Structural Insight into Chromatin Recognition by Multiple Domains of the Tumor Suppressor RBBP1

Retinoblastoma-binding protein 1 (RBBP1) is involved in gene regulation, epigenetic regulation, and disease processes. RBBP1 contains five domains with DNA-binding or histone-binding activities, but how RBBP1 specifically recognizes chromatin is still unknown. An AT-rich interaction domain (ARID) in RBBP1 was proposed to be the key region for DNA-binding and gene suppression. Here, we first determined the solution structure of a tandem PWWP-ARID domain mutant of RBBP1 after deletion of a long flexible acidic loop L12 in the ARID domain. NMR titration results indicated that the ARID domain interacts with DNA with no GC- or AT-rich preference. Surprisingly, we found that the loop L12 binds to the DNA-binding region of the ARID domain as a DNA mimic and inhibits DNA binding. The loop L12 can also bind weakly to the Tudor and chromobarrel domains of RBBP1, but binds more strongly to the DNA-binding region of the histone H2A-H2B heterodimer. Furthermore, both the loop L12 and DNA can enhance the binding of the chromobarrel domain to H3K4me3 and H4K20me3. Based on these results, we propose a model of chromatin recognition by RBBP1, which highlights the unexpected multiple key roles of the disordered acidic loop L12 in the specific binding of RBBP1 to chromatin.     

An Algorithm for Calculation of n-Dimensional Nonlinear Dependencies – Behaviour Tests on Rats

The evaluation of the data obtained during the behaviour tests always leads to the problem of multiple correlation, very often with non-linear dependencies on the target. All mathematical and statistical procedures that have been used so far are based on the assumption of an equation for the desired correlation for which parameters and related statistical equivalents are determined eventually. The MODAK system applied here (MODAK = algorithms of modelling for the calculation of multi-dimensional non-linear mathematical models) breaks down a complex correlation into individual dependencies in a mathematical and statistical way and selects suitable equations for each of them independently and determines the corresponding parameters. The numerical example evaluates data of behaviour tests on rats. First results obtained on the correlations of various behaviour tests indicate both the possibility of selecting suitable tests independent of each other and a better interpretation of the observed patterns of behaviour taking into account the interrelations between the tests. In addition, MODAK is a method which can be applied as a matter of course in a general way to all cases which call for the reduction and analysis of data occurring in process and system analysis and in the evaluation of test results requiring statistical modelling. So far, MODAK applications range from engineering sciences to medicine.     

The coupling of biogeochemical cycles of nutrients

For any element which is incorporated into biomass, the biogeochemical cycle of that element in a given ecosystem will be coupled to that of any other element similarly incorporated. The mutual interaction of two such cycles is examined using a simple model in which each cycle is constrained into four compartments. In each cycle the assimilation rate (primary productivity) is related in a non-linear fashion to the two nutrients and to biomass. The interactions are represented by combining a hyperbolic dependence for each nutrient (involving a "Michaelis constant") with a logistic equation governing the dependence of rate on biomass (involving a "carrying capacity"). The response of the model to perturbation (e.g. mobilization of an abiotic reserve) is strongly governed by the values assigned to these constants. The coupled cycles can exhibit positive feed-back with anomalous responses of the steady state and time-dependent solutions may exhibit complex oscillatory behaviour. Both the steady-state sensitivity and the kinetic behaviour of such coupled systems are simplified if the range of atomic ratios permitted by the assimilation process is restricted. It will therefore be of importance to determine under what conditions the assimilation rates for different elements are governed by mass-action effects (Liebig's Law) or by stoichiometric constraints (Redfield ratios).     

Deme formation in scale insects: a test with the pinyon needle scale and a review of other evidence

ABSTRACT. 1. Deme formation is the transformation of a generalist population into one which is adapted to its local conditions. This adaptation has been inferred from many things but should be inferred from higher survival or fecundity of scale insects on their natal tree compared to that of immigrant scales on the same tree.
2. Transfers of the scale insect Matsucoccus acalyptus Herbert within and between infested host trees ( Pinus monophylla (Torr. & Frem.) resulted in significant differences in scale survivorship among recipient trees. Survival on individual trees was correlated across years, indicating stable differences in tree susceptibility to scale.
3. A significant natal tree colonized tree interaction was observed for late stage scale survival in one experiment but the interaction was not caused by superior survivorship of scales transferred back to the natal tree. Hence, we found no evidence of deme formation in M.acalyptus.
4. Previous studies have concluded that deme formation occurs in the black pineleaf scale based on a significant natal tree by colonized tree interaction in scale survival. We question this conclusion because the experimental design employed did not include transfers back onto the natal tree. Other indirect evidence for deme formation in scale insects is critically discussed.     

