Homemakers and heights. Intra-household resource allocation and male stature in the Netherlands, 1860-1930.

In this article we test the hypothesis that the secular increase in heights in the course of the second half of the nineteenth century was associated with the rise of the breadwinner-homemaker household. In these 'modern' households, women raised the living standards (quality and quantity of food, hygiene and care) for all members, especially the children. We model the assumed contributions to the family budget by age and gender of household members, and find that a strong imbalance between consumers and producers in the household put severe strains on effective resource allocation, leading to lower net nutrition and lower young adult heights. We suggest a carefully calibrated consumer/producer ratio as an indicator to capture these effects. The ratio is not meant to replace others, and we show that sibling rank order as well as gender preferences also played a role in intra-household resource allocation. For our research, we have used a database with reconstructed life histories (including co-residence) of 3003 Dutch army recruits. Our results indicate that the consumer/producer ratio as experienced by recruits in their early life indeed had a strong impact (-1,8 cm) on their heights. However, this effect differed by social class, which can be explained by differences in acceptance of the income pooling model.

A lost family-planning regime in eighteenth-century Ceylon.

Based on Dutch colonial registers (thombos), this paper reconstructs fertility for two districts in Ceylon, 1756-68. It overcomes challenges in data quality by establishing the outer bounds of plausible estimates in a series of scenarios. Among these, total fertility rates (TFRs) averaged 5.5 in one district, but only 2.7 in the other. These figures exclude the victims of infanticide, a custom noted in European travelogues between about 1660 and 1820. Sex ratios among children differed depending on the number of older siblings, and overall, 27 per cent of girls are missing in one district and 57 per cent in the other. There was little significant variation either in the TFR or the sex ratio by socio-economic status, suggesting that poverty was not a key factor in motivating infanticides. Instead, we argue that at least parts of Ceylon had a forward-looking culture of family planning in the eighteenth century, which was lost in subsequent decades.

Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?

Protein investment costs are considered a major driver for the choice of alternative metabolic strategies. We tested this premise in Lactococcus lactis, a bacterium that exhibits a distinct, anaerobic version of the bacterial Crabtree/Warburg effect; with increasing growth rates it shifts from a high yield metabolic mode [mixed-acid fermentation; 3 adenosine triphosphate (ATP) per glucose] to a low yield metabolic mode (homolactic fermentation; 2 ATP per glucose). We studied growth rate-dependent relative transcription and protein ratios, enzyme activities, and fluxes of L. lactis in glucose-limited chemostats, providing a high-quality and comprehensive data set. A three- to fourfold higher growth rate rerouted metabolism from acetate to lactate as the main fermentation product. However, we observed hardly any changes in transcription, protein levels and enzyme activities. Even levels of ribosomal proteins, constituting a major investment in cellular machinery, changed only slightly. Thus, contrary to the original hypothesis, central metabolism in this organism appears to be hardly regulated at the level of gene expression, but rather at the metabolic level. We conclude that L. lactis is either poorly adapted to growth at low and constant glucose concentrations, or that protein costs play a less important role in fitness than hitherto assumed.

A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.

BACKGROUND: In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed. RESULTS: A number of validation experiments were performed on Lactococcus lactis IL1403 amplicon-based DNA-microarrays. Using the validation scheme and ANOVA, the factors contributing to the variance in normalized DNA-microarray data were estimated. Day-to-day as well as experimenter-dependent variances were shown to contribute strongly to the variance, while dye and culturing had a relatively modest contribution to the variance. CONCLUSION: Even in cases where 90% of the data were kept for analysis and the experiments were performed under challenging conditions (e.g. on different days), the CV was at an acceptable 25%. Clustering experiments showed that trends can be reliably detected also from genes with very low expression levels. The validation scheme thus allows determining conditions that could be improved to yield even higher DNA-microarray data quality.

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

MOTIVATION: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. RESULTS: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. AVAILABILITY: http://www.molgenis.nl