metabolism, environmentally-induced cellular processes, and subcellular isotope localization, this technique offers widespread applications across a variety of disciplines including microbial ecology, biophysics, biopharmaceuticals, medicinal science, and cancer research.

Six months of voluntary alcohol consumption in male cynomolgus macaques reduces intracortical bone porosity without altering mineralization or mechanical properties.

Chronic heavy alcohol consumption is a risk factor for low trauma bone fracture. Using a non-human primate model of voluntary alcohol consumption, we investigated the effects of 6 months of ethanol intake on cortical bone in cynomolgus macaques (Macaca fascicularis). Young adult (6.4 ± 0.1 years old, mean ± SE) male cynomolgus macaques (n = 17) were subjected to a 4-month graded ethanol induction period, followed by voluntary self-administration of water or ethanol (4 % w/v) for 22 h/d, 7 d/wk. for 6 months. Control animals (n = 6) consumed an isocaloric maltose-dextrin solution. Tibial response was evaluated using densitometry, microcomputed tomography, histomorphometry, biomechanical testing, and Raman spectroscopy. Global bone response was evaluated using biochemical markers of bone turnover. Monkeys in the ethanol group consumed an average of 2.3 ± 0.2 g/kg/d ethanol resulting in a blood ethanol concentration of 90 ± 12 mg/dl in longitudinal samples taken 7 h after the daily session began. Ethanol consumption had no effect on tibia length, mass, density, mechanical properties, or mineralization (p > 0.642). However, compared to controls, ethanol intake resulted in a dose-dependent reduction in intracortical bone porosity (Spearman rank correlation = -0.770; p < 0.0001) and compared to baseline, a strong tendency (p = 0.058) for lower plasma CTX, a biochemical marker of global bone resorption. These findings are important because suppressed cortical bone remodeling can result in a decrease in bone quality. In conclusion, intracortical bone porosity was reduced to subnormal values 6 months following initiation of voluntary ethanol consumption but other measures of tibia architecture, mineralization, or mechanics were not altered.

Sensorimotor mechanisms selective to numerosity derived from individual differences.

We have previously shown that after few seconds of adaptation by finger-tapping, the perceived numerosity of spatial arrays and temporal sequences of visual objects displayed near the tapping region is increased or decreased, implying the existence of a sensorimotor numerosity system (Anobile et al., 2016). To date, this mechanism has been evidenced only by adaptation. Here, we extend our finding by leveraging on a well-established covariance technique, used to unveil and characterize 'channels' for basic visual features such as colour, motion, contrast, and spatial frequency. Participants were required to press rapidly a key a specific number of times, without counting. We then correlated the precision of reproduction for various target number presses between participants. The results showed high positive correlations for nearby target numbers, scaling down with numerical distance, implying tuning selectivity. Factor analysis identified two factors, one for low and the other for higher numbers. Principal component analysis revealed two bell-shaped covariance channels, peaking at different numerical values. Two control experiments ruled out the role of non-numerical strategies based on tapping frequency and response duration. These results reinforce our previous reports based on adaptation, and further suggest the existence of at least two sensorimotor number channels responsible for translating symbolic numbers into action sequences.

Disambiguating vision with sound.

An important task for the visual system is to identify and segregate objects from background. Figure-ground illusions, such as Edgar Rubin's bistable 'vase-faces illusion'1, make the point clearly: we see either a central vase or lateral faces, alternating spontaneously, but never both images simultaneously. The border is perceptually assigned to either faces or vase, which become figure, the other shapeless background2. The stochastic alternation between figure and ground probably reflects mutual inhibitory processes that ensure a single perceptual outcome3. Which shape dominates perception depends on many factors, such as size, symmetry, convexity, enclosure, and so on, as well as attention and intention4. Here we show that the assignment of the visual border can be strongly influenced by auditory input, far more than is possible by voluntary intention. VIDEO ABSTRACT.

Adaptation to numerosity affects the pupillary light response.

