Functional and Structural Responses of a Degradative Microbial Community to Substrates with Varying Degrees of Complexity in Chemical Structure

Abstract The objective of the present study was to determine whether cultivation of a degradative community on substrates with varying degrees of chlorination and complexity in chemical structure, as well as cultivation in batch and flow cell culture, would alter the community's functional capability. The community was isolated from oil-contaminated soil and maintained in the laboratory on 2,4,6-trichlorobenzoic acid for 5 months before its ability to grow on 15 different chemicals as sole carbon source was evaluated in batch and flow cell systems. While the community could grow and develop biofilms in flow cells on all the substrates, only 11 of the 15 substrates could support growth in batch culture. Although biofilm development was less extensive on chemicals such as pentachlorophenol (2.09% average area covered by biofilm; average biofilm depth = 3 μm) than on 2,4,6-trichlorobenzoic acid (50.84% area covered; biofilm depth = 6.4 μm), no correlation was observed between the degree of chlorination, or number of rings, and the number of planktonic cells or biofilm biomass. In contrast, physicochemical characteristics such as the octanol/water partition coefficient had a significant effect on the development of biofilm biomass. In the case of planktonic communities, the degree of chlorination and ring number also had no effect on the BIOLOG carbon utilization profiles of the resulting communities. Although the sessile communities generally clustered separately from their planktonic counterparts, principal component analysis of carbon utilization profiles of the sessile communities showed different grouping between growth on chlorinated and nonchlorinated substrates. Analysis of the degradative community maintained on 2,4,6-trichlorobenzoic acid over an extended period further showed that adaptation to a new chemical environment is a rather slow process, since the substrate utilization profiles did not stabilize even after 12 months. These results demonstrate the flexibility in metabolic ability and community structure found in microbial communities. Received: 30 November 1998; Accepted: 19 May 1999     

Parallel Genetic Evolution Within and Between Bacteriophage Species of Varying Degrees of Divergence

Parallel evolution is the acquisition of identical adaptive traits in independently evolving populations. Understanding whether the genetic changes underlying adaptation to a common selective environment are parallel within and between species is interesting because it sheds light on the degree of evolutionary constraints. If parallel evolution is perfect, then the implication is that forces such as functional constraints, epistasis, and pleiotropy play an important role in shaping the outcomes of adaptive evolution. In addition, population genetic theory predicts that the probability of parallel evolution will decline with an increase in the number of adaptive solutions—if a single adaptive solution exists, then parallel evolution will be observed among highly divergent species. For this reason, it is predicted that close relatives—which likely overlap more in the details of their adaptive solutions—will show more parallel evolution. By adapting three related bacteriophage species to a novel environment we find (1) a high rate of parallel genetic evolution at orthologous nucleotide and amino acid residues within species, (2) parallel beneficial mutations do not occur in a common order in which they fix or appear in an evolving population, (3) low rates of parallel evolution and convergent evolution between species, and (4) the probability of parallel and convergent evolution between species is strongly effected by divergence.     

Evaluation and Interpretation of the Effects of Environmental Enrichment Utilizing Varying Degrees of Sampling Effort

Documenting the effects of novel forms of enrichment is becoming increasingly important within the field of environmental enrichment. Appropriate documentation and evaluation must accompany any enrichment research project in order for accurate results to be obtained. The objective of the present study was to provide an example of how the level of effort in documenting the effect of enrichment is linked to how it is evaluated. This study was carried out on eight cheetahs (Acinonyx jubatus) at Fota Wildlife Park, Ireland. Temporal feeding variation was the enrichment type used during this study. Behavior data were collected in five different ways in order to simulate varying degrees of effort. Randomization tests were utilized to analyze behavior data. Significant behavioral differences were observed in the first four sampling methods with patterns of behavior remaining similar in all five methods. However, only the most time intensive method concurred with findings previously published utilizing this form of enrichment. No significant differences in behavior were detected when the least time intensive method was used. Between 1 and 2 hr of data collection daily is necessary to evaluate temporal feeding variation accurately. However, 30–45 min of data collection also gave an insight into the effectiveness of the enrichment. Methods of evaluation can influence the interpretations of the strength of the enriching effect of the treatment. Appropriate evaluation and accurate reporting of enrichment is crucial for the future development of the environmental enrichment field. Zoo Biol 32:262–268, 2013. © 2012 Wiley Periodicals, Inc.     

