Photosensory Adaptation in Plants

Photosensory adaptation (range adjustment) is of great importance in plants (including fungi and various microorganisms) that operate in large intensity ranges. The adaptation mechanisms of plants have some features in common with those of vertebrates and invertebrates. As with those systems, plants have biphasic exponential dark-adaptation kinetics, that are much slower than the corresponding light adaptation kinetics. One needs to distinguish between sensor adaptation, which regulates range adjustment, and effector adaptation (habituation), which regulates the motor apparatus of the organism (flagellar movement or cell wall growth). In Phycomyces, and perhaps Stentor, sensor adaptation is mediated by the photoreceptor system. In contrast to vertebrates and invertebrates, dark adaptation can be controlled in some plants by special photoreceptors. In Phycomyces, these can be either photo-products of the actinic photoreceptor(s) or not yet identified receptor pigments. In higher plants phytochrome can alter the state of adaptation.     

Testing Local Host Adaptation and Phenotypic Plasticity in a Herbivore When Alternative Related Host Plants Occur Sympatrically

Host race formation in phytophagous insects can be an early stage of adaptive speciation. However, the evolution of phenotypic plasticity in host use is another possible outcome. Using a reciprocal transplant experiment we tested the hypothesis of local adaptation in the aphid Brevicoryne brassicae. Aphid genotypes derived from two sympatric host plants, Brassica oleracea and B. campestris, were assessed in order to measure the extent of phenotypic plasticity in morphological and life history traits in relation to the host plants. We obtained an index of phenotypic plasticity for each genotype. Morphological variation of aphids was summarized by principal components analysis. Significant effects of recipient host on morphological variation and life history traits (establishment, age at first reproduction, number of nymphs, and intrinsic growth rate) were detected. We did not detected genotype × host plant interaction; in general the genotypes developed better on B. campestris, independent of the host plant species from which they were collected. Therefore, there was no evidence to suggest local adaptation. Regarding plasticity, significant differences among genotypes in the index of plasticity were detected. Furthermore, significant selection on PC1 (general aphid body size) on B. campestris, and on PC1 and PC2 (body length relative to body size) on B. oleracea was detected. The elevation of the reaction norm of PC1 and the slope of the reaction norm for PC2 (i.e., plasticity) were under directional selection. Thus, host plant species constitute distinct selective environments for B. brassicae. Aphid genotypes expressed different phenotypes in response to the host plant with low or nil fitness costs. Phenotypic plasticity and gene flow limits natural selection for host specialization promoting the maintenance of genetic variation in host exploitation.     

Transarterial Chemoembolization in Combination with Local Therapies for Hepatocellular Carcinoma: A Meta-Analysis

Background

In previous randomized trials, transarterial chemoembolization (TACE) has shown an improvement of survival rate in hepatocellular carcinoma (HCC) when combined with radiofrequency ablation (RFA), percutaneous ethanol injection (PEI) or other therapies. The aim of this meta-analysis was to evaluate the effectiveness of combination therapy of TACE with RFA, PEI, radiotherapy (RT), three-dimensional conformal radiation therapy (3D-CRT) or High-Intensity Focused Ultrasound (HIFU).

Methods

Randomized or nonrandomized studies comparing TACE combined with RFA, PEI, RT, 3D-CRT or HIFU with TACE alone for HCC were included. Meta-analysis was performed using a fix-effects model in RCTs and a random-effects model among the observational studies.

