Influence of DNA end structure on the mechanism of initiation of DNA unwinding by the Escherichia coli RecBCD and RecBC helicases

Escherichiacoli RecBCD is a bipolar DNA helicase possessing two motor subunits (RecB, a 3′-to-5′ translocase, and RecD, a 5′-to-3′ translocase) that is involved in the major pathway of recombinational repair. Previous studies indicated that the minimal kinetic mechanism needed to describe the ATP-dependent unwinding of blunt-ended DNA by RecBCD in vitro is a sequential n-step mechanism with two to three additional kinetic steps prior to initiating DNA unwinding. Since RecBCD can “melt out” ∼ 6 bp upon binding to the end of a blunt-ended DNA duplex in a Mg²⁺-dependent but ATP-independent reaction, we investigated the effects of noncomplementary single-stranded (ss) DNA tails [3′-(dT)₆ and 5′-(dT)₆ or 5′-(dT)₁₀] on the mechanism of RecBCD and RecBC unwinding of duplex DNA using rapid kinetic methods. As with blunt-ended DNA, RecBCD unwinding of DNA possessing 3′-(dT)₆ and 5′-(dT)₆ noncomplementary ssDNA tails is well described by a sequential n-step mechanism with the same unwinding rate (mk_U = 774 ± 16 bp s^− 1) and kinetic step size (m = 3.3 ± 1.3 bp), yet two to three additional kinetic steps are still required prior to initiation of DNA unwinding (k_C = 45 ± 2 s^− 1). However, when the noncomplementary 5′ ssDNA tail is extended to 10 nt [5′-(dT)₁₀ and 3′-(dT)₆], the DNA end structure for which RecBCD displays optimal binding affinity, the additional kinetic steps are no longer needed, although a slightly slower unwinding rate (mk_U = 538 ± 24 bp s^− 1) is observed with a similar kinetic step size (m = 3.9 ± 0.5 bp). The RecBC DNA helicase (without the RecD subunit) does not initiate unwinding efficiently from a blunt DNA end. However, RecBC does initiate well from a DNA end possessing noncomplementary twin 5′-(dT)₆ and 3′-(dT)₆ tails, and unwinding can be described by a simple uniform n-step sequential scheme, without the need for the additional k_C initiation steps, with a similar kinetic step size (m = 4.4 ± 1.7 bp) and unwinding rate (mk_obs = 396 ± 15 bp s^− 1). These results suggest that the additional kinetic steps with rate constant k_C required for RecBCD to initiate unwinding of blunt-ended and twin (dT)₆-tailed DNA reflect processes needed to engage the RecD motor with the 5′ ssDNA.     

Effects of root zone temperature on aluminium toxicity in two cultivars of spring wheat with different resistance to aluminium

Manifestations of aluminium (Al) toxicity in two cultivars of wheat ( Triticum aestivum L. cvs Kadett [relatively Al-resistant] and WW 20299 [relatively Al-sensitive]) were investigated at two root zone temperatures (RZT) that may occur in the field. The plants were grown for 9 days at 10 or 25°C RZT. Mineral nutrients other than CaSO₄ were supplied daily in exponentially increasing amounts to meet the demand of the plants. Al was added as Al₂(SO₄)₃ at the beginning of the culture period at concentrations ranging from 0 to 100 μ M . pH was kept constant at 4.1. Experimental data were analysed for interactions between Al and RZT on a fresh weight basis by the nonlinear Weibull function. Cultivar Kadett, when grown at 25°C RZT, was more resistant to Al than when grown at 10°C RZT. Cultivar WW 20299 was equally sensitive to Al at 10 and 25°C RZT but generally more sensitive to Al than cv. Kadett. It is suggested that cv. Kadett, in contrast to cv. WW 20299, possesses a mechanism for Al resistance that is less effective at 10°C than at 25°C RZT and therefore may be metabolically dependent. In roots, the concentrations of K, P, Mg and Ca were not negatively affected by Al or by RZT. In shoots of both cultivars the concentrations of Ca and Mg became comparatively low when the plants were treated with Al or at low RZT, the effect being larger for Ca than for Mg. At 10°C RZT under Al stress, the Ca concentrations in shoots approached the critical concentration where growth may be inhibited. As no Al was detected in the shoots, it is suggested that Al in the roots inhibits shoot growth by reducing transport of Ca from roots to shoots.     