Cooperative Adaptive Responses in Gene Regulatory Networks with Many Degrees of Freedom

Cells generally adapt to environmental changes by first exhibiting an immediate response and then gradually returning to their original state to achieve homeostasis. Although simple network motifs consisting of a few genes have been shown to exhibit such adaptive dynamics, they do not reflect the complexity of real cells, where the expression of a large number of genes activates or represses other genes, permitting adaptive behaviors. Here, we investigated the responses of gene regulatory networks containing many genes that have undergone numerical evolution to achieve high fitness due to the adaptive response of only a single target gene; this single target gene responds to changes in external inputs and later returns to basal levels. Despite setting a single target, most genes showed adaptive responses after evolution. Such adaptive dynamics were not due to common motifs within a few genes; even without such motifs, almost all genes showed adaptation, albeit sometimes partial adaptation, in the sense that expression levels did not always return to original levels. The genes split into two groups: genes in the first group exhibited an initial increase in expression and then returned to basal levels, while genes in the second group exhibited the opposite changes in expression. From this model, genes in the first group received positive input from other genes within the first group, but negative input from genes in the second group, and vice versa. Thus, the adaptation dynamics of genes from both groups were consolidated. This cooperative adaptive behavior was commonly observed if the number of genes involved was larger than the order of ten. These results have implications in the collective responses of gene expression networks in microarray measurements of yeast Saccharomyces cerevisiae and the significance to the biological homeostasis of systems with many components.     

Anoxic Responses of Seedling Roots of Rice Cultivars Varying in Tolerance to Submergence

Differences in tolerance to submergence and anoxia exhibited by cultivar-specific rice (Oryza sativa L.) extend to the primary root tips and axes of 3-day-old seedlings. This paper considers the physiological mechanisms which might account for rice root intolerance to anoxia, particularly those implicated in pH regulation and sugar metabolism in relation to hypoxic acclimation. Hypoxic treatment and the presence of glucose during anoxia did not permit root tips and axes of intolerant cultivars to survive 24-h anoxia. The absence of typical glycolytic and fermentative enzyme induction together with no improvement of ethanol production and energy status during anoxia suggest that intolerant cultivars are not capable of hypoxic acclimation at the level of energy and sugar metabolism. However, root tip survival was enhanced in buffered medium after hypoxic treatment, suggesting a relationship between hypoxic treatment and improved pH regulation.     

Apical Dominance in the Tomato: Some Further Observations on Isogenic Lines Showing Varying Degrees of Side-shoot Development

A study has been made of the distribution of substances resemblingindol-3-ylacetic acid (IAA), abscisic acid (ABA) and cytokinin-likesubstances in the stem tissue of Craigella tomato plants ascompared with that found in two isogenic lines of this variety,Craigella Blind (blbl) and Craigella Lateral Suppressor (lsls),in both of which side shoot growth is suppressed to varyingdegrees. There was no evidence to suggest that the distributionof these hormones in the stem had any association with the differentpatterns of side shoot development of the three types, thoughsome of the lateral suppressor plants which exhibited only partialbud inhibition did show a relation between high auxin and abscisicacid levels and lack of side shoot development from the centralnodes of the shoot. Decapitation led to a stimulation of bud outgrowth from allnodes of the Craigella plants but the lateral suppressor plantsremained inhibited. The blind plants were found to initiatebud primordia at the cotyledonary nodes only when the severedapex was replaced by exogenous IAA. The results are discussed in relation to our knowledge of themechanisms controlling apical dominance in the tomato. Lycopersicon esculentumL, tomato, apical dominance, growth regulation, indol-3-ylacetic acid, abscisic acid, cytokinins     

Photopigment,Absorption, and Growth Responses of Marine Cryptophytes to Varying Spectral Irradiance

The underwater light field of lakes, estuaries, and oceans may vary greatly in spectral composition. Phytoplankton in these environments must contain pigments that absorb the available colors of light. If spectral quality changes, acclimation to the new spectral environment would confer an ecological advantage in terms of photosynthesis and growth. Here, we explored the capacity of eight marine cryptophytes to adjust pigmentation in response to changes in spectral irradiance and related effects on light absorption, photosynthetically useable radiation (PUR), and growth rate. The pigment composition of all species changed in some way in response to shifts in spectral irradiance, but not all pigment changes could be considered advantageous in the context of chromatic acclimation. For most species, absorption by chl-a and chl-c₂ resulted in highest absorption in the blue region, highest PUR values for blue-light grown cells, and highest growth rates in blue light. The exception was Chroomonas mesostigmatica (CCMP 1168), which contains a high percentage of Cryptophyte-Phycocyanin (Cr-PC) 645, absorbs strongly in the orange-to-red region of the spectrum, and grew fastest under red light. The position and magnitude of the maximum and secondary absorption peak of Cr-PC 569, the phycobiliprotein pigment of Hemiselmis cryptochromatica, varied with spectral irradiance. The underlying cause remains unknown, but may represent a mechanism by which cryptophytes optimize photon capture.     

