The Minimal Complexity of Adapting Agents Increases with Fitness

What is the relationship between the complexity and the fitness of evolved organisms, whether natural or artificial? It has been asserted, primarily based on empirical data, that the complexity of plants and animals increases as their fitness within a particular environment increases via evolution by natural selection. We simulate the evolution of the brains of simple organisms living in a planar maze that they have to traverse as rapidly as possible. Their connectome evolves over 10,000s of generations. We evaluate their circuit complexity, using four information-theoretical measures, including one that emphasizes the extent to which any network is an irreducible entity. We find that their minimal complexity increases with their fitness.     

Long-term survival after adoptive bone marrow T cell therapy of advanced metastasized breast cancer: follow-up analysis of a clinical pilot trial

Background

The bone marrow (BM) of breast cancer patients harbors tumor-reactive memory T cells (TCs) with therapeutic potential. We recently described the immunologic effects of adoptive transfer of ex vivo restimulated tumor-reactive memory TCs from the BM of 12 metastasized breast cancer patients in a clinical phase-I study. In this trial, adoptive T cell transfer resulted in the occurrence of circulating tumor antigen-reactive type-1 TCs. We here describe the long-term clinical outcome and its correlation with tumor-specific cellular immune response in 16 metastasized breast cancer patients, including 12 included in the original study.

Methods

Sixteen metastatic breast cancer patients with preexisting tumor-reactive BM memory TCs were included into the study. The study protocol involved one transfusion of TCs which were reactivated in vitro with autologous dendritic cells pulsed with lysates of MCF-7 breast cancer cells as source of tumor antigens. The presence of tumor-reactive memory TCs was analyzed by IFN-γ ELISpot assays.

Results

Tumor-reactive memory TCs in the peripheral blood were induced de novo in 7/16 patients (44 %) after adoptive TC transfer. These patients were considered immunologic responders to the therapy. Positive adoptive immunotherapy (ADI) response was observed significantly more often in patients without bone metastases (p = 0.0051), in patients with high levels of tumor-reactive BM TCs prior to therapy (p = 0.036) and correlated significantly with the estimated numbers of transferred tumor-reactive TCs (p = 0.0021). After the treatment, we observed an overall median survival of 33.8 months in the total cohort with three patients alive at last follow-up and more than 7 years after ADI. Numbers of transferred tumor-reactive TCs correlated significantly with the overall survival of patients (p = 0.017). Patients with an immunologic response to ADI in the peripheral blood had a significantly longer median survival than nonresponders (median survival 58.6 vs. 13.6 months; p = 0.009).

Conclusion

In metastasized breast cancer patients, adoptive transfer of BM TCs can induce the presence of tumor antigen-reactive type-1 TCs in the peripheral blood. Patients with immunologic response after ADI show a significantly longer overall survival. Patients with bone metastases significantly less frequently respond to the treatment and, therefore, might not be optimal candidates for ADI. Although the present study does not yet prove the therapeutic effect of ADI, these findings shed light on the relation between immune response and cancer prognosis and suggest that transfer of reactivated BM TCs might bear therapeutic potential.     

Pharmacological postconditioning by bolus injection of phosphodiesterase-5 inhibitors vardenafil and sildenafil

Postconditioning enables cardioprotection against ischemia/reperfusion injury either by application of short, repetitive ischemic periods or by pharmacological intervention prior to reperfusion. Pharmacological postconditioning has been described for phosphodiesterase-5 inhibitors when the substances were applied as a permanent infusion. For clinical purposes, application of a bolus is more convenient. In a rat heart in situ model of ischemia reperfusion vardenafil or sildenafil were applied as a bolus prior to reperfusion. Cardioprotective effects were found over a broad dosage range. In accordance with current hypotheses on pharmacological postconditioning signaling, the protective effect was mediated by extracellular signal-regulated kinase and protein kinase C pathway. Interestingly, the extent of protection was independent of the concentration applied for both substances. Full protection comparable to ischemic postconditioning was reached with half-maximal human equivalence dose. In contrast, mean arterial pressure dropped upon bolus application in a dose-dependent manner. Taken together, the current study extends previous findings obtained in a permanent infusion model to bolus application. This is an important step toward clinical application of pharmacological postconditioning with sildenafil and vardenafil, especially because the beneficial effects were proven for concentrations with reduced hemodynamic side effects compared to the dosage applied for erectile dysfunction treatment.     