We recently showed that the gain of the pupillary light response depends on numerosity, with weaker responses to fewer items. Here we show that this effect holds when the stimuli are physically identical but are perceived as less numerous due to numerosity adaptation. Twenty-eight participants adapted to low (10 dots) or high (160 dots) numerosities and subsequently watched arrays of 10-40 dots, with variable or homogeneous dot size. Luminance was constant across all stimuli. Pupil size was measured with passive viewing, and the effects of adaptation were checked in a separate psychophysical session. We found that perceived numerosity was systematically lower, and pupillary light responses correspondingly smaller, following adaptation to high rather than low numerosities. This is consistent with numerosity being a primary visual feature, spontaneously encoded even when task irrelevant, and affecting automatic and unconscious behaviours like the pupillary light response.

Investigating cross-orientation inhibition with continuous tracking.

We investigated cross-orientation inhibition with the recently developed continuous tracking technique. We designed an experiment where participants tracked the horizontal motion of a narrow vertical grating. The target was superimposed on one of three different backgrounds, in separate sessions: a uniform gray background or a sinusoidal grating oriented either parallel or orthogonal to the target. Both mask and target where phase reversed. We cross-correlated target and mouse movements and compared the peaks and lags of response with the different masks. Our results are in agreement with previous findings on cross-orientation inhibition: The orthogonal mask had a weak effect on the peaks and lags of correlation as a function of target contrast, consistently with a divisive effect of the mask, while the parallel mask acted subtractively on the response. Interestingly, lags of correlation decreased approximately linearly with contrast, with decrements of the order of 100 ms, even at 10 times the detection threshold, confirming that it is possible to investigate behavioral differences above threshold using the continuous tracking paradigm.

Serial Dependence in Perception.

Much evidence has shown that perception is biased towards previously presented similar stimuli, an effect recently termed serial dependence. Serial dependence affects nearly every aspect of perception, often causing gross perceptual distortions, especially for weak and ambiguous stimuli. Despite unwanted side-effects, empirical evidence and Bayesian modeling show that serial dependence acts to improve efficiency and is generally beneficial to the system. Consistent with models of predictive coding, the Bayesian priors of serial dependence are generated at high levels of cortical analysis, incorporating much perceptual experience, but feed back to lower sensory areas. These feedback loops may drive oscillations in the alpha range, linked strongly with serial dependence. The discovery of top-down predictive perceptual processes is not new, but the new, more quantitative approach characterizing serial dependence promises to lead to a deeper understanding of predictive perceptual processes and their underlying neural mechanisms.

The role of neural oscillations in visuo-motor communication at the time of saccades.

Saccadic eye-movements are fundamental for active vision, allowing observers to purposefully scan the environment with the high-resolution fovea. In this brief perspective we outline a series of experiments from our laboratories investigating the role of eye-movements and their consequences to active perception. We show that saccades lead to suppression of visual sensitivity at saccadic onset, and that this suppression is accompanied by endogenous neural oscillations in the delta range. Similar oscillations are initiated by purposeful hand movements, which lead to measurable changes in responsivity in area V1, and in the connectivity with motor area M1. Saccades also lead to clear distortions in apparent position, but only for verbal reports, not when participants respond with rapid pointing, consistent with the action of two separate visual systems in neurotypical adults. At the time of saccades, serial dependence, the positive influence on perception of previous stimulus attributes (such as orientation) is particularly strong. Again, these processes are accompanied by neural oscillations, in the alpha and low beta range. In general, oscillations seem to be tightly linked to serial dependence in perception, both in auditory judgments (around 10 Hz), and for visual judgements of face gender (14 Hz for female, 17 Hz for male). Taken together, the studies show that neural oscillations play a fundamental role in dynamic, active vision.

The role of non-numerical information in the perception of temporal numerosity.

