13 Viral control of phytoplankton

Since the separation of the Trachelomonas subgroup "Saccatae" into a new genus, Strombomonas Deflandre (1930), there has been some question as to its validity. Deflandre's separation was based on morphological characteristics such as the shape of the lorica, lack of a distinctive collar, possession of a tailpiece, lack of ornamentation, and ability to aggregate particles on the lorica. Recent molecular analyses indicated that the loricate taxa were monophyletic, but few species have been sampled. The LSU rDNA from eleven Strombomonas and thirty-eight Trachelomonas species was sequenced to evaluate the monophyly of the two genera. Bayesian and maximum-likelihood analyses found one monophyletic clade for each genus. The Trachelomonas clade was weakly supported, but had five strongly supported subclades. Morphological characters, such as lorica development and pellicle strip reduction, also supported separation of the genera. Lorica development in Strombomonas occurred from the anterior of the cell to the posterior, forming a shroud over the protoplast whereas in Trachelomonas , a layer of mucilage was excreted over the entire protoplast, followed by creation of the collar at the anterior end. Taxa from both genera underwent exponential strip reduction at the anterior and posterior poles. In Strombomonas , only one reduction was visible in the anterior pole, while in most Trachelomonas species, two reductions were visible. Likewise, Strombomonas species possessed two whorls of strip reduction in their posterior end compared to a single whorl of strip reduction in Trachelomonas species. The combined morphological and molecular data support the retention of Trachelomonas and Strombomonas as separate genera.     

ISOLATION OF A NON‐PHAGE‐LIKE LYTIC VIRUS INFECTING AUREOCOCCUS ANOPHAGEFFERENS1

We have been working to characterize viruses that infect the HAB‐forming pelagophyte Aureococcus anophagefferens Hargraves et Sieburth. Field samples were collected during brown‐tide events in 2002 and tested for the presence of lytic agents. Here, we describe a recently isolated, lytic virus‐like particle (VLP) that is morphologically similar to particles observed in thin sections of infected A. anophagefferens cells from natural samples. TEM and SEM have revealed VLPs consistent with the morphological characteristics of previously described Phycodnaviridae. Large icosahedral particles (～140 nm) of similar shape and morphology dominate cell lysates and are accompanied by smaller phage‐like particles and heterotrophic prokaryotes that appear to be incurable from our cultures. To determine which of these particles interacts with the Aureococcus cells, we preserved cultures during the early stage of infection so that SEM could be used to visualize those particles that attach to the surface of naïve cultures. SEM revealed that 63% of the large icosahedral‐shaped particles attached to A. anophagefferens cells after only 30 min of exposure, while no significant frequency of attachment to the alga was observed for the phage‐like particles. The results of these observations are in contrast to previous studies, where phage‐like particles were reported to infect cells. When considered in conjunction with field observations, the results suggest that this newly isolated virus represents the dominant virus‐morphotype associated with bloom collapse and termination.     

Estimates of protozoan- and viral-mediated mortality of bacterioplankton in Lake Bourget (France)

1. We performed three, 1‐week in situ experiments in March‐April (expt 1), May (expt 2) and August (expt 3) 2003 in order to assess protozoan and virus‐induced mortality of heterotrophic bacteria in a French lake. Viral and bacterial abundances were obtained using flow cytometry (FCM) while protozoa were counted using epifluorescence microscopy (EFM). 2. A dilution approach, applied to pretreated grazer‐free samples, allowed us to estimate that viral lysis could be responsible for 60% (expt 1), 35% (expt 2) and 52% (expt 3) of daily heterotrophic bacterial mortality. Flagellate (both mixotrophic and heterotrophic) grazing in untreated samples, was responsible for 56% (expt 1), 63% (expt 2) and 18% (expt 3) of daily heterotrophic bacteria removal. 3. These results therefore suggest that both viral lysis and flagellate grazing had a strong impact on bacterial mortality, and this impact varied seasonally. 4. From parallel transmission electron microscopy (TEM) analysis, we found that the burst size (i.e. the number of viruses potentially released per lysed cell) ranged from nine to 25 (expt 1), 10 to 35 (expt 2) and eight to 25 (expt 3). The percentage of infected heterotrophic bacteria was 5.7% (expt 1), 3.4% (expt 2) and 5.7% (expt 3) so that the calculated percentage of bacterial mortality induced by viruses was 6.3% (expt 1), 3.7% (expt 2) and 6.3% (expt 3). 5. It is clear that the dilution‐FCM and TEM methods yielded different estimates of viral impact, although both methods revealed an increased impact of viruses during summer.     

