How well do laboratory experiments explain field patterns of zooplankton emergence?

1. We conducted a laboratory experiment to explore potential mechanisms driving variation in zooplankton emergence from diapausing eggs observed in Oneida Lake, NY, U.S.A. We hypothesized that variation in timing of ice-out (date of thawing of ice) between 1994 and 1995, which resulted in variation in photoperiod–temperature cues, contributed to the differences in the observed field patterns. Environmental chambers were used to establish weekly photoperiod–temperature combinations that reproduced natural conditions in Oneida Lake in 1994 and 1995. In addition, a third treatment ('dark') exposed eggs only to the changes in temperature. We recorded zooplankton emergence for 2.5 simulated ice-free seasons.
2. Nine cladoceran taxa were found to hatch, but only Daphnia pulicaria in large numbers. Hatching of D. pulicaria was recorded throughout the season in the two light treatments and sporadically in the dark treatment. The early ice-out treatment had the highest emergence, followed by the late ice-out and dark treatments. Among taxa, there was temporal segregation with five hatching in the early weeks of sampling and two taxa hatching during the middle weeks. Alona hatched late in the first year, but earlier in the second year.
3. We compared our laboratory results of D. pulicaria hatching with the field data obtained by Cáceres (1998) . Hatching was continuous in the laboratory, whereas a synchronous spring emergence was found in the field. However, in both the laboratory and the field, more D. pulicaria hatched under conditions reflecting ice-out occurring in March as opposed to April. Because differences in rates and timing of emergence can affect the population and community dynamics of pelagic systems, we suggest caution when applying laboratory results to field populations.     

Are there allelopathic interactions in zooplankton? Laboratory experiments with Daphnia

Summary Daphnia hyalina and Daphnia cucullata were kept in flow-through chambers in lake water (I), water from mass cultures of D. hyalina (II) and water from mass cultures of D. cucullata (III). A good correlation between body length and clutch size of the Daphnia was found in all cases. The regression lines of the different treatments were compared with respect to different slopes and different intercepts. D. hyalina showed the same reaction to medium II and III, but a lower regression coefficient and higher intercept in medium I. In contrast D. cucullata showed the same reaction to medium I and II, but a higher regression coefficient in medium III.     

Primary glioblastoma cultures: can profiling of stem cell markers predict radiotherapy sensitivity?

Human glioblastomas may be hierarchically organized. Within this hierarchy, glioblastoma‐initiating cells have been proposed to be more resistant to radiochemotherapy and responsible for recurrence. Here, established stem cell markers and stem cell attributed characteristics such as self‐renewal capacity and tumorigenicity have been profiled in primary glioblastoma cultures to predict radiosensitivity. Furthermore, the sensitivity to radiotherapy of different subpopulations within a single primary glioblastoma culture was analyzed by a flow cytometric approach using Nestin, SRY (sex‐determining region Y)‐box 2 (SOX2) and glial fibrillary acidic protein. The protein expression of Nestin and SOX2 as well as the mRNA levels of Musashi1, L1 cell adhesion molecule, CD133, Nestin, and pleiomorphic adenoma gene‐like 2 inversely correlated with radioresistance in regard to the clonogenic potential. Only CD44 protein expression correlated positively with radioresistance. In terms of proliferation, Nestin protein expression and Musashi1, pleiomorphic adenoma gene‐like 2, and CD133 mRNA levels are inversely correlated with radioresistance. Higher expression of stem cell markers does not correlate with resistance to radiochemotherapy in the cancer genome atlas glioblastoma collective. SOX2 expressing subpopulations exist within single primary glioblastoma cultures. These subpopulations predominantly form the proliferative pool of the primary cultures and are sensitive to irradiation. Thus, profiling of established stem cell markers revealed a surprising result. Except CD44, the tested stem cell markers showed an inverse correlation between expression and radioresistance.

     

What can we learn from Daphnia filtering screens?

