经典与非经典生物操纵理论及其应用

湖泊是我国的重要水资源之一,为人类提供了无法替代的生态及社会服务功能。但我国湖泊富营养化日趋严重。以食物网为基础的经典与非经典生物操纵成为湖泊富营养化修复的重要理论支撑。论文综述了经典与非经典生物操纵理论的原理、发展与应用,分析了鱼类(肉食性、滤食性)、浮游动物在控制藻类数量上发挥的功能,并讨论了两种理论的适用条件及实际应用中遇到的问题,以期为我国富营养化湖泊修复工作提供参考。经典与非经典生物操纵理论均是通过改变食物网结构控制藻类,分别利用浮游动物、滤食性鱼类控制藻类数量,但两者都未降低水中N、P含量。因此,实施有效的藻类水华生物操纵应与其它修复措施联合使用。     

The fish community of the Loosdrecht Lakes and the perspective for biomanipulation

In a two-year-study, the fish community of the Loosdrecht Lakes area was characterized with regard to the professional fishery and the forage base. The lakes are shallow (mean depth 2 m) and eutrophic to hypertrophic. The bream,Abramis brama, dominates the fish biomass. The pikeperch,Stizostedion lucioperca, is the main predator.Bream up to 30 cm have a slow growth rate and are in a bad condition. A faster growth rate and a better condition are shown by bream of 30 cm and more. The small bream feeds on chironomid larvae, benthic cladocerans and zooplankton. The better condition of bream over 30 cm is explained by the more efficient feeding of larger bream onChironomus plumosus larvae. Pikeperch show a fast growth rate and a good condition. Recruitment is limited by the low densities of smelt,Osmerus eperlanus, leaving cannibalism as the most important way for the 0+ pikeperch to become piscivorous and to manifest a fast growth.The impact of the professional gillnet fishery on bream and pikeperch is small because the mesh sizes in use are as large as 75–100 mm bar mesh.The planktivorous 0+ pikeperch consumes mainly the carnivorous zooplanktersLeptodora kindtii and cyclopoids. The zooplankton community lacks large herbivorous species likeDaphnia hyalina, capable of consuming bluegreens. A possible experiment in biomanipulation with a view to find out whether the development ofD.hyalina is depressed by the small planktivorous cyprinids, is predator enhancement with the aid of a stocking programme for indoor-raised 0+ pikeperch in early summer.     

The relevance of size efficiency to biomanipulation theory: a field test under hypertrophic conditions

The superiority of large zooplankton in suppressingphytoplankton growth has often been inferred from theSize Efficiency Hypothesis (S.E.H.). The S.E.H. hasoriginally been formulated to account for thecompetitive superiority of large to small zooplanktonunder food limiting conditions. Extrapolation of itspredictions to the suppression of phytoplankton byzooplankton under high food availability, should bedone with care. In an attempt to assess the relevanceof the S.E.H. to biomanipulation theory inhypertrophic systems, a fish exclosure experiment wascarried out in which the efficiency of two differentlystructured zooplankton communities in reducingphytoplankton biomass was examined. By inoculatingpart of the enclosures with laboratory grownDaphnia magna, a community dominated by this largecladoceran species could be compared with a communitymainly consisting of Bosmina and smallerDaphnia species. After the exclusion of fish, therewas an exponential increase of total zooplanktonbiomass. Phytoplankton growth was efficientlysuppressed to equal levels in both treatments, thoughthere was a difference in timing: chlorophyll-a levelsin the enclosures inoculated with D. magnadropped one week earlier than in non-inoculatedenclosures. The time-lag was even more pronounced whenlarge phytoplankton was considered. In accordance withthe S.E.H., the time lags could be explained bydifferences in population growth potential as well asby differences in zooplankton grazing rates(indirectly measured as the minimal zooplanktonbiomass needed to suppress phytoplankton growth) andfood particle size range.     

Adding physiological realism to dynamic state variable models of parasitoid host feeding

Summary The behavioural decisions of insect parasitoids have been the subject of dynamic state variable models, which explicitly incorporate the physiological state of the parasitoid, e.g. her age and egg load (number of mature eggs). Such models have been most recently applied to parasitoid host feeding, the consumption of host body fluids or tissues by the adult female wasp. The models developed to date, and recent empirical work withAphytis melinus, have highlighted the importance of the physiology associated with host feeding to the behavioural decision whether to host feed or oviposit. Below, I develop a new dynamic state variable model which incorporates the physiological features associated with host feeding inAphytis. My intention is to make qualitative predictions about the effects of various physiological featues on host-feeding behaviour and to make quantitative predictions about the relationship between egg load and host feeding inAphytis.     

