Somatic mutations inferred from RNA-seq data highlight the contribution of replication timing to mutation rate variation in a model plant.

Variation in the rates and characteristics of germline and somatic mutations across the genome of an organism is informative about DNA damage and repair processes and can also shed light on aspects of organism physiology and evolution. We adapted a recently developed method for inferring somatic mutations from bulk RNA-seq data and applied it to a large collection of Arabidopsis thaliana accessions. The wide range of genomic data types available for A. thaliana enabled us to investigate the relationships of multiple genomic features with the variation in the somatic mutation rate across the genome of this model plant. We observed that late replicated regions showed evidence of an elevated rate of somatic mutation compared to genomic regions that are replicated early. We identified transcriptional strand asymmetries, consistent with the effects of transcription-coupled damage and/or repair. We also observed a negative relationship between the inferred somatic mutation count and the H3K36me3 histone mark which is well documented in the literature of human systems. In addition, we were able to support previous reports of an inverse relationship between inferred somatic mutation count and guanine-cytosine content as well as a positive relationship between inferred somatic mutation count and DNA methylation for both cytosine and noncytosine mutations.

Implementation of probe rheology simulation technique in atomistically detailed molecular dynamics simulations.

The probe rheology simulation technique is a technique for measuring the viscosity of a fluid by measuring the motion of an inserted probe particle. This approach has the benefit of greater potential accuracy at a lower computational cost than other conventional simulation techniques used for the calculation of mechanical properties, such as the Green-Kubo approach and nonequilibrium molecular dynamics simulations, and the potential to allow for sampling local variations of properties. This approach is implemented and demonstrated for atomistically detailed models. The viscosity of four different simple Newtonian liquids is calculated from both the Brownian motion (passive mode) and the forced motion (active mode) of an embedded probe particle. The probe particle is loosely modeled as a nano-sized diamond particle: a rough sphere cut out of an FCC lattice made of carbon atoms. The viscosities obtained from the motion of the probe particle are compared with those obtained from the periodic perturbation method, and good agreement between the two sets of values is observed once the probe-fluid interaction strength (i.e., ε ij in the pair-wise Lennard-Jones interaction) is two times higher than their original values, and the artificial hydrodynamic interactions between the probe particle and its periodic images are accounted for. The success of the proposed model opens new opportunities for applying such a technique in the rheological characterization of local mechanical properties in atomistically detailed molecular dynamics simulations, which can be directly compared with or help guide experiments of similar nature.

Visuomotor learning promotes visually evoked activity in the medial prefrontal cortex.

The medial prefrontal cortex (mPFC) is necessary for executing many learned associations between stimuli and movement. It is unclear, however, how activity in the mPFC evolves across learning, and how this activity correlates with sensory stimuli and the learned movements they evoke. To address these questions, we record cortical activity with widefield calcium imaging while mice learned to associate a visual stimulus with a forelimb movement. After learning, the mPFC shows stimulus-evoked activity both during task performance and during passive viewing, when the stimulus evokes no action. This stimulus-evoked activity closely tracks behavioral performance across training, with both exhibiting a marked increase between days when mice first learn the task, followed by a steady increase with further training. Electrophysiological recordings localized this activity to the secondary motor and anterior cingulate cortex. We conclude that learning a visuomotor task promotes a route for visual information to reach the prefrontal cortex.

Topologically Precise and Discrete Bottlebrush Polymers: Synthesis, Characterization, and Structure-Property Relationships.

As the complexity of polymer structure grows, so do the challenges for developing an accurate understanding of their structure-property relationships. Here, the synthesis of bottlebrush polymers with topologically precise and fully discrete structures is reported. A key feature of the strategy is the synthesis of discrete macromonomer libraries for their polymerization into topologically precise bottlebrushes that can be separated into discrete bottlebrushes (D = 1.0). As the system becomes more discrete, packing efficiency increases, distinct three-phase Langmuir-Blodgett isotherms are observed, and its glass transition temperature becomes responsive to side-chain sequence. Overall, this work presents a versatile strategy to access a range of precision bottlebrush polymers and unravels the impact of side-chain topology on their macroscopic properties. Precise control over side chains opens a pathway for tailoring polymer properties without changing their chemical makeup.

