The Scientific Impact of Developing Nations

This paper analyzes science productivity for nine developing countries. Results show that these nations are reducing their science gap, with R&D investments and scientific impact growing at more than double the rate of the developed world. But this “catching up” hides a very uneven picture among these nations, especially on what they are able to generate in terms of impact and output relative to their levels of investment and available resources. Moreover, unlike what one might expect, it is clear that the size of the nations and the relative scale of their R&D investments are not the key drivers of efficiency.     

Density- and frequency-dependent predation of artificial bird nests

Predators are often expected to vary their relative predation rates according to the frequency of prey types in the environment (frequency-dependent predation). The underlying cause for this must lie in some dependency of absolute predation rates on the density of prey types in the environment (density-dependent predation). However, frequency-dependent predation may either be caused by 'simple' density-dependent predation, in which the absolute predation rate on a given prey type depends purely on the density of that type, or by more complex responses in which absolute rates depend also on the density of other prey types. It is usually difficult to distinguish the underlying cause of frequency-dependent predation, because frequencies tend to change as densities change. Here, we describe the results of an experiment conducted to disentangle these phenomena under two prey richness (low and high) conditions. We used artificial bird nests (placed on shrubs and on saplings) baited with quail eggs placed in natural forests as models of natural bird nests. Our results indicate that both the absolute and relative predation rates on the prey types may vary in complex ways. Predation rates depend on a complex interaction between the prey's own density, other prey density and the diversity of prey in the environment. Neglecting to include, or consider, these complexities into analyses may lead to erroneous conclusions in studies of absolute or relative predation rates.     

LOH at 6p21.3 region and HLA class altered phenotypes in bladder carcinomas

Alterations in HLA class I antigen expression have been frequently described in different epithelial tumors and are thought to favor tumor immune escape from T lymphocyte recognition. Multiple molecular mechanisms are responsible for these altered HLA class I tumor phenotypes. Some are structural defects that produce unresponsiveness to treatment with interferons. Others include alterations in regulatory mechanisms that can be switched on by treatment of tumor cells with different cytokines. One important mechanism belonging to the first group is loss of heterozygosity (LOH) at chromosome region 6p21.3, which can lead to HLA haplotype loss. In this investigation, the frequency of LOH at 6p21 chromosome region was studied in 69 bladder carcinomas. Short tandem repeat analysis showed that 35% of cases had LOH in this chromosome region. By considering these results together with immunohistological findings previously published by our group, we identified a distribution pattern of HLA class I altered phenotypes in bladder cancer. The most frequently altered phenotype in bladder carcinomas was total loss of HLA class I expression (17 cases, 25%), followed by phenotype II associated with HLA haplotype loss (12 cases, 17.5%), and HLA allelic loss (ten cases, 14.5%). Nine cases (13%) were classified as having a compound phenotype, five cases (7%) as having HLA locus loss, and in 16 cases (23%) no alteration in HLA expression was detected. An important conclusion of this report is that a combination of different molecular and immunohistological techniques is required to precisely define which HLA alleles are lost during tumor progression and to characterize the underlying mechanisms of these losses. These studies should be performed when a cancer patient is to be included in an immunotherapy protocol that aims to stimulate different immune effector mechanisms.     

Phenotype Matching and Early Social Conditions Affect Shoaling and Exploration Decisions

Early social conditions are vital for the establishment of future social interactions. Less, however, is known about how differences in early social conditions contribute to the process of individual recognition and subsequently in the decision of associating and exploring behaviours. In this study, we address this gap in the Trinidadian guppy Poecilia reticulata and test the prediction that fish would show a higher tendency to recognize and associate with individuals of similar phenotype. This prediction was tested by comparing the likelihood of association and latency to explore a novel area in males and females when in the presence of individuals that were familiar (reared together but from different populations), from the same population of origin (from the same population but deprived of interaction with each other), or were unfamiliar (different population and have never interacted). Both early social conditions and population of origin (phenotype matching) affected the tendency to shoal and explore. Females, but not males, exhibited identical preference to associate either with unfamiliar females as with familiar females from a different population. Importantly, female preference did not occur with unfamiliar individuals from a different population. In contrast with our prediction, tendency to shoal did not predict exploration propensity. Males always start exploration before the group whenever unfamiliar males composed the group. Females on the other hand only moved to the novel area after seeing the group doing so, revealing sexual dimorphism in exploratory behaviour. Our results provide evidence for a familiarity and phenotypic matching recognition mechanism at the population level and also highlight the importance of accounting for differences between sexes when investigating the effects of early social conditions.     

