Mouse urogenital development: a practical approach

A detailed knowledge of the developmental anatomy of the embryonic mouse urogenital tract is required to recognize mutant urogenital phenotypes in transgenic and knock-out mice. Accordingly, the purpose of this article is to review urogenital development in the mouse embryo and to give an illustrated methodological protocol for the dissection of urogenital organ rudiments at 12-13 days of gestation (E12-13) to isolate the urogenital ridge and at E16 to isolate the seminal vesicle, Müllerian duct, Wolffian duct, and prostatic rudiment, the urogenital sinus (UGS). The UGS can be cultured and, in the presence of testosterone, prostatic buds form in vitro. Because of the importance of mesenchymal-epithelial interactions in urogenital development, methods for the isolation of epithelium and mesenchyme from the embryonic urogenital sinus are also described. Urogenital sinus mesenchyme (UGM) and urogenital sinus epithelium (UGE) can be used to construct tissue recombinants that can either be grown in vitro or grafted in vivo for the study of epithelial-mesenchymal interactions in prostatic development.     

Observing copepods through a genomic lens

Background

Copepods outnumber every other multicellular animal group. They are critical components of the world's freshwater and marine ecosystems, sensitive indicators of local and global climate change, key ecosystem service providers, parasites and predators of economically important aquatic animals and potential vectors of waterborne disease. Copepods sustain the world fisheries that nourish and support human populations. Although genomic tools have transformed many areas of biological and biomedical research, their power to elucidate aspects of the biology, behavior and ecology of copepods has only recently begun to be exploited.

Discussion

The extraordinary biological and ecological diversity of the subclass Copepoda provides both unique advantages for addressing key problems in aquatic systems and formidable challenges for developing a focused genomics strategy. This article provides an overview of genomic studies of copepods and discusses strategies for using genomics tools to address key questions at levels extending from individuals to ecosystems. Genomics can, for instance, help to decipher patterns of genome evolution such as those that occur during transitions from free living to symbiotic and parasitic lifestyles and can assist in the identification of genetic mechanisms and accompanying physiological changes associated with adaptation to new or physiologically challenging environments. The adaptive significance of the diversity in genome size and unique mechanisms of genome reorganization during development could similarly be explored. Genome-wide and EST studies of parasitic copepods of salmon and large EST studies of selected free-living copepods have demonstrated the potential utility of modern genomics approaches for the study of copepods and have generated resources such as EST libraries, shotgun genome sequences, BAC libraries, genome maps and inbred lines that will be invaluable in assisting further efforts to provide genomics tools for copepods.

Summary

Genomics research on copepods is needed to extend our exploration and characterization of their fundamental biological traits, so that we can better understand how copepods function and interact in diverse environments. Availability of large scale genomics resources will also open doors to a wide range of systems biology type studies that view the organism as the fundamental system in which to address key questions in ecology and evolution.     

Precision networking: a look through the eyes of a fly.

The establishment of the proper connectivity in the nervous system requires specific target selection between individual presynaptic and postsynaptic cells. It has been postulated that cell adhesion molecules likely participate in these local recognition events. However, the broad developmental roles of many of these molecules have presented an obstacle for loss-of-function analyses. A recent series of genetic studies in the Drosophila visual system has demonstrated roles for several cell adhesion molecules, including N-cadherin and the receptor protein tyrosine phosphatase LAR in proper synaptic targeting of photoreceptor axons.     

Environment and sustainable development indicators in Lebanon: A practical municipal level approach