The potential for biomanipulation using fry communities in a lowland reservoir: concordance between water quality and optimal recruitment

The fry community in a temperate lowland reservoir was monitored for seven years. The variation in reproductive success of the dominant perch and cyprinids was correlated with the variation of the water level. During summer the main food of perch wasDaphnia. In the year with the highest density of perch, a decline in the density of cladocerans and in the percentage ofDaphnia eaten was observed. This resulted in low stomach fullness and poor fry growth. Simultaneously, the amount of phytoplankton increased. An optimal recruitment curve was found for maintaining water quality with optimal recruitment of fish stocks, assuming that a high rate of fry growth is essential for high survival during winter. Regulation of fry densities can be achieved by the manipulation of water levels during the reproductive and early ontogeny period.     

The importance of sediment phosphorus release in the restoration of very shallow lakes (The Norfolk Broads,England) and implications for biomanipulation

Phosphorus release from the sediments of very shallow lakes, the Norfolk Broads, can be as high as 278 mgP m^-2 d^-1. These high rates are associated with high total sediment Fe:P ratios and occur when sulphide from sulphate reduction removes Fe(II) from the pore water. There is also evidence that bioturbation from benthic chironomids can enhance phosphorus release rates, particularly in sediments low in total iron. The release of phosphorus from the sediments of these lakes is delaying restoration following the control of phosphorus from sewage discharges. Biomanipulation is being used in these lakes to create clear water and re-establish aquatic macrophytes. This removal of fish has allowed larger populations of benthic chironomid larvae to develop which may result in an increase in the rate of phosphorus release and changes to the pore profiles of dissolved phosphorus, soluble iron and free sulphide.     

Stocking piscivores to improve fishing and water clarity: a synthesis of the Lake Mendota biomanipulation project

SUMMARYY 1. A total of 2.7 × 10⁶ walleye fingerlings and 1.7 × 10⁵ northern pike fingerlings were stocked during 1987–99 in eutrophic Lake Mendota. The objectives of the biomanipulation were to improve sport fishing and to increase piscivory to levels that would reduce planktivore biomass, increase Daphnia grazing and ultimately reduce algal densities in the lake. The combined biomass of the two piscivore species in the lake increased rapidly from < 1 kg ha^?1 and stabilised at 4–6 kg ha^?1 throughout the evaluation period. 2. Restrictive harvest regulations (i.e. increase in minimum size limit and reduction in bag limit) were implemented in 1988 to protect the stocked piscivores. Further restrictions were added in 1991 and 1996 for walleye and northern pike, respectively. These restrictions were essential because fishing pressure on both species (especially walleye) increased dramatically during biomanipulation. 3. Commencing in 1987 with a massive natural die‐off of cisco and declining yellow perch populations, total planktivore biomass dropped from about 300–600 kg ha^?1 prior to the die‐off and the fish stocking, to about 20–40 kg ha^?1 in subsequent years. These low planktivore biomasses lasted until a resurgence in the perch population in 1999. 4. During the period prior to biomanipulation when cisco were very abundant, the dominant Daphnia species was the smaller‐bodied D. galeata mendotae, which usually reached a biomass maximum in June and then crashed shortly thereafter. Beginning in 1988, the larger‐bodied D. pulicaria dominated, with relatively high biomasses occurring earlier in the spring and lasting well past mid‐summer of many years. 5. In many years dominated by D. pulicaria, Secchi disc readings were greater during the spring and summer months when compared with years dominated by D. galeata mendotae. During the biomanipulation evaluation period, phosphorus (P) levels also changed dramatically thus complicating our analysis. Earlier research on Lake Mendota had shown that Daphnia grazing increased summer Secchi disc readings, but P concentrations linked to agricultural and urban runoff and to climate‐controlled internal mixing processes were also important factors affecting summer readings. 6. The Lake Mendota biomanipulation project has been a success given that high densities of the large‐bodied D. pulicaria have continued to dominate for over a decade, and the diversity of fishing opportunities have improved for walleye, northern pike and, more recently, yellow perch. 7. Massive stocking coupled with very restrictive fishing regulations produced moderate increases in piscivore densities. Larger increases could be realised by more drastic restrictions on sport fishing, but these regulations would be very controversial to anglers. 8. If the lake's food web remains in a favourable biomanipulation state (i.e. high herbivory), further improvements in water clarity are possible with future reductions in P loadings from a recently initiated non‐point pollution abatement programme in the lake's drainage basin.     

