Self-organization of collective escape in pigeon flocks

Bird flocks under predation demonstrate complex patterns of collective escape. These patterns may emerge by self-organization from local interactions among group-members. Computational models have been shown to be valuable for identifying what behavioral rules may govern such interactions among individuals during collective motion. However, our knowledge of such rules for collective escape is limited by the lack of quantitative data on bird flocks under predation in the field. In the present study, we analyze the first GPS trajectories of pigeons in airborne flocks attacked by a robotic falcon in order to build a species-specific model of collective escape. We use our model to examine a recently identified distance-dependent pattern of collective behavior: the closer the prey is to the predator, the higher the frequency with which flock members turn away from it. We first extract from the empirical data of pigeon flocks the characteristics of their shape and internal structure (bearing angle and distance to nearest neighbors). Combining these with information on their coordination from the literature, we build an agent-based model adjusted to pigeons’ collective escape. We show that the pattern of turning away from the predator with increased frequency when the predator is closer arises without prey prioritizing escape when the predator is near. Instead, it emerges through self-organization from a behavioral rule to avoid the predator independently of their distance to it. During this self-organization process, we show how flock members increase their consensus over which direction to escape and turn collectively as the predator gets closer. Our results suggest that coordination among flock members, combined with simple escape rules, reduces the cognitive costs of tracking the predator while flocking. Such escape rules that are independent of the distance to the predator can now be investigated in other species. Our study showcases the important role of computational models in the interpretation of empirical findings of collective behavior.     

Effect of Erythropoietic Stimulation of the Chamber Host On the Growth of Haemopoietic Colonies In Plasma Clot Diffusion Chambers (PCDC)

Murine marrow cells were cultured in Millipore diffusion chambers implanted into the peritoneal cavity of variously conditioned murine hosts. Preirradiation (350 cGy), bleeding (0.5 ml) and phenylhydrazine injection (75 mg/kg i.v.) when performed together on the chamber host, induced better growth of erythropoietic and granulopoietic colonies inside the PCDCs than either of these manoeuvres alone. Small erythrocytic colonies (CFU-E derived) and small granulocytic colonies were observed at day 3 of marrow culture. Erythropoietic bursts and large granulocytic colonies were observed at day 8 of chamber culture. Colonies of macrophage-like cells, fibroblast-like cells, mixed erythro-granulopoietic colonies and megakaryoblasts were observed less regularly in chambers incubated in these conditions. the study provides a standardized, relatively reproducible PCDC culture system for studies of both erythro- and granulopoiesis, and does not require a hypoxic chamber.     

Effect of erythropoietic stimulation of the chamber host on the growth of haemopoietic colonies in plasma clot diffusion chambers (PCDC)

Murine marrow cells were cultured in Millipore diffusion chambers implanted into the peritoneal cavity of variously conditioned murine hosts. Preirradiation (350 cGy), bleeding (0.5 ml) and phenylhydrazine injection (75 mg/kg i.v.) when performed together on the chamber host, induced better growth of erythropoietic and granulopoietic colonies inside the PCDCs than either of these manoeuvres alone. Small erythrocytic colonies (CFU-E derived) and small granulocytic colonies were observed at day 3 of marrow culture. Erythropoietic bursts and large granulocytic colonies were observed at day 8 of chamber culture. Colonies of macrophage-like cells, fibroblast-like cells, mixed erythro-granulopoietic colonies and megakaryoblasts were observed less regularly in chambers incubated in these conditions. The study provides a standardized, relatively reproducible PCDC culture system for studies of both erythro- and granulopoiesis, and does not require a hypoxic chamber.     

Growth of in vitro colony-forming cells from normal human peripheral blood leukocytes cultured in diffusion chambers

The growth of granulopoietic progenitor cells (CFU-C) in diffusion chambers during culture of peripheral blood leukocytes from 10 normal subjects has been studied. At various times after initiation of diffusion chamber culture, cells harvested from the chambers were transferred to agar culture for measurement of CFU-C concentration. Under these conditions colonies could be grown successfully in agar culture provided pronase, necessary for the chamber harvesting procedure, was first removed by careful washing. A marked increase in the number of CFU-C, up to 25-fold the initial value, was observed in 8 out of 10 subjects. Here the growth pattern was similar, independent of the initial CFU-C values, with an immediate rise to a maximum between 6 and 13 days of culture followed by a decrease. In the other two subjects the growth of CFU-C throughout the diffusion chamber culture period was very poor. The growth of CFU-C from a given individual's blood was shown to be reproducible in repeated studies in 2 subjects, one of whom showed a proliferative and the other a non-proliferative pattern. Evidence suggests that the increase in CFU-C in diffusion chambers is the result of both self-renewal of these cells and influx from a more primitive compartment, although the present data do not allow an estimate of the relative magnitude of each.     