Evolutionary history of the Coccolithoviridae

We recently determined the genome sequence of the Coccolithoviridae strain Emiliania huxleyi virus 86 (EhV-86), a giant double-stranded DNA (dsDNA) algal virus from the family Phycodnaviridae that infects the marine coccolithophorid E. huxleyi. Here, we determine the phylogenetic relationship between EhV-86 and other large dsDNA viruses. Twenty-five core genes common to nuclear-cytoplasmic large dsDNA virus genomes were identified in the EhV-86 genome; sequence from eight of these genes were used to create a phylogenetic tree in which EhV-86 was placed firmly with the two other members of the Phycodnaviridae. We have also identified a 100-kb region of the EhV-86 genome which appears to have transferred into this genome from an unknown source. Furthermore, the presence of six RNA polymerase subunits (unique among the Phycodnaviridae) suggests both a unique evolutionary history and a unique lifestyle for this intriguing virus.     

Temporal organization of phytoplankton communities linked to physical forcing

The performance of individual phytoplankton species is strongly governed by the thermal stratification’s impact on vertical mixing within the water column, which alters the position of phytoplankton relative to nutrients and light. The present study documents shifts in phytoplankton structure and vertical positioning that have accompanied intensified long-term stratification in a natural ecosystem. Ordination analysis is used to extract gradients in phytoplankton composition in Lake Tahoe, an extremely nutrient-poor lake, over a 23-year period of records. Community structure in the 1980s was associated most strongly with resource availability (low nitrogen to phosphorus ratios, deeper euphotic zone depth), while intensified stratification dominated the phytoplankton structure since the late 1990s. Within diatoms, small-sized cells increased with reduced mixing, suggesting that suppressed turbulence provides them with a competitive advantage over large-sized cells. Among the morphologically diverse chlorophytes, filamentous and coenobial forms were favored under intensified stratification. The selection for small-sized diatoms is accompanied by a shoaling trend in their vertical position in the water column. In contrast, the motile flagellates displayed a deeper vertical positioning in recent years, indicating that optimal growth conditions shifted likely due to reduced upwelling of nutrients. As the thermal stratification of lakes and oceans is strongly linked to climate variables, the present study confirms that climate warming will alter phytoplankton structure and dynamics largely through effects on nutrient availability and sinking velocities. Intensified stratification should favor the expansion of small-sized species and species with the capability of buoyancy regulation, which may alter primary productivity, nutrient recycling, and higher trophic productivity. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Photoheterotrophy in the production of phytoplankton organisms

Interest is growing in algae as sources of medicinal and other potentially useful compounds, as well as their use in fish rearing. We are interested in their production of polyunsaturated fatty acids (PUFA). Photoautotrophic growth gives the highest levels of unsaturation in the fatty acid pool, but biomass concentrations are low. Heterotrophy on sugars gives higher biomass but seems to give more saturation in the fatty acids. In freshwater algae acetate has proved to be a good carbon source for photoheterotrophic growth, giving a crop with reasonably high levels of PUFA. In addition it is possible to regulate acetic acid addition through the pH change as acetate is used up in a well-aerated system, so achieving high biomass yields in the presence of relatively low acetate concentration. When we attempted to extend this to marine algae (principally species used in fish farming), we found that acetic acid was ineffective or sometimes toxic to most species tested, even at high pH. However, glycerol stimulated growth in a number of the algae. We report on this stimulation, and on the fatty acid composition of the resulting algal crop, discuss the problems in regulating the addition of this metabolite to algal cultures, and speculate on applications in the production of other useful algal metabolites. We also show that some of these algae used in fish farming grow best when the salinity of the water is rather less than that found in standard sea water.     

