Mechanism of cell-mediated cytotoxicity at the single cell level. VIII. Kinetics of lysis of target cells bound by more than one cytotoxic T lymphocyte

We measured the effects of having multiple cytotoxic T lymphocytes (CTL) bound to one target cell by using the single-cell cytotoxicity in agarose assay. We found that even though there is variability in the time at which individual target cells are lysed, we can identify a general trend: the mean rate of lysis increases with the number of CTL bound per target cell, reaching a maximum when the CTL-target cell ratio is three. Combining a quantitative model for the rate of lethal hitting in multicellular conjugates with a multi-event model for the rate of target cell disintegration, we developed a new multistage kinetic model for predicting the rate of target cell lysis in multiple lymphocyte-target cell conjugates. The variability in the time at which target cells are hit and the variability in the time until they disintegrate are incorporated into the model. By analyzing our measured data in the context of the multistage kinetic model, we were able to estimate via nonlinear least squares regression the target cell disintegration rate, but not the lethal hitting rate. Lethal hitting appeared to be too fast, when compared with disintegration, to significantly affect the time of target cell lysis. By using previously determined values of the lethal hitting rate for single lymphocyte-target cell conjugates and by postulating that lymphocytes act independently of each other in delivering lethal hits, we were able to estimate the rate at which target cells are hit in multiple-lymphocyte single target cell conjugates. By using this estimate of the lethal hitting rate and the regression estimate of the disintegration rate, the multistage kinetic model gave a quantitative fit to our data. From this analysis, we found that the rate at which a target cell disintegrates after being lethally hit increases with the number of CTL per conjugate. This result is quite surprising, because once the first hit has been received, a target cell can disintegrate in a killer cell-independent manner. Under the conditions of our experiment, it appears as if target cell disintegration is not killer cell-independent. Furthermore, our analysis of the time course of target cell disintegration suggests that the process is not governed by simple first order kinetics, but rather by a more complex multistep mechanism.     

Charcoal as a habitat for microbes and its effect on the microbial community of the underlying humus

Wildfires produce a charcoal layer, which has an adsorbing capacity resembling activated carbon. After the fire a new litter layer starts to accumulate on top of the charcoal layer, which liberates water‐soluble compounds that percolate through the charcoal and the unburned humus layer. We first hypothesized that since charcoal has the capacity to adsorb organic compounds it may form a new habitat for microbes, which decompose the adsorbed compounds. Secondly, we hypothesized that the charcoal may cause depletion of decomposable organic carbon in the underlying humus and thus reduce the microbial biomass. To test our hypotheses we prepared microcosms, where we placed non‐heated humus and on top one of the adsorbents: non‐adsorptive pumice (Pum), charcoal from Empetrum nigrum (EmpCh), charcoal from humus (HuCh) or activated carbon (ActC). We watered them with birch leaf litter extract. The adsorbing capacity increased in the order Pumorg in the litter extract, respectively. After one month, all adsorbents harboured microbes, but their amount and basal respiration was largest in EmpCh and HuCh, and smallest in Pum. In addition, different kinds of microbial communities with respect to their phospholipid fatty acid and substrate utilization patterns were formed in the adsorbents. The amount of microbial biomass and number of bacteria did not differ between humus under different adsorbents, although different microbial communities developed in humus under EmpCh compared with Pum, which is obviously related to the increased pH of the humus under EmpCh, and also ActC. We suggest that charcoal from burning can support microbial communities, which are small in size but have a higher specific growth rate than those of the humus. Although the charcoal layer induces changes in the microbial community of the humus, it does not reduce the amount of humus microbes.     

