The co-evolution of phytoplankton and trace element cycles in the oceans

The composition of the oceans and of its biota have influenced each other through Earth's history. Of all the biologically essential elements, nitrogen is the only one whose seawater concentration is clearly controlled biologically; this is presumably the main reason why the stoichiometry of nitrogen (defined as its mol ratio to phosphorus), but not that of the trace nutrients manganese, iron, cobalt, nickel, copper, zinc and cadmium, is the same in seawater and in the plankton. Like the major nutrients, the trace nutrients are depleted in surface seawater as a result of quasi-complete utilization by the biota. This is made possible in part by the ability of marine phytoplankton to replace one trace metal by another in various biochemical functions. This replacement also results in an equalization of the availability of most essential trace metals in surface seawater. The difference in the stoichiometric composition of the plankton and of deep seawater, which is the dominant source of new nutrients to the surface, indicates that some nutrients are likely recycled with different efficiencies in the photic zone. The difference in the composition of the ocean and its biota provides insight into the coupling of biochemistry and biogeochemistry in seawater.     

Environmental variability drives phytoplankton assemblage persistence in a subtropical reservoir

Temporal changes of assemblages may result from environmental variability and reflect seasonal dynamics of their ecosystem. In the subtropics, the hydrological regime is usually characterized by well‐defined wet and dry seasons, regulating discharge and influencing a series of environmental variables that affect phytoplankton persistence. Therefore, we may expect that dry seasons are environmentally more stable than wet seasons. We analysed interannual phytoplankton assemblage variability (or, inversely, persistence) in a subtropical reservoir sampled every austral summer and winter during 5 years. We tested (i) if phytoplankton assemblage structure differed between the dry (summer) and wet (winter) seasons; (ii) if assemblage persistence differed between the seasons; (iii) if assemblage persistence was related to environmental stability; and (iv) if assemblage dissimilarity increased over time. Phytoplankton assemblages differed between the summer and winter seasons. Winter indicator species were mostly Bacillariophyceae or Cryptophyceae, whereas Cyanophyceae and Chlorophyceae taxa were more frequent and abundant in summer. Assemblages in the dry season were more persistent among years than those occurring during rainy periods. Similarly, environmental variability tended to be lower among dry than among rainy seasons. The relation between the phytoplankton temporal cycle and the temporal patterns of environmental variability supports our prediction that high environmental stability results in more persistent assemblages. Assemblage dissimilarity increased as sampling years were farther apart, for both seasons. Additionally, assemblages in the rainy periods showed a more pronounced increase in dissimilarity, as their changes among years were less predictable. We found a clear temporal pattern and an increased dissimilarity over time in the phytoplankton assemblage structure. Unravelling these temporal patterns may improve our understanding of phytoplankton temporal dynamics, and may have implications for management and monitoring programs. High dissimilarity of assemblages among years, particularly among rainy periods, can obscure human impacts, and monitoring programs should take this into account.     

Temporal variability of phytoplankton in tropical lakes

Summary Temporal variability of ecological systems continues to receive theoretical and empirical attention but remains inadequately documented at low latitudes. Results of my comparative investigation of photosynthetic rates of phytoplankton in 6 equatiorial African lakes and similar information from 20 South American, Asian and African lakes studied by others provide the data for an assessment of the range of seasonal variability (expressed as coefficients of variation, CV) among tropical lakes. Sampling intervals varied from 1 week to 3 months and usually spanned at least one year. Within Africa the coefficient of variation ranged from 15% to 61%, and among all the lakes the coefficient of variation ranged from 15% to 86%. The Spearman rank correlation coefficient of the CV's of photosynthesis versus latitude is 0.24 and is not significant at the 0.05 level.Coefficients of variation of photosynthetic rates of phytoplankton in a diverse set of 45 temperate and arctic lakes ranged from 29% to 155% and were significantly different from the set of 26 tropical lakes by the Mann-Whitney U test. When all 71 lakes are compared, the Spearman rank correlation coefficient of CV's of photosynthesis versus latitude is 0.71 and is significant at the 0.0005 level.Three temporal patterns were recognized among tropical lakes. Most tropical lakes exhibit pronounced seasonal fluctuations that usually correspond with variations in rainfall, river discharges or vertical mixing. A second pattern occurs in lakes with muted fluctuations (coefficient of variation less than 20%) in which diel changes often exceed month to month changes. A third pattern is distinguished by an abrupt change from one persistent algal assemblage (i.e., extant for at least 10 generations) and level of photosynthetic activity to another persistent condition.     