The relative filtering setae length (RFSL the length of filteringsetae on the third pair of thoracic limbs expressed as a percent of carapace length) was determined in three developmentalcategories of a reservoir population of Daphnia galeata andits relationship to phytoplankton fluctuation. RFSL of adultfemales immediately after moulting reflects the current foodconditions in the reservoir (higher RFSL at lower food level,and vice versa), whereas RFSL of adult females close to moultingreflects the food conditions several days or weeks ago. RFSLof juvenile animals reacts the most quickly to changing foodconditions, provided the temperature allows frequent moulting.Higher RFSL can also indicate poor-quality food for daphnids,in situations when food quantitative parameters (such as chlorophylla) show high values.     

Continental scale patterns of biodiversity: can higher taxa accurately predict African plant distributions?

The distribution maps of a total of 3563 species, which represent 8.9% of the known African angiosperm flora, were entered into cells representing a one-degree latitude–longitude grid of Sub-Saharan Africa. The computer programme WORLDMAP was used to explore continental scale patterns of biodiversity. The maps were used to assess the use of higher taxa as a surrogate measure for predicting patterns of species richness. Genera were found to predict species richness distributions most closely, with higher taxa (families, orders, subclasses) exhibiting progressively worse correlations. However in two areas, the Cape Region of South Africa and coastal Cameroon, there was a higher species to genus ratio than in other areas of Africa. In the Cape Region this meant that generic richness failed to predict species richness. Hotspots, defined as the 5% of grid cells with the highest scores for richness and range-size rarity, were identified for species and higher taxa. Whilst a high percentage of species richness hotspots were predicted by higher taxa, there were important exceptions like the Cape Region. Species range-size rarity hotspots were not well predicted by higher taxa. Hotspots of higher taxa (families and orders) do not therefore accurately predict the location of species hotspots. Higher taxa appear to provide a powerful and accurate tool that can be used to predict large scale patterns of species biodiversity in Sub-Saharan Africa. However care must be taken when using taxa higher than genera, especially if selecting areas of highest conservation priority. The special case of the Cape Region indicates the danger of extending predictive generalizations as the ecological mechanisms that promote and retain species may not be the same in all places. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 138 , 225–235.     

How reliably can we predict the reliability of protein structure predictions?

Background  

Comparative methods have been the standard techniques for in silico protein structure prediction. The prediction is based on a multiple alignment that contains both reference sequences with known structures and the sequence whose unknown structure is predicted. Intensive research has been made to improve the quality of multiple alignments, since misaligned parts of the multiple alignment yield misleading predictions. However, sometimes all methods fail to predict the correct alignment, because the evolutionary signal is too weak to find the homologous parts due to the large number of mutations that separate the sequences.     

The < folding problem >: can one predict the structure of proteins?

A protein's three-dimensional structure is encoded in its amino acid sequence. The < folding problem > consists in predicting one based on the other. This classic problem of molecular biology has seen important steps forward in recent years. The raw power of today's computers, along with the mobilization of thousands of internauts, have allowed several small proteins to be literally folded up in a computer, through simulations. Moreover, international programs for structural genomics aim to determine the experimental structures of hundreds of proteins in several organisms, and to model the others by homology to known structures. This will lead to a nearly-complete map of the protein structure universe, shedding light on the past evolution and current functions of today's proteins, and suggesting new targets for therapeutic strategies.     

Critical swimming speed of sterlet (Acipenser ruthenus): Does intraspecific hybridization affect swimming performance?

We studied the effect of intraspecific hybridization on swimming performance in sterlet, hypothesizing that such hybridization increases the performance by inducing the hybrid vigor. A total of 12 purebred and hybrid crosses were reproduced from Danube (D) and Volga (V) populations of Acipenser ruthenus. Within each cross, one group of fish was exposed to temperature challenges mimicking the temperature variation in the natural environment during summer. Temperature challenges comprised a constant increase from 19°C to 24°C and then return to 19°C within 12 hr (dT<1°C/hr), and were carried out every third day over the experimental period of 20 days. As a control, fish from each cross were kept at a constant temperature of 19°C. Critical swimming speed (U_crit) was assessed on day 0 (29 days post hatch, dph), 10 (39 dph) and 20 (49 dph). The critical swimming speeds ranged from 5.12 cm/s (1.63 TL/s) to 16.44 cm/s (2.4 TL/s) during the experimental period (29–49 dph). There were no significant differences observed in U_crit between repeatedly temperature challenged and control groups, indicating that the temperature challenge did not alter the swimming performance. The critical swimming speed showed positive relationship with total body length. Comparing intraspecific hybrid crosses with purebred crosses, no significant difference in swimming performance was observed. It is thus concluded that swimming performance is a family specific trait. There is no indication that intraspecific hybridization affects swimming performance nor that close‐to‐natural temperature regimes increase swimming performance.     