Temperature dependence of single channel currents and the peptide libration mechanism for ion transport through the gramicidin A transmembrane channel

Summary A study of the temperature dependence of gramicidin A conductance of K⁺ in diphytanoyllecithin/n-decane membranes shows the plot of In (single channel conductance) as a function of reciprocal temperature to be nonlinear for the most probable set of conductance, states. These results are considered in terms of a series of barriers, of the dynamics of channel conformation,vis-a-vis the peptide libration mechanism, and of the effect of lipid viscosity on side chain motions again as affecting the energetics of peptide libration.     

Do you hear what I see? Vocalization relative to visual detection rates of Hawaiian hoary bats (Lasiurus cinereus semotus)

Bats vocalize during flight as part of the sensory modality called echolocation, but very little is known about whether flying bats consistently call. Occasional vocal silence during flight when bats approach prey or conspecifics has been documented for relatively few species and situations. Bats flying alone in clutter‐free airspace are not known to forgo vocalization, yet prior observations suggested possible silent behavior in certain, unexpected situations. Determining when, why, and where silent behavior occurs in bats will help evaluate major assumptions of a primary monitoring method for bats used in ecological research, management, and conservation. In this study, we recorded flight activity of Hawaiian hoary bats (Lasiurus cinereus semotus) under seminatural conditions using both thermal video cameras and acoustic detectors. Simultaneous video and audio recordings from 20 nights of observation at 10 sites were analyzed for correspondence between detection methods, with a focus on video observations in three distance categories for which accompanying vocalizations were detected. Comparison of video and audio detections revealed that a high proportion of Hawaiian hoary bats “seen” on video were not simultaneously “heard.” On average, only about one in three visual detections within a night had an accompanying call detection, but this varied greatly among nights. Bats flying on curved flight paths and individuals nearer the cameras were more likely to be detected by both methods. Feeding and social calls were detected, but no clear pattern emerged from the small number of observations involving closely interacting bats. These results may indicate that flying Hawaiian hoary bats often forgo echolocation, or do not always vocalize in a way that is detectable with common sampling and monitoring methods. Possible reasons for the low correspondence between visual and acoustic detections range from methodological to biological and include a number of biases associated with the propagation and detection of sound, cryptic foraging strategies, or conspecific presence. Silent flight behavior may be more prevalent in echolocating bats than previously appreciated, has profound implications for ecological research, and deserves further characterization and study.     

Causality in Complex Systems

Systems involving many interacting variables are at the heart of the natural and social sciences. Causal language is pervasive in the analysis of such systems, especially when insight into their behavior is translated into policy decisions. This is exemplified by economics, but to an increasing extent also by biology, due to the advent of sophisticated tools to identify the genetic basis of many diseases. It is argued here that a regularity notion of causality can only be meaningfully defined for systems with linear interactions among their variables. For the vastly more important class of nonlinear systems, no such notion is likely to exist. This thesis is developed with examples of dynamical systems taken mostly from mathematical biology. It is discussed with particular reference to the problem of causal inference in complex genetic systems, systems for which often only statistical characterizations exist.     

鸣禽发声学习记忆与即刻早期基因

鸣禽受到声音信号的刺激或自身表现出发声行为时,脑内即刻早期基因(immediate early gene,IEG)能迅速被激活而表达.其中zenk、c-fos和c-jun表达的脑区及水平与鸟在鸣唱时神经元的活动区域及活动程度相一致,暗示IEG在鸣禽发声学习记忆中起重要作用.     

Feedback of coastal marshes to climate change: Long‐term phenological shifts

Coastal marshes are important carbon sinks facing serious threats from climatic stressors. Current research reveals that the growth of individual marsh plants is susceptible to a changing climate, but the responses of different marsh systems at a landscape scale are less clear. Here, we document the multi‐decadal changes in the phenology and the area of the extensive coastal marshes in Louisiana, USA, a representative of coastal ecosystems around the world that currently experiencing sea‐level rise, temperature warming, and atmospheric CO₂ increase. The phenological records are constructed using the longest continuous satellite‐based record of the Earth's ecosystems, the Landsat data, and an advanced modeling technique, the nonlinear mixed model. We find that the length of the growing seasons of the intermediate and brackish marshes increased concomitantly with the atmospheric CO₂ concentration over the last 30 years, and predict that such changes will continue and accelerate in the future. These phenological changes suggest a potential increase in CO₂ uptake and thus a negative feedback mechanism to climate change. The areas of the freshwater and intermediate marshes were stable over the period studied, but the areas of the brackish and saline marshes decreased substantially, suggesting ecosystem instability and carbon storage loss under the anticipated sea‐level rise. The marshes' phenological shifts portend their potentially critical role in climate mitigation, and the different responses among systems shed light on the underlying mechanisms of such changes.