Numerosity perception refers to the ability to make rapid but approximate estimates of the quantity of elements in a set (spatial numerosity) or presented sequentially (temporal numerosity). Whether numerosity is directly perceived or indirectly recomputed from non-numerical features is a highly debated issue. In the spatial domain, area and density have been suggested as the main parameters through which numerosity would be recomputed. In the temporal domain, stimuli duration and temporal frequency could be similarly exploited to retrieve numerosity. By adapting a psychophysical technique previously exploited in the spatial domain, we investigated whether temporal visual numerosity is directly perceived. Adult participants observed sequences of visual impulses sampled from a stimulus space spanning several levels of temporal frequency and duration (and hence numerosity), and then reproduced the sequence as accurately as possible via a series of keypresses. Crucially, participants were not asked to reproduce any particular property (such as number of impulses) but were free to choose any available cue (such as total duration, or temporal frequency). The results indicate that while the overall sequence duration was barely considered, numerosity and temporal frequency were both spontaneously used as the main cues to reproduce the sequences, with a slight but significant dominance of numerosity. Overall, the results are in line with previous literature suggesting that numerosity is directly encoded, even for temporal sequences, but a non-numerical feature (temporal frequency) is also used in reproducing sequences.

Serial dependence in orientation judgments at the time of saccades.

We actively seek information from the environment through saccadic eye movements, necessitating continual integration of presaccadic and postsaccadic signals, which are displaced on the retina by each saccade. We tested whether trans-saccadic integration may be related to serial dependence (a measure of how perceptual history influences current perception) by measuring how viewing a presaccadic stimulus affects the perceived orientation of a subsequent test stimulus presented around the time of a saccade. Participants reproduced the position, and orientation of a test stimulus presented around a 16° saccade. The reproduced position was mislocalized toward the saccadic target, agreeing with previous work. The reproduced orientation was attracted toward the prior stimulus and regressed to the mean orientation. These results suggest that both short- and long-term past information affects trans-saccadic perception, most strongly when the test stimulus is presented perisaccadically. This study unites the fields of serial dependence and trans-saccadic perception, leading to potential new insights of how information is transferred and accumulated across saccades.

Serial dependence improves performance and biases confidence-based decisions.

Perception depends on both the current sensory input and on the preceding stimuli history, a mechanism referred to as serial dependence (SD). One interesting, and somewhat controversial, question is whether serial dependence originates at the perceptual stage, which should lead to a sensory improvement, or at a subsequent decisional stage, causing solely a bias. Here, we studied the effects of SD in a novel manner by leveraging on the human capacity to spontaneously assess the quality of sensory information. Two noisy-oriented Gabor stimuli were simultaneously presented along with two bars of the same orientation as the Gabor stimuli. Participants were asked to choose which Gabor stimulus to judge and then make a forced-choice judgment of its orientation by selecting the appropriate response bar. On all trials, one of the Gabor stimuli had the same orientation as the Gabor in the same position on the previous trial. We explored whether continuity in orientation and position affected choice and accuracy. Results show that continuity of orientation leads to a persistent (up to four back) accuracy advantage and a higher preference in the selection of stimuli with the same orientation, and this advantage accumulates over trials. In contrast, analysis of the continuity of the selected position indicated that participants had a strong tendency to choose stimuli in the same position, but this behavior did not lead to an improvement in accuracy.

Future space experiment platforms for astrobiology and astrochemistry research.

Space experiments are a technically challenging but a scientifically important part of astrobiology and astrochemistry research. The International Space Station (ISS) is an excellent example of a highly successful and long-lasting research platform for experiments in space, that has provided a wealth of scientific data over the last two decades. However, future space platforms present new opportunities to conduct experiments with the potential to address key topics in astrobiology and astrochemistry. In this perspective, the European Space Agency (ESA) Topical Team Astrobiology and Astrochemistry (with feedback from the wider scientific community) identifies a number of key topics and summarizes the 2021 "ESA SciSpacE Science Community White Paper" for astrobiology and astrochemistry. We highlight recommendations for the development and implementation of future experiments, discuss types of in situ measurements, experimental parameters, exposure scenarios and orbits, and identify knowledge gaps and how to advance scientific utilization of future space-exposure platforms that are either currently under development or in an advanced planning stage. In addition to the ISS, these platforms include CubeSats and SmallSats, as well as larger platforms such as the Lunar Orbital Gateway. We also provide an outlook for in situ experiments on the Moon and Mars, and welcome new possibilities to support the search for exoplanets and potential biosignatures within and beyond our solar system.

