MIPHENO: data normalization for high throughput metabolite analysis

Background  

High throughput methodologies such as microarrays, mass spectrometry and plate-based small molecule screens are increasingly used to facilitate discoveries from gene function to drug candidate identification. These large-scale experiments are typically carried out over the course of months and years, often without the controls needed to compare directly across the dataset. Few methods are available to facilitate comparisons of high throughput metabolic data generated in batches where explicit in-group controls for normalization are lacking.     

Euclidean distances discriminatively predict short-term and long-term attraction to potential mates

We tested the ability of a Euclidean algorithm to predict attraction to potential mates—a relatively upstream domain in the temporal sequence of the mating process. Participants in two studies reported their ideal mate preferences using a 23-item preference instrument. Separately, they rated their attraction to profiles of potential mates that varied on those 23 dimensions. Study 1 (N = 522) found that Euclidean distances predicted attraction to potential mates both in terms of (1) overall mate value and (2) unique mate value. Study 2 (N = 411) replicated these effects and further found that Euclidean mate values discriminatively predict between short- and long-term attraction. Across both studies, a Euclidean model outperformed a variety of alternative models for predicting attraction to potential mates. These results suggest that a Euclidean algorithm is a good model for how multiple preferences are integrated in mate choice.     

A Method for Injecting Insect Tracheae Permanently

By the use of an alcohol insoluble dye (trypan blue), acetic acid, and a detergent (“Santomerse No. 3”), a resulting dye solution is obtained which will completely penetrate the tracheal system of an insect. The dye is injected by the use of a vacuum and by the pressure produced when the air is allowed to re-enter the dye vessel. The dye itself is permanently fixed in the tracheae by means of a fixing solution containing alcohol, acetic acid and barium chloride as its components. The material must be properly preserved after staining. It may be stored indefinitely in 70% alcohol, xylol, cedar oil or clove oil, depending on whether the material is to be used for sectioning or for whole mounts. Injected material may be sectioned in either celloidin or paraffin, or may be cleared and mounted in toto.     

Transmission Genetics of Allorecognition in Hydractinia Symbiolongicarpus (Cnidaria: Hydrozoa)

Allorecognition is ubiquitous, or nearly so, amongst colonial invertebrates. Despite the prominent role that such phenomena have played both in evolutionary theory and in speculations on the origin of the vertebrate immune system, unambiguous data on the transmission genetics of fusibility (i.e., the ability of two individuals to fuse upon tissue contact) is lacking for any metazoan outside of the phylum Chordata. We have developed lines of the hydroid Hydractinia symbiolongicarpus (Phylum Cnidaria) inbred for fusibility and here report results of breeding experiments establishing that fusibility segregates as expected for a single locus with codominantly expressed alleles, with one shared allele producing a fusible phenotype. Surveys of fusibility in field populations and additional breeding experiments indicate the presence of an extensive allele series.     

INTERSPECIFIC INCOMPATIBILITY IN GOSSYPIUM. IV. TEMPERATURE-CONDITIONAL LETHALITY IN HYBRIDS OF G. KLOTZSCHIANUM

A number of interspecific hybrids involving G. klotzschianum are embryo-lethal or seedling-lethal at temperatures considered optimal for cotton culture (26–32 C). At temperatures between 33–37 C, lethal symptoms (cell-necrosis and vascular plugging) for both stages of lethality are greatly ameliorated and at 40 C lethal symptoms are absent and hybrid ontogeny is normal for embryo- and seedling-lethals. Temperature-repressed lethals revert to type within 12–24 h after being returned to a non-repressive temperature regime.     

Dying Cells Protect Survivors from Radiation-Induced Cell Death in Drosophila

We report a phenomenon wherein induction of cell death by a variety of means in wing imaginal discs of Drosophila larvae resulted in the activation of an anti-apoptotic microRNA, bantam. Cells in the vicinity of dying cells also become harder to kill by ionizing radiation (IR)-induced apoptosis. Both ban activation and increased protection from IR required receptor tyrosine kinase Tie, which we identified in a genetic screen for modifiers of ban. tie mutants were hypersensitive to radiation, and radiation sensitivity of tie mutants was rescued by increased ban gene dosage. We propose that dying cells activate ban in surviving cells through Tie to make the latter cells harder to kill, thereby preserving tissues and ensuring organism survival. The protective effect we report differs from classical radiation bystander effect in which neighbors of irradiated cells become more prone to death. The protective effect also differs from the previously described effect of dying cells that results in proliferation of nearby cells in Drosophila larval discs. If conserved in mammals, a phenomenon in which dying cells make the rest harder to kill by IR could have implications for treatments that involve the sequential use of cytotoxic agents and radiation therapy.     

DdcA antagonizes a bacterial DNA damage checkpoint

Bacteria coordinate DNA replication and cell division, ensuring a complete set of genetic material is passed onto the next generation. When bacteria encounter DNA damage, a cell cycle checkpoint is activated by expressing a cell division inhibitor. The prevailing model is that activation of the DNA damage response and protease‐mediated degradation of the inhibitor is sufficient to regulate the checkpoint process. Our recent genome‐wide screens identified the gene ddcA as critical for surviving exposure to DNA damage. Similar to the checkpoint recovery proteases, the DNA damage sensitivity resulting from ddcA deletion depends on the checkpoint enforcement protein YneA. Using several genetic approaches, we show that DdcA function is distinct from the checkpoint recovery process. Deletion of ddcA resulted in sensitivity to yneA overexpression independent of YneA protein levels and stability, further supporting the conclusion that DdcA regulates YneA independent of proteolysis. Using a functional GFP‐YneA fusion we found that DdcA prevents YneA‐dependent cell elongation independent of YneA localization. Together, our results suggest that DdcA acts by helping to set a threshold of YneA required to establish the cell cycle checkpoint, uncovering a new regulatory step controlling activation of the DNA damage checkpoint in Bacillus subtilis.