Aerosol responses to precipitation along North American air trajectories arriving at Bermuda.

North American pollution outflow is ubiquitous over the western North Atlantic Ocean, especially in winter, making this location a suitable natural laboratory for investigating the impact of precipitation on aerosol particles along air mass trajectories. We take advantage of observational data collected at Bermuda to seasonally assess the sensitivity of aerosol mass concentrations and volume size distributions to accumulated precipitation along trajectories (APT). The mass concentration of particulate matter with aerodynamic diameter less than 2.5 µm normalized by the enhancement of carbon monoxide above background (PM2.5/ΔCO) at Bermuda was used to estimate the degree of aerosol loss during transport to Bermuda. Results for December-February (DJF) show that most trajectories come from North America and have the highest APTs, resulting in a significant reduction (by 53 %) in PM2.5/ΔCO under high-APT conditions (> 13.5 mm) relative to low-APT conditions (< 0.9 mm). Moreover, PM2.5/ΔCO was most sensitive to increases in APT up to 5 mm (-0.044 µg m-3 ppbv-1 mm-1) and less sensitive to increases in APT over 5 mm. While anthropogenic PM2.5 constituents (e.g., black carbon, sulfate, organic carbon) decrease with high APT, sea salt, in contrast, was comparable between high- and low-APT conditions owing to enhanced local wind and sea salt emissions in high-APT conditions. The greater sensitivity of the fine-mode volume concentrations (versus coarse mode) to wet scavenging is evident from AErosol RObotic NETwork (AERONET) volume size distribution data. A combination of GEOS-Chem model simulations of the 210Pb submicron aerosol tracer and its gaseous precursor 222Rn reveals that (i) surface aerosol particles at Bermuda are most impacted by wet scavenging in winter and spring (due to large-scale precipitation) with a maximum in March, whereas convective scavenging plays a substantial role in summer; and (ii) North American 222Rn tracer emissions contribute most to surface 210Pb concentrations at Bermuda in winter (~75 %-80 %), indicating that air masses arriving at Bermuda experience large-scale precipitation scavenging while traveling from North America. A case study flight from the ACTIVATE field campaign on 22 February 2020 reveals a significant reduction in aerosol number and volume concentrations during air mass transport off the US East Coast associated with increased cloud fraction and precipitation. These results highlight the sensitivity of remote marine boundary layer aerosol characteristics to precipitation along trajectories, especially when the air mass source is continental outflow from polluted regions like the US East Coast.

An Aerosol Climatology and Implications for Clouds at a Remote Marine Site: Case Study Over Bermuda.

Aerosol characteristics and aerosol-cloud interactions remain uncertain in remote marine regions. We use over a decade of data (2000-2012) from the NASA AErosol RObotic NETwork, aerosol and wet deposition samples, satellite remote sensors, and models to examine aerosol and cloud droplet number characteristics at a representative open ocean site (Bermuda) over the Western North Atlantic Ocean (WNAO). Annual mean values were as follows: aerosol optical depth (AOD) = 0.12, Ångström Exponent (440/870 nm) = 0.95, fine mode fraction = 0.51, asymmetry factor = 0.72 (440 nm) and 0.68 (1020 nm), and Aqua-MODIS cloud droplet number concentrations = 51.3 cm-3. The winter season (December-February) was characterized by high sea salt optical thickness and the highest aerosol extinction in the lowest 2 km. Extensive precipitation over the WNAO in winter helps contribute to the low FMFs in winter (~0.40-0.50) even though air trajectories often originate over North America. Spring and summer had more pronounced influence from sulfate, dust, organic carbon, and black carbon. Volume size distributions were bimodal with a dominant coarse mode (effective radii: 1.85-2.09 µm) and less pronounced fine mode (0.14-0.16 µm), with variability in the coarse mode likely due to different characteristic sizes for transported dust (smaller) versus regional sea salt (larger). Extreme pollution events highlight the sensitivity of this site to long-range transport of urban emissions, dust, and smoke. Differing annual cycles are identified between AOD and cloud droplet number concentrations, motivating a deeper look into aerosol-cloud interactions at this site.