A predictive framework to assess spatio‐temporal variability of infestations by the European spruce bark beetle

Natural disturbances are key factors for the development of forest ecosystems. In forests of central Europe and Scandinavia, the European spruce bark beetle Ips typographus is the most devastating biotic disturbance agent in Norway spruce Picea abies, but our understanding of the factors determining its spatio‐temporal dynamics is still quite limited. To quantify the drivers of bark beetle dynamics, we analyzed a survey dataset with annual resolution that covers 17 yr and 469 forest districts (10 860 km² of forest area) all over Switzerland. We used Poisson log‐normal models in a Bayesian framework to analyze the spatio‐temporal dynamics of bark beetle infestation spots at the forest district level. Bark beetle infestations increased with increasing heat sum (> 8.3°C), volume of standing Norway spruce stock, and the number of infestation spots of the previous year. Precipitation tended to slightly affect the risk of bark beetle infestations. Two major storm events further increased the spatio‐temporal variability of bark beetle infestations. Spruce abundance, storm damage and temperature are known to be important factors influencing the population dynamics of the European spruce bark beetle. Our study is the first to quantify the combined effects of spruce abundance and heat sum, whereby the heat sum turned out to be the most important and consistent predictor. Because our study area encompasses large ecological and climatological gradients, our model is likely to be applicable to Norway spruce forests in other regions of central Europe and Scandinavia.     

A comparison of the strength of biodiversity effects across multiple functions

In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 % of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination.     

Wavelength-dependent photodamage to <Emphasis Type="Italic">Chlorella</Emphasis> investigated with a new type of multi-color PAM chlorophyll fluorometer

A new type of multi-color PAM chlorophyll fluorometer (Schreiber et al. 2012) was applied for measurements of photodamage to photosystem II (PS II) in optically thin suspensions of Chlorella (200 μg Chl l^?1) in the presence of 1 mM lincomycin. An action spectrum of the relative decrease of F _v/F _m in the 440–625 nm range was measured, which not only showed the expected high activity in the blue, but at a lower level also substantial activity above 540 nm. With the same dilute suspension, a PS II absorption spectrum was derived via measurements of the O-I₁ rise kinetics induced by differently colored strong light at defined incident quantum flux densities. After normalization of the two spectra at 625 nm, the relative extent of photodamage at 440–480 nm proved substantially higher than absorption by PS II, whereas the two spectra were close to identical in the 540–625 nm range. Hence, overall photodamage to PS II appears to consist of two components, one of which is due to light absorbed by PS II pigments, whereas the other one is likely to involve direct light absorption by Mn in the oxygen-evolving complex (Hakala et al. Biochim Biophys Acta 1706:68–80, 2005). Based on this rationale, an action spectrum of the Mn mechanism of photodamage was deconvoluted from the overall action spectrum, declining steeply above 480 nm. An almost identical Mn-spectrum was derived by another approach with the PAR of the various colors being adjusted to give identical rates of PS II turnover, PAR _II. The tentative, basic assumption of negligibly small contribution of the Mn mechanism to photodamage above 540 nm was supported by supplementary measurements using an external 665 nm lamp. 665 nm not only gave about two times PS II turnover as compared to 625 nm, but also about two times photodamage.     