Humus Form Development during Forest Restoration in Exclosures of the Tigray Highlands, Northern Ethiopia

Forest restoration in protected exclosures has become a common practice to fight land degradation in the highlands of northern Ethiopia. Insights into ecosystem processes governing restoration in these formerly degraded areas are gained through the study of humus forms and factors influencing humus formation during vegetation recovery. Humus forms of 135 sample plots located in different land use types were morphologically described. The subsequent classification into six humus form types was based on principal component analysis and cluster analysis. Where areas are closed for a longer time, humus profiles are commonly more developed and higher organic matter accumulation is noticed as well as increased nutrient stocks. The combined effects of seasonal drought conditions and low fresh litter quality account for an overall slow decomposition, which explains the high importance of litter input for organic matter accumulation. Based on a correlation analysis, vegetation cover, litter production, litter quality, soil nutrient content, soil moisture, and topography were identified as important factors influencing humus formation. It is inferred that humus formation leads to improvements in soil fertility and structure, microclimate development, and soil protection and therefore forms part of the restoration processes taking place in exclosures.     

Ecology of nematophagous fungi: vertical distribution in a deciduous woodland

Summary The distribution of nematophagous fungi in soil collected from a deciduous woodland is compared to various biotic and abiotic soil factors. The microfungi are isolated at all depths down to a maximum of 35 cm. Predators forming constricting rings, adhesive branches and adhesive knobs are restricted to the upper litter and humus layers. The net forming predators and endoparasites are isolated at all depths, although they are significantly more abundant in the lower mineral rich soils. A much greater species diversity of nematophagous fungi is recorded in the upper organic zones.Preliminary soil analysis indicates thatCephalosporium balanoides is independent of all soil variables, while predators able to form traps spontaneously are restricted to the organic soils which are rich in nematodes. Non-spontaneous trap forming predators, which are excellent saprophytes, are isolated from the deeper soils which are low in nutrients. The ecological significance of these results is discussed.     

The degree of CTL-induced DNA solubilization is not determined by the human vs mouse origin of the target cell

CTL-mediated lysis is unique among lytic mechanisms in inducing rapid, prelytic nuclear disintegration. Target cell DNA can be solubilized within minutes as a result of degradation, which can proceed to the nucleosomal level, presumably mediated by endonucleases that are either endogenous or injected by the CTL. Nuclear disintegration has been reported for mouse lymphoid target cells by several groups. However, previous studies in which human target cells were studied saw little or no DNA solubilization. We here report rapid, extensive CTL-induced solubilization of DNA in human lymphoid target cells; on the other hand, we found that three mouse cell lines exhibit little or no nuclear disintegration. We conclude that the degree of nuclear disintegration depends on the nature of the target cell, but is not determined by the species of origin of the target cell.     

Anthropogenic N Deposition Increases Soil C Storage by Decreasing the Extent of Litter Decay: Analysis of Field Observations with an Ecosystem Model

Recent meta-analyses of experimental studies simulating increased anthropogenic nitrogen (N) deposition in forests reveal greater soil carbon (C) storage under elevated levels of atmospheric N deposition. However, these effects have not yet been included in ecosystem-scale models of soil C and N cycling and it is unclear whether increased soil C storage results from slower decomposition rates or a reduced extent of decomposition (for example, an increase in the amount of litter entering slowly decaying humus pools). To test these alternatives, we conducted a meta-analysis of litter decomposition data. We then used the results from our meta-analysis to model C and N cycling in four sugar maple forests in Michigan using an ecosystem process model (TRACE). We compared model results testing our alternative hypotheses to field data on soil C storage from a 17-year N deposition experiment. Using data from published litter decomposition studies in forests, we determined that, on average, exogenous N inputs decreased lignin decomposition rates by 30% and increased cellulose decomposition by 9%. In the same set of litter decomposition studies increased exogenous N availability increased the amount of litter entering slowly decaying humus pools in a manner significantly related to the lignocellulose index of decaying litter. Incorporating changes to decomposition rates in TRACE did not accurately reproduce greater soil C storage observed in our field study with experimentally elevated N deposition. However, when changes in the extent of decomposition were incorporated in TRACE, the model produced increased soil C storage by increasing the amount of litter entering the humus pool and accurately represented C storage in plant and soil pools under experimental N deposition. Our modeling results and meta-analysis indicate that the extent of litter decay as humus is formed, rather than slower rates of litter decay, is likely responsible for the accumulation of organic matter, and hence soil C storage, under experimental N deposition. This effect should be incorporated in regional to global-scale models simulating the C balance of forest ecosystems in regions receiving elevated N deposition.     

