Density, short-range order and the quark-gluon plasma

We study the thermal part of the energy density spatial correlator in the quark-gluon plasma. We describe its qualitative form at high temperatures. We then calculate it out to distances approx. 1.5/T in SU(3) gauge theory lattice simulations for the range of temperatures 0.9<= T/T_c<= 2.2. The vacuum-subtracted correlator exhibits non-monotonic behavior, and is almost conformal by 2T_c. Its broad maximum at r approx. 0.6/T suggests a dense medium with only weak short-range order, similar to a non-relativistic fluid near the liquid-gas phase transition, where eta/s is minimal.Comment: 4 pages, 4 figure

Interpreting two-photon imaging data of lymphocyte motility

Recently, using two-photon imaging it has been found that the movement of B and T cells in lymph nodes can be described by a random walk with persistence of orientation in the range of 2 minutes. We interpret this new class of lymphocyte motility data within a theoretical model. The model considers cell movement to be composed of the movement of subunits of the cell membrane. In this way movement and deformation of the cell are correlated to each other. We find that, indeed, the lymphocyte movement in lymph nodes can best be described as a random walk with persistence of orientation. The assumption of motility induced cell elongation is consistent with the data. Within the framework of our model the two-photon data suggest that T and B cells are in a single velocity state with large stochastic width. The alternative of three different velocity states with frequent changes of their state and small stochastic width is less likely. Two velocity states can be excluded

Cutting edge: back to "one-way" germinal centers

The present status of germinal center (GC) research is revisited using in silico simulations based on recent lymphocyte motility data in mice. The generally adopted view of several rounds of somatic hypermutations and positive selection is analyzed with special emphasis on the spatial organization of the GC reaction. We claim that the development of dark zones is not necessary for successful GC reactions to develop. We find that a recirculation of positively selected centrocytes to the dark zone is rather unlikely. Instead we propose a scenario that combines a multiple-step mutation and selection concept with a "one-way" GC in the sense of cell migration

TOPEX satellite concept. TOPEX option study report

Candidate bus equipment from the Viking, Applications Explorer Mission, and Small Scientific Satellite programs for application to the TOPEX mission options is assessed. Propulsion module equipment and subsystem candidates from the Applications Explorer Mission satellites and the Small Scientific Satellite spacecraft are evaluated for those TOPEX options. Several subsystem concepts appropriate to the TOPEX options are described. These descriptions consider performance characteristics of the subsystems. Cost and availability information on the candidate equipment and subsystems are also provided

Road blocks on paleogenomes - polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA

Although the last few years have seen great progress in DNA sequence retrieval from fossil specimens, some of the characteristics of ancient DNA remain poorly understood. This is particularly true for blocking lesions, i.e. chemical alterations that cannot be bypassed by DNA polymerases and thus prevent amplification and subsequent sequencing of affected molecules. Some studies have concluded that the vast majority of ancient DNA molecules carry blocking lesions, suggesting that the removal, repair or bypass of blocking lesions might dramatically increase both the time depth and geographical range of specimens available for ancient DNA analysis. However, previous studies used very indirect detection methods that did not provide conclusive estimates on the frequency of blocking lesions in endogenous ancient DNA. We developed a new method, polymerase extension profiling (PEP), that directly reveals occurrences of polymerase stalling on DNA templates. By sequencing thousands of single primer extension products using PEP methodology, we have for the first time directly identified blocking lesions in ancient DNA on a single molecule level. Although we found clear evidence for blocking lesions in three out of four ancient samples, no more than 40% of the molecules were affected in any of the samples, indicating that such modifications are far less frequent in ancient DNA than previously thought

An analysis of B cell selection mechanisms in germinal centres

Affinity maturation of antibodies during immune responses is achieved by multiple rounds of somatic hypermutation and subsequent preferential selection of those B cells that express B cell receptors with improved binding characteristics for the antigen. The mechanism underlying B cell selection has not yet been defined. By employing an agent-based model, we show that for physiologically reasonable parameter values affinity maturation can be driven by competition for neither binding sites nor antigen—even in the presence of competing secreted antibodies. Within the tested mechanisms, only clonal competition for T cell help or a refractory time for the interaction of centrocytes with follicular dendritic cells is found to enable affinity maturation while generating the experimentally observed germinal centre characteristics and tolerating large variations in the initial antigen density

NMDA Currents Modulate the Synaptic Input–Output Functions of Neurons in the Dorsal Nucleus of the Lateral Lemniscus in Mongolian Gerbils

Neurons in the dorsal nucleus of the lateral lemniscus (DNLL) receive excitatory and inhibitory inputs from the superior olivary complex (SOC) and convey GABAergic inhibition to the contralateral DNLL and the inferior colliculi. Unlike the fast glycinergic inhibition in the SOC, this GABAergic inhibition outlasts auditory stimulation by tens of milliseconds. Two mechanisms have been postulated to explain this persistent inhibition. One, an “integration-based” mechanism, suggests that postsynaptic excitatory integration in DNLL neurons generates prolonged activity, and the other favors the synaptic time course of the DNLL output itself. The feasibility of the integration-based mechanism was tested in vitro in DNLL neurons of Mongolian gerbils by quantifying the cellular excitability and synaptic input–output functions (IO-Fs). All neurons were sustained firing and generated a near monotonic IO-F on current injections. From synaptic stimulations, we estimate that activation of approximately five fibers, each on average liberating ∼18 vesicles, is sufficient to trigger a single postsynaptic action potential. A strong single pulse of afferent fiber stimulation triggered multiple postsynaptic action potentials. The steepness of the synaptic IO-F was dependent on the synaptic NMDA component. The synaptic NMDA receptor current defines the slope of the synaptic IO-F by enhancing the temporal and spatial EPSP summation. Blocking this NMDA-dependent amplification during postsynaptic integration of train stimulations resulted into a ∼20% reduction of the decay time course of the GABAergic inhibition. Thus, our data show that the NMDA-dependent amplification of the postsynaptic activity contributes to the GABAergic persistent inhibition generated by DNLL neurons

Analysis of B cell selection mechanisms in the adaptive immune response

The essential task of a germinal centre reaction is the selection of those B cells that bind the antigen with high affinity. The exact mechanisms of B cell selection is still unknown and rather difficult to be accessed in experiment. With the help of an already established agent-based model for the space-time-dynamics of germinal centre reactions [1,2] we compare the most important hypotheses for what the limiting factor for B cell rescue may be. We discuss competition for antigen sites on follicular dendritic cells, a refractory time for centrocytes after every encounter with follicular dendritic cells, competition for the antigen itself, the role of antigen masking with soluble antibodies, and competition for T cell help. The unexpected result is that neither competition for interaction sites nor competition for antigen nor antigen masking are in agreement with present experimental data on germinal centre reactions. We show that these most popular selection mechanisms do not lead to sufficient affinity maturation and do not respect the observed robustness against changes of initial conditions. However, the best agreement with data was found for the newly hypothesized centrocyte refractory time and for competition for T cell help. Thus the in silico experiments point towards selection mechanisms that are not in the main focus of current germinal centre research. Possible experiments to test these hypotheses are proposed