The vertical distribution of phytoplankton in stratified water columns

What determines the vertical distribution of phytoplankton in different aquatic environments remains an open question. To address this question, we develop a model to explore how phytoplankton respond through growth and movement to opposing resource gradients and different mixing conditions. We assume stratification creates a well-mixed surface layer on top of a poorly mixed deep layer and nutrients are supplied from multiple depth-dependent sources. Intraspecific competition leads to a unique strategic equilibrium for phytoplankton, which allows us to classify the distinct vertical distributions that can exist. Biomass can occur as a benthic layer (BL), a deep chlorophyll maximum (DCM), or in the mixed layer (ML), or as a combination of BL+ML or DCM+ML. The ML biomass can be limited by nutrients, light, or both. We predict how the vertical distribution, relative resource limitation, and biomass of phytoplankton will change across environmental gradients. We parameterized our model to represent potentially light and phosphorus limited freshwater lakes, but the model is applicable to a broad range of vertically stratified systems. Increasing nutrient input from the sediments or to the mixed layer increases light limitation, shifts phytoplankton towards the surface, and increases total biomass. Increasing background light attenuation increases light limitation, shifts the phytoplankton towards the surface, and generally decreases total biomass. Increasing mixed layer depth increases, decreases, or has no effect on light limitation and total biomass. Our model is able to replicate the diverse vertical distributions observed in nature and explain what underlying mechanisms drive these distributions.     

湿地中的藻类生态学研究进展

从湿地中藻类的种群结构、藻类在湿地中的功能、湿地中的藻类生产力及其影响因素等方面综述了天然湿地中的藻类生态学研究进展．湿地植物区系主要有附泥藻类、附植藻类、后周丛藻类和浮游植物4种类型,其中常见的是附泥藻类的硅藻、绿藻和蓝藻．藻类最显著的作用是作为湿地食物网中的初级生产者,也作为湿地环境污染的生物指示物．影响藻类生产力的因素有水力学因素、营养、温度、光、大型植物及草食动物和其它动物．未来对藻类的研究应侧重于湿地藻类生物多样性、藻类生物量、生产力、种群组成的环境控制及其相互关系,以及藻类作为水环境及湿地污染程度指标的研究,“基因治藻”也将是未来研究的新方向．     

Grazing rates and behaviors of Neocalanus plumchrus: implications for phytoplankton control in the subarctic Pacific

Grazing rates and behaviors of the copepod Neocalanus plumchrus were investigated in shipboard experiments during the first SUPER Program cruise (May, 1984). N. plumchrus can exploit cells in the 2 to 30 m size range with equal clearance efficiency but displays considerable flexibility in responding to changes in concentration and size composition. Its functional response helps to stabilize phytoplankton at low densities. In 60-liter microcosms, a density of one copepod liter^–1 was sufficient to maintain the ambient abundance and structure of the phytoplankton community for a week. In the absence of the copepod, phytoplankton bloomed to unnaturally high levels, and the community composition was dramatically altered. Despite its grazing potential, N. plumchrus was not present in sufficient density to control phytoplankton blooms in the subarctic Pacific. However, the copepod may have an important role in regulating the abundance of smaller grazers and the size structure of the phytoplankton community.Contribution No. 2002 from Hawaii Institute of Geophysics, University of Hawaii, Honolulu, HI 96822     

Viral diseases in commercially exploited crabs: a review

Viruses and viral diseases of crabs were observed and investigated earlier than the first observation of viruses in shrimp. In fact, crabs were used as biological models to investigate crustacean virology at the beginning of shrimp aquaculture development. More than 30 viruses have been reported in crabs, including those related to the known virus families Reoviridae, Bunyaviridae, Roniviridae and a group of Bacilliform enveloped nuclear viruses. This review reports data on several important viral diseases of crabs, particularly those associated with pathology of organs and tissues of commercially and ecologically significant host species.     