A multistage model for the action of cytotoxic T lymphocytes in multicellular conjugates

We propose a multistage stochastic model to explain data on the kinetics of target cell lysis by cytotoxic T lymphocytes in multicellular conjugates. A novel feature of our model is that we explicitly consider both the lethal hitting stage and the target cell disintegration stage of the cytolytic process. Further, we allow for the possibility that target cell disintegration is itself a complex process composed of many events. The comparison of our model with the data of other investigators suggests that cytotoxic T cells deliver lethal hits at random to undamaged target cells. Having received a lethal hit, the target cell disintegrates over a variable length of time. The disintegration times of target cells from different conjugates appear to be randomly distributed and to be consistent with a model in which disintegration occurs by at least two major, sequential, rate-limiting events. For conjugates containing one lymphocyte and multiple target cells, the mean rate at which a lethally hit target cell disintegrates is found to be independent of the total number of target cells in the conjugate. Our model predicts that in such multicellular conjugates, individual target cells lyse one by one, on average at approximately 30-min intervals, thus agreeing closely with previously reported experimental observations.     

Nuclear disintegration induced by cytotoxic T lymphocytes. Evidence against damage to the nuclear envelope of the target cell

CTL and NK cells induce nuclear disintegration in their target cells. This phenomenon, which is seen as extensive fragmentation and solubilization of target cell DNA, is not seen with most other means of inducing cytolysis, including antibody- and complement-mediated cytolysis. We have previously shown that the degree of DNA solubilization is dependent upon the nature of the target cell. We here investigate the possibility that CTL induce, in all targets, damage to the nuclear envelope, which in turn leads to nuclear disintegration in only some of them. We reasoned that damage to the nuclear envelope would render nuclear DNA more accessible to exogenous DNase. Therefore, we determined the susceptibility of target DNA to exogenous DNase I after cytolysis by various means. We found no difference in DNA susceptibility for cells lysed by CTL vs methods (such as complement-mediated lysis or nonionic detergent) incapable of inducing nuclear disintegration. As a positive control, freezing and thawing dramatically enhanced susceptibility of the DNA. In conclusion, we found no evidence that the nuclear envelope is damaged by CTL in target cell types (or in the subpopulation of nuclei) that do not undergo nuclear disintegration.     

Variation in the herb species response and the humus quality across a 200-year chronosequence of beech and oak plantations in Belgium

The present study aimed at exploring the long-term impact of pure and mixed beech Fagus sylvatica and oak Quercus robur stands on the forest floor by documenting changes in the herb species' behaviour and in humus index across a 200-yr chronosequence of forest stands. The research was conducted in central Belgium, in a 4383 ha beech-dominated forest. Analyses were carried out in stands which are replicated, of the same age, managed in the same way, and growing on the same soil type with the same land-use history. The results of this study indicate that stand aging is an important determinant of herb species occurrence in the studied area. Most of the species studied show a different response to stand age in pure compared to mixed stands. Our results clearly show a decrease of the humus quality with age in pure stands (beech as well as oak). On the other hand, we found that mixing beech and oak maintained or improved the humus status along the chronosequence according to the proportion of each tree. So the addition of some oak to the beech made it possible to keep a constant quality of the humus. We found that, even if the understory tree species is very scarce, it may be sufficient to maintain the humus status on the long term. In the present study, a cover of 1% oak in a beech stand was sufficient to show an effect of the minor species on these soils. This pattern contrasts with the widespread idea that substantial effects of the minor tree species on soils might not develop if the ratio of major/minor species is low.     

Digital contact tracing and network theory to stop the spread of COVID-19 using big-data on human mobility geolocalization

The spread of COVID-19 caused by the SARS-CoV-2 virus has become a worldwide problem with devastating consequences. Here, we implement a comprehensive contact tracing and network analysis to find an optimized quarantine protocol to dismantle the chain of transmission of coronavirus with minimal disruptions to society. We track billions of anonymized GPS human mobility datapoints to monitor the evolution of the contact network of disease transmission before and after mass quarantines. As a consequence of the lockdowns, people’s mobility decreases by 53%, which results in a drastic disintegration of the transmission network by 90%. However, this disintegration did not halt the spreading of the disease. Our analysis indicates that superspreading k-core structures persist in the transmission network to prolong the pandemic. Once the k-cores are identified, an optimized strategy to break the chain of transmission is to quarantine a minimal number of ‘weak links’ with high betweenness centrality connecting the large k-cores.     