Results

10 randomized trials and 18 observational studies matched the selection criteria, including 2497 patients (682 in RCTs, 1815 in non-RCTs). Meta-analysis of RCTs showed that the combination of TACE and PEI ((RR)_{1 -}year=1.10, 95%CI=0.99-1.22, p=0.073; (RR)_{3 -}year=2.32, 95%CI=1.52-3.53, p<0.001), TACE+RT ((RR)_{1 -}year=1.37, 95%CI=1.11-1.70, p=0.004; (RR)_{3 -}year=2.32, 95%CI=1.44-3.75, p=0.001) were associated with higher survival rates. The results of observational studies were in good consistency with that of RCTs. Furthermore, TACE plus 3D-CRT ((RR)_{1 -}year=1.22, 95%CI=1.06-1.41, p=0.005; (RR)_{3 -}year=2.05, 95%CI=1.48-2.84, p<0.001) and TACE plus HIFU ((RR)_{1 -}year=1.16, 95%CI=1.01-1.33, p=0.033; (RR)_{3 -}year=1.66, 95%CI=1.12-2.45, p=0.011) have introduced marked survival benefit when pooling results from observational studies.

Conclusions

This meta-analysis demonstrated that TACE combined with local treatments, especially PEI, HIFU or 3D-CRT could improve the overall survival status than performing TACE alone. Importantly, these results need to be validated in further high-quality clinical trials.     

Robust Identification of Local Adaptation from Allele Frequencies

Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of “standardized allele frequencies” that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to F_ST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools—a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org.     

Phylogenetic Meta-Analysis of the Functional Traits of Clonal Plants Foraging in Changing Environments

Foraging behavior, one of the adaptive strategies of clonal plants, has stimulated a tremendous amount of research. However, it is a matter of debate whether there is any general pattern in the foraging traits (functional traits related to foraging behavior) of clonal plants in response to diverse environments. We collected data from 97 published papers concerning the relationships between foraging traits (e.g., spacer length, specific spacer length, branch intensity and branch angle) of clonal plants and essential resources (e.g., light, nutrients and water) for plant growth and reproduction. We incorporated the phylogenetic information of 85 plant species to examine the universality of foraging hypotheses using phylogenetic meta-analysis. The trends toward forming longer spacers and fewer branches in shaded environments were detected in clonal plants, but no evidence for a relation between foraging traits and nutrient availability was detected, except that there was a positive correlation between branch intensity and nutrient availability in stoloniferous plants. The response of the foraging traits of clonal plants to water availability was also not obvious. Additionally, our results indicated that the foraging traits of stoloniferous plants were more sensitive to resource availability than those of rhizomatous plants. In consideration of plant phylogeny, these results implied that the foraging traits of clonal plants (notably stoloniferous plants) only responded to light intensity in a general pattern but did not respond to nutrient or water availability. In conclusion, our findings on the effects of the environment on the foraging traits of clonal plants avoided the confounding effects of phylogeny because we incorporated phylogeny into the meta-analysis.     

Nitrogen Containing Compounds and Adaptation of Plants to Salinity Stress

A number of nitrogen containing compounds (NCC) accumulate in plants exposed to salinity stress. The most frequently accumulating NCC include amino acids, amids, imino acids, proteins, quarternary ammonium compounds (QAC) and polyamines. The specific NCC that accumulate in saline environment vary with the plant species. Osmotic adjustment, protection of cellular macromolecules, storage form of nitrogen, maintaining cellular pH, detoxification of the cells, and scavenging of free radicals are proposed functions for these compounds under stress conditions. NCC accumulation is usually correlated with plant salt tolerance, even though this correlation is based on untested hypotheses.     

高山植物对其环境的生理生态适应性研究进展

高山林线植物(林木和草本)由于生长环境特殊而形成其独特的适应环境的生理生态特性.该文对近年来国内外有关高山植物、特别是林线林木在形态解剖结构、光合作用、养分利用和碳水化合物及抗氧化系统等方面对高山环境的生理生态适应性的研究进展进行综述,指出了林线树种生理生态适应性研究方面的不足,并提出了今后高山林线树种生理生态需要研究的方向,以期为研究气候变化下高山林线植物的应对策略和适应机制提供参考.     