Nest architecture shapes the collective behaviour of harvester ants

Structures influence how individuals interact and, therefore, shape the collective behaviours that emerge from these interactions. Here I show that the structure of a nest influences the collective behaviour of harvester ant colonies. Using network analysis, I quantify nest architecture and find that as chamber connectivity and redundancy of connections among chambers increase, so does a colony''s speed of recruitment to food. Interestingly, the volume of the chambers did not influence speed of recruitment, suggesting that the spatial organization of a nest has a greater impact on collective behaviour than the number of workers it can hold. Thus, by changing spatial constraints on social interactions organisms can modify their behaviour and impact their fitness.     

Diffusion chamber and spleen colony assay of murine haematopoietic stem cells

Mouse bone marrow cells have been cultured in diffusion chambers and their capacity to form spleen colonies in irradiated mice investigated after different culture periods. The number of spleen colony-forming units (CFU) in the chambers decreased during the first day of culture. The number then increased rapidly to a level significantly above the original chamber value on the third to fifth day of culture. By that time large numbers of granulocytes and macrophages had also appeared. Histological examination of spleen colonies showed that prior culturing did not alter the ratio between the different types of colonies. Cultured bone marrow cells which were transferred to new chambers retained granulopoietic capacity. This capacity increased between the first and second day of primary culturing. At this time hydroxyurea injections to chamber hosts revealed that the progenitor cells were proliferating. The results show that the granulopoietic progenitor cells of the chambers are stem cells, and that one progenitor cell type is identical with the CFU.     

Spatiotemporal dynamics of growth and death within spherical bacterial colonies

Bacterial growth within colonies and biofilms is heterogeneous. Local reduction of growth rates has been associated with tolerance against various antibiotics. However, spatial gradients of growth rates are poorly characterized in three-dimensional bacterial colonies. Here, we report two spatially resolved methods for measuring growth rates in bacterial colonies. As bacteria grow and divide, they generate a velocity field that is directly related to the growth rates. We derive profiles of growth rates from the velocity field and show that they are consistent with the profiles obtained by single-cell-counting. Using these methods, we reveal that even small colonies initiated with a few thousand cells of the human pathogen Neisseria gonorrhoeae develop a steep gradient of growth rates within two generations. Furthermore, we show that stringent response decelerates growth inhibition at the colony center. Based on our results, we suggest that aggregation-related growth inhibition can protect gonococci from external stresses even at early biofilm stages.     

A new in vitro assay for cell motility and proliferation

We have described and characterized a new micropore membrane assay for migration and proliferation of cells of various tumourigenic potential. The assay was developed to facilitate analysis of some aspects of cancer invasion and metastasis. Tumorigenic and non-tumorigenic C3H/10 T 1/2 cells grow in and migrate out of a culture chamber during a 1-11 day period, the shorter periods are used for chambers with 6 micron thick polycarbonate membranes, the longer ones for 140 micron thick cellulose nitrate membranes. Cell growth within the chambers, in their micropore membranes and on the outside of the membranes, was assessed with microscopy, electronic cell counting, flow cytometry of propidium iodide (PI) stained cells, and 3H-thymidine [( 3H]TdR) incorporation. A complete retrieval of intact cells that have traversed the membraneous chamber wall is possible, and these cells can be recultured or used in other studies. The tumorigenic cells had a steeper growth curve in vitro than the non transformed cells, but the relative sizes of the emigrated subpopulations were not significantly different. The subpopulation of tumorigenic cells that emigrated spontaneously from the chambers was less able than the subpopulation retained to populate secondary chamber cultures, suggesting that the clonogenic (stem) tumour cells are 'slow movers'.     

Simple quantification of bacterial envelope-associated extracellular materials

We have developed a simple method for distinguishing between bacterial cultures that produce different amount of exopolysaccharide. It is based upon small differences in pellet volume formed by those cultures upon centrifugation. For that we have constructed a special centrifugation tube consisting of two connected chambers: an upper 12 ml chamber connected to a lower capillary chamber. Cells are applied to the upper chamber and following centrifugation, sink to its bottom and are forced into the capillary so that the height they fill can be measured. This procedure has been developed in order to demonstrate differences in volume of centrifugation pellet formed by similar number of Escherichia coli K12 wild type, rpoS mutant and yjbG rpoS double mutant cells. These differences are further shown to be a result of overproduction of colanic acid exopolysaccharide in the mutant strains. We suggest that this simple method can be employed to detect differences in other cell surface structures and to estimate biomass when optical density measurement or microscopic count is not applicable.     

