Population analysis in mass cultures of Tubifex tubifex

Mass cultures of Tubifex tubifex from Lake Orta were kept in the lab at 20 °C starting with different initial densities (10, 45, 86, 161 ind · jar^–1), with the aim of evaluating the effect of density on population numbers and on population parameters. The results show that density mainly controls fecundity, growth, maturation and ovigeration rates. Growth rates and mean number of eggs laid/ovigerous (R₀) are inversely related to density, but generation time appears to be directly related. Very low or very high initial densities display, at different times of the culture history, efficient density controls. Intermediate N₀ seem to bring about situations of bad control, easily leading to numerical overshoots. A possible implementation of a population dynamics model (Bonomi & Di Cola, 1980), originally used for laboratory observations on T. tubifex cohorts was considered, including some density control functions derived from our observations on cohort and mass cultures in some transfer rates and in fecundity rate.     

Leaf Water Relations and Sapflow in Eastern Cottonwood (Populus deltoides Bartr.) Trees Planted for Phytoremediation of a Groundwater Pollutant

Plants that remediate groundwater pollutants may offer a feasible alternative to the traditional and more expensive practices. Because its success depends on water use, this approach requires a complete understanding of species-specific transpiration patterns. The objectives of this study were (1) to quantify tree and stand-level transpiration in two age classes (whips and 1-year-old seedlings) of eastern cottonwoods (Populus deltoides Bartr.), and (2) to determine climatic and physiological driving variables at the Carswell Air Force Base in central Texas, USA. Trichloroethylene (TCE) was detected in shallow (2 to 3 m) groundwater in the early 1980s. Cottonwood whips and 1-year-old potted seedlings were planted in two separate 0.15-ha plantations in spring 1996. Sapflow gauges determined sapflow on 14 to 16 trees in May, June, July, August, and October 1997. Without adjusting for differences in tree size, sapflow rates were greater for 1-year-old trees than whips (peak values were 0.75 and 0.53 kg hr^-1 tree^-1, respectively). When adjusted for tree size, the pattern reversed, with whips having significantly greater sapflow rates than 1-year-old trees (peak values were 0.053 and 0.045 kg cm^-2 hr^-1, respectively). Temporal variation (diurnal and seasonal) in sapflow rates was principally related to VPD, solar radiation, and leaf conductance. Extrapolating to the stand and across the growing season, the plantations transpired ~25 cm of water. Early attainment of high levels of transpiration indicates that the stands will transpire considerably more water as leaf area and root exploitation increases with stand development.     

Biotic effects dominate the inter-annual variability in ecosystem carbon exchange in a Tibetan alpine meadow

青藏高寒草甸生态系统碳交换年际变异主要受生物效应影响 位于西藏的高寒草甸生态系统具有敏感脆弱的特点,在全球气候变化背景下,其碳汇功能的变化受到了广泛的关注。因此,本研究旨在明确高寒草甸碳通量的年际变异特征,并进一步量化各驱动因素对碳通量变异的贡献。本研究基于7年(2012–2018)的碳通量与气象因子和生物因子数据,采用一组查表法(look-up tables,LUTs)对高寒草甸碳通量的年际变异来源进行了拆分和量化,并进一步利用线性扰动分析法量化了各个关键因子对碳通量变异的贡献。2012–2018年,高寒草甸生态系统净生产力(net ecosystem productivity, NEP)、总初级生产力(gross primary productivity, GPP)和生态系统呼吸(ecosystem respiration, Re)多年平均值分别为3.31 ± 26.90、210.18 ± 48.35和206.88 ± 28.45 g C m⁻² y⁻¹,表现出了较大的年际变异。本研究通过区分和量化气象因子和生物因子对碳通量年际变异的贡献,发现了生物因子对年际变异的主控作用。此外,发现了气象因子和生物因子之间的负反馈作用。在气象因子中,只有土壤水分对年际变异的贡献相对较大,并在气象因子和生物因子的相互作用中发挥着调节作用。这些结果表明,在气候变化背景下,若要准确估算碳通量,需考虑生物因子的作用。     

A guide to the perplexed on the specificity of antibodies

Many investigators are unaware of the potential problems with specificity of antibodies and the need to document antibody characterization meticulously for each antibody that is used. In this review, I consider the principles of antibody action and how they define a set of rules for what information should be obtained by the investigator before using an antibody in a serious scientific investigation.     

