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Biological classification embodies the most fundamental idea in all of biology, especially evolution. The contrast between biological classifications and those of manufactured objects for instance hardware-based collection of screws, nails and bolts, help illustrate the central biological ideas and induce student interest, however, this could be misleading, as taxonomic classifications of organisms are fundamentally different from the classifications of other things.

Benthic marine primary producers affect the chemistry of their surrounding environment through metabolic processes. Photosynthesis and respiration will elevate or depress the concentration of oxygen in the diffusive boundary layer. Likewise, acid-base regulation and biomineralization/dissolution for calcifying species can alter the relative concentration of inorganic carbon species and thus pH. Here, we measured the relative ability of several common benthic primary producers from coral reef systems of the central Pacific and the Caribbean to simultaneously affect seawater oxygen concentration and pH values. Repeated measurements over a diel cycle confirmed that several primary producers substantially alter surrounding seawater chemistry over time. The majority of fleshy algae exhibited a stoichiometric ratio of oxygen to hydrogen ions not significantly different from one during daylight hours. In contrast, calcifiers exhibited significantly lower oxygen to hydrogen ion ratios that were unique for each species and were inversely correlated with known rates of calcification. These data provide the first quantitative estimates of the simultaneous influence of several species of benthic primary producers on water column oxygen concentrations and pH across different tropical reef systems. Finally, because more productive fleshy taxa have the potential to raise both oxygen and pH during the day to a greater extent than calcified species, our results suggest that some fleshy taxa may provide a buffering capacity to future ocean acidification scenarios., Introduction Coral reefs are subjected to local anthropogenic stressors [e.g. overfishing, sedimentation; (Nystrom et al. 2000; Bellwood et al. 2004)] as well as global warming and seawater acidification due to [...]

Byline: Bradley M. Hersh (a)(b), Craig E. Nelson (c), Samantha J. Stoll (a), Jason E. Norton (d), Thomas J. Albert (d), Sean B. Carroll (a) Keywords: Hox protein; Ultrabithorax; Drosophila; Wing; Haltere; Anachronism Abstract: Hox proteins have been proposed to act at multiple levels within regulatory hierarchies and to directly control the expression of a plethora of target genes. However, for any specific Hox protein or tissue, very few direct in vivo-regulated target genes have been identified. Here, we have identified target genes of the Hox protein Ultrabithorax (UBX), which modifies the genetic regulatory network of the wing to generate the haltere, a modified hindwing. We used whole-genome microarrays and custom arrays including all predicted transcription factors and signaling molecules in the Drosophila melanogaster genome to identify differentially expressed genes in wing and haltere imaginal discs. To elucidate the regulation of selected genes in more detail, we isolated cis-regulatory elements (CREs) for genes that were specifically expressed in either the wing disc or haltere disc. We demonstrate that UBX binds directly to sites in one element, and these sites are critical for activation in the haltere disc. These results indicate that haltere and metathoracic segment morphology is not achieved merely by turning off the wing and mesothoracic development programs, but rather specific genes must also be activated to form these structures. The evolution of haltere morphology involved changes in UBX-regulated target genes, both positive and negative, throughout the wing genetic regulatory network. Author Affiliation: (a) Howard Hughes Medical Institute and University of Wisconsin-Madison, 1525 Linden Drive, Madison, WI 53703, USA (b) Clemson University, 132 Long Hall, Clemson, SC 29634, USA (c) University of Connecticut, 91 North Eagleville Road, Storrs, CT 06269, USA (d) NimbleGen Systems, Inc., 1 Science Ct., Madison, WI 53711, USA Article History: Received 8 September 2006; Revised 20 October 2006; Accepted 3 November 2006