Virustat, a device for continuous production of viruses

Methods for continuous production of viruses, and operation of the virustat, an apparatus in which such production was accomplished, were studied. Continuous production requires a separate continuous host growth chamber, such as the chemostat, and a multiunit virus growth chamber into which the virus-inoculated host cells are led. Successful continuous output of MS-2 and ϕX174 viruses, the latter in lysates, over periods of several days and at titers approximating those of batch lysates, was observed. Design problems include chamber sizes and flow rates, growth of resistant mutants within both virus and host growth chambers, clogging by lysis debris, and the phenomenon of self-inoculation. The latter represents virus growth in the first section of the chamber in excess of the washout rate, leading to lack of need for virus inoculation after an initial period. Use of the virustat for production and research purposes will require some attention to the formation of resistant bacterial colonies at pockets and surface sites of limited washout. With the virustat as a continuous virus production device, continuous purification methods are desirable. Research use of the virustat in continuous mutagenic population studies would require suppression of self-inoculation by use of many sections in the chamber, and improved servo control of host populations at low concentrations.     

A new in vitro assay for cell motility and proliferation

Abstract. We have described and characterized a new micropore membrane assay for migration and proliferation of cells of various tumourigenic potential. The assay was developed to facilitate analysis of some aspects of cancer invasion and metastasis. Tumorigenic and non-tumorigenic C3H/10 T1/2 cells grow in and migrate out of a culture chamber during a 1–11 day period, the shorter periods are used for chambers with 6 μ m thick polycarbonate membranes, the longer ones for 140 μ m thick cellulose nitrate membranes. Cell growth within the chambers, in their micropore membranes and on the outside of the membranes, was assessed with microscopy, electronic cell counting, flow cytometry of propidium iodide (PI) stained cells, and ³H-thymidine ([³H]TdR) incorporation. A complete retrieval of intact cells that have traversed the membraneous chamber wall is possible, and these cells can be recultured or used in other studies. The tumorigenic cells had a steeper growth curve in vitro than the non transformed cells, but the relative sizes of the emigrated subpopulations were not significantly different. The subpopulation of tumorigenic cells that emigrated spontaneously from the chambers was less able than the subpopulation retained to populate secondary chamber cultures, suggesting that the clonogenic (stem) tumour cells are 'slow movers'.     

Buckling instability in ordered bacterial colonies

Bacterial colonies often exhibit complex spatio-temporal organization. This collective behavior is affected by a multitude of factors ranging from the properties of individual cells (shape, motility, membrane structure) to chemotaxis and other means of cell-cell communication. One of the important but often overlooked mechanisms of spatio-temporal organization is direct mechanical contact among cells in dense colonies such as biofilms. While in natural habitats all these different mechanisms and factors act in concert, one can use laboratory cell cultures to study certain mechanisms in isolation. Recent work demonstrated that growth and ensuing expansion flow of rod-like bacteria Escherichia coli in confined environments leads to orientation of cells along the flow direction and thus to ordering of cells. However, the cell orientational ordering remained imperfect. In this paper we study one mechanism responsible for the persistence of disorder in growing cell populations. We demonstrate experimentally that a growing colony of nematically ordered cells is prone to the buckling instability. Our theoretical analysis and discrete-element simulations suggest that the nature of this instability is related to the anisotropy of the stress tensor in the ordered cell colony.     

The significances of bacterial colony patterns

Bacteria do many things as organized populations. We have recently learned much about the molecular basis of intercellular communication among prokaryotes. Colonies display bacterial capacities for multicellular coordination which can be useful in nature where bacteria predominantly grow as films, chains, mats and colonies. E. coli colonies are organized into differentiated non-clonal populations and undergo complex morphogenesis. Multicellularity regulates many aspects of bacterial physiology, including DNA rearrangement systems. In some bacterial species, colony development involves swarming (active migration of cell groups). Swarm colony development displays precise geometrical controls and periodic phenomena. Motile E. coli cells in semi-solid media form organized patterns due to chemotactic autoaggregation. On poor media, B. subtilis forms branched colonies using group motility and longrange chemical signalling. The significances of bacterial colony patterns thus reside in a deeper understanding of prokaryotic biology and evolution and in experimental systems for studying self-organization and morphogenesis.     