Haematopoietic stem cell transplantation: can our genes predict clinical outcome?

Haematopoietic stem cell transplantation (HSCT) is currently the only curative treatment for many patients with malignant and non-malignant haematological diseases. The success of HSCT is greatly reduced by the development of complications, which include graft-versus-host disease (GVHD), relapse and infection. Human leukocyte antigen (HLA) matching of patients and donors is essential, but does not completely prevent these complications; non-HLA genes may also have an impact upon transplant outcome. Polymorphisms within genes that are associated with an individual's capability to mount an immune response to alloantigen and infectious pathogens and/or response to drugs (pharmacogenomics) are all currently being studied for their association with HSCT outcome. This review summarises the potential role of non-HLA polymorphisms in predicting HSCT outcome, from studies on retrospective transplant cohorts of HLA-identical siblings and matched unrelated donors. The clinical relevance and interpretation of non-HLA genetics, and how these could be used alongside clinical risk factors in HSCT, are also discussed.     

Do small-scale exclosure/enclosure experiments predict the effects of large-scale extirpation of freshwater migratory fauna?

A variety of theoretical and empirical studies indicate that the abilities of small-scale experiments to predict responses to large-scale perturbations vary. Small-scale experiments often do not predict the directions of large-scale responses, and relatively few empirical studies have examined whether small-scale experiments predict the magnitudes of large-scale responses. Here we present an empirical example of small-scale manipulations predicting not only the directions but also the magnitudes of the effects of whole-catchment, decades-long decimation of migratory freshwater shrimp populations. In streams of Puerto Rico (USA), we used arena sizes of < 2 m² in 1- to 4-week exclosure/enclosure experiments. Effects of small-scale experiments largely matched those of large-scale shrimp loss above dams for a variety of response variables (abiotic and biotic factors including epilithic fine sediments, algae and organic matter, and invertebrate grazers, detritivores, and predators). The results of our extrapolation contrast with studies of small- versus large-scale perturbations in the temperate zone. Our findings are likely explained by: a set of response variables that are more dominated by within-patch processes than exchange processes, an experimental manipulation that encompassed the characteristic scales of response variables, our use of open arenas lacking cage artifacts, and/or our combination of two distinct experimental approaches (exclosures and enclosures). Based on our study design, we suggest that extrapolation across experimental scales can be greatly enhanced by embedding open arenas within large-scale conditions that represent all treatment levels. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

Do laboratory studies predict parasitoid interaction outcomes in the field?

Studying competitive interactions among natural enemies is important to elucidate the success and non-target impact of candidate biological control agents. Increased regulation of new introductions requires that studies on non-target species be carried out in confined conditions. Hypotheses about potential impacts of biological control agents in the field are based on data from Petri dish or small cage experiments conducted in the laboratory. This study compared the performance of the diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), parasitoids Diadegma insulare (Cresson) (Hymenoptera: Ichneumonidae) and Microplitis plutellae (Muesebeck) (Hymenoptera: Braconidae) in experiments conducted in small cages in the laboratory and in large cages in the field. Results showed no significant differences between laboratory and field outcomes for D. insulare alone and when D. insulare and M. plutellae were combined. For M. plutellae alone, parasitism in the laboratory cages was significantly less than in the field cages. These results demonstrate that laboratory studies may be useful to develop hypotheses on competitive interactions of candidate parasitoid biological control agents.     

Tadpole mortality varies across experimental venues: do laboratory populations predict responses in nature?