Biosynthesis of eicosanoids and transcellular metabolism of leukotrienes in murine bone marrow cells

Leukotriene B(4) (LTB(4)) biosynthesis by polymorphonuclear leukocytes (PMNs) is an important factor of inflammatory responses. PMNs also release LTA(4), an unstable intermediate that can be taken up by neighboring cells and metabolized into LTC(4). Most studies of LT synthesis have been carried out using human PMNs, but very little information is available about mouse PMNs. Mouse bone marrow PMNs were found to synthesize eicosanoids upon stimulation with A23187, fMLP, or zymosan. The major eicosanoids produced are LTB(4) and 5-hydroxyeicosatetraenoic acid, with some nonenzymatic products of LTA(4) hydrolysis. No cysteinyl leukotrienes were produced, in contrast to what was observed with human blood neutrophil preparations. Human megakaryoblast-like MEG-01 cells synthesized thromboxane B(2) and prostaglandin E(2) in response to A23187 but produced no 5-lipoxygenase (5-LO)-derived eicosanoids. When mouse bone marrow cells (mBMCs) and MEG-01 cells were stimulated during coincubation, LTC(4) and LTD(4) were produced. Mouse peritoneal macrophages from 5-LO-deficient mice were able to synthesize LTC(4) when incubated with mBMCs from wild-type mice, demonstrating transcellular exchange of LTA(4) from mBMCs into murine peritoneal macrophages. These data demonstrate that murine bone marrow PMNs are a valid model for the study of LT biosynthesis, which now offers the possibility to investigate specific biochemical pathways through the use of transgenic mice.     

Estimation of coancestry in Iberian pigs using molecular markers

Genetic markers provide a useful tool toestimate pairwise coancestry betweenindividuals in the absence of a known pedigree. Inthe present work 62 pigs from two relatedstrains of Iberian breed, Guadyerbas andTorbiscal, belonging to a conservationprogramme with completely known pedigrees since1945, have been genotyped for 49microsatellites. Four coefficients thatsummarise molecular resemblance betweenindividuals together with eightestimators of coancestry have been calculatedfrom this information. Their values werecompared with the genealogical coancestry,calculated from the complete or partialpedigree. The eight estimations obtained usingmolecular information substantiallyunderestimate the coancestry calculated usingthe genealogical analysis. The correlationbetween the estimates and the genealogicalvalues was also calculated. This correlationwas high, between 0.78 and 0.93 for differentestimators, when all pairwise comparisons amongthe 62 animals were considered. However, thecorrelation decreases remarkably to 0.49–0.69and 0.37–0.47 for the Guadyerbas and Torbiscalpopulations respectively, when they wereanalysed separately. All the correlations weresimilar to those obtained when using simplecoefficients of molecular resemblance such asmolecular coancestry or similarity indexes.Finally, simulations were carried out tofurther explore the results obtained. It isconcluded that lack of information on theallele frequencies in the base population mayexplain the bias of these estimators inpopulations with complex pedigrees.     