Acclimation in dynamic models based on structural relationships

1. A number of recent tree growth models have been based on the assumption that tree structure follows certain empirical rules and carbon allocation is performed so as to maintain these rules when growth and senescence occur simultaneously. This paper introduces a method of combining structural rules with adaptive regulation in a carbon balance model.
2. The method is based on regulating gross growth but situations are analysed where increased senescence of tissue functions as an alternative means of re-establishing the balance.
3. The model does not aim to be mechanistic but merely to describe the process of regulation, or acclimation to changing environments and situations, as constrained by the carbon balance. The method incorporates parameters that describe the rate of returning to the balance after disturbance or after a change in the goal, which can be determined empirically.
4. Two models are given as examples of the use of the method, and the requirements and limitations of control in a carbon balance framework are discussed.
5. The method is best applied as a technical tool to describe variations and disturbance in balanced growth models when the variations are present but not very large. In addition, it can be used as a theoretical framework for the analysis of regulation as constrained by the conservation of mass.     

Comparison of losses of planktivorous fish by predation and seine-fishing in a lake undergoing long-term biomanipulation

SUMMARY 1. Piscivore stocking at artificially high densities and fishing are the two common approaches to reduce the amount of planktivorous and benthivorous fish in lake biomanipulation programmes. Both measures have advantages and disadvantages, but their relative efficacy has not previously been directly compared.
2. We calculated the average annual catch of roach and bream in a lake undergoing long-term biomanipulation (Feldberger Haussee, Germany) by seining each year between 1992 and 1998. We compared this value with a bioenergetics estimate of annual consumption rates of the dominant cohorts of piscivores, pikeperch and pike, in 1997 and 1998. We also determined species composition and length distribution of prey fish in stomachs of the piscivores.
3. Roach was the dominant prey species of both pikeperch and pike, whereas bream was rarely taken by either piscivorous species. Seining removed on average larger specimens of roach than were found in the stomachs of the piscivores.
4. Based on stocking densities of the piscivores, published mortality rates, and individual consumption rates, feeding of pikeperch and pike on roach exceeded the manual removal of roach by seining by a factor of 4–15 (biomass) in 1997 and 1998.
5. Based on these results, a combination of fishing and piscivore enhancement is recommended. Whereas the stocks of adult roach and bream have to be reduced mainly by fishing, the predation of piscivores should be directed predominantly towards the juvenile zooplanktivorous fish. Therefore, small size-classes of piscivorous fish should be promoted by fisheries management, including stocking and harvest regulations.     

The influence of biomanipulation on fish community development in a southeastern United States cooling reservoir

L Lake, a reactor cooling reservoir in South Carolina, USA was managed after filling to promote the development of healthy ecological communities similar to those in mature regional cooling reservoirs. Two types of biomanipulation were undertaken to achieve this goal, the introduction of typical southeastern US reservoir fishes (bluegill and largemouth bass) and artificial planting of native aquatic macrophytes. Fish assemblages were monitored by electrofishing from reservoir filling in 1986 until 1998. Multivariate analysis divided the fish samples into five sequential periods resulting from species replacements and additions. Small species that colonized L Lake from a feeder stream predominated in the first period but were mostly eliminated, as bluegill, largemouth bass, and other lentic species increased in the second period. A rapid increase in threadfin shad abundance characterized the third period, and small littoral zone and phytophilous fishes increased during the fourth and fifth periods coincident with the proliferation of aquatic macrophytes. Analysis of Bray-Curtis similarities and the species accumulation rate indicated that the rate of fish community change decreased with time and that fish community structure changed little during the last several years of the study. By the end of the study, community structure was similar to that in a nearby cooling reservoir that supported diverse and resilient biota. Biomanipulation contributed to the rapid establishment of lentic species and later increases in small littoral and phytophilous species suggesting that biomanipulation may be useful in accelerating fish community development in new cooling reservoirs.     