SENESCENCE IN NATURAL POPULATIONS OF MAMMALS: A COMPARATIVE STUDY

Here, I use published mortality data from 56 natural populations of mammals to examine evidence for senescence, an increase in the probability of mortality with age. Data on extent of senescence and life history characteristics are compared across taxa in an attempt to test theories for the evolution of senescence in natural populations. In accord with theoretical expectation, senescence is highest in short-lived species with short generation times. In contrast to theoretical expectation, however, senescent increases in mortality rate do not begin until well after age at maturity in most cases. I also present evidence in support of the hypothesis that senescence will be lower in large-brained taxa.     

RNA 沉默的病毒抑制子

RNA 沉默是一种在真核生物体内普遍保守的、通过核酸序列特异性的相互作用来抑制基因表达的调控机制 . RNA 沉默的一种重要生物学效应是防御病毒的侵染,而针对寄主的这种防御机制,许多植物病毒已演化通过编码 RNA 沉默的抑制子来克服这种防御反应 . 目前,已从植物、动物和人类病毒中鉴定了 20 多种 RNA 沉默的抑制子,围绕抑制子的鉴定和作用机理研究已成为病毒学研究的一个热点 . 对 RNA 沉默抑制子的发现、鉴定方法、作用机理及与病毒病症状形成的关系、动物病毒的沉默抑制子等方面的最新进展做了综述,并对沉默抑制子的应用和存在的问题进行了讨论 .     

Viral diseases of the giant fresh water prawn Macrobrachium rosenbergii: a review

The giant freshwater prawn Macrobrachium rosenbergii is cultivated essentially in Southern and South-eastern Asian countries such as continental China, India, Thailand and Taiwan. To date, only two viral agents have been reported from this prawn. The first (HPV-type virus) was observed by chance 25 years ago in hypertrophied nuclei of hepatopancreatic epithelial cells and is closely related to members of the Parvoviridae family. The second, a nodavirus named MrNV, is always associated with a non-autonomous satellite-like virus (XSV), and is the origin of so-called white tail disease (WTD) responsible for mass mortalities and important economic losses in hatcheries and farms for over a decade. After isolation and purification of these two particles, they were physico-chemically characterized and their genome sequenced. The MrNV genome is formed with two single linear ss-RNA molecules, 3202 and 1250 nucleotides long, respectively. Each RNA segment contains only one ORF, ORF1 coding for the RNA-dependant RNA polymerase located on the long segment and ORF2 coding for the structural protein CP-43 located on the small one. The XSV genome (linear ss-RNA), 796 nucleotides long, contains a single ORF coding for the XSV coat protein CP-17. The XSV does not contain any RdRp gene and consequently needs the MrNV polymerase to replicate.     

Leading indicators of phytoplankton transitions caused by resource competition

Many important transitions in phytoplankton composition of lakes and oceans are related to shifts in nutrient supply ratios. Some phytoplankton transitions, such as cyanobacteria blooms in freshwater supplies and red tides in coastal oceans, are important for aquatic resource management. Therefore, it would be useful to have leading indicators which precede phytoplankton shifts and could be readily monitored in the field. We investigated potential indicators using a well-understood model of phytoplankton dynamics parameterized to mimic the transition toward cyanobacteria blooms in freshwater lakes. In stationary distributions, performance of the indicators depends on whether the species are capable of stable coexistence over a certain range of nutrient inputs. In transient simulations, however, indicators show consistent responses regardless of the possibility of stable coexistence. Leading indicators occurring 10 to 40 days prior to species shift include shift of lag-1 autoregression coefficient toward 0, low standard deviation, fluctuating skewness, and high kurtosis. These responses are different from those reported for critical transitions such as fold bifurcations. Thus, the indicators reveal clues to the mechanisms of important ecosystem transitions. In practice, indicators should be measured for multiple ecosystem variables, and interpretation of the indicators should be guided by experiments and mechanistic site-specific models to help resolve potential ambiguities.     