Resistance Responses of Potato to Vesicular-Arbuscular Mycorrhizal Fungi under Varying Abiotic Phosphorus Levels

In mycorrhizal symbioses, susceptibility of a host plant to infection by fungi is influenced by environmental factors, especially the availability of soil phosphorus. This study describes morphological and biochemical details of interactions between a vesicular-arbuscular mycorrhizal (VAM) fungus and potato (Solanum tuberosum L. cv Russet Burbank) plants, with a particular focus on the physiological basis for P-induced resistance of roots to infection. Root infection by the VAM fungus Glomus fasciculatum ([Thaxt. sensu Gerdemann] Gerdemann and Trappe) was extensive for plants grown with low abiotic P supply, and plant biomass accumulation was enhanced by the symbiosis. The capacity of excised roots from P-deficient plants to produce ethylene in the presence or absence of exogenous 1-amino cyclopropane-1-carboxylic acid (ACC) was markedly reduced by VAM infection. This apparent inhibition of ACC oxidase (ACC_ox) activity was localized to areas containing infected roots, as demonstrated in split-root studies. Furthermore, leachate from VAM roots contained a potent water-soluble inhibitor of ethylene generation from exogenous ACC by nonmycorrhizal (NM) roots. The leachate from VAM-infected roots had a higher concentration of phenolics, relative to that from NM roots. Moreover, the rates of ethylene formation and phenolic concentration in leachates from VAM roots were inversely correlated, suggesting that this inhibitor may be of a phenolic nature. The specific activity of extracellular peroxidase recovered in root leachates was not stimulated by VAM infection, although activity on a fresh weight basis was significantly enhanced, reflecting the fact that VAM roots had higher protein content than NM roots. Polyphenol oxidase activity of roots did not differ between NM and VAM roots. These results characterize the low resistance response of P-deficient plants to VAM infection. When plants were grown with higher abiotic P supply, the relative benefit of the VAM symbiosis to plant growth decreased and root infection was lower. The in vivo ACC_ox activity was also greater in roots of plants grown on high levels of P compared with those grown on low levels, although the influence of VAM infection was partially to counteract the nutritional effect of P on ACC_ox activity. Similar to ACC_ox activity, extracellular peroxidase activity of roots increased linearly with increasing abiotic P supply, thus indicating a greater potential for resistance to VAM infection. These findings suggest that VAM fungi may alter phenolic metabolism of roots so as to hinder ethylene production and the root's ability to invoke a defense response. Raising the abiotic P supply to plants at least partially restores the capacity of roots to produce ethylene and may, in this way, increase the root's resistance to VAM infection.     

Spatially Pooled Contrast Responses Predict Neural and Perceptual Similarity of Naturalistic Image Categories

The visual world is complex and continuously changing. Yet, our brain transforms patterns of light falling on our retina into a coherent percept within a few hundred milliseconds. Possibly, low-level neural responses already carry substantial information to facilitate rapid characterization of the visual input. Here, we computationally estimated low-level contrast responses to computer-generated naturalistic images, and tested whether spatial pooling of these responses could predict image similarity at the neural and behavioral level. Using EEG, we show that statistics derived from pooled responses explain a large amount of variance between single-image evoked potentials (ERPs) in individual subjects. Dissimilarity analysis on multi-electrode ERPs demonstrated that large differences between images in pooled response statistics are predictive of more dissimilar patterns of evoked activity, whereas images with little difference in statistics give rise to highly similar evoked activity patterns. In a separate behavioral experiment, images with large differences in statistics were judged as different categories, whereas images with little differences were confused. These findings suggest that statistics derived from low-level contrast responses can be extracted in early visual processing and can be relevant for rapid judgment of visual similarity. We compared our results with two other, well- known contrast statistics: Fourier power spectra and higher-order properties of contrast distributions (skewness and kurtosis). Interestingly, whereas these statistics allow for accurate image categorization, they do not predict ERP response patterns or behavioral categorization confusions. These converging computational, neural and behavioral results suggest that statistics of pooled contrast responses contain information that corresponds with perceived visual similarity in a rapid, low-level categorization task.     

