COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms

We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.

Shoot tip necrosis of in vitro plant cultures: a reappraisal of possible causes and solutions.

MAIN CONCLUSION: Shoot tip necrosis is a physiological condition that negatively impacts the growth and development of in vitro plant shoot cultures across a wide range of species. Shoot tip necrosis is a physiological condition and disorder that can arise in plantlets or shoots in vitro that results in death of the shoot tip. This condition, which can spread basipetally and affect the emergence of axillary shoots from buds lower down the stem, is due to the cessation of apical dominance. STN can occur at both shoot multiplication and rooting stages. One of the most common factors that cause STN is nutrient deficiency or imbalance. Moreover, the presence or absence of plant growth regulators (auxins or cytokinins) at specific developmental stages may impact STN. The cytokinin to auxin ratio within an in vitro plant can be modified by varying the concentration of cytokinins used in the culture medium. The supply of nutrients to in vitro shoots or plantlets might also affect their hormonal balance, thus modifying the occurrence of STN. High relative humidity within culture vessels and hyperhydricity are associated with STN. An adequate supply of calcium as the divalent cation (Ca2+) can hinder STN by inhibiting the accumulation of phenolic compounds and thus programmed cell death. Moreover, the level of Ca2+ affects auxin transport and ethylene production, and higher ethylene production, which can occur as a result of high relative humidity in or poor ventilation of the in vitro culture vessel, induces STN. High relative humidity can decrease the mobility of Ca2+ within a plant, resulting in Ca2+ deficiency and STN. STN of in vitro shoots or plantlets can be halted or reversed by altering the basal medium, mainly the concentration of Ca2+, adjusting the levels of auxins or cytokinins, or modifying culture conditions. This review examines the literature related to STN, seeks to discover the associated factors and relations between them, proposes practical solutions, and attempts to better understand the mechanism(s) underlying this condition in vitro.

Selenate tolerance and selenium hyperaccumulation in the monocot giant reed (Arundo donax), a biomass crop plant with phytoremediation potential.

The response of giant reed (Arundo donax L.) to selenium (Se), added as selenate, was studied. The development, stress response, uptake, translocation, and accumulation of Se were documented in three giant reed ecotypes STM (Hungary), BL (USA), and ESP (Spain), representing different climatic zones. Plantlets regenerated from sterile tissue cultures were grown under greenhouse conditions in sand supplemented with 0, 2.5, 5, and 10 mg Se kg-1 added as sodium selenate. Total Se content was measured in different plant parts using hydride generation atomic fluorescence spectroscopy. All plants developed normally in the 0-5.0 mg Se kg-1 concentration range regardless of ecotype, but no growth occurred at 10.0 mg Se kg-1. There were no signs of chlorosis or necrosis, and the photosynthetic machinery was not affected as evidenced by no marked differences in the structure of thylakoid membranes. There was no change in the maximum quantum yield of photosystem II (Fv/Fm ratio) in the three ecotypes under Se stress, except for a significant negative effect in the ESP ecotype in the 5.0 mg Se kg-1 treatment. Glutathione peroxidase (GPx) activity increased as the Se concentration increased in the growth medium. GPx activity was higher in the shoot system than the root system in all Se treatments. All ecotypes showed great capacity of take up, translocate and accumulate selenium in their stem and leaf. Relative Se accumulation is best described as leaf ˃˃ stem ˃ root. The ESP ecotype accumulated 1783 µg g-1 in leaf, followed by BL with 1769 µg g-1, and STM with 1606 µg g-1 in the 5.0 mg Se kg-1 treatment. All ecotypes showed high values of translocation and bioaccumulation factors, particularly the ESP ecotype (10.1 and 689, respectively, at the highest tolerated Se supplementation level). Based on these findings, Arundo donax has been identified as the first monocot hyperaccumulator of selenium, because Se concentration in the leaves of all three ecotypes, and also in the stem of the ESP ecotype, is higher than 0.1% (dry weight basis) under the conditions tested. Tolerance up to 5.0 mg Se kg-1 and the Se hyperaccumulation capacity make giant reed a promising tool for Se phytoremediation.

High Accumulation and Subcellular Distribution of Thallium in Green Cabbage (Brassica Oleracea L. Var. Capitata L.).

