Ecological studies of spores of aquatic hyphomycetes in the cringle brook,lincs

The aquatic Hyphomycete spora of the Cringle Brook, Lincs, was examined by foam sampling and by the use of cellophane impaction traps between August, 1968 and January, 1970.The species most frequently found (Tetracladium marchalianum, Alatospora acuminata and Flagellospora curvula) were generally in agreement with those found by other workers in temperate areas. Impaction trap samples generally contained fewer species than foam samples but filiform spore types such as Flagellospora were more frequently found on traps than in foam suggesting that impaction is more selective towards the filiform spore type than is foam. Many species increased in frequency in autumn accompanying and following leaf fall, and the winter spora was dominated by Alatospora acuminata, Clavariopsis aquatica, Clavatospora stellata, Flagellospora curvula and Lemonniera aquatica. During the summer the spora was dominated by Tetracladium marchalianum.The role of foam and impaction in the balance of aquatic spore populations is discussed in relation to techniques available for their study.     

Effect of population size on the estimation of QTL: a test using resistance to barley stripe rust

The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n=409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods—resampling, selective genotyping, and selective phenotyping—to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping. Electronic Supplementary Material Supplementary material is available for this article at     

Reciprocal influence of connexins and apical junction proteins on their expressions and functions

Membranes of adjacent cells form intercellular junctional complexes to mechanically anchor neighbour cells (anchoring junctions), to seal the paracellular space and to prevent diffusion of integral proteins within the plasma membrane (tight junctions) and to allow cell-to-cell diffusion of small ions and molecules (gap junctions). These different types of specialised plasma membrane microdomains, sharing common adaptor molecules, particularly zonula occludens proteins, frequently present intermingled relationships where the different proteins co-assemble into macromolecular complexes and their expressions are co-ordinately regulated. Proteins forming gap junction channels (connexins, particularly) and proteins fulfilling cell attachment or forming tight junction strands mutually influence expression and functions of one another.     

Enhancing estimation methods for integrating probability and nonprobability survey samples with machine-learning techniques. An application to a Survey on the impact of the COVID-19 pandemic in Spain

Web surveys have replaced Face-to-Face and computer assisted telephone interviewing (CATI) as the main mode of data collection in most countries. This trend was reinforced as a consequence of COVID-19 pandemic-related restrictions. However, this mode still faces significant limitations in obtaining probability-based samples of the general population. For this reason, most web surveys rely on nonprobability survey designs. Whereas probability-based designs continue to be the gold standard in survey sampling, nonprobability web surveys may still prove useful in some situations. For instance, when small subpopulations are the group under study and probability sampling is unlikely to meet sample size requirements, complementing a small probability sample with a larger nonprobability one may improve the efficiency of the estimates. Nonprobability samples may also be designed as a mean for compensating for known biases in probability-based web survey samples by purposely targeting respondent profiles that tend to be underrepresented in these surveys. This is the case in the Survey on the impact of the COVID-19 pandemic in Spain (ESPACOV) that motivates this paper. In this paper, we propose a methodology for combining probability and nonprobability web-based survey samples with the help of machine-learning techniques. We then assess the efficiency of the resulting estimates by comparing them with other strategies that have been used before. Our simulation study and the application of the proposed estimation method to the second wave of the ESPACOV Survey allow us to conclude that this is the best option for reducing the biases observed in our data.     

Living with observational data in biological anthropology

The establishment of cause and effect relationships is a fundamental objective of scientific research. Many lines of evidence can be used to make cause–effect inferences. When statistical data are involved, alternative explanations for the statistical relationship need to be ruled out. These include chance (apparent patterns due to random factors), confounding effects (a relationship between two variables because they are each associated with an unmeasured third variable), and sampling bias (effects due to preexisting properties of compared groups). The gold standard for managing these issues is a controlled randomized experiment. In disciplines such as biological anthropology, where controlled experiments are not possible for many research questions, causal inferences are made from observational data. Methods that statisticians recommend for this difficult objective have not been widely adopted in the biological anthropology literature. Issues involved in using statistics to make valid causal inferences from observational data are discussed.     