Interannual variability in phytoplankton biomass and species composition in a subtropical reservoir

• 1 The interannual variability of the dominant phytoplankton populations is described in a subtropical reservoir in Queensland using weekly data for a 16-year period between 1978 and 1994. North Pine Dam, Brisbane, is in an area characterized by strong interannual variability in rainfall. This variability is linked to El Nino Southern Oscillation (ENSO) events. Between 1978 and 1994 periods of drought (during strong ENSO events) were interspersed by periods of flooding rains. Rainfall on the catchment and temperature and oxygen within the dam showed strong 40-day periodicities which also varied in strength interannually in response to ENSO events. Similar patterns of fluctuations in the 40-day periodicity have been found elsewhere in SE Australia. Seasonal cycles of stratification in the dam were a function of both hydrographic and hydrological events. Intermittent rain storms caused partial turnovers and large outflows. As much as 90% of the dam volume was exchanged in a single flood event.
• 2 The dominant phytoplankton species were similar to those frequently found in tropical and subtropical lakes and reservoirs. The phytoplankton community switched between cyanobacterial blooms (Cylindrospermopsis, Microcystis) during drought and falling water levels and diatom blooms (Aulacoseira) in response to inflows and seasonal turnovers. There appeared to be a subtle interaction between inflows, water column stability, the periodic overturns and the occurrence of the dominant species. All the dominant species showed long periods (2–4 years) of exponential increase or decrease superimposed on top of the seasonal fluctuations in abundance. These patterns of abundance led to marked interannual variability in the phytoplankton biomass. Climate variability had a major impact on the seasonal and interannual changes of the dominant phytoplankton species.
• 3 Phytoplankton biomass tended to be depressed for about 3 months after individual storm events but the data also displayed long-term lag effects (2–4 years) which destroyed any significant correlation between water residence time and biomass. Summer maxima of biomass dominated by cyanobacteria disappeared between 1985 and 1990 and were replaced by smaller winter peaks. The data presented here are not capable of unequivocally identifying the precise reason for these longer-term effects. Because of the implications for water quality management in subtropical and tropical reservoirs they warrant further study.

     

Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms

Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large‐scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual‐based structuring algorithms discern geographical structuring. Model‐based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.     

Receptor-mediated delivery of engineered nucleases for genome modification

Engineered nucleases, which incise the genome at predetermined sites, have a number of laboratory and clinical applications. There is, however, a need for better methods for controlled intracellular delivery of nucleases. Here, we demonstrate a method for ligand-mediated delivery of zinc finger nucleases (ZFN) proteins using transferrin receptor-mediated endocytosis. Uptake is rapid and efficient in established mammalian cell lines and in primary cells, including mouse and human hematopoietic stem-progenitor cell populations. In contrast to cDNA expression, ZFN protein levels decline rapidly following internalization, affording better temporal control of nuclease activity. We show that transferrin-mediated ZFN uptake leads to site-specific in situ cleavage of the target locus. Additionally, despite the much shorter duration of ZFN activity, the efficiency of gene correction approaches that seen with cDNA-mediated expression. The approach is flexible and general, with the potential for extension to other targeting ligands and nuclease architectures.     