Comprehensive Comparison of Multiple-Detector Computed Tomography and Dynamic Magnetic Resonance Imaging in the Diagnosis of Hepatocellular Carcinoma with Varying Degrees of Fibrosis

Methods841 patients with liver tumor who had liver CT or dynamic MRI examinations followed by surgical resection were included in the study. We defined typical HCC imaging characteristics as early enhancement in the artery phase and early washout in the venous phase. The tumor size was recorded based on pathological examination after surgery. The pathologic fibrosis score was verified by the METAVIR scoring classification.ResultsAmong the 841 patients, 756 underwent liver CT and 204 underwent dynamic liver MRI before surgery. The etiologies of chronic liver disease included hepatitis B virus, hepatitis C virus, hepatitis B and C virus, and non-hepatitis B or C virus. The sensitivity and accuracy of liver CT or MRI for HCC diagnosis was approximately 80%~90%. Liver CT had a diagnostic accuracy for HCC similar to that of dynamic MRI, and liver fibrosis stage did not influence their diagnostic efficacies.ConclusionsThe application of 4-phase dynamic CT and MRI exhibit similar diagnostic accuracy for hepatocellular carcinoma, in tumors of sizes 1 to 2 cm and >2 cm. Liver fibrosis status did not affect the diagnostic accuracy of liver CT or MRI for HCC. The AASLD and EASL restrictions of dynamic imaging studies for HCC diagnosis to cirrhotic patients alone are unnecessary.     

Measures of Stability (Trait) and Mutability (State) of Binary Responses in Pre-post-treatment Fourfold Tables

For the discussion of binary responses in pre-post-treatment we define new, simple measures for the stability (Trait) and mutability (State) of the responses, which have very nice and simple properties. We show the important fact that under certain conditions these two measures are uncorrelated. Because of the simplicity of the measures we derive the exact and limit distributions for testing the one respectively the two sample case.     

车八岭保护区及其邻近地区的木兰科植物种群及其保护现状

报道了广东省始兴县车八岭国家级自然保护区及其邻近地区木兰科植物种群特点及保护现状。木兰科植物通常位于人为破坏较轻 ,林相保存较好 ,以壳斗科、樟科、茶科为主要建群种的中亚热带常绿阔叶林中。共设置了 9个面积为 4 0 0 m2的样方。在样方中共记录了 3种木兰科植物 :观光木 ( Tsoongiodendron odor-um Chun)、深山含笑 ( Michelia maudiae Dunn)和金叶含笑 ( M.foveolata Merr.ex Dandy)。其中 ,深山含笑的种群较大 ,呈稳定结构 ,但主要局限于保护区内保护较好的地域 ;金叶含笑种群面临濒危 ,种群小 ,在保护区呈零星分布 ;观光木的分布区域相对较广 ,在保护区内外均见分布 ,但种群较小 ,特别是在保护区外的种群 ,由于人为的干扰 ,种群在急剧减少。大多数木兰科植物的种群在原生境均表现出自然更新不良 ,必须加以保护。分析了影响车八岭及其邻近地区木兰科植物种群及其群落发展的主要限制因素 ,建议加强自然保护知识的宣传和木兰科植物的人工保育 ,促进该区域木兰科植物资源的管理和发展     

Polyfunctional T Cell Responses in Children in Early Stages of Chronic Trypanosoma cruzi Infection Contrast with Monofunctional Responses of Long-term Infected Adults

Background

Adults with chronic Trypanosoma cruzi exhibit a poorly functional T cell compartment, characterized by monofunctional (IFN-γ-only secreting) parasite-specific T cells and increased levels of terminally differentiated T cells. It is possible that persistent infection and/or sustained exposure to parasites antigens may lead to a progressive loss of function of the immune T cells.

Methodology/Principal Findings

To test this hypothesis, the quality and magnitude of T. cruzi-specific T cell responses were evaluated in T. cruzi-infected children and compared with long-term T. cruzi-infected adults with no evidence of heart failure. The phenotype of CD4⁺ T cells was also assessed in T. cruzi-infected children and uninfected controls. Simultaneous secretion of IFN-γ and IL-2 measured by ELISPOT assays in response to T. cruzi antigens was prevalent among T. cruzi-infected children. Flow cytometric analysis of co-expression profiles of CD4⁺ T cells with the ability to produce IFN-γ, TNF-α, or to express the co-stimulatory molecule CD154 in response to T. cruzi showed polyfunctional T cell responses in most T. cruzi-infected children. Monofunctional T cell responses and an absence of CD4⁺TNF-α⁺-secreting T cells were observed in T. cruzi-infected adults. A relatively high degree of activation and differentiation of CD4⁺ T cells was evident in T. cruzi-infected children.