Cyanide Binding to [FeFe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway.

Hydrogenases are H2 converting enzymes that harbor catalytic cofactors in which iron (Fe) ions are coordinated by biologically unusual carbon monoxide (CO) and cyanide (CN- ) ligands. Extrinsic CO and CN- , however, inhibit hydrogenases. The mechanism by which CN- binds to [FeFe]-hydrogenases is not known. Here, we obtained crystal structures of the CN- -treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum. The high resolution of 1.39 Šallowed us to distinguish intrinsic CN- and CO ligands and to show that extrinsic CN- binds to the open coordination site of the cofactor where CO is known to bind. In contrast to other inhibitors, CN- treated crystals show conformational changes of conserved residues within the proton transfer pathway which could allow a direct proton transfer between E279 and S319. This configuration has been proposed to be vital for efficient proton transfer, but has never been observed structurally.

Vision: Neuronal mechanisms enabling stable perception.

Eye movements cause rapid motion of the retinal image, potentially confusable with external motion. A recent study shows that neurons in mouse primary visual cortex distinguish self-generated from external motion by combining sensory input with saccade-related signals from the thalamic pulvinar nucleus.

Evidence of Serial Dependence from Decoding of Visual Evoked Potentials.

It is well known that recent sensory experience influences perception, recently demonstrated by a phenomenon termed "serial dependence." However, its underlying neural mechanisms are poorly understood. We measured ERP responses to pairs of stimuli presented randomly to the left or right hemifield. Seventeen male and female adults judged whether the upper or lower half of the grating had higher spatial frequency, independent of the horizontal position of the grating. This design allowed us to trace the memory signal modulating task performance and also the implicit memory signal associated with hemispheric position. Using classification techniques, we decoded the position of the current and previous stimuli and the response from voltage scalp distributions of the current trial. Classification of previous responses reached full significance only 700 ms after presentation of the current stimulus, consistent with retrieval of an activity-silent memory trace. Cross-condition classification accuracy of past responses (trained on current responses) correlated with the strength of serial dependence effects of individual participants. Overall, our data provide evidence for a silent memory signal that can be decoded from the EEG potential, which interacts with the neural processing of the current stimulus. This silent memory signal could be the physiological substrate subserving at least one type of serial dependence.SIGNIFICANCE STATEMENT The neurophysiological underpinnings of how past perceptual experience affects current perception are poorly understood. Here, we show that recent experience is reactivated when a new stimulus is presented and that the strength of this reactivation correlates with serial biases in individual participants, suggesting that serial dependence is established on the basis of a silent memory signal.

Visual priming and serial dependence are mediated by separate mechanisms.

Perceptual history influences current perception, readily revealed by visual priming (the facilitation of responses on repeated presentations of similar stimuli) and by serial dependence (systematic biases toward the previous stimuli). We asked whether the two phenomena shared perceptual mechanisms. We modified the standard "priming of pop-out" paradigm to measure both priming and serial dependence concurrently. The stimulus comprised three grating patches, one or two red, and the other green. Participants identified the color singleton (either red or green), and reproduced its orientation. Trial sequences were designed to maximize serial dependence, and long runs of priming color and position. The results showed strong effects of priming, both on reaction times and accuracy, which accumulated steadily over time, as generally reported in the literature. The serial dependence effects were also strong, but did not depend on previous color, nor on the run length. Reaction times measured under various conditions of repetition or change of priming color or position were reliably correlated with imprecision in orientation reproduction, but reliably uncorrelated with magnitude of serial dependence. The results suggest that visual priming and serial dependence are mediated by different neural mechanisms. We propose that priming affects sensitivity, possibly via attention-like mechanisms, whereas serial dependence affects criteria, two orthogonal dimensions in the signal detection theory.