Striatal activity topographically reflects cortical activity.

The cortex projects to the dorsal striatum topographically1,2 to regulate behaviour3-5, but spiking activity in the two structures has previously been reported to have markedly different relations to sensorimotor events6-9. Here we show that the relationship between activity in the cortex and striatum is spatiotemporally precise, topographic, causal and invariant to behaviour. We simultaneously recorded activity across large regions of the cortex and across the width of the dorsal striatum in mice that performed a visually guided task. Striatal activity followed a mediolateral gradient in which behavioural correlates progressed from visual cue to response movement to reward licking. The summed activity in each part of the striatum closely and specifically mirrored activity in topographically associated cortical regions, regardless of task engagement. This relationship held for medium spiny neurons and fast-spiking interneurons, whereas the activity of tonically active neurons differed from cortical activity with stereotypical responses to sensory or reward events. Inactivation of the visual cortex abolished striatal responses to visual stimuli, supporting a causal role of cortical inputs in driving the striatum. Striatal visual responses were larger in trained mice than untrained mice, with no corresponding change in overall activity in the visual cortex. Striatal activity therefore reflects a consistent, causal and scalable topographical mapping of cortical activity.

Cortical State Fluctuations during Sensory Decision Making.

In many behavioral tasks, cortex enters a desynchronized state where low-frequency fluctuations in population activity are suppressed. The precise behavioral correlates of desynchronization and its global organization are unclear. One hypothesis holds that desynchronization enhances stimulus coding in the relevant sensory cortex. Another hypothesis holds that desynchronization reflects global arousal, such as task engagement. Here, we trained mice on tasks where task engagement could be distinguished from sensory accuracy. Using widefield calcium imaging, we found that performance-related desynchronization was global and correlated better with engagement than with accuracy. Consistent with this link between desynchronization and engagement, rewards had a long-lasting desynchronizing effect. To determine whether engagement-related state changes depended on the relevant sensory modality, we trained mice on visual and auditory tasks and found that in both cases desynchronization was global, including regions such as somatomotor cortex. We conclude that variations in low-frequency fluctuations are predominately global and related to task engagement.

Phase behavior of AB/CD diblock copolymer blends via coarse-grained simulation.

The phase diagram of equimolar blends of AB and CD diblock copolymers has been studied using dissipative particle dynamics. All unlike blocks interacted with the same χ, except for the B-C interaction, for which χBC < 0 in order to prevent macrophase separation. The BC interaction was able to prevent macrophase separation except for low volume fractions of B and C (φBC⪅ 0.1) and relatively equal fractions of A and D. For high φBC (φBC⪆ 0.92), a disordered state was obtained. For all microphase separated states the shapes/morphologies were described by the ratios of the eigenvalues of the radius of gyration tensor and their sphericity. These were used to classify the domains as forming sphere, cylinders, lamellae, or branched/gyroidal structures. For φBC < 0.5 the BC domains acted as an interfacial region which compatibilized the A and D domains, while for φBC > 0.5 the BC domain filled in the space between A and D domains. Several interesting structures were formed including a novel connected/branched spheres morphology, hierarchical lamellae, concentric spheres/cylinders, and a combination of cylinders/lamellae. Comparisons are made with the linear diblock and linear triblock phase diagrams.

Aberrant Cortical Activity in Multiple GCaMP6-Expressing Transgenic Mouse Lines.

