Effect of ice fraction and dilution factor on the antifreeze activity in the hemolymph of the cerambycid beetle Rhagium inquisitor

The freezing-melting hysteresis in a given volume of hemolymph from the cerambycid beetle Rhagium inquisitor was linearly and negatively related to the logarithm of the mass fraction of ice in the sample. When the ice fraction dropped by a factor of 10, the hysteresis activity increased by about 2 degrees C. When the hemolymph was diluted, the hysteresis activity was linearly and negatively related to the logarithm of the dilution factor. Dilution of the hemolymph by a factor of 2 led to a 1 degree C reduction in hysteresis activity. In the diluted samples, the ice growth took place along the a-axes, implying that the antifreeze peptides of insects block ice growth along the c-axis, in addition to the a-axis.     

Optimizing stringency for expression microarrays

While several studies have reported methods to optimize expression microarray protocols, none have dealt directly with hybridization wash stringency. We designed a series of experiments to determine the optimal stringency conditions for microarray experiments, using reproducibility and magnitudes of log2 (test/reference) ratio values as measures of quality. Low-stringency wash conditions of cell line hybridizations led to nonspecific binding, resulting in increased intensities, decreased magnitude of ratios, and poor reproducibility. Relatively high-stringency wash conditions were found to give the best reproducibility and large magnitude ratio changes, although increasing the stringency beyond this point led to lower magnitude ratios and poorer reproducibility. The expression levels of the ERBB2 oncogene in the BT474 versus MCF7 cell lines showed that high-stringency wash conditions gave the best agreement with real-time quantitative PCR, although the magnitude of the changes by microarray was smaller than for real-time quantitative PCR. Analysis of a series of cell lines washed at the optimized stringency indicated that the rank order of relative expression levels for ERBB2 microarray clones agreed well with the rank order of ERBB2 levels, as measured by quantitative PCR. These results indicate that the optimization of stringency conditions will improve microarray reproducibility and give more representative expression values.     

Bipolar cells use kainate and AMPA receptors to filter visual information into separate channels

Unlike cone photoreceptors, whose light responses have a uniform time course, retinal ganglion cells are tuned to respond to different temporal components in a changing visual scene. The signals in a mammalian cone flow to three to five morphologically distinct "OFF" bipolar cells at a sign-conserving, glutamatergic synapse. By recording simultaneously from pairs of synaptically connected cones and OFF bipolar cells, I now show that each morphological type of OFF bipolar cell receives its signal through a different AMPA or kainate receptor. The characteristic rate at which each receptor recovers from desensitization divides the cone signal into temporal components. Temporal processing begins at the first synapse in the visual system.     

AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions

Background  

Replication origins are considered important sites for understanding the molecular mechanisms involved in DNA replication. Many computational methods have been developed for predicting their locations in archaeal, bacterial and eukaryotic genomes. However, a prediction method designed for a particular kind of genomes might not work well for another. In this paper, we propose the AT excursion method, which is a score-based approach, to quantify local AT abundance in genomic sequences and use the identified high scoring segments for predicting replication origins. This method has the advantages of requiring no preset window size and having rigorous criteria to evaluate statistical significance of high scoring segments.     

Identification and characterization of GIV, a novel Galpha i/s-interacting protein found on COPI, endoplasmic reticulum-Golgi transport vesicles

In this report, we characterize GIV (Galpha-interacting vesicle-associated protein), a novel protein that binds members of the Galpha(i) and Galpha subfamilies of heterotrimeric G proteins. The Galpha(s) interaction site was mapped to an 83-amino acid region of GIV that is enriched in highly charged amino acids. BLAST searches revealed two additional mammalian family members, Daple and an uncharacterized protein, FLJ00354. These family members share the highest homology at the Galpha binding domain, are homologous at the N terminus and central coiled coil domain but diverge at the C terminus. Using affinity-purified IgG made against two different regions of the protein, we localized GIV to COPI, endoplasmic reticulum (ER)-Golgi transport vesicles concentrated in the Golgi region in GH3 pituitary cells and COS7 cells. Identification as COPI vesicles was based on colocalization with beta-COP, a marker for these vesicles. GIV also codistributes in the Golgi region with endogenous calnuc and the KDEL receptor, which are cis Golgi markers and with Galpha(i3)-yellow fluorescent protein expressed in COS7 cells. By immunoelectron microscopy, GIV colocalizes with beta-COP and Galpha(i3) on vesicles found in close proximity to ER exit sites and to cis Golgi cisternae. In cell fractions prepared from rat liver, GIV is concentrated in a carrier vesicle fraction (CV2) enriched in ER-Golgi transport vesicles. beta-COP and several Galpha subunits (Galpha(i1-3), Galpha(s)) are also most enriched in CV2. Our results demonstrate the existence of a novel Galpha-interacting protein associated with COPI transport vesicles that may play a role in Galpha-mediated effects on vesicle trafficking within the Golgi and/or between the ER and the Golgi.     