In close coordination and collaboration with the Lebanese Environment and Development Observatory at the Ministry of Environment, the Faculty of Health Science at the University of Balamand developed an action plan to “establish a decentralized environment and sustainable development monitoring network through local authorities using agreed upon environment and development indicators”. This effort was part of a pilot regional project involving six Mediterranean countries with funds provided by the Ministry of Environment, Greece through the University of Athens to establish a “Mediterranean Environmental Reporting, Monitoring and Information System” for Mediterranean countries. According to a well-defined selection process, a total of 44 municipalities out of more than 700 municipalities belonging to three unions representing three different regions in Lebanon qualified for inclusion in the project with 17 choosing to participate in MED-ERMIS-Lebanon. Meetings with concerned public officials at all levels were then held to ensure the support of all relevant governmental institutions and therefore the success of the project. Applying a participatory approach, local government officers and representatives from concerned ministries, universities, research centers and non-governmental organizations were invited to attend the different workshops at the municipality level to produce the appropriate lists of indicators. A total of 110 indicators were generated and grouped into four major categories adopted by the national indicator system: (1) population and socio-economics; (2) economic activities; (3) environment; and (4) sustainable development activities and policies. “Indicator data sheets”, a “door-to-door questionnaire” and a “municipality archive survey” were developed for data compilation, calculation, and presentation; and a total of 6250 surveys were filled (≈20%). Field surveying was carried out by trained teams using the “Multistage Cluster Systematic Random Sampling” technique and data entered for analysis. Data is being currently interpreted, and a user-friendly software application hosted on the University of Balamand web-site to facilitate the updating of indicators and the dissemination of indicator data on the World Wide Web has been developed allowing access to information by all interested parties.     

Estimating the power of a proposed linkage study: a practical computer simulation approach.

I describe a simulation method to estimate the power to detect linkage given a set of pedigrees of known structure and for which family history data may be available. This method can be applied to autosomal and X-linked dominant diseases; depending on the pedigrees under consideration, it will often be applicable for autosomal and X-linked recessive diseases. This power calculation can most usefully be undertaken after family history data are gathered, but prior to examination and testing of pedigree members to obtain marker information. Of key importance, the power calculation is straightforward to carry out and not too time-consuming; it is practical even on a microcomputer. The result of the power calculation is an objective answer to the question: Will my families be sufficient to demonstrate linkage?     

Protection goals in environmental risk assessment: a practical approach

Policy protection goals are set up in most countries to minimise harm to the environment, humans and animals caused by human activities. Decisions on whether to approve new agricultural products, like pesticides or genetically modified (GM) crops, take into account these policy protection goals. To support decision-making, applications for approval of commercial uses of GM crops usually comprise an environmental risk assessment (ERA). These risk assessments are analytical tools, based on science, that follow a conceptual model that includes a problem formulation step where policy protection goals are considered. However, in most countries, risk assessors face major problems in that policy protection goals set in the legislation are stated in very broad terms and are too ambiguous to be directly applicable in ERAs. This means that risk assessors often have to interpret policy protection goals without clear guidance on what effects would be considered harmful. In this paper we propose a practical approach that may help risk assessors to translate policy protection goals into unambiguous (i.e., operational) protection goals and to establish relevant assessment endpoints and risk hypotheses that can be used in ERAs. Examples are provided to show how this approach can be applied to two areas of environmental concern relevant to the ERAs of GM crops.     

Plant protoplast isolation - a practical approach

A method for the isolation of plant protoplasts is presented that uses inexpensive sources of enzymes. It is suitable for student use in Biotechnology.     

Nematode development: an evolutionary fugue

Recent studies of vulva development in the nematode Pristionchus pacificus have identified cell interactions that do not appear to occur in Caenorhabditis elegans. The new results underscore the diversity of patterning mechanisms that can produce structures with similar cellular morphology.     

Biological complexity and drug discovery: a practical systems biology approach

Drugs fail in clinical studies most often from lack of efficacy or unexpected toxicities. These failures result from an inadequate understanding of drug action and follow, in part, from our dependence on drug discovery technologies that do not take into account the complexity of human disease biology. Biological systems exhibit many features of complex engineering systems, including modularity, redundancy, robustness, and emergent properties. Addressing these features has contributed to the successful design of an improved biological assay technology for inflammation drug discovery. This approach, termed Biologically Multiplexed Activity Profiling (BioMAP), involves the statistical analysis of protein datasets generated from novel complex primary human cell-based assay systems. Compound profiling in these systems has revealed that a surprisingly large number of biological mechanisms can be detected and distinguished. Features of these assays relevant to the behaviour of complex systems are described.     

A practical approach to the synthesis of hairpin polyamide-peptide conjugates through the use of a safety-catch linker

Hairpin polyamides are high-affinity, sequence selective DNA binders. The use of a safety-catch linker for the solid phase synthesis of hairpin polyamides allows for easy preparation of derivatives ready for chemoselective ligation with unprotected peptides. Examples of ligations reported include thioether bond formation and thioester-mediated amide bond formation ('Native Chemical Ligation').