Increasing the effectiveness of spring trap crops for Leptinotarsa decemlineata

Insecticide resistance problems have increased interest in trap crops as a cultural control strategy for overwintered Colorado potato beetle adults, Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae). Growers in the north central United States have noticed and treated concentrations of adults at the edge of some of their potato fields each spring. Based on sampling in commercial potato fields over a 2-year period, early planted fields that are adjacent to the previous year's potato crop are most likely to have concentrations of adults at the field edge. Frequency of fields with significantly more adults at the edges than in the center sections as well as adult population density in the center sections of fields declined with both distance from the previous potato field and later planting date. The effects of both physical and chemical barriers to movement into potato fields from the field edges were studied in small plot trials and at the edges of commercial potato fields. In small plot trials, physical barriers had a greater impact than chemical barriers on adult beetle movement from a potato trap crop to the protected potatoes beyond the barrier. Barrier treatments reduced beetle numbers in and just beyond the barrier in commercial fields, but the effects were localized and no significant reduction of beetles was observed further into the field. Beetle flight was hypothesized to be responsible for the localized effects of barrier treatments and the lack of edge concentrations in later planted and more distantly rotated fields. In field studies, larger potato plants attracted more colonizing potato beetles than smaller plants. Attracting Colorado potato beetles to trap crops containing potato plants that were larger than those in the remainder of the field, however, provided no significant reduction of beetles in the remainder of the field. We found little opportunity to reduce beetle populations with trap crops at the edges of potato fields without controlling the adults in the trap crop itself. Growers can exploit naturally occurring concentrations of adults at the edges of early and adjacent potato plantings if they are prepared to monitor and regularly treat the field edges.     

Controls for Immunohistochemistry: The Histochemical Society’s Standards of Practice for Validation of Immunohistochemical Assays

Immunohistochemistry is widely used in biomedical research to localize specific epitopes of molecules in cells and tissues. The validity of interpretations based on immunohistochemistry requires appropriate positive and negative controls that are often not reported in publications. This omission may lead to incorrect interpretations and irreproducible results in the literature and contribute to wasted time, effort, and resources as well as erosion of confidence in scientific investigation by the general public, legislative bodies and funding agencies. The present article summarizes essential controls required for validation of immunohistochemical findings and represents a standard of practice for the use of immunohistochemistry in research and diagnostic investigations. Adherence to the guidelines described in the present article can be cited by authors as support for the validity of interpretations of the immunohistochemistry reported in their publications.     

Interannual variability of NDVI and its relationship to climate for North American shrublands and grasslands

Abstract. Our objective was to analyse the interannual variability of different characteristics of the seasonal dynamics of NDVI and their relationships with climatic variables for grassland and shrubland sites of North America. We selected twenty-five sites located in relatively undisturbed areas. We analysed the variability of seven traits derived from the annual dynamics of the NDVI at each site: the annual integral, the difference between maximum and minimum NDVI, the dates of the inflection points of a double logistic model fitted to the NDVI curve, the difference between these dates, the date of maximum NDVI, and the coefficient of determination of the double logistic model. The temporal variability of traits that integrated aspects of primary productivity over the year was lower than those related to seasonality. This suggests that from year to year, grassland and shrubland ecosystems would differ more in the timing of production and senescence than in the total amount of carbon fixed. The integral of NDVI showed less temporal variability than annual precipitation. The coefficient of variation of both precipitation and the NDVI integral were positively related. The slope of the relationship was significantly lower than 1, indicating that the variability of ecosystem function is a lower proportion of the variability of annual precipitation in areas with a high relative variability of this climatic variable than in areas of low variability. The variability of most of the NDVI traits analysed showed a negative and, in general, non-linear relationship with annual precipitation. The same kind of relationship has been reported elsewhere for annual precipitation and its coefficient of variation. Mean annual precipitation has been reported as the main control of above-ground net primary production in grassland and shrubland ecosystems. Our results suggest that this climatic variable is also associated with the interannual variability of carbon gains, such as the primary production and its seasonality.     

