Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types.

Neural circuit function is shaped both by the cell types that comprise the circuit and the connections between those cell types 1 . Neural cell types have previously been defined by morphology 2, 3 , electrophysiology 4, 5 , transcriptomic expression 6-8 , connectivity 9-13 , or even a combination of such modalities 14-16 . More recently, the Patch-seq technique has enabled the characterization of morphology (M), electrophysiology (E), and transcriptomic (T) properties from individual cells 17-20 . Using this technique, these properties were integrated to define 28, inhibitory multimodal, MET-types in mouse primary visual cortex 21 . It is unknown how these MET-types connect within the broader cortical circuitry however. Here we show that we can predict the MET-type identity of inhibitory cells within a large-scale electron microscopy (EM) dataset and these MET-types have distinct ultrastructural features and synapse connectivity patterns. We found that EM Martinotti cells, a well defined morphological cell type 22, 23 known to be Somatostatin positive (Sst+) 24, 25 , were successfully predicted to belong to Sst+ MET-types. Each identified MET-type had distinct axon myelination patterns and synapsed onto specific excitatory targets. Our results demonstrate that morphological features can be used to link cell type identities across imaging modalities, which enables further comparison of connectivity in relation to transcriptomic or electrophysiological properties. Furthermore, our results show that MET-types have distinct connectivity patterns, supporting the use of MET-types and connectivity to meaningfully define cell types.

Characterizing export of land-based microplastics to the estuary - Part II: Sensitivity analysis of an integrated geospatial microplastic transport modeling assessment of tire and road wear particles.

Integrated models addressing microplastic (MP) generation, terrestrial distribution, and freshwater transport are useful tools characterizing the export of MP to marine waters. In Part I of this study, a baseline watershed-scale MP mass balance model was developed for tire and road wear particles (TRWP) in the Seine watershed. In Part II, uncertainty and sensitivity analysis (SA) methods were used to identify the parameters that determine the transport of these particles to the estuary. Local differential, local range and global first-order variance-based SA identified similar key parameters. The global SA (1000 Monte Carlo simulations) indicated that most of the variance in TRWP exported to the estuary can be apportioned to TRWP diameter (76%), TRWP density (5.6%), the fraction of TRWP directed to combined sewers with treatment (3.9%), and the fraction of TRWP distributed to runoff (versus roadside soil; 2.2%). The export fraction was relatively insensitive to heteroaggregation processes and the rainfall intensity threshold for road surface washoff. The fraction of TRWP exported to estuary in the probabilistic assessment was centered on the baseline estimate of 2%. This fraction ranged from 1.4 to 4.9% (central tendency defined as 25th to 75th percentile) and 0.97% to 13% (plausible upper bound defined as 10th to 90th percentiles). This study emphasizes the importance of in situ characterization of TRWP diameter and density, and confirms the baseline mass balance presented in Part I, which indicated an appreciable potential for capture of TRWP in freshwater sediment.

Characterizing export of land-based microplastics to the estuary - Part I: Application of integrated geospatial microplastic transport models to assess tire and road wear particles in the Seine watershed.

Human and ecological exposure to micro- and nanoplastic materials (abbreviated as MP, < 5 mm) occurs in both aquatic and terrestrial environments. Recent reviews prioritize the need for assessments linking spatially distributed MP releases with terrestrial and freshwater transport processes, thereby providing a better understanding of the factors affecting MP distribution to the sea. Tire and road wear particles (TRWP) have an estimated generation rate of 1 kg tread inhabitant-1 year-1 in Europe, but the fate of this MP source in watersheds has not been systematically assessed. An integrated temporally and geospatially resolved watershed-scale MP modeling methodology was applied to TRWP fate and transport in the Seine (France) watershed. The mass balance considers TRWP generation and terrestrial transport to soil, air, and roadways, as well as freshwater transport processes including particle heteroaggregation, degradation and sedimentation within subcatchments. The per capita TRWP mass release estimate in the Seine watershed was 1.8 kg inhabitant-1 yr-1. The model estimates indicated that 18% of this release was transported to freshwater and 2% was exported to the estuary, which demonstrated the potential for appreciable capture, degradation, and retention of TRWP prior to export. The modeled pseudo-steady state sediment concentrations were consistent with measurements from the Seine watershed supporting the plausibility of the predicted trapping efficiency of approximately 90%. The approach supported the efficient completion of local and global sensitivity analyses presented in Part II of this study, and can be adapted to the assessment of other MPs.

