Classification and nomenclature of all human homeobox genes

Background

The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described.

Results

We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes. We describe 300 human homeobox loci, which we divide into 235 probable functional genes and 65 probable pseudogenes. These totals include 3 genes with partial homeoboxes and 13 pseudogenes that lack homeoboxes but are clearly derived from homeobox genes. These figures exclude the repetitive DUX1 to DUX5 homeobox sequences of which we identified 35 probable pseudogenes, with many more expected in heterochromatic regions. Nomenclature is established for approximately 40 formerly unnamed loci, reflecting their evolutionary relationships to other loci in human and other species, and nomenclature revisions are proposed for around 30 other loci. We use a classification that recognizes 11 homeobox gene 'classes' subdivided into 102 homeobox gene 'families'.

Conclusion

We have conducted a comprehensive survey of homeobox genes and pseudogenes in the human genome, described many new loci, and revised the classification and nomenclature of homeobox genes. The classification scheme may be widely applicable to homeobox genes in other animal genomes and will facilitate comparative genomics of this important gene superclass.     

Agricultural Landscape Transformation Needed to Meet Water Quality Goals in the Yahara River Watershed of Southern Wisconsin

Ecosystems - Balancing agricultural production with other ecosystem services is a vexing challenge. The Yahara River watershed in southern Wisconsin is a place where tensions among farmers,...     

Lysosomal neutral red retention time as a biomarker of organophosphate exposure in the earthworm Aporrectodea caliginosa: laboratory and semi-field experiments

Aporrectodea caliginosa is the most common endogeic (topsoil) earthworm in New Zealand and, because of its habitat, is potentially vulnerable to surface-applied pesticides. Lysosomal damage to earthworms, which can be visualized by the use of the neutral red retention assay (NRRA) has been evaluated in this species as a biomarker of organophosphate exposure. Earthworms were exposed in the laboratory to sub-lethal concentrations of chlorpyrifos and diazinon. In a semi-field experiment, earthworms were placed in mesocosms in a field sprayed with these pesticides at the rate recommended for a vegetable crop. In the laboratory, the neutral red retention time (NRRT) was significantly reduced following exposure to both pesticides compared with controls. In the semi-field experiment, earthworm NRRT was significantly reduced by both pesticides. These experiments have shown that the NRRA is very sensitive to exposure to chlorpyrifos and diazinon even at field rates. It therefore shows promise as a potential biomarker of contamination of soil by organophosphates.     

ANG II is required for optimal overload-induced skeletal muscle hypertrophy

ANG II mediates the hypertrophic response of overloaded cardiac muscle, likely via the ANG II type 1 (AT(1)) receptor. To examine the potential role of ANG II in overload-induced skeletal muscle hypertrophy, plantaris and/or soleus muscle overload was produced in female Sprague-Dawley rats (225-250 g) by the bilateral surgical ablation of either the synergistic gastrocnemius muscle (experiment 1) or both the gastrocnemius and plantaris muscles (experiment 2). In experiment 1 (n = 10/group), inhibiting endogenous ANG II production by oral administration of an angiotensin-converting enzyme (ACE) inhibitor during a 28-day overloading protocol attenuated plantaris and soleus muscle hypertrophy by 57 and 96%, respectively (as measured by total muscle protein content). ACE inhibition had no effect on nonoverloaded (sham-operated) muscles. With the use of new animals (experiment 2; n = 8/group), locally perfusing overloaded soleus muscles with exogenous ANG II (via osmotic pump) rescued the lost hypertrophic response in ACE-inhibited animals by 71%. Furthermore, orally administering an AT(1) receptor antagonist instead of an ACE inhibitor produced a 48% attenuation of overload-induced hypertrophy that could not be rescued by ANG II perfusion. Thus ANG II may be necessary for optimal overload-induced skeletal muscle hypertrophy, acting at least in part via an AT(1) receptor-dependent pathway.     

Reconstruction of coral reef fisheries catches in American Samoa, 1950–2002

Fisheries catches from Pacific Island coral reefs are rarely recorded in official statistics. Reconstruction of catch estimates with limited hard data requires interpolation and assumptions, justifiable only by the unsatisfactory alternative of continued substitution of zero catches, a common policy interpretation for ‘no data’. Uncertainties associated with reconstructions are high, requiring conservative estimation. American Samoan domestic fisheries consist of an artisanal, small-boat sector, whose commercial catches are reported, and a shore-based subsistence sector, with no regular reporting. Our catch reconstruction (with large pelagic species removed) suggested a 79% decrease in catches between 1950 (752 t) and 2002 (155 t). Accounting for rapid human population growth on the main island, the per capita catch rate may have declined from 36.3 kg·person⁻¹ year⁻¹ in 1950 to 1.3 kg·person⁻¹ year⁻¹ by 2002, while the catch rate for the inhabited outer islands has been independently reported as 58.6 kg·person⁻¹ year⁻¹. Catch per area of coral reef (to 50-m depth) may have declined from 5.5 to 0.7 t km⁻² year⁻¹ for the main island, and from 9.1 to 4.9 t km⁻² year⁻¹ for the outer islands, for 1950 and 2002, respectively. Summed for 1950–2002, our reconstruction suggested a 17-fold difference between reconstructed estimates and reported statistics.     

Identification of indole compounds secreted byFrankia HFPArI3 in defined culture medium

Indole compounds secreted byFrankia sp. HFPArI3 in defined culture medium were identified with gas chromatography-mass spectrometry (GC-MS). WhenFrankia was grown in the presence of¹³C(ring-labelled)-L-tryptophan,¹³C-labelled indole-3-acetic acid (IAA), indole-3-ethanol (IEtOH), indole-3-lactic acid (ILA), and indole-3-methanol (IMeOH) were identified.High performance liquid chromatography (HPLC) and GC-MS with selected ion monitoring were used to quantify levels of IAA and IEtOH inFrankia culture medium. IEtOH was present in greater abundance than IAA in every experiment. When no exogenous trp was supplied, no or only low levels of indole compounds were detected.Seedling roots ofAlnus rubra incubated in axenic conditions in the presence of indole-3-ethanol formed more lateral roots than untreated plants, indicating that IEtOH is utilized by the host plant, with physiological effects that modify patterns of root primordium initiation.     

Calcium-sensitive, lipid-binding cytoskeletal proteins of the human placental microvillar region

In this study we describe a group of Ca2+-sensitive proteins located in the microvillar region of the human placental syncytiotrophoblast. By following the distribution of proteins between the particulate and supernatant phases of detergent-solubilized microvilli in the presence of defined concentrations of free Ca2+, we demonstrate a class of proteins of subunit molecular weights 72,000, 69,000, 38,000, 36,000, and 32,000 that associate with both the cytoskeleton and lipid at high concentrations of free Ca2+. These proteins can be released from microvilli using EGTA-containing buffers. Although they do not bind to phenyl-Sepharose, they will bind to phospholipids immobilized on phenyl-Sepharose columns in a Ca2+-dependent manner and show a marked preference for phospholipids with negatively charged headgroups. The results provide evidence for a sequence of events which may occur within the microvillus as the localized concentration of intracellular free Ca2+ rises.