Uniform magnetic fields and double-wrapped coil systems: improved techniques for the design of bioelectromagnetic experiments.

A common mistake in biomagnetic experimentation is the assumption that Helmholtz coils provide uniform magnetic fields; this is true only for a limited volume at their center. Substantial improvements on this design have been made during the past 140 years with systems of three, four, and five coils. Numerical comparisons of the field uniformity generated by these designs are made here, along with a table of construction details and recommendations for their use in experiments in which large volumes of uniform intensity magnetic exposures are needed. Double-wrapping, or systems of bifilar windings, can also help control for the non-magnetic effects of the electric coils used in many experiments. In this design, each coil is wrapped in parallel with two separate, adjacent strands of copper wire, rather than the single strand used normally. If currents are flowing in antiparallel directions, the magnetic fields generated by each strand will cancel and yield virtually no external magnetic field, whereas parallel currents will yield an external field. Both cases will produce similar non-magnetic effects of ohmic heating, and simple measures can reduce the small vibration and electric field differences. Control experiments can then be designed such that the only major difference between treated and untreated groups is the presence or absence of the magnetic field. Double-wrapped coils also facilitate the use of truly double-blind protocol, as the same apparatus can be used either for experimental or control groups.     

An analysis of soil respiration across northern hemisphere temperate ecosystems

Over two-thirds of terrestrial carbon is stored belowground and a significant amount of atmospheric CO₂ is respired by roots and microbes in soils. For this analysis, soil respiration (Rs) data were assembled from 31 AmeriFlux and CarboEurope sites representing deciduous broadleaf, evergreen needleleaf, grasslands, mixed deciduous/evergreen and woodland/savanna ecosystem types. Lowest to highest rates of soil respiration averaged over the growing season were grassland and woodland/savanna < deciduous broadleaf forests < evergreen needleleaf, mixed deciduous/evergreen forests with growing season soil respiration significantly different between forested and non-forested biomes (p < 0.001). Timing of peak respiration rates during the growing season varied from March/April in grasslands to July–September for all other biomes. Biomes with overall strongest relationship between soil respiration and soil temperature were from the deciduous and mixed forests (R² ≥ 0.65). Maximum soil respiration was weakly related to maximum fine root biomass (R² = 0.28) and positively related to the previous years’ annual litterfall (R² = 0.46). Published rates of annual soil respiration were linearly related to LAI and fine root carbon (R² = 0.48, 0.47), as well as net primary production (NPP) (R² = 0.44). At 10 sites, maximum growing season Rs was weakly correlated with annual GPP estimated from eddy covariance towersites (R² = 0.29; p < 0.05), and annual soil respiration and total growing season Rs were not correlated with annual GPP (p > 0.1). Yet, previous studies indicate correlations on shorter time scales within site (e.g., weekly, monthly). Estimates of annual GPP from the Biome-BGC model were strongly correlated with observed annual estimates of soil respiration for six sites (R² = 0.84; p < 0.01). Correlations from observations of Rs with NPP, LAI, fine root biomass and litterfall relate above and belowground inputs to labile pools that are available for decomposition. Our results suggest that simple empirical relationships with temperature and/or moisture that may be robust at individual sites may not be adequate to characterize soil CO₂ effluxes across space and time, agreeing with other multi-site studies. Information is needed on the timing and phenological controls of substrate availability (e.g., fine roots, LAI) and inputs (e.g., root turnover, litterfall) to improve our ability to accurately quantify the relationships between soil CO₂ effluxes and carbon substrate storage.For this study, these authors received significant contributions from: M. Aubinet, D. Baldocchi, C. Bernhofer, P. Bolstad, A. Bosc, J.L. Campbell, Y. Cheng, J. Curiel Yuste, P. Curtis, E.A. Davidson, D. Epron, A. Granier, T. Grünwald, D. Hollinger, I.A. Janssens, B. Longdoz, D. Loustau, J. Martin, R. Monson, W. Oechel, J. Pippen, F. Ponti, R. Ryel, K. Savage, L. Scott-Denton, J.-A. Subke, J. Tang, J. Tenhunen, V. Turcu, C. S. Vogel.     