Chronic cellular imaging of mouse visual cortex during operant behavior and passive viewing.

Nearby neurons in mammalian neocortex demonstrate a great diversity of cell types and connectivity patterns. The importance of this diversity for computation is not understood. While extracellular recording studies in visual cortex have provided a particularly rich description of behavioral modulation of neural activity, new methods are needed to dissect the contribution of specific circuit elements in guiding visual perception. Here, we describe a method for three-dimensional cellular imaging of neural activity in the awake mouse visual cortex during active discrimination and passive viewing of visual stimuli. Head-fixed mice demonstrated robust discrimination for many hundred trials per day after initial task acquisition. To record from multiple neurons during operant behavior with single-trial resolution and minimal artifacts, we built a sensitive microscope for two-photon calcium imaging, capable of rapid tracking of neurons in three dimensions. We demonstrate stable recordings of cellular calcium activity during discrimination behavior across hours, days, and weeks, using both synthetic and genetically encoded calcium indicators. When combined with molecular and genetic technologies in mice (e.g., cell-type specific transgenic labeling), this approach allows the identification of neuronal classes in vivo. Physiological measurements from distinct classes of neighboring neurons will enrich our understanding of the coordinated roles of diverse elements of cortical microcircuits in guiding sensory perception and perceptual learning. Further, our method provides a high-throughput, chronic in vivo assay of behavioral influences on cellular activity that is applicable to a wide range of mouse models of neurologic disease.

The use of live-animal micro-computed tomography to determine the effect of a novel phospholipase A2 inhibitor on alveolar bone loss in an in vivo mouse model of periodontitis.

BACKGROUND AND OBJECTIVE: Live-animal micro-computed tomography is a new and promising technique that can be used to quantify changes in bone volume for periodontal disease models. The major aim of this study was to develop the methodology of live-animal micro-computed tomography and to determine the effect of a novel secretory phospholipase A2 inhibitor on alveolar bone loss. MATERIAL AND METHODS: Periodontitis was induced in mice by oral infection with Porphyromonas gingivalis over a period of 13 wk, and live-animal micro-computed tomography scans were taken at different time-points to determine bone volume changes with disease progression. This enabled conclusions to be made as to when treatment was most likely to be effective. In addition, the model was used to investigate a novel drug, the secretory phospholipase A2 inhibitor, KHO64, and its potential ability to inhibit osteoclast bone resorption and treat periodontitis. RESULTS: The results from live-animal micro-computed tomography scans revealed greater, statistically significant, bone volume loss in diseased mice compared with normal mice (p < 0.05). This corresponded to a larger area from the cemento-enamel junction to the alveolar bone crest, as assessed by stereo imaging (p < 0.001). These techniques can therefore detect and quantify alveolar bone loss. Both methods revealed that KHO64 had no significant effect on the volume of bone resorption. CONCLUSION: Live-animal micro-computed tomography is a robust, reproducible technique that clearly demonstrates significant time-dependent changes in alveolar bone volume in a small-animal model of periodontitis.

Inhibition of immune-complex mediated dermal inflammation in rats following either oral or topical administration of a small molecule C5a receptor antagonist.