The accumulation of thallium (Tl) in brassicaceous crops is widely known, but both the uptake extents of Tl by the individual cultivars of green cabbage and the distribution of Tl in the tissues of green cabbage are not well understood. Five commonly available cultivars of green cabbage grown in the Tl-spiked pot-culture trials were studied for the uptake extent and subcellular distribution of Tl. The results showed that all the trial cultivars mainly concentrated Tl in the leaves (101∼192 mg/kg, DW) rather than in the roots or stems, with no significant differences among cultivars (p = 0.455). Tl accumulation in the leaves revealed obvious subcellular fractionation: cell cytosol and vacuole >> cell wall > cell organelles. The majority (∼ 88%) of leaf-Tl was found to be in the fraction of cytosol and vacuole, which also served as the major storage site for other major elements such as Ca and Mg. This specific subcellular fractionation of Tl appeared to enable green cabbage to avoid Tl damage to its vital organelles and to help green cabbage tolerate and detoxify Tl. This study demonstrated that all the five green cabbage cultivars show a good application potential in the phytoremediation of Tl-contaminated soils.

Spatial variation of contaminant elements of roadside dust samples from Budapest (Hungary) and Seoul (Republic of Korea), including Pt, Pd and Ir.

Roadside dusts were studied to explain the spatial variation and present levels of contaminant elements including Pt, Pd and Ir in urban environment and around Budapest (Hungary) and Seoul (Republic of Korea). The samples were collected from six sites of high traffic volumes in Seoul metropolitan city and from two control sites within the suburbs of Seoul, for comparison. Similarly, road dust samples were obtained two times from traffic focal points in Budapest, from the large bridges across the River Danube, from Margitsziget (an island in the Danube in the northern part of Budapest, used for recreation) as well as from main roads (no highways) outside Budapest. The samples were analysed for contaminant elements by ICP-AES and for Pt, Pd and Ir by ICP-MS. The highest Pt, Pd and Ir levels in road dusts were found from major roads with high traffic volume, but correlations with other contaminant elements were low, however. This reflects automobile catalytic converter to be an important source. To interpret the obtained multi-element results in short, pollution index, contamination index and geo-accumulation index were calculated. Finally, the obtained data were compared with total concentrations encountered in dust samples from Madrid, Oslo, Tokyo and Muscat (Oman). Dust samples from Seoul reached top level concentrations for Cd-Zn-As-Co-Cr-Cu-Mo-Ni-Sn. Just Pb was rather low because unleaded gasoline was introduced as compulsory in 1993. Concentrations in Budapest dust samples were lower than from Seoul, except for Pb and Mg. Compared with Madrid as another continental site, Budapest was higher in Co-V-Zn. Dust from Oslo, which is not so large, contained more Mn-Na-Sr than dust from other towns, but less other metals.

Distinct dendritic arborization and in vivo firing patterns of parvalbumin-expressing basket cells in the hippocampal area CA3.

Hippocampal CA3 area generates temporally structured network activity such as sharp waves and gamma and theta oscillations. Parvalbumin-expressing basket cells, making GABAergic synapses onto cell bodies and proximal dendrites of pyramidal cells, control pyramidal cell activity and participate in network oscillations in slice preparations, but their roles in vivo remain to be tested. We have recorded the spike timing of parvalbumin-expressing basket cells in areas CA2/3 of anesthetized rats in relation to CA3 putative pyramidal cell firing and activity locally and in area CA1. During theta oscillations, CA2/3 basket cells fired on the same phase as putative pyramidal cells, but, surprisingly, significantly later than downstream CA1 basket cells. This indicates a distinct modulation of CA3 and CA1 pyramidal cells by basket cells, which receive different inputs. We observed unexpectedly large dendritic arborization of CA2/3 basket cells in stratum lacunosum moleculare (33% of length, 29% surface, and 24% synaptic input from a total of ∼35,000), different from the dendritic arborizations of CA1 basket cells. Area CA2/3 basket cells fired phase locked to both CA2/3 and CA1 gamma oscillations, and increased firing during CA1 sharp waves, thus supporting the role of CA3 networks in the generation of gamma oscillations and sharp waves. However, during ripples associated with sharp waves, firing of CA2/3 basket cells was phase locked only to local but not CA1 ripples, suggesting the independent generation of fast oscillations by basket cells in CA1 and CA2/3. The distinct spike timing of basket cells during oscillations in CA1 and CA2/3 suggests differences in synaptic inputs paralleled by differences in dendritic arborizations.

Early post-operative thrombosis of the prosthetic mitral valve in patient with heparin-induced thrombocytopenia.