Continuous ECS-indicated recording of the proton-motive charge flux in leaves

Technical features and examples of application of a special emitter–detector module for highly sensitive measurements of the electrochromic pigment absorbance shift (ECS) via dual-wavelength (550–520 nm) transmittance changes (P515) are described. This device, which has been introduced as an accessory of the standard, commercially available Dual-PAM-100 measuring system, not only allows steady-state assessment of the proton motive force (pmf) and its partitioning into ΔpH and ΔΨ components, but also continuous recording of the overall charge flux driven by photosynthetic light reactions. The new approach employs a double-modulation technique to derive a continuous signal from the light/dark modulation amplitude of the P515 signal. This new, continuously measured signal primarily reflects the rate of proton efflux via the ATP synthase, which under quasi-stationary conditions corresponds to the overall rate of proton influx driven by coupled electron transport. Simultaneous measurements of charge flux and CO₂ uptake as a function of light intensity indicated a close to linear relationship in the light-limited range. A linear relationship between these two signals was also found for different internal CO₂ concentrations, except for very low CO₂, where the rate of charge flux distinctly exceeded the rate of CO₂ uptake. Parallel oscillations in CO₂ uptake and charge flux were induced by high CO₂ and O₂. The new device may contribute to the elucidation of complex regulatory mechanisms in intact leaves.     

Shadow enhancers flanking the HoxB cluster direct dynamic Hox expression in early heart and endoderm development

The products of Hox genes function in assigning positional identity along the anterior–posterior body axis during animal development. In mouse embryos, Hox genes located at the 3′ end of HoxA and HoxB complexes are expressed in nested patterns in the progenitors of the secondary heart field during early cardiogenesis and the combined activities of both of these clusters are required for proper looping of the heart. Using Hox bacterial artificial chromosomes (BACs), transposon reporters, and transgenic analyses in mice, we present the identification of several novel enhancers flanking the HoxB complex which can work over a long range to mediate dynamic reporter expression in the endoderm and embryonic heart during development. These enhancers respond to exogenously added retinoic acid and we have identified two retinoic acid response elements (RAREs) within these control modules that play a role in potentiating their regulatory activity. Deletion analysis in HoxB BAC reporters reveals that these control modules, spread throughout the flanking intergenic region, have regulatory activities that overlap with other local enhancers. This suggests that they function as shadow enhancers to modulate the expression of genes from the HoxB complex during cardiac development. Regulatory analysis of the HoxA complex reveals that it also has enhancers in the 3′ flanking region which contain RAREs and have the potential to modulate expression in endoderm and heart tissues. Together, the similarities in their location, enhancer output, and dependence on retinoid signaling suggest that a conserved cis-regulatory cassette located in the 3′ proximal regions adjacent to the HoxA and HoxB complexes evolved to modulate Hox gene expression during mammalian cardiac and endoderm development. This suggests a common regulatory mechanism, whereby the conserved control modules act over a long range on multiple Hox genes to generate nested patterns of HoxA and HoxB expression during cardiogenesis.     

Phase control of circadian activity in the antelope ground squirrel

Abstract

Wheel‐running activity of forty antelope ground squirrels, Ammospermophilus leucurus, was monitored for several months in both an outdoor cage and in the laboratory. The squirrels demonstrated a highly diurnal pattern which persisted in “constant conditions.” After removal from the field the initial free‐running period was close to 24 hrs, but typically lengthened in a nearly linear fashion at least for the first few months. There was no evidence of any difference in this trend for squirrels, in D/D, L/L 100 lx, 250 lx or 1200 lx. Eventually, about 90 percent of the squirrels had periods longer than 24 hrs.

The synchronizing capacity of the natural photoperiod was used to “catch the free‐running rhythm” and thereby demonstrate a response curve. Synchronization occurred by a shortening of the period when the time of sunrise was between 125° and 0° (subjective night) and by a lengthening of the period when the time of sunrise was between 0° and 125° (subjective day).

To more thoroughly examine the underlying mechanisms of phase control, phase‐response curves based on sixty one light‐pulse experiments were constructed. Comparisons of curves based on 6‐hr and 15‐min pulses, showed that the integral action of light is important (i.e., the entire pulse is involved in phase shifting). It was found that light pulses not only affected the phase of the rhythm but also the phase. Large phase shifts were usually associated with decreases in free‐running period. Several hypotheses on the controlling mechanisms were advanced.