1. Initiation of a peritoneal Arthus reaction by deposition of immune-complexes results in vascular leakage, polymorphonuclear leukocyte (PMN) infiltration, and tumour necrosis factor alpha (TNFalpha) and interleukin-6 (IL-6) production. We now demonstrate in rats that oral administration of the C5a receptor antagonist AcPhe[Orn-Pro-D-Cyclohexylalanine-Trp-Arg] (AcF-[OPdChaWR]; 1 - 10 mg kg(-1) 30 min prior to immune-complex deposition) inhibits these inflammatory markers in the peritoneal Arthus reaction. 2. Initiation of a dermal Arthus reaction resulted in a significant increase in vascular leakage, PMN infiltration, systemic production of TNFalpha and pathological changes in the dermis. 3. Pretreatment of rats with AcF-[OPdChaWR] either intravenously (1 mg kg(-1) 10 min prior to immune-complex deposition) or orally (1 - 10 mg kg(-1) 30 min prior to immune-complex deposition) significantly inhibited immune-complex mediated dermal vascular leakage and systemic cytokine production. Topical pretreatment with AcF-[OPdChaWR] (400 microg site(-1) in 10% dimethyl sulphoxide 10 min prior to immune-complex deposition) also inhibited vascular leakage, as well as histopathological changes associated with a dermal Arthus reaction. 4. Oral administration of 3 mg kg(-1) AcF-[OPdChaWR] resulted in the appearance of the drug in plasma within 5 min, with peak blood levels approximately 0.3 microM reached within 20 min. The plasma elimination half-life was approximately 70 min. The oral activity and bioavailability of AcF-[OPdChaWR], its activity when applied topically to the skin, suggest that small molecule C5a receptor antagonists may have therapeutic utility in dermal inflammatory disorders involving complement activation. 5. This is the first demonstration for either an orally or topically active C5a receptor antagonist, and suggests that small molecule C5a antagonists may have therapeutic utility when given by multiple routes of application.

Predicting every spike: a model for the responses of visual neurons.

In the early visual system, neuronal responses can be extremely precise. Under a wide range of stimuli, cells in the retina and thalamus fire spikes very reproducibly, often with millisecond precision on subsequent stimulus repeats. Here we develop a mathematical description of the firing process that, given the recent visual input, accurately predicts the timing of individual spikes. The formalism is successful in matching the spike trains from retinal ganglion cells in salamander, rabbit, and cat, as well as from lateral geniculate nucleus neurons in cat. It adapts to many different response types, from very precise to highly variable. The accuracy of the model allows a compact description of how these neurons encode the visual stimulus.

Rules of connectivity between geniculate cells and simple cells in cat primary visual cortex.

Hundreds of thalamic axons ramify within a column of cat visual cortex; yet each layer 4 neuron receives input from only a fraction of them. We have examined the specificity of these connections by recording simultaneously from layer 4 simple cells and cells in the lateral geniculate nucleus with spatially overlapping receptive fields (n = 221 cell pairs). Because of the precise retinotopic organization of visual cortex, the geniculate axons and simple-cell dendrites of these cell pairs should have overlapped within layer 4. Nevertheless, monosynaptic connections were identified in only 33% of all cases, as estimated by cross-correlation analysis. The visual responses of monosynaptically connected geniculate cells and simple cells were closely related. The probability of connection was greatest when a geniculate center overlapped a strong simple-cell subregion of the same sign (ON or OFF) near the center of the subregion. This probability was further increased when the time courses of the visual responses were similar. In addition, the connections were strongest when the simple-cell subregion and the geniculate center were matched in position, sign, and size. The rules of connectivity between geniculate afferents and simple cells resemble those found for retinal afferents to geniculate cells. The connections along the retinogeniculocortical pathway, therefore, show a precision that goes beyond simple retinotopy to include many other response properties, such as receptive-field sign, timing, subregion strength, and size. This specificity in wiring emphasizes the need for developmental mechanisms (presumably correlation-based) that can select among afferents that differ only slightly in their response properties.

Low response variability in simultaneously recorded retinal, thalamic, and cortical neurons.

The response of a cortical cell to a repeated stimulus can be highly variable from one trial to the next. Much lower variability has been reported of retinal cells. We recorded visual responses simultaneously from three successive stages of the cat visual system: retinal ganglion cells (RGCs), thalamic (LGN) relay cells, and simple cells in layer 4 of primary visual cortex. Spike count variability was lower than that of a Poisson process at all three stages but increased at each stage. Absolute and relative refractory periods largely accounted for the reliability at all three stages. Our results show that cortical responses can be more reliable than previously thought. The differences in reliability in retina, LGN, and cortex can be explained by (1) decreasing firing rates and (2) decreasing absolute and relative refractory periods.