Trace element and strontium isotopic analysis of Gulf Sturgeon fin rays to assess habitat use

Trace element and ⁸⁷Sr/⁸⁶Sr isotope analyses of fish pectoral fin rays offer non-destructive methods for determining habitat use. In this study, water and fin ray samples were analyzed for Gulf Sturgeon Acipenser oxyrinchus desotoi from the Choctawhatchee River Basin (FL and AL, USA) and compared with reference samples from Atlantic Sturgeon A. o. oxyrinchus held at controlled salinities (0, 10, 33 ppt). Samples were analyzed using inductively coupled plasma mass spectrometry, with a multi-collector for ⁸⁷Sr/⁸⁶Sr. In water, Sr, Ba, Mn and Zn differed between freshwater and saline habitats, with increases in Sr and decreases in Ba, Mn and Zn. ⁸⁷Sr/⁸⁶Sr decreased upstream to downstream with lowest values in saline habitats. In the reference study, water trace element concentrations and ⁸⁷Sr/⁸⁶Sr corresponded to those in pectoral fin rays. ⁸⁷Sr/⁸⁶Sr was higher in pectoral fin ray than water, due to influence of diet, which differed with salinity. In wild fish, trace elements in pectoral fin rays indicated freshwater emigration to saline habitats primarily occurred in the second to third growth zone with some heterogeneity in the population (4% <0.3 years, 39% 0.5–1.3 years, 39% 1.5–2.3 years, 17% 2.5–3.3 years). Analyses of ⁸⁷Sr/⁸⁶Sr indicated initial locations of Gulf Sturgeon were in the middle river, with few fish in the upper or lower river. Most (74%) juvenile Gulf Sturgeon utilized more than one river region prior to freshwater emigration and 48% moved upstream temporarily based on increased ⁸⁷Sr/⁸⁶Sr. After initial freshwater emigration, fish utilized lower-river to saline habitats. Collectively, these studies demonstrate the usefulness of trace element and ⁸⁷Sr/⁸⁶Sr analyses in sturgeon pectoral fin rays.     

Developmental changes in myelin-induced proliferation of cultured Schwann cells

Schwann cell proliferation induced by a myelin-enriched fraction was examined in vitro. Although nearly all the Schwann cells contained material that was recognized by antisera to myelin basic protein after 24 h, only 1% of the cells were synthesizing DNA. 72 h after the addition of the mitogen a maximum of 10% of the cells incorporated [3H]thymidine. If the cultures were treated with the myelin-enriched fraction for 24 h and then washed, the number of proliferating Schwann cells decreased by 75% when compared with those cells that were incubated with the mitogen continuously. When Schwann cells were labeled with [14C]thymidine followed by a pulse of [3H]thymidine 24 h later, every Schwann cell labeled with [3H]thymidine was also labeled with [14C]thymidine. Although almost every Schwann cell can metabolize the myelin membranes within 24 h of exposure, a small population of cell initially utilizes the myelin as a mitogen, and this population continues to divide only if myelin is present in the extracellular media. The percentage of the Schwann cells that initially recognize the myelin-enriched fraction as a mitogen is dependent upon the age of the animal from which the cells were prepared.     

1-Oleoyl-2-Acetylglycerol and A23187 Potentiate Axolemma-and Myelin-Induced Schwann Cell Proliferation

The effects of 1-oleoyl-2-acetylglycerol (OAG) and the calcium ionophore A23187 on the proliferation of Schwann cells stimulated with either a myelin-enriched membrane fraction (MEF) or an axolemma-enriched membrane fraction (AEF) have been examined. Using incorporation of [3H]thymidine as an index of proliferation, 16% of the cells became labeled after incubation with MEF (20 micrograms protein/ml) and AEF (40 micrograms protein/ml) for 72 h. Only 0.5% of the cells became labeled in cultures which were not exposed to the membrane fractions. Addition of OAG (10-500 microM) or A23187 (1.9-190 nM) in the absence of the membrane mitogens had no effect on the proliferative response of quiescent cultures of Schwann cells. When added simultaneously, however, OAG and A23187 were able to induce proliferation of the cells, although the response was only 30% of the response achieved with maximal doses of either AEF or MEF. Both OAG and A23187 were able to potentiate the mitogenicity of AEF or MEF, but only when AEF and MEF were added at submaximal concentrations. When Schwann cells were prelabeled with [3H]glycerol and then stimulated to proliferate with AEF or MEF, the amount of [3H]diacylglycerol was increased two- to threefold above that in control cultures for time periods up to 1 h. These results suggest that the proliferation of Schwann cells induced by either AEF or MEF is partially mediated through the combined effects of diacylglycerol and an increase in intracellular calcium.