The genome editing toolbox: a spectrum of approaches for targeted modification

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New tools for genome modification in human embryonic stem cells

Two recent papers outline improvements in gene editing technology that may facilitate the analysis of signaling networks important for development. The systems developed by both Thyagarajan and coworkers (Thyagarajan et al., 2007) in Nature Biotechnology, and Lombardo and colleagues (Lombardo et al., 2007) in Stem Cells, have the potential to advance our understanding of human embryonic stem cells.     

人工锌指核酸酶介导的基因组定点修饰技术

锌指核酸酶(ZFN)由锌指蛋白(ZFP)结构域和Fok I核酸内切酶的切割结构域人工融合而成,是近年来发展起来的一种可用于基因组定点改造的分子工具。ZFN可识别并结合特定的DNA序列,并通过切割这一序列的特定位点造成DNA的双链断裂(DSB)。在此基础上,人们可以对基因组的特定位点进行各种遗传操作,包括基因打靶、基因定点插入、基因修复等,从而能够方便快捷地对基因组实现靶向遗传修饰。这种新的基因组定点修饰方法的突出优势是适用性好,对物种没有选择性,并且可以在细胞和个体水平进行遗传操作。文章综述了ZFN技术的研究进展及应用前景,重点介绍ZFN的结构与作用机制、现有的靶点评估及锌指蛋白库的构建与筛选方法、基因组定点修饰的策略,以及目前利用这一技术已成功实现突变的物种及内源基因,为开展这一领域的研究工作提供参考。     

Atypically larger variability of resource allocation accounts for visual working memory deficits in schizophrenia

Working memory (WM) deficits have been widely documented in schizophrenia (SZ), and almost all existing studies attributed the deficits to decreased capacity as compared to healthy control (HC) subjects. Recent developments in WM research suggest that other components, such as precision, also mediate behavioral performance. It remains unclear how different WM components jointly contribute to deficits in schizophrenia. We measured the performance of 60 SZ (31 females) and 61 HC (29 females) in a classical delay-estimation visual working memory (VWM) task and evaluated several influential computational models proposed in basic science of VWM to disentangle the effect of various memory components. We show that the model assuming variable precision (VP) across items and trials is the best model to explain the performance of both groups. According to the VP model, SZ exhibited abnormally larger variability of allocating memory resources rather than resources or capacity per se. Finally, individual differences in the resource allocation variability predicted variation of symptom severity in SZ, highlighting its functional relevance to schizophrenic pathology. This finding was further verified using distinct visual features and subject cohorts. These results provide an alternative view instead of the widely accepted decreased-capacity theory and highlight the key role of elevated resource allocation variability in generating atypical VWM behavior in schizophrenia. Our findings also shed new light on the utility of Bayesian observer models to characterize mechanisms of mental deficits in clinical neuroscience.     

微生物基因组精简优化的研究进展

微生物基因组精简优化是构建合成生物学底盘细胞的重要策略.文中从基因组精简的整体设计出发,归纳了微生物的必需基因及其确定方法,重点介绍了各种微生物基因组精简策略,分析了多种基因组精简菌株的特点,充分展示了基因组精简优化在构建合成生物学底盘细胞中的重要作用.     

Irradiance-induced variability in light scatter from marine phytoplankton in culture