Laboratory experiments are widely used to study how populations in nature might respond to various biological interactions, but the relevance of experiments in artificial venues is not known. We compiled mortality and growth data from 424 anuran populations carried out under laboratory, mesocosm, field enclosure, and field settings to determine if major differences exist amongst experimental venues and how this might influence experimental responses of tadpoles amongst venues. Our results show that there are fundamental differences in survival amongst venues, with the highest mortality occurring in field populations and the lowest in laboratory populations. Separation of mesocosm and field enclosure data based on the possibility of predatory interactions indicates that predation is an important factor leading to increased mortality in natural populations. Comparisons of size distributions across venues (although size data were limited for field populations) suggest that variation in tadpole size is low in natural populations compared to populations in artificial venues. We infer from this that mortality has a homogenizing effect on size in nature, resulting in natural populations that are not a random sample of hatched individuals. This finding suggests that populations reared under controlled laboratory conditions in the absence of predation (and other selective pressures) may not be representative of natural populations.     

Power requirements of swimming: do new methods resolve old questions?

A recurring question in the study of fish biomechanics and energeticsis the mechanical power required for tail-swimming at the highspeeds seen among aquatic vertebrates. The quest for answershas been driven by conceptual advances in fluid dynamics, startingwith ideas on the boundary layer and drag initiated by Prandtl,and in measurement techniques starting with force balances focussingon drag and thrust. Drag (=thrust) from measurements on physicalmodels, carcasses, kinematics as inputs to hydromechanical models,and physiological power sources vary from less than that expectedfor an equivalent rigid reference to over an order of magnitudegreater. Estimates of drag and thrust using recent advanceslargely made possible by increased computing power have notresolved the discrepancy. Sources of drag and thrust are notseparable in axial undulatory self propulsion, are open to interpretationand Froude efficiency is zero. Wakes are not easily interpreted,especially for thrust evaluation. We suggest the best measuresof swimming performance are velocity and power consumption forwhich 2D inviscid simulations can give realistic predictions.Steady swimming power is several times that required for towingan equivalent flat plate at the same speed.     

Assay conditions in laboratory experiments: is the use of constant rather than fluctuating temperatures justified when investigating temperature-induced plasticity?

Temperature is an important selective agent in nature. Consequently, temperature-induced plasticity which may help buffering detrimental effects of temperature variation has received considerable attention over recent decades. Laboratory studies have almost exclusively used constant temperatures, while in nature, temperature typically shows pronounced daily fluctuations. Using a factorial design with constant versus fluctuating temperatures and a higher versus a lower mean temperature, we here investigate in the butterfly Lycaena tityrus whether the use of constant temperatures is justified. Fluctuating compared to constant temperatures caused shorter development times, increased heat but decreased cold stress resistance, decreased heat-shock protein expression, and increased immunocompetence. Thus, overall, fluctuating temperatures were more beneficial to the butterflies compared to constant ones. However, despite substantial variation across temperature regimes, the ranking of trait values among treatments remained largely unaffected (e.g. lower constant as well as fluctuating temperatures caused increased pupal mass). Thus, we tentatively conclude that there is no general reason for concern about using constant temperatures in studies investigating phenotypic plasticity, which seem to comprise a fair proxy. However, substantial differences in mean values as well as interactive effects suggest that one needs to be cautious. We further demonstrate negative effects of high temperatures on butterfly immune function, which seem to result from a trade-off between the latter and the heat shock response.     

Intra-annual rainfall variability and grassland productivity: can the past predict the future?