Synthesis, stability, antiviral activity, and protease-bound structures of substrate-mimicking constrained macrocyclic inhibitors of HIV-1 protease.

Three new peptidomimetics (1-3) have been developed with highly stable and conformationally constrained macrocyclic components that replace tripeptide segments of protease substrates. Each compound inhibits both HIV-1 protease and viral replication (HIV-1, HIV-2) at nanomolar concentrations without cytotoxicity to uninfected cells below 10 microM. Their activities against HIV-1 protease (K(i) 1.7 nM (1), 0.6 nM (2), 0.3 nM (3)) are 1-2 orders of magnitude greater than their antiviral potencies against HIV-1-infected primary peripheral blood mononuclear cells (IC(50) 45 nM (1), 56 nM (2), 95 nM (3)) or HIV-1-infected MT2 cells (IC(50) 90 nM (1), 60 nM (2)), suggesting suboptimal cellular uptake. However their antiviral potencies are similar to those of indinavir and amprenavir under identical conditions. There were significant differences in their capacities to inhibit the replication of HIV-1 and HIV-2 in infected MT2 cells, 1 being ineffective against HIV-2 while 2 was equally effective against both virus types. Evidence is presented that 1 and 2 inhibit cleavage of the HIV-1 structural protein precursor Pr55(gag) to p24 in virions derived from chronically infected cells, consistent with inhibition of the viral protease in cells. Crystal structures refined to 1.75 A (1) and 1.85 A (2) for two of the macrocyclic inhibitors bound to HIV-1 protease establish structural mimicry of the tripeptides that the cycles were designed to imitate. Structural comparisons between protease-bound macrocyclic inhibitors, VX478 (amprenavir), and L-735,524 (indinavir) show that their common acyclic components share the same space in the active site of the enzyme and make identical interactions with enzyme residues. This substrate-mimicking minimalist approach to drug design could have benefits in the context of viral resistance, since mutations which induce inhibitor resistance may also be those which prevent substrate processing.

Small peptides Do not inhibit human non-pancreatic secretory phospholipase-A(2) (Type IIA).

Seven small peptides, that are among the most potent reported inhibitors of secreted mammalian phospholipases A(2), were found not to inhibit processing of a small phospholipid substrate by human non-pancreatic secretory phospholipase A(2) (type IIa), under conditions where certain non-peptides are potent inhibitors at nanomolar concentrations.

Temporal coding of visual information in the thalamus.

The amount of information a sensory neuron carries about a stimulus is directly related to response reliability. We recorded from individual neurons in the cat lateral geniculate nucleus (LGN) while presenting randomly modulated visual stimuli. The responses to repeated stimuli were reproducible, whereas the responses evoked by nonrepeated stimuli drawn from the same ensemble were variable. Stimulus-dependent information was quantified directly from the difference in entropy of these neural responses. We show that a single LGN cell can encode much more visual information than had been demonstrated previously, ranging from 15 to 102 bits/sec across our sample of cells. Information rate was correlated with the firing rate of the cell, for a consistent rate of 3.6 +/- 0.6 bits/spike (mean +/- SD). This information can primarily be attributed to the high temporal precision with which firing probability is modulated; many individual spikes were timed with better than 1 msec precision. We introduce a way to estimate the amount of information encoded in temporal patterns of firing, as distinct from the information in the time varying firing rate at any temporal resolution. Using this method, we find that temporal patterns sometimes introduce redundancy but often encode visual information. The contribution of temporal patterns ranged from -3.4 to +25.5 bits/sec or from -9.4 to +24.9% of the total information content of the responses.

Synaptic interactions between thalamic inputs to simple cells in cat visual cortex.