Heparin-induced thrombocytopenia (HIT) is one of the most common immune-mediated adverse drug reactions, with frequencies as high as 2-3% for certain groups of post-cardiac surgery patients. We report on an 50-year-old woman with early post-operative thrombosis of the prosthetic mitral valve due to heparin-induced thrombocytopenia. Non-invasive imaging (two-dimensional transesophageal echocardiography; 2D-TEE) allowed the exact localisation of thrombotic masses and revealed the increase of the mean diastolic mitral gradient. The HIT diagnosis was proved by the clinical scoring system, and with the identification of heparin platelet factor 4-induced antibodies. After the withdrawal of LMWH therapy and the start of intravenous lepirudin treatment, the patient's medical condition improved continuously. Follow-up echocardiography showed a step-wise decrease in the severity of the mean diastolic mitral valve gradient and a complete resolution of thrombus formations. Perhaps we may remind ourselves that, whilst HIT is one of the most common immune-mediated adverse drug reactions for certain groups of post-cardiac surgery patients, it can be managed successfully. We would also stress the importance of serial 2D-TEE examinations in the early post-operative period.

Platinum pollution in road dusts, roadside soils, and tree barks in Seoul, Korea.

This study presents the level of platinum in urban environment in and around Seoul, the capital city of Korea. Road dust, roadside soil, and tree bark samples were collected from the sites of various traffic volumes and from control sites in the suburbs. The above samples were analyzed for Pt by ICP-MS and other heavy metals by ICP-OES. Platinum levels in road dusts and roadside soils from Seoul were in the range of 3.8-444 ng/g (av. 115.0 ng/g) and 0.7-221 ng/g (av. 49.7 ng/g), respectively, whereas those in the suburbs were in the range of 2.3-5.2 ng/g (av. 3.9 ng/g) in road dusts and 0.4-5.1 ng/g (av. 2.4 ng/g) in roadside soils. The highest Pt levels in road dusts were found from major roads with high traffic volume. The remarkable difference in average Pt level between heavy traffic roads (av. 132.2 ng/g) and light traffic roads (av. 22.8 ng/g) reflects that an important source of Pt in roadside environment is automobile catalytic converter. High Pt level in road dust was found from the site of erratic stop-start driving condition, for example, 178 ng/g Pt in road dust around a vehicle crossing gate. Platinum level in tree barks ranged from 0.9 to 4.5 ng/g, which indicates the existence of Pt-containing particulate matter in the atmosphere. Road dusts with high Pt level were enriched in traffic-related heavy metals.

Crop demand of manganese.

The objectives of this study were to evaluate some of the popular rotation crops grown in Hungary for tolerance to low external Mn(2+) levels and to determine the critical tissue concentration of Mn(2+) deficiency during early stages of growth. The minimum Mn(2+) concentration required in soil nutrient contents was 42.5 mg kg(-1) for sunflower, 24.3 mg kg(-1) for tobacco and 10.2 mg kg(-1) for triticale. Sunflower, tobacco and triticale achieved optimum growth at 48.0-65.0 mg Mn(2+) kg(-1), 24.9-32.1 mg Mn( n+) kg(-1) and 28.7 to 29.6 mg Mn(2+) kg(-1), respectively. Critical shoot Mn(2+) concentration at early stages of growth was 53.6 mg kg(-1) in sunflower, 458.0 mg kg(-1) in tobacco and 193.8 mg kg(-1) in triticale. Our results demonstrate that the tolerance to low external Mn(2+) (triticale: <30.2 mg kg(-1); sunflower: <56.2 mg kg(-1); tobacco: <69.3 mg kg(-1)) and the critical tissue Mn(2+) levels for deficiency varied significantly between crop species tested.

Parkinsonian beta oscillations in the external globus pallidus and their relationship with subthalamic nucleus activity.