Transgenic mouse lines are invaluable tools for neuroscience but, as with any technique, care must be taken to ensure that the tool itself does not unduly affect the system under study. Here we report aberrant electrical activity, similar to interictal spikes, and accompanying fluorescence events in some genotypes of transgenic mice expressing GCaMP6 genetically encoded calcium sensors. These epileptiform events have been observed particularly, but not exclusively, in mice with Emx1-Cre and Ai93 transgenes, of either sex, across multiple laboratories. The events occur at >0.1 Hz, are very large in amplitude (>1.0 mV local field potentials, >10% df/f widefield imaging signals), and typically cover large regions of cortex. Many properties of neuronal responses and behavior seem normal despite these events, although rare subjects exhibit overt generalized seizures. The underlying mechanisms of this phenomenon remain unclear, but we speculate about possible causes on the basis of diverse observations. We encourage researchers to be aware of these activity patterns while interpreting neuronal recordings from affected mouse lines and when considering which lines to study.

Reorganization of corticospinal output during motor learning.

Motor learning is accompanied by widespread changes within the motor cortex, but it is unknown whether these changes are ultimately funneled through a stable corticospinal output channel or whether the corticospinal output itself is plastic. We investigated the consistency of the relationship between corticospinal neuron activity and movement through in vivo two-photon calcium imaging in mice learning a lever-press task. Corticospinal neurons exhibited heterogeneous correlations with movement, with the majority of movement-modulated neurons decreasing activity during movement. Individual cells changed their activity across days, which led to changed associations between corticospinal activity and movement. Unlike previous observations in layer 2/3, activity accompanying learned movements did not become more consistent with learning; instead, the activity of dissimilar movements became more decorrelated. These results indicate that the relationship between corticospinal activity and movement is dynamic and that the types of activity and plasticity are different from and possibly complementary to those in layer 2/3.

Learning in the Rodent Motor Cortex.

The motor cortex is far from a stable conduit for motor commands and instead undergoes significant changes during learning. An understanding of motor cortex plasticity has been advanced greatly using rodents as experimental animals. Two major focuses of this research have been on the connectivity and activity of the motor cortex. The motor cortex exhibits structural changes in response to learning, and substantial evidence has implicated the local formation and maintenance of new synapses as crucial substrates of motor learning. This synaptic reorganization translates into changes in spiking activity, which appear to result in a modification and refinement of the relationship between motor cortical activity and movement. This review presents the progress that has been made using rodents to establish the motor cortex as an adaptive structure that supports motor learning.

Stable isotopes in the atmospheric marine boundary layer water vapour over the Atlantic Ocean, 2012-2015.

The water vapour isotopic composition (1H216O, H218O and 1H2H16O) of the Atlantic marine boundary layer has been measured from 5 research vessels between 2012 and 2015. Using laser spectroscopy analysers, measurements have been carried out continuously on samples collected 10-20 meter above sea level. All the datasets have been carefully calibrated against the international VSMOW-SLAP scale following the same protocol to build a homogeneous dataset covering the Atlantic Ocean between 4°S to 63°N. In addition, standard meteorological variables have been measured continuously, including sea surface temperatures using calibrated Thermo-Salinograph for most cruises. All calibrated observations are provided with 15-minute resolution. We also provide 6-hourly data to allow easier comparisons with simulations from the isotope-enabled Global Circulation Models. In addition, backwards trajectories from the HYSPLIT model are supplied every 6-hours for the position of our measurements.

Marine biogenic source of atmospheric organic nitrogen in the subtropical North Atlantic.