Influence of agricultural soil management on humus composition and dynamics: Classical and modern analytical techniques

In-source pyrolysis-field ionization mass spectrometry (Py-FIMS), in combination with complementary elemental, wet-chemical, biochemical, and microbiological data, has been used to characterize humus composition and dynamics in soil samples from several field plots that have been cultivated in long-term experiments under different management conditions. Thermograms and Py-FI mass spectra of whole-soil samples from field plots that under very different management show significant differences in humus composition, which may be due to varying stages of decomposition of plant residues and humus genesis. The intensity of soil management significantly affects high-molecular-weight subunits such as dimeric lignin0, arylalkyl-, and aliphatic constituents, even though humus quantity is similar for plots under more practically oriented management, such as crop rotation. The differences in molecular humus subunits of soil samples from different plots, in combination with complementary data, demonstrated that less parent (i.e. primary) material is incorporated in the humus matrix under intense soil management conditions. Samples from different field plots can thus be objectively differentiated on the basis of humus properties using multivariate statistical techniques such as principal component and cluster analyses. This statistical discrimination, using Py-FI mass spectra of the samples, corresponds well with microbial biomasses but is somewhat inconsistent with elemental data and results of chemical degradation procedures. The microflora populations in soils under intense management are limited by low availability and/or quality of carbon substrates. The resulting restricted internal nitrogen cycle causes those soils to have a reduced capacity to immobilize N, leading to relative enrichment of heterocyclic nitrogen compounds that are resistant to mineralization.     

Local and regional trends in the ground vegetation of beech forests

We sampled moss and vascular forest vegetation in five ancient beech forests from northwest France, embracing in each a wide array of environmental conditions. Indirect (PCA) and direct (RDA) gradient analysis were used to discern local and regional ecological factors which explain the observed variation in species composition. Our results point to a global factor encompassing a large array of soil and light conditions, unravelled when local particularities of studied forests are singled out. The humus form, numerically expressed by the Humus Index, explains a large part of the observed variation in ground vegetation. Our study confirmed opposite trends in vascular and moss species richness according to humus condition. Ecological factors to which vascular and moss forest species respond at the regional level can be estimated directly in the field by visually inspecting humus forms and vegetation strata despite of the confounding influence of local factors.     

Spatial Distribution of Optical Near-Fields in Plasmonic Gold Sphere Segment Voids

We present a comprehensive experimental and computational study on the electromagnetic field distribution in sphere segment void arrays. Surface plasmon polaritons can be excited in these void arrays, resulting in greatly enhanced electromagnetic fields. With the scanning near-field optical microscope (SNOM) we are able to measure the electromagnetic field distribution at the sample surface. For this purpose, an array of relatively large voids with a sphere diameter of 900 nm was fabricated, allowing for an easy access of the scanning glass-fibre tip and yielding very detailed scans. Complementary, finite-difference time-domain (FDTD) calculations on a complete void array have been performed and compared with the SNOM intensity maps and experimental reflectivity data. We show in a direct way both the existence of extended and localised modes in the Au void array for three different void depths. We also show and discuss the changes that the modes undergo for the different void depths and excitation wavelengths. Moreover, since the simulations were performed for two different void geometries, one containing perfectly spherical void surfaces and another more realistic one, which considers the presence of interstitial wall holes and other imperfections, as observed in scanning electron micrographs, we were able to determine by comparison with the experiment under which conditions an array of idealised sphere segment voids is a meaningful model. This demonstrates that both SNOM and FDTD simulations are powerful tools for understanding the plasmonic response of metallic nanostructures, thus enabling, for instance, a design for applications in ultra-sensitive optical detection.     