Meta-Analysis of the Reduction of Norovirus and Male-Specific Coliphage Concentrations in Wastewater Treatment Plants

Human norovirus (NoV) is the leading cause of foodborne illness in the United States and Canada. Wastewater treatment plant (WWTP) effluents impacting bivalve mollusk-growing areas are potential sources of NoV contamination. We have developed a meta-analysis that evaluates WWTP influent concentrations and log₁₀ reductions of NoV genotype I (NoV GI; in numbers of genome copies per liter [gc/liter]), NoV genotype II (NoV GII; in gc/liter), and male-specific coliphage (MSC; in number of PFU per liter), a proposed viral surrogate for NoV. The meta-analysis included relevant data (2,943 measurements) reported in the scientific literature through September 2013 and previously unpublished surveillance data from the United States and Canada. Model results indicated that the mean WWTP influent concentration of NoV GII (3.9 log₁₀ gc/liter; 95% credible interval [CI], 3.5, 4.3 log₁₀ gc/liter) is larger than the value for NoV GI (1.5 log₁₀ gc/liter; 95% CI, 0.4, 2.4 log₁₀ gc/liter), with large variations occurring from one WWTP to another. For WWTPs with mechanical systems and chlorine disinfection, mean log₁₀ reductions were −2.4 log₁₀ gc/liter (95% CI, −3.9, −1.1 log₁₀ gc/liter) for NoV GI, −2.7 log₁₀ gc/liter (95% CI, −3.6, −1.9 log₁₀ gc/liter) for NoV GII, and −2.9 log₁₀ PFU per liter (95% CI, −3.4, −2.4 log₁₀ PFU per liter) for MSCs. Comparable values for WWTPs with lagoon systems and chlorine disinfection were −1.4 log₁₀ gc/liter (95% CI, −3.3, 0.5 log₁₀ gc/liter) for NoV GI, −1.7 log₁₀ gc/liter (95% CI, −3.1, −0.3 log₁₀ gc/liter) for NoV GII, and −3.6 log₁₀ PFU per liter (95% CI, −4.8, −2.4 PFU per liter) for MSCs. Within WWTPs, correlations exist between mean NoV GI and NoV GII influent concentrations and between the mean log₁₀ reduction in NoV GII and the mean log₁₀ reduction in MSCs.     

Local Scale Comparisons of Biodiversity as a Test for Global Protected Area Ecological Performance: A Meta-Analysis

Terrestrial protected areas (PAs) are cornerstones of global biodiversity conservation. Their efficacy in terms of maintaining biodiversity is, however, much debated. Studies to date have been unable to provide a general answer as to PA conservation efficacy because of their typically restricted geographic and/or taxonomic focus, or qualitative approaches focusing on proxies for biodiversity, such as deforestation. Given the rarity of historical data to enable comparisons of biodiversity before/after PA establishment, many smaller scale studies over the past 30 years have directly compared biodiversity inside PAs to that of surrounding areas, which provides one measure of PA ecological performance. Here we use a meta-analysis of such studies (N = 86) to test if PAs contain higher biodiversity values than surrounding areas, and so assess their contribution to determining PA efficacy. We find that PAs generally have higher abundances of individual species, higher assemblage abundances, and higher species richness values compared with alternative land uses. Local scale studies in combination thus show that PAs retain more biodiversity than alternative land use areas. Nonetheless, much variation is present in the effect sizes, which underscores the context-specificity of PA efficacy.     

From Local Adaptation to Ecological Speciation in Copepod Populations from Neighboring Lakes