Generative models versus underlying symmetries to explain biological pattern

Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative models confirm the plausibility of an explanation and make testable hypotheses for further experiments. However, studies rarely consider the broad family of alternative models that match the same observed pattern. The symmetries that define the broad class of matching models are in fact the only aspects of information truly revealed by observed pattern. Commonly observed patterns derive from simple underlying symmetries. This article illustrates the problem by showing the symmetry associated with the observed rate of increase in fitness in a constant environment. That underlying symmetry reveals how each particular generative model defines a single example within the broad class of matching models. Further progress on the relation between pattern and process requires deeper consideration of the underlying symmetries.     

Long-term changes in the rotifer fauna after biomanipulation in Haussee (Feldberg,Germany, Mecklenburg-Vorpommern) and its relationship to the crustacean and phytoplankton communities

In Feldberg Haussee, an anthropogenic eutrophicated lake, biomanipulation was executed for restoration. To increase the biomass of crustaceans, fish grazing on zooplankton was reduced by catching small fishes and introducing pike-perch. After biomanipulation rotifer biomass from a wide range of species decreased to a small spring maximum with three dominant species. The development of food in spring and food competition between crustaceans probably controlled the rotifer development.     

Structure and feeding activities of zooplankton community in Lake Zwemlust,in the two years after biomanipulation

The biomanipulation study in Lake Zwemlust (area 1.5 ha; mean depth 1.5 m) is among the series of such investigations initiated recently in The Netherlands. The effects of the lake's reffilling (after it was first completely drained empty) almost entirely the nutrient-rich seepage water from the River Vecht flowing nearby and of removal of the planktivorous bream (Abramis brama), on zooplankton community structure and feeding activities of crustaceans were monitored for two successive years (1987, 1988). In these years a classical pattern of succession occurred, with the rotifer spring maximum preceding the crustacean maximum by about 3 weeks. Among the fiveDaphnia species, which appeared in quick succession during May–July, two were large-bodied forms (D. magna; D. pulex). OnlyD. pulex persisted and was the important grazer species in the second year, especially in spring. In the first year the crustacean grazing, with several values >100%.d^–1, contributed significantly to the lake's improved water clarity, with Secchi-disc transparencies of 1.5 m and more almost throughout the summer, compared with 0.3 m before the biomanipulation. Even though the water clarity climate in the second year was quite similar to that in the first, the causal factor was high macrophytic vegetation, rather than zooplankton grazing. The lake developed a rich littoral flora and fauna in the second year in response to the optimal light and nutrient conditions. Apparently, the predation by the introduced planktivorous rudd (Scardinius erythrophthalmus) on zooplankton was an important factor in the changes in zooplankton structure, and in the reduced role of zooplankton in seston elimination during the second year. There is some evidence from bioassay work that, simultaneously with the littoral development, nitrogen limitation of the phytoplankton also contributed to the improved light situation in the second year.     

Performance of the marginal structural models under various scenarios of incomplete marker's values: A simulation study

Marginal structural models (MSMs) have been proposed for estimating a treatment's effect, in the presence of time‐dependent confounding. We aimed to evaluate the performance of the Cox MSM in the presence of missing data and to explore methods to adjust for missingness. We simulated data with a continuous time‐dependent confounder and a binary treatment. We explored two classes of missing data: (i) missed visits, which resemble clinical cohort studies; (ii) missing confounder's values, which correspond to interval cohort studies. Missing data were generated under various mechanisms. In the first class, the source of the bias was the extreme treatment weights. Truncation or normalization improved estimation. Therefore, particular attention must be paid to the distribution of weights, and truncation or normalization should be applied if extreme weights are noticed. In the second case, bias was due to the misspecification of the treatment model. Last observation carried forward (LOCF), multiple imputation (MI), and inverse probability of missingness weighting (IPMW) were used to correct for the missingness. We found that alternatives, especially the IPMW method, perform better than the classic LOCF method. Nevertheless, in situations with high marker's variance and rarely recorded measurements none of the examined method adequately corrected the bias.     