腐殖质呼吸作用及其生态学意义

腐殖质呼吸是厌氧环境中普遍存在的一种微生物呼吸代谢模式.自1996年发现以来,日益成为生态学与环境科学领域的研究热点.在厌氧条件下,一些微生物能以腐殖质作为唯一电子受体,氧化环境中的有机质或者甲苯等环境有毒物质,产生CO2,参与碳循环;同时,腐殖质呼吸作用产生的还原态腐殖质可以还原环境中的一些氧化态物质,如Fe(III)、Mn(IV)、Cr(VI)、U(VI) 、硝基芳香化合物和多卤代污染物.因此,腐殖质呼吸能够影响环境中C、N、Fe、Mn以及一些痕量金属元素的生物地球化学循环,并且能够促进重金属以及有机污染物的脱毒,在水体自净、污染土壤原位修复、污水处理等方面具有积极作用.     

Humus functioning types in evergreen coniferous forests of the French Inner Alps

Three humus forms that are widespread in the Inner Alps, a dysmull below Pinus sylvestris, an oligomull below Abies alba and a mor below Pinus cembra, were studied by following mineral nitrogen production and uptake and by a characterization of the pedofauna. Due to the production and uptake of nitrogen, mainly as nitrates and also due to the dominance of Lumbricids versus Arthropods, the oligomull was the sole humus form that functioned as a mull. Nevertheless relatively weak mineral nitrogen production and the dominance of endogeic soil-dwelling earthworms versus anecic earthworms demonstrated the moderate activity of this mull, which is representative of humus forms of old growth forests and cold climates. There was a discrepancy between the very low biological activity of the dysmull and its status of mull, while an observed bifunctioning between the different layers of this humus also differentiated it from the mor.     

Interaction of lactoferrin and lysozyme with casein micelles

On addition of lactoferrin (LF) to skim milk, the turbidity decreases. The basic protein binds to the caseins in the casein micelles, which is then followed by a (partial) disintegration of the casein micelles. The amount of LF initially binding to casein micelles follows a Langmuir adsorption isotherm. The kinetics of the binding of LF could be described by first-order kinetics and similarly the disintegration kinetics. The disintegration was, however, about 10 times slower than the initial adsorption, which allowed investigating both phenomena. Kinetic data were also obtained from turbidity measurements, and all data could be described with one equation. The disintegration of the casein micelles was further characterized by an activation energy of 52 kJ/mol. The initial increase in hydrodynamic size of the casein micelles could be accounted for by assuming that it would go as the cube root of the mass using the adsorption and disintegration kinetics as determined from gel electrophoresis. The results show that LF binds to casein micelles and that subsequently the casein micelles partly disintegrate. All micelles behave in a similar manner as average particle size decreases. Lysozyme also bound to the casein micelles, and this binding followed a Langmuir adsorption isotherm. However, lysozyme did not cause the disintegration of the casein micelles.     

Relationship between decomposition of cellulose strips and chemical properties of humus layer in natural boreal forests

The relationships between the decomposition of cellulose strips buried completely within the humus layer (Of + Oh) for two 1-year periods and humus layer properties were studied at forested sites with minimal anthropogenic influence. The 18 study sites are clustered in four catchments located between 61° and 69° N in Finland. The stands were composed of varying proportions of Scots pine, Norway spruce and deciduous species. Of the 23 humus layer properties studied, significant correlations were found between decomposition and soil pH, effective cation exchange capacity, base saturation, C/N ratio, the concentrations of P, Mn, Pb, Zn and Cu. The relationships, however, were inconsistent except for heavy metal concentrations which were positive in all cases. Decomposition was more strongly and consistently correlated to tree stand characteristics (mean height and stem volume) than to the humus layer properties. Both the decomposition of cellulose strips and the concentrations of heavy metals were intercorrelated with climate and the stand characteristics. Partial correlation analysis revealed that the relationships between decomposition and humus layer heavy metal concentrations were more strongly affected by the tree stand characteristics than by climate. After the statistical elimination of the effects of stand characteristics, no significant positive correlations between decomposition and humus layer heavy metal concentrations remained and, in some cases for total and extractable Zn, the correlations became significant and negative. Results from litterfall chemistry (nutrients and heavy metals) also underlined that any specific effects of humus layer heavy metal concentrations on decomposition may be masked if the effects of stand characteristics are not accounted for. We conclude that the relationships between decomposition and soil chemical properties can not be elucidated without considering stand structure and composition of the forest stand.     