Continental copepods have been derived from several independent invasive events from the sea, but the subsequent evolutionary processes that account for the current diversity in lacustrine environments are virtually unknown. Salinity is highly variable among lakes and constitutes a source of divergent selection driving potential reproductive isolation. We studied four populations of the calanoid copepod Leptodiaptomus cf. sicilis inhabiting four neighboring lakes with a common history (since the Late Pleistocene) located in the Oriental Basin, Mexico; one lake is shallow and varies in salinity periodically (1.4–10 g L^-1), while three are deep and permanent, with constant salinity (0.5, 1.1 and 6.5 g L^-1, respectively). We hypothesized that (1) these populations belong to a different species than L. sicilis sensu stricto and (2) are experiencing ecologically based divergence due to salinity differences. We assessed morphological and molecular (mtDNA) COI variation, as well as fitness differences and tests of reproductive isolation. Although relationships of the Mexican populations with L. sicilis s.s. could not be elucidated, we identified a clear pattern of divergent selection driven by salinity conditions. The four populations can still be considered a single biological species (sexual recognition and hybridization are still possible in laboratory conditions), but they have diverged into at least three different phenotypes: two locally adapted, specialized in the lakes of constant salinity (saline vs. freshwater), and an intermediate generalist phenotype inhabiting the temporary lake with fluctuating salinity. The specialized phenotypes are poorly suited as migrants, so prezygotic isolation due to immigrant inviability is highly probable. This implication was supported by molecular evidence that showed restricted gene flow, persistence of founder events, and a pattern of allopatric fragmentation. This study showed how ecologically based divergent selection may explain diversification patterns in lacustrine copepods.     

Personality Consistency in Dogs: A Meta-Analysis

Personality, or consistent individual differences in behavior, is well established in studies of dogs. Such consistency implies predictability of behavior, but some recent research suggests that predictability cannot be assumed. In addition, anecdotally, many dog experts believe that ‘puppy tests’ measuring behavior during the first year of a dog''s life are not accurate indicators of subsequent adult behavior. Personality consistency in dogs is an important aspect of human-dog relationships (e.g., when selecting dogs suitable for substance-detection work or placement in a family). Here we perform the first comprehensive meta-analysis of studies reporting estimates of temporal consistency of dog personality. A thorough literature search identified 31 studies suitable for inclusion in our meta-analysis. Overall, we found evidence to suggest substantial consistency (r = 0.43). Furthermore, personality consistency was higher in older dogs, when behavioral assessment intervals were shorter, and when the measurement tool was exactly the same in both assessments. In puppies, aggression and submissiveness were the most consistent dimensions, while responsiveness to training, fearfulness, and sociability were the least consistent dimensions. In adult dogs, there were no dimension-based differences in consistency. There was no difference in personality consistency in dogs tested first as puppies and later as adults (e.g., ‘puppy tests’) versus dogs tested first as puppies and later again as puppies. Finally, there were no differences in consistency between working versus non-working dogs, between behavioral codings versus behavioral ratings, and between aggregate versus single measures. Implications for theory, practice, and future research are discussed.     

From Local Checklists to Online Identification Portals: A Case Study on Vascular Plants

Checklists, the result of time-consuming exploration and painstaking bibliographic research, can be easily converted into online databases, which have the advantage of being updatable online in real time, and of reaching a much wider audience. However, thousands of local checklists (Natural Parks, protected areas, etc.) are still available on paper only, and most of those published online appear as dry lists of latin names, which strongly reduces their outreach for a wider audience. The University of Trieste has recently started the publication of several local checklists in a way that may be more appealing for the general public, by linking species'' names to archives of digital resources, and especially to digital identification tools produced by software FRIDA (FRiendly IDentificAtion). The query interfaces were developed on the basis of feedback from a wide range of users. The result is no longer a simple list of names accessible on the Web, but a veritable multimedial, interactive portal to the biodiversity of a given area. This paper provides an example of how relevant added value can be given to local lists of taxa by embedding them in a complex system of biodiversity-related resources, making them usable for a much wider audience than a restricted circle of specialists, as testified by the almost 1.000.000 unique visitors reached in 2014. A critical mass of digital resources is also put at disposal of the scientific community by releasing them under a Creative Commons license.     