Translocation boost protein-folding efficiency of double-barreled chaperonins

Incorrect folding of proteins in living cells may lead to malfunctioning of the cell machinery. To prevent such cellular disasters from happening, all cells contain molecular chaperones that assist nonnative proteins in folding into the correct native structure. One of the most studied chaperone complexes is the GroEL-GroES complex. The GroEL part has a "double-barrel" structure, which consists of two cylindrical chambers joined at the bottom in a symmetrical fashion. The hydrophobic rim of one of the GroEL chambers captures nonnative proteins. The GroES part acts as a lid that temporarily closes the filled chamber during the folding process. Several capture-folding-release cycles are required before the nonnative protein reaches its native state. Here we report molecular simulations that suggest that translocation of the nonnative protein through the equatorial plane of the complex boosts the efficiency of the chaperonin action. If the target protein is correctly folded after translocation, it is released. However, if it is still nonnative, it is likely to remain trapped in the second chamber, which then closes to start a reverse translocation process. This shuttling back and forth continues until the protein is correctly folded. Our model provides a natural explanation for the prevalence of double-barreled chaperonins. Moreover, we argue that internal folding is both more efficient and safer than a scenario where partially refolded proteins escape from the complex before being recaptured.     

“Wall-papering” and elaborate nest architecture in the ponerine antHarpegnathos saltator

Summary Excavation of 18 nests ofHarpegnathos saltator from southern India revealed an unusually complex architecture for a ponerine ant. The inhabited chambers are not deep in the ground. The uppermost chamber is protected by a thick vaulted roof, on the outside of which is an intervening space serving as isolation from the surrounding soil. In large colonies, the vaulted roof is extended into a shell which encloses several superimposed chambers. Little openings, which may be encircled by moulded flanges, occur in the upper region of the shell. The inside of the chambers is partly or completely lined with strips of empty cocoons. A refuse chamber is always found deeper than the inhabited chambers; live dipteran larvae (family Milichiidae) are typically present. These elaborate nests represent a large energetic investment, and we speculate therefore that nest emigration is unlikely in this species. Consequently, colony fission may never occur, unlike other ants where gamergates reproduce.     

FETAL HEMOPOIESIS IN DIFFUSION CHAMBER CULTURES

The growth pattern of fetal liver (FL), normal adult bone marrow (NABM) and regenerating (post Velban treatment) adult bone marrow (RABM) colony forming units (CFU) cultured in diffusion chambers (DC) was studied. When twenty CFU were implanted into DC the recovery of CFU after 4 days with FL, NABM or RABM was 133 ± 7, 19 + 2 and 34 ± 2 CFU, respectively. The transplantation fraction of CFU from NABM decreased from 10-4% on day 0 to 6–9 % on day 4; that of FL did not change from the initial 6-2%. The growth rate of CFU derived from FL was substantially greater than that from NABM. The relative growth of FL and RABM CFU was clearly inhibited when the concentration of cells cultured was increased. Spleen colonies from FL cells before culture were larger (P < 0–005) than colonies from NABM but after 7 days of culture there was no difference between the two groups. Histological examination of spleen colonies showed that after DC culture FL and NABM CFU were differentiating along the three normal pathways. These data suggest that intrinsic differences exist between fetal and adult stem cells in the in vivo diffusion chamber culture system.     

Investigation of an Iron-Oxidizing Microbial Mat Community Located near Aarhus, Denmark: Laboratory Studies

We constructed a small flow chamber in which suboxic medium containing 60 to 120 μM FeCl₂ flowed up through a sample well into an aerated reservoir, thereby creating an suboxic-oxic interface similar to the physicochemical conditions that exist in natural iron seeps. When microbial mat material from the Marselisborg iron seep that contained up to 10⁹ bacterial cells per cm³ (D. Emerson and N. P. Revsbech, Appl. Environ. Microbiol. 60:4022-4031, 1994) was placed in the sample well of the chamber, essentially all of the Fe²⁺ flowing through the sample well was oxidized at rates of up to 1,200 nmol of Fe²⁺ oxidized per h per cm³ of mat material. The oxidation rates of samples of the mat that were pasteurized prior to inoculation were only about 20 to 50% of the oxidation rates of unpasteurized samples. Sodium azide also significantly inhibited oxidation. These results suggest that at least 50% and up to 80% of the Fe oxidation in the chamber were actively mediated by the microbes in the mat. It also appeared that Fe stimulated the growth of the community since chambers fed with FeCl₂ accumulated masses of either filamentous or particulate growth, both in the sample well and attached to the walls of the chamber. Control chambers that did not receive FeCl₂ showed no sign of such growth. Furthermore, after 4 to 5 days the chambers fed with FeCl₂ contained 35 to 75% more protein than chambers not supplemented with FeCl₂. Leptothrix ochracea and, to a lesser extent, Gallionella spp. were responsible for the filamentous growth, and the sheaths and stalks, respectively, of these two organisms harbored large numbers of Fe-encrusted, nonappendaged unicellular bacteria. In chambers where particulate growth predominated, the unicellular bacteria alone appeared to be the primary agents of iron oxidation. These results provide the first clear evidence that the “iron bacteria” commonly found associated with neutral-pH iron seeps are responsible for most of the iron oxidation and that the presence of ferrous iron appears to stimulate the growth of these organisms.     