Inappropriately synchronized beta (beta) oscillations (15-30 Hz) in the subthalamic nucleus (STN) accompany movement difficulties in idiopathic Parkinson's disease (PD). The cellular and network substrates underlying these exaggerated beta oscillations are unknown but activity in the external globus pallidus (GP), which forms a candidate pacemaker network with STN, might be of particular importance. Using a clinically relevant rat model of PD, we demonstrate that oscillatory activity in GP neuronal networks becomes excessively and selectively synchronized at beta frequencies in a spatially widespread and brain state-dependent manner after lesion of dopamine neurons. Although synchronization of GP unit activity increased by almost 100-fold during beta oscillations, the mean firing rate of GP neurons decreased compared with controls. Importantly, in parkinsonian animals, two main types of GP neuron were identified according to their distinct and inversely related firing rates and patterns. Moreover, neurons of the same type tended to fire together, with small phase differences, whereas different types of neuron tended not to do so. This functional dichotomy in temporal coupling persisted across extreme brain states, suggesting that maladaptive interactions are dominated by hardwiring. Finally, the precisely timed discharges of GP and STN neurons indicated that rhythmic sequences of recurrent excitation and inhibition in the STN-GP network, and lateral inhibition between GP neurons, could actively support abnormal beta oscillations. We propose that GP neurons, by virtue of their spatiotemporal synchronization, widespread axon collaterals and feed-back/feed-forward mechanisms, are well placed to orchestrate and propagate exaggerated beta oscillations throughout the entire basal ganglia in PD.

Rhythmically active enkephalin-expressing GABAergic cells in the CA1 area of the hippocampus project to the subiculum and preferentially innervate interneurons.

Enkephalins (ENKs) are endogenous opioids that regulate synaptic excitability of GABAergic networks in the cerebral cortex. Using retrograde tracer injections in the subiculum, we identified a hippocampal population of ENK-expressing projection neurons. In situ hybridization for GAD shows that ENK-expressing cells are a small GABAergic subpopulation. Furthermore, by extracellular recording and juxtacellular labeling in vivo, we identified an ENK-expressing cell in stratum radiatum of the CA1 area by its complete axodendritic arborization and characteristic spike timing during network oscillations. The somatodendritic membrane was immunopositive for mGluR1alpha, and there was both a rich local axon in CA1 and subicular-projecting branches. The boutons showed cell-type- and layer-specific innervation, i.e., interneurons were the main targets in the alveus, both interneurons and pyramidal cell dendrites were innervated in the other layers, and interneurons were exclusive targets in the subiculum. Parvalbumin-, but not somatostatin-, calbindin-, or cholecystokinin-expressing interneurons were preferred synaptic targets. During network activity, the juxtacellularly labeled ENK-expressing cell was phase modulated throughout theta oscillations, but silenced during sharp-wave/ripple episodes. After these episodes the interneuron exhibited rebound activity of high-frequency spike bursts, presumably causing peptide release. The ENK-expressing interneurons innervating parvalbumin-positive interneurons might contribute to the organization of the sharp-wave/ripple episodes by decreased firing during and rebound activity after the ripple episodes, as well as to the coordination of activity between the CA1 and subicular areas during network oscillations.

Ivy cells: a population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity.

In the cerebral cortex, GABAergic interneurons are often regarded as fast-spiking cells. We have identified a type of slow-spiking interneuron that offers distinct contributions to network activity. "Ivy" cells, named after their dense and fine axons innervating mostly basal and oblique pyramidal cell dendrites, are more numerous than the parvalbumin-expressing basket, bistratified, or axo-axonic cells. Ivy cells express nitric oxide synthase, neuropeptide Y, and high levels of GABA(A) receptor alpha1 subunit; they discharge at a low frequency with wide spikes in vivo, yet are distinctively phase-locked to behaviorally relevant network rhythms including theta, gamma, and ripple oscillations. Paired recordings in vitro showed that Ivy cells receive depressing EPSPs from pyramidal cells, which in turn receive slowly rising and decaying inhibitory input from Ivy cells. In contrast to fast-spiking interneurons operating with millisecond precision, the highly abundant Ivy cells express presynaptically acting neuromodulators and regulate the excitability of pyramidal cell dendrites through slowly rising and decaying GABAergic inputs.

Neuronal diversity in GABAergic long-range projections from the hippocampus.

The formation and recall of sensory, motor, and cognitive representations require coordinated fast communication among multiple cortical areas. Interareal projections are mainly mediated by glutamatergic pyramidal cell projections; only few long-range GABAergic connections have been reported. Using in vivo recording and labeling of single cells and retrograde axonal tracing, we demonstrate novel long-range GABAergic projection neurons in the rat hippocampus: (1) somatostatin- and predominantly mGluR1alpha-positive neurons in stratum oriens project to the subiculum, other cortical areas, and the medial septum; (2) neurons in stratum oriens, including somatostatin-negative ones; and (3) trilaminar cells project to the subiculum and/or other cortical areas but not the septum. These three populations strongly increase their firing during sharp wave-associated ripple oscillations, communicating this network state to the septotemporal system. Finally, a large population of somatostatin-negative GABAergic cells in stratum radiatum project to the molecular layers of the subiculum, presubiculum, retrosplenial cortex, and indusium griseum and fire rhythmically at high rates during theta oscillations but do not increase their firing during ripples. The GABAergic projection axons have a larger diameter and thicker myelin sheet than those of CA1 pyramidal cells. Therefore, rhythmic IPSCs are likely to precede the arrival of excitation in cortical areas (e.g., subiculum) that receive both glutamatergic and GABAergic projections from the CA1 area. Other areas, including the retrosplenial cortex, receive only rhythmic GABAergic CA1 input. We conclude that direct GABAergic projections from the hippocampus to other cortical areas and the septum contribute to coordinating oscillatory timing across structures.