The Ethical Use of Placebo Controls in Clinical Research: The Declaration of Helsinki

Medical ethicists have questioned the use of no-treatment (placebo and sham procedure) controlled studies of new therapies when safe and effective standard therapies are available for use as an active or equivalence control. Current ethical principles of conduct for biomedical research specifically prohibit designs that withhold or deny the best proven diagnostic and therapeutic treatment to any participant in a clinical study, including those individuals who consent to randomization into a control group. Studies of psychophysiological therapies are often criticized on the grounds they lack a placebo or sham treatment control group. This paper briefly reviews the history of the problem and discusses the ethical standards that govern human research as derived from the Nuremberg Code and the Declaration of Helsinki. An examination of the problem with regard to research involving EEG biofeedback therapy for Attention-Deficit/Hyperactivity Disorder, Traumatic Brain Injury, and depression serves to highlight the issues. It is concluded that the active treatment control (treatment equivalence) design is most appropriate for those clinical studies examining disorders for which there is a known, effective treatment. Sham- or placebo-controlled studies are ethically acceptable for those disorders for which no effective treatment is available.     

Modelling the effectiveness of contraception for controlling introduced populations of elephant in South Africa

Re‐introduced African elephant (Loxodonta africana Blumenbach) populations are growing at very high rates in many of southern Africa’s reserves, have attained densities higher than previously thought possible and may be exhibiting irruptive growth. Active management of such populations is necessary to prevent the potentially negative effects on habitat and biodiversity that are associated with elephant overpopulation. One potentially feasible method of elephant management is immunocontraception, but very little is known about the long‐term effectiveness of this method. Using demographic data from three South African elephant populations, we made model projections of the effects of contraception on population growth rates to determine whether contraception may be a feasible management tool for elephant. In comparison with noncontracepted populations, realistic reductions in population growth rate after 20 years of contraception were projected to be up to c. 64%, with 50% being a very feasible target. Through its ability to reduce population growth rates, immunocontraception should be an effective tool for preventing or minimizing irruption in elephants and, perhaps, other introduced ungulate species.     

Lake Erie Microcystis: Relationship between microcystin production, dynamics of genotypes and environmental parameters in a large lake

Cyanobacteria of genus Microcystis sp. have been commonly found in Lake Erie waters during recent summer seasons. In an effort to elucidate relationships between microcystin production, genotypic composition of Microcystis community and environmental parameters in a large lake ecosystem, we collected DNA samples and environmental data during a three-year (2003–2005) survey within Lake Erie and used the data to perform a series of correlation analyses. Cyanobacteria and Microcystis genotypes were quantified using quantitative real-time PCR (qPCR). Our data show that Microcystis in Lake Erie forms up to 42% of all cyanobacteria, and that Microcystis exists as a mixed population of potentially toxic and (primarily) non-toxic genotypes. In the entire lake, the total abundance of Microcystis as well as the abundance of microcystin-producing Microcystis is strongly correlated with the abundance of cyanobacteria suggesting that Microcystis is a significant component of the cyanobacterial community in Lake Erie during summer seasons. The proportion of total Microcystis of all cyanobacteria was strongly linked to the microcystin concentrations, while the percentage of microcystin-producing genotypes within Microcystis population showed no correlation with microcystin concentrations. Correlation analysis indicated that increasing total phosphorus concentrations correlate strongly with increasing microcystin concentrations as well as with the total abundance of Microcystis and microcystin-producing Microcystis.     