Characterization of Humus Microbial Communities in Adjacent Forest Types That Differ in Nitrogen Availability

To address the link between soil microbial community composition and soil processes, we investigated the microbial communities in forest floors of two forest types that differ substantially in nitrogen availability. Cedar-hemlock (CH) and hemlock-amabilis fir (HA) forests are both common on northern Vancouver Island, B.C., occurring adjacently across the landscape. CH forest floors have low nitrogen availability and HA high nitrogen availability. Total microbial biomass was assessed using chloroform fumigation-extraction and community composition was assessed using several cultivation-independent approaches: denaturing gradient gel electrophoresis (DGGE) of the bacterial communities, ribosomal intergenic spacer analysis (RISA) of the bacterial and fungal communities, and phospholipid fatty acid (PLFA) profiles of the whole microbial community. We did not detect differences in the bacterial communities of each forest type using DGGE and RISA, but differences in the fungal communities were detected using RISA. PLFA analysis detected subtle differences in overall composition of the microbial community between the forest types, as well as in particular groups of organisms. Fungal PLFAs were more abundant in the nitrogen-poor CH forests. Bacteria were proportionally more abundant in HA forests than CH in the lower humus layer, and Gram-positive bacteria were proportionally more abundant in HA forests irrespective of layer. Bacterial and fungal communities were distinct in the F, upper humus, and lower humus layers of the forest floor and total biomass decreased in deeper layers. These results indicate that there are distinct patterns in forest floor microbial community composition at the landscape scale, which may be important for understanding nutrient availability to forest vegetation.     

Relationship between plant life forms and ecological indices in a lacustrine ecosystem

This study is the first to analyze the relationship between ecological indices (substrate moisture, nutrient content, substrate dispersion/aeration, substrate pH and humus content) and life forms of the vascular flora in and around Lake Provala; these relationships may serve as reliable indicators of the ecological conditions prevailing in this ecosystem. Since the development of certain life forms, in addition to climatic conditions, depends on plant requirements for several major environmental factors expressed as ecological indices, we established the relationship between the ecological index and life form of vascular plants collected over an eight year period in this system using correspondence analysis. We found a significant correlation between the development of certain life forms and levels of substrate moisture, nutrient content and substrate dispersion/aeration. These relationships help explain the predominance of hemicryptophytes and hydro-helophytes in the riparian zone of the lake, as these forms are perfectly adapted to water-saturated or aquatic environments rich in nutrients and relatively well aerated. There was no significant relationship between life forms and substrate pH or the content of organo-mineral compounds (humus) in the soil.     

Contrasting preferences of arbuscular mycorrhizal and dark septate fungi colonizing boreal and subarctic Avenella flexuosa

Arbuscular mycorrhizal (AM) and dark septate endophytic (DSE) fungi are ubiquitous in grass roots, but their colonizations may vary according to latitudinal gradient and site conditions. We investigated how vegetation zone (boreal vs. subarctic), humus thickness, and site openness affect root fungal colonizations of the grass Avenella flexuosa. More precisely, we hypothesized that AM and DSE fungal colonizations would have different responses to environmental conditions such that AM fungi could be more common in boreal zone, whereas we expected DSE fungi to be more affected by the amount of humus. We found site openness to affect AM and DSE fungi in a contrasting manner, in interaction with the vegetation zone. AM colonization was high at open coastal dunes, whereas DSE fungi were more common at forested sites, in the boreal zone. Humus thickness affected AM fungi negatively and DSE fungi positively. To conclude, the observed AM and DSE fungal colonization patterns were largely contrasting. AM fungi were favored in seashore conditions characterized by thin humus layer, whereas DSE fungi were favored in conditions of higher humus availability.