Transgenic Spartina alterniflora for phytoremediation.

Perennial monoculture forming grasses are very important natural remediators of pollutants. Their genetic improvement is an important task because introduction of key transgenes can dramatically improve their remediation potential. Transfer of key genes for mercury phytoremediation into the salt marsh cordgrass (Spartina alterniflora) is reported here. S. alterniflora plays an important role in the salt marsh by cycling of elements, both nutrients and pollutants, protects the coastline from erosion, is a keystone species in the salt marsh supporting a large food web, which in turn supports a significant segment of economy, including tourism, has an impact on cloud formation and consequently on global weather, and is thus an ecologically important species relevant for our life-support systems. Embryogenic callus of S. alterniflora was co-inoculated with a pair of Agrobacterium strains LBA4404 carrying the organomercurial lyase (merB) and mercuric reductase (merA) genes, respectively, in order to co-introduce both the merA and the merB genes. Seven stable geneticin resistant lines were recovered. The presence of merA and merB genes was verified by PCR and Southern blotting. All but one transgenic lines contained both the merA and the merB sequences proving that co-introduction into Spartina of two genes from separate Agrobacterium strains is feasible and frequent, although the overall frequency of transformation is low. Northern blotting showed differences in relative expression of the two transgenes among individual transformants. The steady-state RNA levels appeared to correlate with the phenotype. Line #7 showed the highest resistance to HgCl(2) (up to 500 microM), whereas line #3 was the most resistant to phenylmercuric acetate (PMA). Wild-type (WT) callus is sensitive to PMA at 50 microM and to HgCl(2) at 225 microM.

Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations.

In the hippocampal CA1 area, a relatively homogenous population of pyramidal cells is accompanied by a diversity of GABAergic interneurons. Previously, we found that parvalbumin-expressing basket, axo-axonic, bistratified, and oriens-lacunosum moleculare cells, innervating different domains of pyramidal cells, have distinct firing patterns during network oscillations in vivo. A second family of interneurons, expressing cholecystokinin but not parvalbumin, is known to target the same domains of pyramidal cells as do the parvalbumin cells. To test the temporal activity of these independent and parallel GABAergic inputs, we recorded the precise spike timing of identified cholecystokinin interneurons during hippocampal network oscillations in anesthetized rats and determined their molecular expression profiles and synaptic targets. The cells were cannabinoid receptor type 1 immunopositive. Contrary to the stereotyped firing of parvalbumin interneurons, cholecystokinin-expressing basket and dendrite-innervating cells discharge, on average, with 1.7 +/- 2.0 Hz during high-frequency ripple oscillations in an episode-dependent manner. During theta oscillations, cholecystokinin-expressing interneurons fire with 8.8 +/- 3.3 Hz at a characteristic time on the ascending phase of theta waves (155 +/- 81 degrees), when place cells start firing in freely moving animals. The firing patterns of some interneurons recorded in drug-free behaving rats were similar to cholecystokinin cells in anesthetized animals. Our results demonstrate that cholecystokinin- and parvalbumin-expressing interneurons make different contributions to network oscillations and play distinct roles in different brain states. We suggest that the specific spike timing of cholecystokinin interneurons and their sensitivity to endocannabinoids might contribute to differentiate subgroups of pyramidal cells forming neuronal assemblies, whereas parvalbumin interneurons contribute to synchronizing the entire network.

Genetic modification of wetland grasses for phytoremediation.