The singularly perturbed Hodgkin-Huxley equations as a tool for the analysis of repetitive nerve activity

A qualitative analysis of the Hodgkin-Huxley model (Hodgkin and Huxley 1952), which closely mimics the ionic processes at a real nerve membrane, is performed by means of a singular perturbation theory. This was achieved by introducing a perturbation parameter that, if decreased, speeds up the fast variables of the Hodgkin-Huxley equations (membrane potential and sodium activation), whereas it does not affect the slow variables (sodium inactivation and potassium activation). In the most extreme case, if the perturbation parameter is set to zero, the original four-dimensional system degenerates to a system with only two differential equations. This degenerate system is easier to analyze and much more intuitive than the original Hodgkin-Huxley equations. It shows, like the original model, an infinite train of action potentials if stimulated by an input current in a suitable range. Additionally, explanations for the increased sensitivity to depolarizing current steps that precedes an action potential can be found by analysis of the degenerate system. Using the theory of Mishchenko and Rozov (1980) it is shown that the degenerate system does not only represent a simplification of the original Hodgkin-Huxley equations but also gives a valid approximation of the original model at least for stimulating currents that are constant within a suitable range.     

Auditory assessment of avian predator threat in semi-captive ringtailed lemurs (Lemur catta)

Antiraptor responses from forest-living ringtailed lemurs to advertisement calls of naturally-occurring red-tailed hawks suggested that the lemurs discriminated these calls from other environmental sounds. A series of playback experiments, using real animal sounds and synthetic sound probes, was conducted to investigate the acoustic basis of this putative discrimination. Two semi-captive groups of ringtails served as study subjects: one group had many years of experience living in the forest, whereas the other group had relatively little such experience. Responses to playbacks suggested that both groups used the same acoustic criteria to discriminate “calls of large hawks” from other sounds, but the range of auditory stimuli that evoked antiraptor responses was broader for the experienced group than for the inexperienced group. Although several interpretations of the experimental results are possible, one that seems particularly compatible with the data is the “prototype” concept of stimulus categorization.     

Evolutionary implications of swimming behaviour in meiobenthic copepods

Body morphology is said to be the all important factor in determining swimming prowess in copepods. Fusion and differentiation of the body (tagmosis) is coupled with advance into the pelagic realm of the Gymnoplea and is thought, by the provision of a rigid thoracic tagma, to promote swimming efficiency. Thus pelagic copepods are believed to be secondarily derived from bottom dwelling predecessors. Experimental evidence is presented to show that the majority of bottom dwelling harpacticoid families, including the most primitive and the most advanced, have representatives that undergo active sustained swimming movements. Such a widespread occurrence is indicative of a conservative evolutionary trait. This primitive behaviour is linked to precopulatory association which takes place necessarily in the water column; it is a feature retained by representatives of all copepod orders. The implication of cephalic appendage vibration (feeding currents) is the essential feature in the swimming success of the Gymnoplea; planktonic efficiency in these is suggested to have evolved coincident with, rather than because of increased tagmosis.     

Chromosome numbers and reproduction inRubus subgen.Malachobatus

A review of current knowledge of chromosome numbers and modes of reproduction in the genusRubus L. is presented. Chromosome numbers from some species of subg.Malachobatus Focke together with results of crossing experiments are reported for the first time.     

Increased straying by adult steelhead trout,Salmo gairdneri,following the 1980 eruption of Mount St. Helens

Synopsis This paper describes the magnitude and geographic dispersion of adult steelhead trout, Salmo gairdneri, diverted from Columbia River tributaries which were impacted by the 1980 volcanic eruption of Mount St. Helens. Compelling circumstantial evidence suggests that for 1–3 yr after the eruption, large numbers of adult steelhead migrating toward affected tributaries entered two non-affected tributaries flowing into the Columbia River upstream of natal streams. Streams downstream of affected tributaries did not appear to receive substantial numbers of displaced fish. I estimated that the percentage of non-natal steelhead migrating into the lower portions of the nearest upstream river increased from 16% pre-eruption to 45% post-eruption. Winter-run steelhead strays probably originated from both the Cowlitz and Toutle rivers, whereas summer-run strays originated predominantly from the Toutle River. Increased natural production in tributaries resulting from the infusion of large numbers of strays was of insufficient magnitude to be detected by the methods of this study.