Reduction of indole‐3‐acetic acid methyltransferase activity compensates for high‐temperature male sterility in Arabidopsis

High temperature is a general stress factor that causes a decrease in crop yield. It has been shown that auxin application reduces the male sterility caused by exposure to higher temperatures. However, widespread application of a hormone with vast effects on plant physiology may be discouraged in many cases. Therefore, the generation of new plant varieties that locally enhance auxin in reproductive organs may represent an alternative strategy. We have explored the possibility of increasing indole‐3‐acetic acid (IAA) in ovaries by reducing IAA methyltransferase1 (IAMT1) activity in Arabidopsis thaliana. The iamt1 mutant showed increased auxin signalling in funiculi, which correlated with a higher growth rate of wild‐type pollen in contact with mutant ovaries and premature ovule fertilization. While the production of seeds per fruit was similar in the wild type and the mutant at 20 °C, exposure to 29 °C caused a more severe decrease in fertility in the wild type than in the mutant. Loss of IAMT1 activity was also associated with the production of more nodes after flowering and higher tolerance of the shoot apical meristem to higher temperatures. As a consequence, the productivity of the iamt1 mutant under higher temperatures was more than double of that of the wild type, with almost no apparent trade‐off.     

A note on the rationale for estimating genealogical coancestry from molecular markers

Background

Genetic relatedness or similarity between individuals is a key concept in population, quantitative and conservation genetics. When the pedigree of a population is available and assuming a founder population from which the genealogical records start, genetic relatedness between individuals can be estimated by the coancestry coefficient. If pedigree data is lacking or incomplete, estimation of the genetic similarity between individuals relies on molecular markers, using either molecular coancestry or molecular covariance. Some relationships between genealogical and molecular coancestries and covariances have already been described in the literature.

Methods

We show how the expected values of the empirical measures of similarity based on molecular marker data are functions of the genealogical coancestry. From these formulas, it is easy to derive estimators of genealogical coancestry from molecular data. We include variation of allelic frequencies in the estimators.

Results

The estimators are illustrated with simulated examples and with a real dataset from dairy cattle. In general, estimators are accurate and only slightly biased. From the real data set, estimators based on covariances are more compatible with genealogical coancestries than those based on molecular coancestries. A frequently used estimator based on the average of estimated coancestries produced inflated coancestries and numerical instability. The consequences of unknown gene frequencies in the founder population are briefly discussed, along with alternatives to overcome this limitation.

Conclusions

Estimators of genealogical coancestry based on molecular data are easy to derive. Estimators based on molecular covariance are more accurate than those based on identity by state. A correction considering the random distribution of allelic frequencies improves accuracy of these estimators, especially for populations with very strong drift.     

Linking Changes in Epithelial Morphogenesis to Cancer Mutations Using Computational Modeling

Most tumors arise from epithelial tissues, such as mammary glands and lobules, and their initiation is associated with the disruption of a finely defined epithelial architecture. Progression from intraductal to invasive tumors is related to genetic mutations that occur at a subcellular level but manifest themselves as functional and morphological changes at the cellular and tissue scales, respectively. Elevated proliferation and loss of epithelial polarization are the two most noticeable changes in cell phenotypes during this process. As a result, many three-dimensional cultures of tumorigenic clones show highly aberrant morphologies when compared to regular epithelial monolayers enclosing the hollow lumen (acini). In order to shed light on phenotypic changes associated with tumor cells, we applied the bio-mechanical IBCell model of normal epithelial morphogenesis quantitatively matched to data acquired from the non-tumorigenic human mammary cell line, MCF10A. We then used a high-throughput simulation study to reveal how modifications in model parameters influence changes in the simulated architecture. Three parameters have been considered in our study, which define cell sensitivity to proliferative, apoptotic and cell-ECM adhesive cues. By mapping experimental morphologies of four MCF10A-derived cell lines carrying different oncogenic mutations onto the model parameter space, we identified changes in cellular processes potentially underlying structural modifications of these mutants. As a case study, we focused on MCF10A cells expressing an oncogenic mutant HER2-YVMA to quantitatively assess changes in cell doubling time, cell apoptotic rate, and cell sensitivity to ECM accumulation when compared to the parental non-tumorigenic cell line. By mapping in vitro mutant morphologies onto in silico ones we have generated a means of linking the morphological and molecular scales via computational modeling. Thus, IBCell in combination with 3D acini cultures can form a computational/experimental platform for suggesting the relationship between the histopathology of neoplastic lesions and their underlying molecular defects.