Micronutrients in HIV: A Bayesian Meta-Analysis

BackgroundApproximately 28.5 million people living with HIV are eligible for treatment (CD4<500), but currently have no access to antiretroviral therapy. Reduced serum level of micronutrients is common in HIV disease. Micronutrient supplementation (MNS) may mitigate disease progression and mortality.ObjectivesWe synthesized evidence on the effect of micronutrient supplementation on mortality and rate of disease progression in HIV disease.MethodsWe searched MEDLINE, EMBASE, the Cochrane Central, AMED and CINAHL databases through December 2014, without language restriction, for studies of greater than 3 micronutrients versus any or no comparator. We built a hierarchical Bayesian random effects model to synthesize results. Inferences are based on the posterior distribution of the population effects; posterior distributions were approximated by Markov chain Monte Carlo in OpenBugs.ConclusionsMNS significantly and substantially slows disease progression in HIV+ adults not on ARV, and possibly reduces mortality. Micronutrient supplements are effective in reducing progression with a posterior probability of 97.9%. Considering MNS low cost and lack of adverse effects, MNS should be standard of care for HIV+ adults not yet on ARV.     

A Meta-Analysis of Oxidative Stress Markers in Depression

ObjectStudies have suggested that depression was accompanied by oxidative stress dysregulation, including abnormal total antioxidant capacity (TAC), antioxidants, free radicals, oxidative damage and autoimmune response products. This meta-analysis aims to analyse the clinical data quantitatively by comparing the oxidative stress markers between depressed patients and healthy controls.MethodsA search was conducted to collect the studies that measured the oxidative stress markers in depressed patients. Studies were searched in Embase, Medline, PsychINFO, Science direct, CBMDisc, CNKI and VIP from 1990 to May 2015. Data were subjected to meta-analysis by using a random effects model for examining the effect sizes of the results. Bias assessments, heterogeneity assessments and sensitivity analyses were also conducted.Results115 articles met the inclusion criteria. Lower TAC was noted in acute episodes (AEs) of depressed patients (p<0.05). Antioxidants, including serum paraoxonase, uric acid, albumin, high-density lipoprotein cholesterol and zinc levels were lower than controls (p<0.05); the serum uric acid, albumin and vitamin C levels were increased after antidepressant therapy (p<0.05). Oxidative damage products, including red blood cell (RBC) malondialdehyde (MDA), serum MDA and 8-F₂-isoprostanes levels were higher than controls (p<0.05). After antidepressant medication, RBC and serum MDA levels were decreased (p<0.05). Moreover, serum peroxide in free radicals levels were higher than controls (p<0.05). There were no differences between the depressed patients and controls for other oxidative stress markers.ConclusionThis meta-analysis supports the facts that the serum TAC, paraoxonase and antioxidant levels are lower, and the serum free radical and oxidative damage product levels are higher than controls in depressed patients. Meanwhile, the antioxidant levels are increased and the oxidative damage product levels are decreased after antidepressant medication. The pathophysiological relationships between oxidative stress and depression, and the potential benefits of antioxidant supplementation deserve further research.     

葡萄幼苗在温度胁迫交叉适应过程中对水杨酸的应答

在温度锻炼诱导葡萄幼苗对交叉温度逆境的适应过程中叶片内源SA变化的结果表明,0℃低温胁迫期间,葡萄幼苗叶片细胞膜系统受到严重伤害,丙二醛(MDA)含量明显升高;此时自由态SA含量呈波动性变化,并随着胁迫进程的延长,内源SA含量明显低于正常叶片水平。而经过高温锻炼的幼苗,在低温胁迫初期自由态SA含量迅速达到一个高峰,之后回落并保持在正常叶片的SA水平,MDA含量也相应降低且相对稳定。结合态SA的变化相对较平稳,并且总SA含量变化趋势与自由态SA含量的变化趋势相吻合。在45℃高温胁迫期间,经过低温锻炼的幼苗的上述各项指标的变化规律与经过高温锻炼的幼苗在低温胁迫期间的变化趋势相似。