We performed experiments in the cat geniculocortical pathway, in vivo, to examine how presynaptic spikes interact to influence the firing of postsynaptic targets. In particular, we asked (1) how do multiple spikes from a single presynaptic neuron interact to influence the firing of a postsynaptic target (homosynaptic interactions), (2) how do spikes from two different presynaptic neurons interact (heterosynaptic interactions), and (3) what is the time course of homosynaptic and heterosynaptic interactions? We found that both homosynaptic and heterosynaptic interactions increase the likelihood of driving a postsynaptic spike, although with different time courses. For two spikes traveling down a single geniculate axon, the second spike is more effective than the first for approximately 15 msec. For two spikes on separate axons, the interaction is faster ( approximately 7 msec duration, approximately 2.5 msec time constant). Thus changes in firing rate are perhaps best relayed by homosynaptic interactions, whereas heterosynaptic interactions may help detect coincident spikes from different thalamic inputs.

The koniocellular pathway in primate vision.

A neurochemically distinct population of koniocellular (K) neurons makes up a third functional channel in primate lateral geniculate nucleus. As part of a general pattern, K neurons form robust layers through the full representation of the visual hemifield. Similar in physiology and connectivity to W cells in cat lateral geniculate nucleus, K cells form three pairs of layers in macaques. The middle pair relays input from short-wavelength cones to the cytochrome-oxidase blobs of primay visual cortex (V1), the dorsal-most pair relays low-acuity visual information to layer I of V1, and the ventral-most pair appears closely tied to the function of the superior colliculus. Throughout each K layer are neurons that innervate extrastriate cortex and that are likely to sustain some visual behaviors in the absence of V1. These data show that several pathways exist from retina to V1 that are likely to process different aspects of the visual scene along lines that may remain parallel well into V1.

Diverse receptive fields in the lateral geniculate nucleus during thalamocortical development.

Most models of thalamocortical development in the visual system assume a homogeneous population of thalamic inputs to the cortex, each with concentric on- or off-center receptive fields. To test this, we made high-resolution spatial maps of receptive fields in the developing ferret lateral geniculate nucleus (LGN). Developing receptive fields (RFs), had a variety of shapes: some concentric, others elongated (like adult cortical receptive fields) and some with 'hot spots' of sensitivity. These receptive fields seemed to arise from convergence of multiple retinal afferents onto LGN neurons. We present a Hebbian model whereby imprecise retinogeniculate connections help refine geniculocortical connections, sharpening both thalamocortical topography and perhaps orientation selectivity.

Visual physiology of the lateral geniculate nucleus in two species of new world monkey: Saimiri sciureus and Aotus trivirgatis.

1. Visual responses were recorded from neurones in the magnocellular and parvocellular layers of the lateral geniculate nucleus (LGN) of the thalamus in two species of New World monkeys - the diurnal squirrel monkey (Saimiri sciureus) and the nocturnal owl monkey (Aotus trivirgatis). Recording sites were reconstructed in postmortem tissue and comparisons were made between the response properties of magnocellular and parvocellular neurones. 2. Receptive fields were characterized with both white noise and drifting gratings. We found that most of the differences between magnocellular and parvocellular neurones that have been described in the macaque monkey hold for the squirrel monkey and owl monkey. In squirrel monkey and owl monkey, receptive fields of magnocellular neurones were larger than those of parvocellular neurones at similar eccentricities. Although visual responses in the owl monkey were significantly slower than in the squirrel monkey, in both species magnocellular neurones differed from parvocellular neurones in that their responses (1) had higher contrast gains, (2) tended to peak at higher temporal frequencies (but with considerable overlap), (3) had shorter response latencies, and (4) were more transient. 3. The strength of a neurone's receptive-field surround was assessed by comparing neuronal responses to gratings of optimal spatial frequency with responses to gratings of low spatial frequency. Using this approach, receptive-field surrounds were found to be equally strong on average for magnocellular and parvocellular neurones. 4. Spatial summation, as measured by a null test, was linear for all magnocellular and parvocellular cells tested; that is, Y cells were not observed in either species. Finally, most magnocellular neurones showed a contrast gain control mechanism, although this was not seen for parvocellular neurones.

Dimensions of care for dementia sufferers in long-term care institutions: are they related to outcomes?