Wetland grasses and grass-like monocots are very important natural remediators of pollutants. Their genetic improvement is an important task because introduction of key transgenes can dramatically improve their remediation potential. Tissue culture is prerequisite for genetic manipulation, and methods are reported here for in vitro culture and micropropagation of a number of wetland plants of various ecological requirements such as salt marsh, brackish water, riverbanks, and various zones of lakes and ponds, and bogs. The monocots represent numerous genera in various families such as Poaceae, Cyperaceae, Juncaceae, and Typhaceae. The reported species are in various stages of micropropagation and Arundo donax is scaled for mass propagation for selecting elite lines for pytoremediation. Transfer of key genes for mercury phytoremediation into the salt marsh cordgrass (Spartina alterniflora) is also reported here. All but one transgenic lines contained both the organomercurial lyase (merB) and mercuric reductase (merA) sequences showing that co-introduction into Spartina of two genes from separate Agrobacterium strains is possible.

Auxin autotrophic tobacco callus tissues resist oxidative stress: the importance of glutathione S-transferase and glutathione peroxidase activities in auxin heterotrophic and autotrophic calli.

Auxin autotrophic and heterotrophic tobacco callus lines were grown on MS medium with or without 100 mmol/L NaCl and growth and some of the stress-related activities, such as GPX, SOD, CAT, GST, GSH-PX, as well as the concentration of ethylene and H2O2, were measured and compared with each other. The auxin autotrophic calli grew slower, however, on the NaCl-containing medium the growth rate was higher than that of the heterotrophic cultures after two weeks of culturing. The stress-related ethylene production was lower in the autotrophic cultures and, contrary to the heterotrophic tissues, its level did not change significantly upon NaCl treatment. The guaiacol peroxidase (GPX) activities were higher in the autotrophic tissues in all cell fractions regardless of the presence of NaCl. Treated with NaCl, the GPX activities elevated in the soluble and covalently-bound fractions in the heterotrophic calli, but were not further increased in the autotrophic line. SOD and CAT activities were higher in the heterotrophic tissues, and were increased further by 100 mmol/L NaCl treatment. The GST and GSH-PX activities were higher in the autotrophic line, which might explain their enhanced stress tolerance. In the autotrophic tissues, the elevated antioxidant activities led to reduced levels of H2O2 and malondialdehyde; under mild NaCl stress, these levels decreased further. The lower growth rate and the effective protection against NaCl stress-induced oxidative damage of the autotrophic line can be explained by the cell wall-bound peroxidase and GSH-PX activities in the auxin autotrophic tissues. Their maintained growth rate indicates that the autotropic cultures were more resistant to exogenous H2O2.

Spike timing of dendrite-targeting bistratified cells during hippocampal network oscillations in vivo.

Behavior-contingent network oscillations bring about transient, functionally coherent neuronal assemblies in the cerebral cortex, including the hippocampus. Inhibitory input on and close to the soma is believed to phase intrinsic oscillations and output of pyramidal cells, but the function of GABA release to pyramidal cell dendrites remains unknown. We recorded the oscillation-locked spike timing of identified bistratified interneurons in rats. These cells mainly innervated small dendritic shafts of pyramidal cells co-aligned with the glutamatergic Schaffer collateral/commissural input. During theta oscillations, bistratified cells fired at a phase when, on average, pyramidal cell dendrites are most hyperpolarized. Interneurons targeting the perisomatic domain discharge at an earlier phase. During sharp wave-associated ripples, bistratified cells fired with high frequency and in-phase with basket cells, on average 1-2 ms after the discharges in pyramidal cell somata and dendrites. Our results indicate that bistratified cells rhythmically modulate glutamatergic input to the dendrites of pyramidal cells to actively promote the precise input/output transformation during network oscillations.

Brain-state- and cell-type-specific firing of hippocampal interneurons in vivo.

Neural-network oscillations at distinct frequencies have been implicated in the encoding, consolidation and retrieval of information in the hippocampus. Some GABA (gamma-aminobutyric acid)-containing interneurons fire phase-locked to theta oscillations (4-8 Hz) or to sharp-wave-associated ripple oscillations (120-200 Hz), which represent different behavioural states. Interneurons also entrain pyramidal cells in vitro. The large diversity of interneurons poses the question of whether they have specific roles in shaping distinct network activities in vivo. Here we report that three distinct interneuron types--basket, axo-axonic and oriens-lacunosum-moleculare cells--visualized and defined by synaptic connectivity as well as by neurochemical markers, contribute differentially to theta and ripple oscillations in anaesthetized rats. The firing patterns of individual cells of the same class are remarkably stereotyped and provide unique signatures for each class. We conclude that the diversity of interneurons, innervating distinct domains of pyramidal cells, emerged to coordinate the activity of pyramidal cells in a temporally distinct and brain-state-dependent manner.