The Role of Viral Mutation in the Pathogenesis of Chronic Viral Hepatitis

The quasispecies nature of hepatitis B and C virus (HBV, HCV) plays an important role in the pathogenesis, immune escape and drug resistance during chronic infection. Although there is still a lack of effective treatment for hepatitis C, a series of nucleoside analogs (NA) have been developed for the treatment of hepatitis B. NA resistant HBV mutants can accumulate during prolonged therapy and lead to the failure of anti-HBV therapy. Switching to other sensitive NAs can inhibit the emerged resistant mutants. Therefore, understanding the evolution of viral quasispecies under drug pressure is crucial for the establishment of antiviral strategy and the monitoring of antiviral process. Immune response and escape are complicated process, during which both host and virus factors may play their roles. Further understanding of the interaction and interrelationship between host and these viruses may lead to optimized prevention, diagnosis and treatment for chronic hepatitis.     

Student's tutorial on bloom hypotheses in the context of phytoplankton annual cycles

Phytoplankton blooms are elements in repeating annual cycles of phytoplankton biomass and they have significant ecological and biogeochemical consequences. Temporal changes in phytoplankton biomass are governed by complex predator–prey interactions and physically driven variations in upper water column growth conditions (light, nutrient, and temperature). Understanding these dependencies is fundamental to assess future change in bloom frequency, duration, and magnitude and thus represents a quintessential challenge in global change biology. A variety of contrasting hypotheses have emerged in the literature to explain phytoplankton blooms, but over time the basic tenets of these hypotheses have become unclear. Here, we provide a “tutorial” on the development of these concepts and the fundamental elements distinguishing each hypothesis. The intent of this tutorial is to provide a useful background and set of tools for reading the bloom literature and to give some suggestions for future studies. Our tutorial is written for “students” at all stages of their career. We hope it is equally useful and interesting to those with only a cursory interest in blooms as those deeply immersed in the challenge of understanding the temporal dynamics of phytoplankton biomass and predicting its future change.     

外体和病毒感染

外体(exosome)是源自细胞内体的小囊泡,可由多种哺乳动物细胞分泌释放,其组分包括蛋白质、脂质、mRNA和microRNA,是细胞间"通讯"交互的工具之一。我们以介绍外体的组成和生物发生为基础,综述了近年来其在病毒感染致病中的研究成果,以期为病毒感染致病机理的研究提供新的切入点。     

Viral control of mitochondrial apoptosis

Throughout the process of pathogen-host co-evolution, viruses have developed a battery of distinct strategies to overcome biochemical and immunological defenses of the host. Thus, viruses have acquired the capacity to subvert host cell apoptosis, control inflammatory responses, and evade immune reactions. Since the elimination of infected cells via programmed cell death is one of the most ancestral defense mechanisms against infection, disabling host cell apoptosis might represent an almost obligate step in the viral life cycle. Conversely, viruses may take advantage of stimulating apoptosis, either to kill uninfected cells from the immune system, or to induce the breakdown of infected cells, thereby favoring viral dissemination. Several viral polypeptides are homologs of host-derived apoptosis-regulatory proteins, such as members of the Bcl-2 family. Moreover, viral factors with no homology to host proteins specifically target key components of the apoptotic machinery. Here, we summarize the current knowledge on the viral modulation of mitochondrial apoptosis, by focusing in particular on the mechanisms by which viral proteins control the host cell death apparatus.     

Collective Infection of Cells by Viral Aggregates Promotes Early Viral Proliferation and Reveals a Cellular-Level Allee Effect

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