OBJECTIVES: This study empirically examined whether dimensions of care cluster in special care units (SCUs) compared with non-SCUs. The relationship between SCU status plus separate measures of the dimensions of care and outcomes for dementia sufferers was then investigated. METHODS: Data were drawn from the Intermediate Care Facility Project. The sample (N = 510) included residents with dementia, aged 65 and older, in intermediate care facilities throughout the province of British Columbia. Canada. Longitudinal data included 6 outcomes: cognitive function, behavioral problems of agitation and social skills, physical functioning, and quality of life measured through affect and expressive language skills. Separate multiple linear regression equations were estimated, relating each of these outcomes to 5 dimensions of care: preadmission and admission procedures. staff training and education, nonuse of physical and chemical restraints, flexible care routines and resident-relevant activities, and the environment. RESULTS: The results showed there is virtually no clustering of dimensions along SCU/non-SCU lines. Neither SCU status nor the individual dimensions were highly predictive of outcomes. Residents' affect at t1 emerged as a characteristic that was significantly correlated with other outcomes. DISCUSSION: This Canadian research can be added to the few but growing number of rigorous studies that suggest SCUs are not homogeneous and do not necessarily provide better care than non-SCUs. Moreover, it raises questions about the benefits of "best practice" dimensions of care, regardless of SCU status.

Conformational selection of inhibitors and substrates by proteolytic enzymes: implications for drug design and polypeptide processing.

Inhibitors of proteolytic enzymes (proteases) are emerging as prospective treatments for diseases such as AIDS and viral infections, cancers, inflammatory disorders, and Alzheimer's disease. Generic approaches to the design of protease inhibitors are limited by the unpredictability of interactions between, and structural changes to, inhibitor and protease during binding. A computer analysis of superimposed crystal structures for 266 small molecule inhibitors bound to 48 proteases (16 aspartic, 17 serine, 8 cysteine, and 7 metallo) provides the first conclusive proof that inhibitors, including substrate analogues, commonly bind in an extended beta-strand conformation at the active sites of all these proteases. Representative superimposed structures are shown for (a) multiple inhibitors bound to a protease of each class, (b) single inhibitors each bound to multiple proteases, and (c) conformationally constrained inhibitors bound to proteases. Thus inhibitor/substrate conformation, rather than sequence/composition alone, influences protease recognition, and this has profound implications for inhibitor design. This conclusion is supported by NMR, CD, and binding studies for HIV-1 protease inhibitors/substrates which, when preorganized in an extended conformation, have significantly higher protease affinity. Recognition is dependent upon conformational equilibria since helical and turn peptide conformations are not processed by proteases. Conformational selection explains the resistance of folded/structured regions of proteins to proteolytic degradation, the susceptibility of denatured proteins to processing, and the higher affinity of conformationally constrained 'extended' inhibitors/substrates for proteases. Other approaches to extended inhibitor conformations should similarly lead to high-affinity binding to a protease.

Specificity and strength of retinogeniculate connections.

Retinal ganglion cells and their target neurons in the principal layers of the lateral geniculate nucleus (LGN) of the thalamus have very similar, center-surround receptive fields. Although some geniculate neurons are dominated by a single retinal afferent, others receive both strong and weak inputs from several retinal afferents. In the present study, experiments were performed in the cat that examined the specificity and strength of monosynaptic connections between retinal ganglion cells and their target neurons. The responses of 205 pairs of retinal ganglion cells and geniculate neurons with overlapping receptive-field centers or surrounds were studied. Receptive fields were mapped quantitatively using a white-noise stimulus; connectivity was assessed by cross-correlating the retinal and geniculate spike trains. Of the 205 pairs, 12 were determined to have monosynaptic connections. Both the likelihood that cells were connected and the strength of connections increased with increasing similarity between retinal and geniculate receptive fields. Connections were never found between cells with <50% spatial overlap between their centers. The results suggest that although geniculate neurons often receive input from several retinal afferents, these multiple afferents represent a select subset of the retinal ganglion cells with overlapping receptive-field centers.