Global models estimate that the anthropogenic component of atmospheric nitrogen (N) deposition to the ocean accounts for up to a third of the ocean's external N supply and 10% of anthropogenic CO2 uptake. However, there are few observational constraints from the marine atmospheric environment to validate these findings. Due to the paucity of atmospheric organic N data, the largest uncertainties related to atmospheric N deposition are the sources and cycling of organic N, which is 20-80% of total N deposition. We studied the concentration and chemical composition of rainwater and aerosol organic N collected on the island of Bermuda in the western North Atlantic Ocean over 18 mo. Here, we show that the water-soluble organic N concentration ([WSON]) in marine aerosol is strongly correlated with surface ocean primary productivity and wind speed, suggesting a marine biogenic source for aerosol WSON. The chemical composition of high-[WSON] aerosols also indicates a primary marine source. We find that the WSON in marine rain is compositionally different from that in concurrently collected aerosols, suggesting that in-cloud scavenging (as opposed to below-cloud "washout") is the main contributor to rain WSON. We conclude that anthropogenic activity is not a significant source of organic N to the marine atmosphere over the North Atlantic, despite downwind transport from large pollution sources in North America. This, in conjunction with previous work on ammonium and nitrate, leads to the conclusion that only 27% of total N deposition to the global ocean is anthropogenic, in contrast to the 80% estimated previously.

Simulation study of the effect of molar mass dispersity on domain interfacial roughness in lamellae forming block copolymers for directed self-assembly.

A coarse-grained molecular dynamics model was used to study the thin film self-assembly and resulting pattern properties of block copolymer (BCP) systems with various molar mass dispersities. Diblock copolymers (i.e. A-b-B type) were simulated in an aligned lamellar state, which is one of the most common patterns of potential use for integrated circuit fabrication via directed self-assembly of BCPs. Effects of the molar mass dispersity (Ð) on feature pitch and interfacial roughness, which are critical lithographic parameters that have a direct impact on integrated circuit performance, were simulated. It was found that for a realistic distribution of polymer molecular weights, modeled by a Wesslau distribution, both line edge roughness (LER) and line width roughness (LWR) increase approximately linearly with increasing Ð, up to ∼45% of the monodisperse value at Р= 1.5. Mechanisms of compensation for increased A-A and B-B roughness were considered. It was found that long and short chain positions were not correlated, and that long chains were significantly deformed in shape. The increase in LWR was due to the increase in LER and a constant correlation between the line edges. Unaligned systems show a correlation between domain width and local molecular weight, while systems aligned on an alternating pattern of A and B lines did not show any correlation. When the volume fraction of individual chains was allowed to vary, similar results were found when considering the Ð of the block as opposed to the Ð of the entire system.

Subtype-specific plasticity of inhibitory circuits in motor cortex during motor learning.

Motor skill learning induces long-lasting reorganization of dendritic spines, principal sites of excitatory synapses, in the motor cortex. However, mechanisms that regulate these excitatory synaptic changes remain poorly understood. Here, using in vivo two-photon imaging in awake mice, we found that learning-induced spine reorganization of layer (L) 2/3 excitatory neurons occurs in the distal branches of their apical dendrites in L1 but not in the perisomatic dendrites. This compartment-specific spine reorganization coincided with subtype-specific plasticity of local inhibitory circuits. Somatostatin-expressing inhibitory neurons (SOM-INs), which mainly inhibit distal dendrites of excitatory neurons, showed a decrease in axonal boutons immediately after the training began, whereas parvalbumin-expressing inhibitory neurons (PV-INs), which mainly inhibit perisomatic regions of excitatory neurons, exhibited a gradual increase in axonal boutons during training. Optogenetic enhancement and suppression of SOM-IN activity during training destabilized and hyperstabilized spines, respectively, and both manipulations impaired the learning of stereotyped movements. Our results identify SOM inhibition of distal dendrites as a key regulator of learning-related changes in excitatory synapses and the acquisition of motor skills.

Emergence of reproducible spatiotemporal activity during motor learning.