A series of laboratory experiments are reported that illustratethe response of beam attenuation ( = 660 nm) and single-celllight scatter ( = 488 nm) properties of several species of marinephytoplankton to light intensity. When unialgal cultures weresubjected to an increase in light intensity, the particle-scatteringcomponent of beam attenuation and near-forward single-cell lightscatter were found to increase rapidly in response. Cell abundanceincreased only slightly over the course of the experiments,leading to the conclusion that the response in beam attenuationwas due to irradiance-induced changes in the single-cell opticalproperties. The percent hourly increase in beam attenuation,normalized to cell abundance, and single-cell light scatterrangedfrom 5% for a culture of the coccolithophore Emiliania huxleyito 25% for a culture of Thalassiosira pseudonana. In a separateset of experiments, carbon-specific beam attenuation (c^*_c; thepaniculate material component of beam attenuation normalizedto the concentration of paniculate organic carbon) was foundto be species specific and, to some extent, sensitive to irradiance.The positive response in phytoplankton light scatter, both atthe population and at the single-cell level, to an increasein light intensity is similar to diet patterns in beam attenuationreported for the near-surface ocean. If a component of the observeddiel pattern in beam attenuation is due to irradiance-induced,carbon-independent optical variability in the phytoplanktonassemblage, as the results of the high-light experiments suggest,neglecting such variability can result in either an overestimationor an underestimation of primary production, depending on theresponse in cc^*_c. Natural variability in cc^*_c is poorly understoodand responses to environmental factors, such as irTadiance,have yet to be addressed outside of the laboratory.     

Seasonal variability of phytoplankton populations in the middle Adriatic sub-basin

The seasonal variability of phytoplankton assemblages in themiddle Adriatic sub-basin is described. The investigated areacrossed the middle Adriatic from the Italian to the Croatiancoasts. Hydrographic data, chlorophyll (Chl) a and phytoplanktonwere collected on a seasonal basis from May 1995 to February1996. Highest phytoplankton densities (up to 6 x 10⁶ cells dm^–3)were observed in spring and autumn in the western side, withinthe diluted waters. The vertical distribution of Chl a exhibiteda pronounced subsurface maximum associated, in coastal waters,with micro-planktonic diatoms. Phytoplankton assemblages weredominated by phytoflagellates in all the periods investigated.Diatom maxima were observed in spring and autumn: their verticaldistribution generally reflected the Chl a pattern and in thewestern coastal area peaks are due to large diatom species (Pseudo-nitzschiaspp.). In offshore waters, dinoflagellates strongly prevailover diatoms and provide a relevant contribution to the totalbiomass, especially in highly stratified conditions. Coccolithophoridswere mostly encountered in surface layers and their highestcontribution to the total biomass was observed in the LevantineIntermediate Water.     

GenDB--an open source genome annotation system for prokaryote genomes

The flood of sequence data resulting from the large number of current genome projects has increased the need for a flexible, open source genome annotation system, which so far has not existed. To account for the individual needs of different projects, such a system should be modular and easily extensible. We present a genome annotation system for prokaryote genomes, which is well tested and readily adaptable to different tasks. The modular system was developed using an object-oriented approach, and it relies on a relational database backend. Using a well defined application programmers interface (API), the system can be linked easily to other systems. GenDB supports manual as well as automatic annotation strategies. The software currently is in use in more than a dozen microbial genome annotation projects. In addition to its use as a production genome annotation system, it can be employed as a flexible framework for the large-scale evaluation of different annotation strategies. The system is open source.     

The role of predation for seasonal variability patterns among phytoplankton and ciliates

Investigating the mechanisms which underlie the biomass fluctuations of populations and communities is important to better understand the processes which buffer community biomass in a variable environment. Based on long-term data of plankton biomass in Lake Constance (Bodensee), this study aims at explaining the different degree of synchrony among populations observed within two freshwater plankton groups, phytoplankton and ciliates. Established measures of temporal variability such as the variance ratio and cross-correlation coefficients were combined with first-order autoregressive models that allow estimating species interactions from time-series data. We found that predation was an important driver of the observed seasonal variability patterns in phytoplankton and ciliates, and that competitive interactions only played a subordinate role. In Lake Constance copepods and cladocerans, two major invertebrate predator groups, focus their grazing pressure at different times of the season. Model results suggested that compensatory dynamics detected in phytoplankton originate from the differential vulnerability of species to either one of these two predator groups. For ciliates model results advocated that synchrony among species occurs because ciliates tend to be vulnerable to both predator groups. Our findings underline the necessity of extending studies of community variability to multiple trophic levels because accounting for predator-prey interactions may often be more important than accounting for competitive interactions at one trophic level.