Crowding results from optimal integration of visual targets with contextual information.

Crowding is the inability to recognize an object in clutter, usually considered a fundamental low-level bottleneck to object recognition. Here we advance and test an alternative idea, that crowding, like predictive phenomena such as serial dependence, results from optimizing strategies that exploit redundancies in natural scenes. This notion leads to several testable predictions: crowding should be greatest for unreliable targets and reliable flankers; crowding-induced biases should be maximal when target and flankers have similar orientations, falling off for differences around 20°; flanker interference should be associated with higher precision in orientation judgements, leading to lower overall error rate; effects should be maximal when the orientation of the target is near that of the average of the flankers, rather than to that of individual flankers. Each of these predictions were supported, and could be simulated with ideal-observer models that maximize performance. The results suggest that while crowding can affect object recognition, it may be better understood not as a processing bottleneck, but as a consequence of efficient exploitation of the spatial redundancies of the natural world.

Symmetry as a grouping cue for numerosity perception.

To estimate the number of objects in an image, each element needs to be segregated as a single unit. Several principles guide the process of element identification, one of the strongest being symmetry. In the current study, we investigated how symmetry affects the ability to rapidly estimate the number of objects (numerosity). Participants judged the numerosity of asymmetric or symmetric arrays of various numerosities. The results show that the numerosity of symmetrical arrays was significantly underestimated at low numerosities, but the effect was greatly reduced at higher numerosities. Adding an additional axis of symmetry (double symmetry) further reduced perceived numerosity. The magnitude of the symmetry-driven underestimation was inversely correlated with autistic personality traits, consistent with previous work associating autistic traits with perceptual grouping. Overall, these results support the idea that perceived numerosity relies on object segmentation and grouping cues, with symmetry playing a key role.

Numerosity perception is tuned to salient environmental features.

Numerosity perception is a key ability to guide behavior. However, current models propose that number units encode an abstract representation of numerosity regardless of the non-numerical attributes of the stimuli, suggesting rather coarse environmental tuning. Here we investigated whether numerosity systems spontaneously adapt to all visible items, or to subsets segregated by salient attributes such as color or pitch. We measured perceived numerosity after participants adapted to highly numerous stimuli with color either matched to or different from the test. Matched colors caused a 25% underestimation of numerosity, while different colors had virtually no effect. This was true both for physically different colors, and for the same colors perceived as different, via a color-assimilation illusion. A similar result occurred in the acoustic domain, where adaptation magnitude was halved when the adaptor and test differed in pitch. Taken together, our results support the idea that numerosity perception is selectively tuned to salient environmental attributes.

Contextual Information Modulates Pupil Size in Autistic Children.

Recent Bayesian models suggest that perception is more "data-driven" and less dependent on contextual information in autistic individuals than others. However, experimental tests of this hypothesis have given mixed results, possibly due to the lack of objectivity of the self-report methods typically employed. Here we introduce an objective no-report paradigm based on pupillometry to assess the processing of contextual information in autistic children, together with a comparison clinical group. After validating in neurotypical adults a child-friendly pupillometric paradigm, in which we embedded test images within an animation movie that participants watched passively, we compared pupillary response to images of the sun and meaningless control images in children with autism vs. age- and IQ-matched children presenting developmental disorders unrelated to the autistic spectrum. Both clinical groups showed stronger pupillary constriction for the sun images compared with control images, like the neurotypical adults. However, there was no detectable difference between autistic children and the comparison group, despite a significant difference in pupillary light responses, which were enhanced in the autistic group. Our report introduces an objective technique for studying perception in clinical samples and children. The lack of statistically significant group differences in our tests suggests that autistic children and the comparison group do not show large differences in perception of these stimuli. This opens the way to further studies testing contextual processing at other levels of perception.