Precipitation quantity has been shown to influence grassland aboveground net primary productivity (ANPP) positively whereas experimental increases in of temporal variability in water availability commonly exhibit a negative relationship with ANPP. We evaluated long term ANPP datasets from the Konza Prairie Long Term Ecological Research (LTER) program (1984–1999) to determine if similar relationships could be identified based on patterns of natural variability (magnitude and timing) in precipitation. ANPP data were analyzed from annually burned sites in native mesic grassland and productivity was partitioned into graminoid (principally C₄ grasses) and forb (C₃ herbaceous) components. Although growing season precipitation amount was the best single predictor of total and grass ANPP (r ²=0.62), several measures of precipitation variability were also significantly and positively correlated with productivity, independent of precipitation amount. These included soil moisture variability, expressed as CV, for June (r ²=0.45) and the mean change in soil moisture between weekly sampling periods in June and August (%wv) (r ²=0.27 and 0.32). In contrast, no significant relationships were found between forb productivity and any of the precipitation variables (p>0.05). A multiple regression model combining precipitation amount and both measures of soil moisture variability substantially increased the fit with productivity (r ²=0.82). These results were not entirely consistent with those of short-term manipulative experiments in the same grassland, however, because soil moisture variability was often positively, not negatively related to ANPP. Differences in results between long and short term experiments may be due to low variability in the historic precipitation record compared to that imposed experimentally as experimental levels of variability exceeded the natural variability of this dataset by a factor of two. Thus, forecasts of ecosystem responses to climate change (i.e. increased climatic variability), based on data constrained by natural and recent historical rainfall patterns may be inadequate for assessing climate change scenarios if precipitation variability in the future is expected to exceed current levels.     

Acoustic signalling in a wolf spider: can signal characteristics predict male quality?

While there has been considerable interest in female choice for male sexual signals, there have been few studies of the underlying information that different aspects of the signal calls convey. Such studies, however, are essential to understand the significance of signals as honest handicaps, arbitrary Fisherian traits and/or in species recognition. We studied the somewhat exceptional system of audible drumming in the wolf spider Hygrolycosa rubrofasciata. We estimated the repeatabilities of signal components, the levels of between-male variance, the symmetry of the signal, the correlations between different aspects of drumming and their correlations with body weight. While in other taxa the frequency of audible signals may convey honest information of male size, in this species signal frequency was not related to male size and had a low repeatability. The pulse rate within each drum was highly repeatable but had a relatively small between-male coefficient of variation. In previous studies on this species, these traits were not important for male mating success. Among the traits directionally preferred by females, signal volume had considerable repeatability. Signal length was repeatable with high variability between males. In one population, signal length and volume were positively correlated with the rate at which males produced the drumming signals, a trait essential for male mating success. Thus, while signal length may reliably indicate male quality, other signal characteristics such as peak frequency and symmetry were not repeatable or were static and not related to any other male traits. Copyright 2000 The Association for the Study of Animal Behaviour.     

Logic of experiments in ecology: is pseudoreplication a pseudoissue?

Hurlbert divides experimental ecologist into ‘those who do not see any need for dispersion (of replicated treatments and controls), and those who do recognize its importance and take whatever measures are necessary to achieve a good dose of it’. Experimental ecologists could also be divided into those who do not see any problems with sacrificing spatial and temporal scales in order to obtain replication, and those who understand that appropriate scale must always have priority over replication. If an experiment is conducted in a spatial or temporal scale, where the predictions of contesting hypotheses are convergent or ambiguous, no amount of technical impeccability can make the work instructive. Conversely, replication can always be obtained afterwards, by conducting more experiments with basically similar design in different areas and by using meta‐analysis. This approach even reduces the sampling bias obtained if resources are allocated to a small number of well‐replicated experiments. For a strict advocate of the hypothetico‐deductive method, replication is unnecessary even as a matter of principle, unless the predicted response is so weak that random background noise is a plausible excuse for a discrepancy between predictions and results. By definition, a prediction is an ‘all‐statement’, referring to all systems within a well‐defined category. What applies to all must apply to any. Hence, choosing two systems and assigning them randomly to a treatment and a control is normally an adequate design for a deductive experiment. The strength of such experiments depends on the firmness of the predictions and their a priori probability of corroboration. Replication is but one of many ways of reducing this probability. Whether the experiment is replicated or not, inferential statistics should always be used, to enable the reader to judge how well the apparent patterns in samples reflect real patterns in statistical populations. The concept ‘pseudoreplication’ amounts to entirely unwarranted stigmatization of a reasonable way to test predictions referring to large‐scale systems.