Maximizing antibody production in a targeted integration host by optimization of subunit gene dosage and position

Historically, therapeutic protein production in Chinese hamster ovary (CHO) cells has been accomplished by random integration (RI) of expression plasmids into the host cell genome. More recently, the development of targeted integration (TI) host cells has allowed for recombination of plasmid DNA into a predetermined genomic locus, eliminating one contributor to clone-to-clone variability. In this study, a TI host capable of simultaneously integrating two plasmids at the same genomic site was used to assess the effect of antibody heavy chain and light chain gene dosage on antibody productivity. Our results showed that increasing antibody gene copy number can increase specific productivity, but with diminishing returns as more antibody genes are added to the same TI locus. Random integration of additional antibody DNA copies in to a targeted integration cell line showed a further increase in specific productivity, suggesting that targeting additional genomic sites for gene integration may be beneficial. Additionally, the position of antibody genes in the two plasmids was observed to have a strong effect on antibody expression level. These findings shed light on vector design to maximize production of conventional antibodies or tune expression for proper assembly of complex or bispecific antibodies in a TI system.     

Community-based processes behind species richness gradients: contrasting abundance–extinction dynamics and sampling effects in areas of low and high productivity

Aim  To consider the role of local colonization and extinction rates in explaining the generation and maintenance of species richness gradients at the regional scale.
Location  A Mediterranean biome (oak forests, deciduous forests, shrublands, pinewoods, firwoods, alpine heathlands, crops) in Catalonia, Spain.
Methods  We analysed the relative importance of direct and indirect effects of community size in explaining species richness gradients. Direct sampling effects of community size on species richness are predicted by Hubbell's neutral theory of biodiversity and biogeography. The greater the number of individuals in a locality, the greater the number of species expected by random direct sampling effects. Indirect effects are predicted by the abundance–extinction hypothesis, which states that in more productive sites increased population densities and reduced extinction rates may lead to high species richness. The study system was an altitudinal gradient of forest bird species richness.
Results  We found significant support for the existence of both direct and indirect effects of community size in species richness. Thus, both the neutral and the abundance–extinction hypotheses were supported for the altitudinal species richness gradient of forest birds in Catalonia. However, these mechanisms seem to drive variation in species richness only in low-productivity areas; in high-productivity areas, species richness was uncorrelated with community size and productivity measures.
Main conclusions  Our results support the existence of a geographical mosaic of community-based processes behind species richness gradients, with contrasting abundance–extinction dynamics and sampling effects in areas of low and high productivity.     

Estimating Size and Trend of the North Interlake Woodland Caribou Population Using Fecal-DNA and Capture-Recapture Models

A critical step in recovery efforts for endangered and threatened species is the monitoring of population demographic parameters. As part of these efforts, we evaluated the use of fecal-DNA based capture–recapture methods to estimate population sizes and population rate of change for the North Interlake woodland caribou herd (Rangifer tarandus caribou), Manitoba, Canada. This herd is part of the boreal population of woodland caribou, listed as threatened under the federal Species at Risk Act (2003) and the provincial Manitoba Endangered Species Act (2006). Between 2004 and 2009 (9 surveys), we collected 1,080 fecal samples and identified 180 unique genotypes (102 females and 78 males). We used a robust design survey plan with 2 surveys in most years and analysed the data with Program MARK to estimate encounter rates (p), apparent survival rates (φ), rates of population change (λ), and population sizes (N). We estimated these demographic parameters for males and females and for 2 genetic clusters within the North Interlake. The population size estimates were larger for the Lower than the Upper North Interlake area and the proportion of males was lower in the Lower (33%) than the Upper North Interlake (49%). Population rate of change for the entire North Interlake area (2005–2009) using the robust design Pradel model was significantly <1.0 (λ = 0.90, 95% CI: 0.82–0.99) and varied between sex and area with the highest being for males in Lower North Interlake (λ = 0.98, 95% CI: 0.83–1.13) and the lowest being for females in Upper North Interlake (λ = 0.83, 95% CI: 0.69–0.97). The additivity of λ between sex and area is supported on the log scale and translates into males having a λ that is 0.09 greater than females and independent of sex, Lower North Interlake having a λ that is 0.06 greater than Upper North Interlake. Population estimates paralleled these declining trends, which correspond to trends observed in other fragmented populations of woodland caribou along the southern part of their range. The results of this study clearly demonstrate the applicability and success of non-invasive genetic sampling in monitoring populations of woodland caribou. © 2012 The Wildlife Society.