Conclusions/Significance

Our observations are compatible with our initial hypothesis that persistent T. cruzi infection promotes eventual exhaustion of immune system, which might contribute to disease progression in long-term infected subjects.     

不同寡聚形式的Aβ42与细胞膜作用显示毒性差异

β-淀粉样蛋白（β-amyloid peptide, Aβ）与神经细胞膜的相互作用是阿尔茨海默症（Alzheimer’s disease, AD）发病的重要事件,但不同寡聚形式的Aβ与细胞膜相互作用的差异仍缺乏直接比较。本文通过膜天平、透射电子显微镜、Thioflavin T(ThT)和细胞毒性实验等方法,检测Aβ42单体、ADDL、原纤维等形式的β-淀粉样蛋白与磷脂膜的作用方式,分析不同形式淀粉样蛋白对细胞的毒性作用。结果显示,（1）单层膜的实验数据可以判断Aβ42单体和寡聚体插膜能力存在差异,Aβ42单体能插入磷脂单层膜内,而Aβ42 ADDL不具备插膜能力;（2）透射电镜和ThT荧光检测,定性定量地分析出不同聚集形式的Aβ42具有不同的纤维化能力,Aβ42单体纤维化能力最强,而Aβ42原纤维的纤维化能力次之,Aβ42ADDL很难形成纤维;（3）Aβ42单体细胞毒性较弱,而Aβ42 ADDL和原纤维的细胞毒性较强。由以上结果可以得出结论：在磷脂膜存在的条件下,Aβ42单体可以插入膜内并迅速形成无毒性的Aβ42纤维,因此,细胞毒性较弱。而ADDL及原纤维不能插入膜内,纤维化能力较弱,从而以寡聚体的形式发挥细胞毒性。将单体、ADDL及原纤维形式的Aβ42与细胞膜相互作用进行分析,将为Aβ42在AD中的毒性机制研究提供一定的参考。但各种寡聚体入胞的方式及毒性机制仍需要进一步研究。     

Simulation of Neuronal Responses Defining Depth Order and Contrast Polarity at Illusory Contours in Monkey Area V2

Neurophysiological, brain imaging, and perceptual studies in animals and humans suggest that illusory (occluding) contours are represented at an early level of visual cortical processing. Comparatively little is known about the mechanisms defining the depth order and the brightness illusion associated with such contours. Baumann et al. (1997) found neurons in area V2 of the alert monkey that signaled not only illusory contours but also the figure-ground direction that human observers perceive at such contours. The majority of these neurons showed this property independent stimulus contrast; a small minority preferred a certain combination of figure-ground direction and contrast polarity at these contours. In this article, we simulate the responses of these neurons by means of a grouping mechanism that uses occlusion cues (line-ends, corners) to define figure-ground direction and contrast polarity at such contours.     

How Far Stationary Contrast Boundaries Can Be Away to Elicit Behavioral Responses in Praying Mantis

The aim of the present study was to investigate the distance at which vertical black and white stripes (contrast boundaries) elicit object-related behavioral responses in 6th instar and adults of the praying mantis Mantis religiosa. The mantids reacted when the contrast boundaries were not further away than 60 cm. However, with increasing distance (>20 cm), the contrast boundaries became progressively less significant for the mantids. Jumps/preparation of jumps could be observed between 10 and 30 cm. The results are supportive for distance measurement of up to 20–30 cm, which corresponds to distance accessible for the insect. It seems that image motion cues induced by peering movements play an important role.     

A New Extension of the Binomial Error Model for Responses to Items of Varying Difficulty in Educational Testing and Attitude Surveys

We put forward a new item response model which is an extension of the binomial error model first introduced by Keats and Lord. Like the binomial error model, the basic latent variable can be interpreted as a probability of responding in a certain way to an arbitrarily specified item. For a set of dichotomous items, this model gives predictions that are similar to other single parameter IRT models (such as the Rasch model) but has certain advantages in more complex cases. The first is that in specifying a flexible two-parameter Beta distribution for the latent variable, it is easy to formulate models for randomized experiments in which there is no reason to believe that either the latent variable or its distribution vary over randomly composed experimental groups. Second, the elementary response function is such that extensions to more complex cases (e.g., polychotomous responses, unfolding scales) are straightforward. Third, the probability metric of the latent trait allows tractable extensions to cover a wide variety of stochastic response processes.