Evaluating methods for estimating local effective population size with and without migration

Effective population size is a fundamental parameter in population genetics, evolutionary biology, and conservation biology, yet its estimation can be fraught with difficulties. Several methods to estimate N_e from genetic data have been developed that take advantage of various approaches for inferring N_e. The ability of these methods to accurately estimate N_e, however, has not been comprehensively examined. In this study, we employ seven of the most cited methods for estimating N_e from genetic data (Colony2, CoNe, Estim, MLNe, ONeSAMP, TMVP, and NeEstimator including LDNe) across simulated datasets with populations experiencing migration or no migration. The simulated population demographies are an isolated population with no immigration, an island model metapopulation with a sink population receiving immigrants, and an isolation by distance stepping stone model of populations. We find considerable variance in performance of these methods, both within and across demographic scenarios, with some methods performing very poorly. The most accurate estimates of N_e can be obtained by using LDNe, MLNe, or TMVP; however each of these approaches is outperformed by another in a differing demographic scenario. Knowledge of the approximate demography of population as well as the availability of temporal data largely improves N_e estimates.     

Power priors based on multiple historical studies for binary outcomes

Incorporating historical information into the design and analysis of a new clinical trial has been the subject of much recent discussion. For example, in the context of clinical trials of antibiotics for drug resistant infections, where patients with specific infections can be difficult to recruit, there is often only limited and heterogeneous information available from the historical trials. To make the best use of the combined information at hand, we consider an approach based on the multiple power prior that allows the prior weight of each historical study to be chosen adaptively by empirical Bayes. This choice of weight has advantages in that it varies commensurably with differences in the historical and current data and can choose weights near 1 if the data from the corresponding historical study are similar enough to the data from the current study. Fully Bayesian approaches are also considered. The methods are applied to data from antibiotics trials. An analysis of the operating characteristics in a binomial setting shows that the proposed empirical Bayes adaptive method works well, compared to several alternative approaches, including the meta‐analytic prior.     

When are genetic methods useful for estimating contemporary abundance and detecting population trends?

The utility of microsatellite markers for inferring population size and trend has not been rigorously examined, even though these markers are commonly used to monitor the demography of natural populations. We assessed the ability of a linkage disequilibrium estimator of effective population size (N_e) and a simple capture-recapture estimator of abundance (N) to quantify the size and trend of stable or declining populations (true N = 100–10,000), using simulated Wright–Fisher populations. Neither method accurately or precisely estimated abundance at sample sizes of S = 30 individuals, regardless of true N. However, if larger samples of S = 60 or 120 individuals were collected, these methods provided useful insights into abundance and trends for populations of N = 100–500. At small population sizes (N = 100 or 250), precision of the N_e estimates was improved slightly more by a doubling of loci sampled than by a doubling of individuals sampled. In general, monitoring N_e proved a more robust means of identifying stable and declining populations than monitoring N over most of the parameter space we explored, and performance of the N_e estimator is further enhanced if the N_e/N ratio is low. However, at the largest population size (N = 10,000), N estimation outperformed N_e. Both methods generally required ≥ 5 generations to pass between sampling events to correctly identify population trend.     

CorrSieve: software for summarizing and evaluating Structure output

The clustering software Structure has been used extensively to infer population structure in natural populations from multilocus genotype data. Determining meaningful values of K, the assumed number of subpopulations is one of the primary challenges of making biological inferences from Structure data. The package CorrSieve summarizes Structure output and performs a number of tests, including both previously reported methods and novel ones, to help determine meaningful values of K.     

A population dynamics model for annual plants subject to inbreeding depression

Summary We present a population dynamics model for annual plants subject to density dependent competition and a decline in mean individual fitness with inbreeding. An analysis of this model provides three distinct sets of parameter values that define the relative influence of inbreeding depression and density on population growth. First, a population with a relatively high finite rate of increase and a relatively small environmental carrying capacity can persist in spite of low levels of inbreeding depression. These types of population may occur during a bottleneck event that is caused by pure predation (or collecting) pressure rather than loss of habitat. Second, there can exist a minimum viable population size when the finite rate of increase is relatively low and the population is also affected by density: the growth or decline of the population will depend on the initial population size. Third, when the population is small enough to be simultaneously effected by density and by inbreeding depression, there can be no viable population.