Structural and grazing responses of zooplankton community to biomanipulation of some Dutch water bodies

Structure and grazing activities of crustacean zooplankton were compared in five lakes undergoing manipulation with several unmanipulated eutrophic (shallow) and mesotrophic (deep) lakes in The Netherlands. The biomanipulated lakes had lesser number of species and their abundance, both of rotifers and crustaceans, and had much larger mean animal size (3–11 μg C ind.⁻¹) than in the unmanipulated eutrophic lakes (0.65 μG C ind.⁻¹). WhereasD. hyalina (=D. galeata) andD. cucullata generally co-occurred in the unmanipulated lakes, in the manipulated lakes bothD. hyalina and other large-bodied daphnids,D. magna,D. pulex (=D. pulicaria), were the important grazers. In the biomanipulated lakes an increase in the individual crustacean size and of zooplankton mass were reflected in a decrease in seston concentration, higher Secchi-disc depth and a marked decrease in the share in phytoplankton biovolume of cyanobacteria. Biomass relationship between seston (150 μm) and zooplankton indicated a Monod type relationship, with an initial part of the curve in which the zooplankton responds linearly to the seston increase up to aboutca. 2 mg C l⁻¹, followed by a saturation of zooplankton mass (0.39 mg C l⁻¹) at 3–4 mg C l⁻¹ seston, and an inhibitory effect on zooplankton mass at seston levels>4 mg C l⁻¹. This latter is related to predominance in the seston of cyanobacteria. In the biomanipulated lakes, the zooplankton grazing rates often exceeded 100% d⁻¹, during the spring, and food levels generally dropped to <0.5 mg C l⁻¹. The computed specific clearance rate (SCR) of zooplankton of 1.9 l mg⁻¹ Zoop C is well within the range of SCR values (1.7–2.2 l mg⁻¹ Zoop C) from deep and mesotrophic waters, but about an order of magnitude higher than in the eutrophic lakes, with the food levels 10-fold higher. For 25% d⁻¹ clearance of lake seston between 35 and 60 ind. l⁻¹ are needed in the biomanipulated lakes against 1200–1300 ind. l⁻¹ in eutrophic lakes. Similarly, about 10 to 15 times more crustacean grazers are required to eliminate the daily primary production in the eutrophic lakes than in the biomanipulated lakes. These numbers are inversely related to the differences in animal size. The corresponding biomass values of zooplankton needed to clear the daily primary production in the eutrophic waters were 0.1–0.2 mg C l⁻¹ in the biomanipulated lakes, but about 0.45 mg C l⁻¹ in the unmanipulated eutrophic waters. Only if the water was kept persistently clear by zooplankton was there a balanced seston budget between the inputvia primary production and elimination by zooplankton. Mostly, however, the input exceeded the assimilatory removal by zooplankton, such that the estimated seston loss could be attributed to sedimentation and mineralization.     

Predicting nucleic acid binding interfaces from structural models of proteins

The function of DNA‐ and RNA‐binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure‐based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high‐resolution three‐dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I‐TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high‐resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I‐TASSER produces high‐quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low‐resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Proteins 2012. © 2011 Wiley Periodicals, Inc.     

Theoretical models of wound healing: past successes and future challenges

The complex biology of wound healing is an area in which theoretical modelling has already made a significant impact. In this review article, the authors describe the key features of wound healing biology, divided into four components: epidermal wound healing, remodelling of the dermal extracellular matrix, wound contraction, and angiogenesis. Within each of these categories, previous modelling work is described, and the authors identify what they regard as the main challenges for future theoretical work.     

Critical analysis of the successes and failures of homology models of G protein‐coupled receptors

We present a critical assessment of the performance of our homology model refinement method for G protein‐coupled receptors (GPCRs), called LITICon that led to top ranking structures in a recent structure prediction assessment GPCRDOCK2010. GPCRs form the largest class of drug targets for which only a few crystal structures are currently available. Therefore, accurate homology models are essential for drug design in these receptors. We submitted five models each for human chemokine CXCR4 (bound to small molecule IT1t and peptide CVX15) and dopamine D3DR (bound to small molecule eticlopride) before the crystal structures were published. Our models in both CXCR4/IT1t and D3/eticlopride assessments were ranked first and second, respectively, by ligand RMSD to the crystal structures. For both receptors, we developed two types of protein models: homology models based on known GPCR crystal structures, and ab initio models based on the prediction method MembStruk. The homology‐based models compared better to the crystal structures than the ab initio models. However, a robust refinement procedure for obtaining high accuracy structures is needed. We demonstrate that optimization of the helical tilt, rotation, and translation is vital for GPCR homology model refinement. As a proof of concept, our in‐house refinement program LITiCon captured the distinct orientation of TM2 in CXCR4, which differs from that of adrenoreceptors. These findings would be critical for refining GPCR homology models in future. Proteins 2013. © 2012 Wiley Periodicals, Inc.