Invasive extravillous trophoblasts restrict intracellular growth and spread of Listeria monocytogenes

Listeria monocytogenes is a facultative intracellular bacterial pathogen that can infect the placenta, a chimeric organ made of maternal and fetal cells. Extravillous trophoblasts (EVT) are specialized fetal cells that invade the uterine implantation site, where they come into direct contact with maternal cells. We have shown previously that EVT are the preferred site of initial placental infection. In this report, we infected primary human EVT with L. monocytogenes. EVT eliminated ～80% of intracellular bacteria over 24-hours. Bacteria were unable to escape into the cytoplasm and remained confined to vacuolar compartments that became acidified and co-localized with LAMP1, consistent with bacterial degradation in lysosomes. In human placental organ cultures bacterial vacuolar escape rates differed between specific trophoblast subpopulations. The most invasive EVT-those that would be in direct contact with maternal cells in vivo-had lower escape rates than trophoblasts that were surrounded by fetal cells and tissues. Our results suggest that EVT present a bottleneck in the spread of L. monocytogenes from mother to fetus by inhibiting vacuolar escape, and thus intracellular bacterial growth. However, if L. monocytogenes is able to spread beyond EVT it can find a more hospitable environment. Our results elucidate a novel aspect of the maternal-fetal barrier.     

Phenotypically determined resistance of Neisseria gonorrhoeae to normal human serum: environmental factors in subcutaneous chambers in guinea pigs.

Some gonococci obtained from human urethral exudate or from subcutaneously implanted chambers in guinea pigs show a resistance to killing by human serum which is lost on sub-culture in vitro after a few generations. The environmental factors which may influence the phenotypic expression of resistance to serum killing were investigated in guinea pig chambers and in chamber fluid in vitro. The redox potential in chambers before and after infection was lower than that of heart blood but conditions were not anaerobic; H2O2 increased the redox potential but did not decrease gonococcal serum resistance. The chambers were slightly alkaline before and after infection. When the concentration of glucose (depleted in infected chambers by the abundant polymorphonuclear cells) was restored to excess, the serum resistance of the gonococci was unaffected. Concentrations of free amino acids in chambers changed little during infection. Gonococci adapted to growth in chambers and subsequently rendered serum-sensitive by growing once on agar reverted to serum-resistance after 0.5 to 1 h incubation in chamber fluid in vitro at 37 degrees C but not at 25 degrees C or 4 degrees C. After 16 to 24 h growth at 37 degrees C, resistance was again lost. The reversion to serum resistance did not occur in a complex laboratory medium. Examination of the chamber fluid after growth of gonococci in vitro showed depletion of lactate, glutamine and proline.     

Diffusion chamber colony-forming unit (CFU-d): a primitive stem cell

Assay of hematopoietic precursor cells in diffusion chambers (DCs) implanted intraperitoneally in experimental animals provides a powerful tool for studying stem cell kinetics in vivo. In this system, the effect of cell migration (which complicates whole animal studies) is eliminated because the membranes utilized in the construction of the chambers are impermeable for cells, while permitting free passage of molecules present in the humoral phase of the host. As judged by light microscopy, conditions in the DC cultures primarily favor macrophage and granulocyte growth. However, the use of in vitro and in vivo subculture to further analyze chamber contents has demonstrated that the system supports proliferation of early hematopoietic progenitors. Additionally, cells capable of rescuing lethally irradiated mice proliferate in DC cultures. Development of the plasma clot DC technique has revealed that most of the growth occurs in colonies which are derived from single cells (CFU-d). Characterization of these cells indicates that they are at least as primitive as other colony-forming cells and, also based on subculture studies, can differentiate along several hematopoietic lineages. In addition to normal CFU-d, both embryonal and leukemic cells can give rise to granulocytes, macrophages, megakaryocytes and erythroid cells in the DC cultures. Evaluation of the effects of humoral factors on hematopoietic cell proliferation and differentiation in the system has led to the identification of both stimulators and inhibitors that may be different from the well-characterized cytokines. Thus, the system seems to be useful for detecting molecules controlling the most primitive stages of hematopoiesis. We believe that the DC culture technique holds enormous potential in the study of stem cell proliferation and differentiation in vivo.