The motor cortex is capable of reliably driving complex movements yet exhibits considerable plasticity during motor learning. These observations suggest that the fundamental relationship between motor cortex activity and movement may not be fixed but is instead shaped by learning; however, to what extent and how motor learning shapes this relationship are not fully understood. Here we addressed this issue by using in vivo two-photon calcium imaging to monitor the activity of the same population of hundreds of layer 2/3 neurons while mice learned a forelimb lever-press task over two weeks. Excitatory and inhibitory neurons were identified by transgenic labelling. Inhibitory neuron activity was relatively stable and balanced local excitatory neuron activity on a movement-by-movement basis, whereas excitatory neuron activity showed higher dynamism during the initial phase of learning. The dynamics of excitatory neurons during the initial phase involved the expansion of the movement-related population which explored various activity patterns even during similar movements. This was followed by a refinement into a smaller population exhibiting reproducible spatiotemporal sequences of activity. This pattern of activity associated with the learned movement was unique to expert animals and not observed during similar movements made during the naive phase, and the relationship between neuronal activity and individual movements became more consistent with learning. These changes in population activity coincided with a transient increase in dendritic spine turnover in these neurons. Our results indicate that a novel and reproducible activity-movement relationship develops as a result of motor learning, and we speculate that synaptic plasticity within the motor cortex underlies the emergence of reproducible spatiotemporal activity patterns for learned movements. These results underscore the profound influence of learning on the way that the cortex produces movements.

Parvalbumin-expressing interneurons linearly control olfactory bulb output.

In the olfactory bulb, odor representations by principal mitral cells are modulated by local inhibitory circuits. While dendrodendritic synapses between mitral and granule cells are typically thought to be a major source of this modulation, the contributions of other inhibitory neurons remain unclear. Here we demonstrate the functional properties of olfactory bulb parvalbumin-expressing interneurons (PV cells) and identify their important role in odor coding. Using paired recordings, we find that PV cells form reciprocal connections with the majority of nearby mitral cells, in contrast to the sparse connectivity between mitral and granule cells. In vivo calcium imaging in awake mice reveals that PV cells are broadly tuned to odors. Furthermore, selective PV cell inactivation enhances mitral cell responses in a linear fashion while maintaining mitral cell odor preferences. Thus, dense connections between mitral and PV cells underlie an inhibitory circuit poised to modulate the gain of olfactory bulb output.

Motion-sensitive responses in visual area V4 in the absence of primary visual cortex.

Neurons in cortical ventral-stream area V4 are thought to contribute to important aspects of visual processing by integrating information from primary visual cortex (V1). However, how V4 neurons respond to visual stimulation after V1 injury remains unclear: While electrophysiological investigation of V4 neurons during reversible V1 inactivation suggests that virtually all responses are eliminated (Girard et al., 1991), fMRI in humans and monkeys with permanent lesions shows reliable V1-independent activity (Baseler et al., 1999; Goebel et al., 2001; Schmid et al., 2010). To resolve this apparent discrepancy, we longitudinally assessed neuronal functions of macaque area V4 using chronically implanted electrode arrays before and after creating a permanent aspiration lesion in V1. During the month after lesioning, we observed weak yet significant spiking activity in response to stimuli presented to the lesion-affected part of the visual field. These V1-independent responses showed sensitivity for motion and likely reflect the effect of V1-bypassing geniculate input into extrastriate areas.

Receptive field focus of visual area V4 neurons determines responses to illusory surfaces.

Illusory figures demonstrate the visual system's ability to infer surfaces under conditions of fragmented sensory input. To investigate the role of midlevel visual area V4 in visual surface completion, we used multielectrode arrays to measure spiking responses to two types of visual stimuli: Kanizsa patterns that induce the perception of an illusory surface and physically similar control stimuli that do not. Neurons in V4 exhibited stronger and sometimes rhythmic spiking responses for the illusion-promoting configurations compared with controls. Moreover, this elevated response depended on the precise alignment of the neuron's peak visual field sensitivity (receptive field focus) with the illusory surface itself. Neurons whose receptive field focus was over adjacent inducing elements, less than 1.5° away, did not show response enhancement to the illusion. Neither receptive field sizes nor fixational eye movements could account for this effect, which was present in both single-unit signals and multiunit activity. These results suggest that the active perceptual completion of surfaces and shapes, which is a fundamental problem in natural visual experience, draws upon the selective enhancement of activity within a distinct subpopulation of neurons in cortical area V4.