Potentially lethal damage repair is due to the difference of DNA double-strand break repair under immediate and delayed plating conditions

Cells plated immediately after irradiation on nutrient agar (immediate plating) exhibit a lower survival than cells which are kept under nongrowth conditions before plating (delayed plating). The difference between the survival curves obtained after immediate plating and delayed plating is considered to exhibit the cell's capacity to repair potentially lethal damage. In yeast evidence has been presented previously for the DNA double-strand break (DSB) as the molecular lesion involved in the repair of potentially lethal damage observed at the cellular level. Radiation-induced DSB are repaired in cells plated on nutrient agar, i.e., under growth conditions, as well as in cells kept under nongrowth conditions. In this paper DSB repair under growth and nongrowth conditions is studied with the help of the yeast mutant rad54-3 which is temperature conditional for DSB repair. It is shown that the extent of repair of potentially lethal damage can be varied by shifting the relative fractions of repair of DSB under growth conditions versus nongrowth conditions. Repair of DSB in cells plated on nutrient agar is promoted when glucose is substituted by Na-succinate as an energy source. As a result the immediate plating survival curve approaches the delayed plating survival curve, thus reducing the operationally defined repair of potentially lethal damage. We show that this reduced potentially lethal damage repair is caused, however, by a higher amount of DSB repair in cells immediately plated on succinate agar as compared to glucose agar.     

Regulation of the mouse organic solute transporter alpha-beta, Ostalpha-Ostbeta, by bile acids

The mechanisms responsible for bile acid regulation of mouse intestinal organic solute transporter alpha-beta (Ostalpha-Ostbeta) expression were investigated. Expression of Ostalpha-Ostbeta mRNA was increased in cecum and proximal colon of cholic acid-fed mice and in chenodeoxycholate-treated mouse CT26 colon adenocarcinoma cells. Sequence analysis revealed potential cis-acting elements for farnesoid X receptor (FXR) and liver receptor homolog-1 (LRH-1) in the mouse Ostalpha and Ostbeta promoters and reporter constructs containing Ostalpha and Ostbeta 5'-flanking sequences were positively regulated by bile acids. Expression of a dominant-negative FXR, reduction of FXR with interfering small RNA (siRNA), or mutation of the potential FXR elements decreased Ostalpha and Ostbeta promoter activity and abolished the induction by chenodeoxycolic acid. Negative regulation of the Ostalpha and Ostbeta promoters by bile acids was mediated through LRH-1 elements. Ostalpha and Ostbeta promoter activities were increased by coexpression of LRH-1 and decreased by coexpression of SHP. Mutation of the potential LRH-1 elements and siRNA-mediated reduction of LRH-1 expression decreased basal promoter activity. As predicted from the promoter analyses, ileal Ostalpha and Ostbeta mRNA expressions were increased in wild-type mice administered the FXR agonist GW4064 and decreased in FXR-null mice. Immunoblotting analysis revealed that Ostalpha and Ostbeta intestinal protein expressions correlated with mRNA expression. The mouse Ostalpha and Ostbeta promoters are unusual in that they contain functional FXR and LRH elements, which mediate, respectively, positive and negative feedback regulation by bile acids. Although the positive regulatory pathway appears to be dominant, this arrangement provides a mechanism to finely titrate Ostalpha-Ostbeta expression to the bile acid flux.     

DDX4 (VASA) is conserved in germ cell development in marsupials and monotremes

DDX4 (VASA) is an RNA helicase expressed in the germ cells of all animals. To gain greater insight into the role of this gene in mammalian germ cell development, we characterized DDX4 in both a marsupial (the tammar wallaby) and a monotreme (the platypus). DDX4 is highly conserved between eutherian, marsupial, and monotreme mammals. DDX4 protein is absent from tammar fetal germ cells but is present from Day 1 postpartum in both sexes. The distribution of DDX4 protein during oogenesis and spermatogenesis in the tammar is similar to eutherians. Female tammar germ cells contain DDX4 protein throughout all stages of postnatal oogenesis. In males, DDX4 is in gonocytes, and during spermatogenesis it is present in spermatocytes and round spermatids. A similar distribution of DDX4 occurs in the platypus during spermatogenesis. There are several DDX4 isoforms in the tammar, resulting from both pre- and posttranslational modifications. DDX4 in marsupials and monotremes has multiple splice variants and polyadenylation motifs. Using in silico analyses of genomic databases, we found that these previously unreported splice variants also occur in eutherians. In addition, several elements implicated in the control of Ddx4 expression in the mouse, including RGG (arginine-glycine-glycine) and dimethylation of arginine motifs and CpG islands within the Ddx4 promoter, are also highly conserved. Collectively these data suggest that DDX4 is essential for the regulation of germ cell proliferation and differentiation across all three extant mammalian groups-eutherians, marsupials, and monotremes.     

Influence of non-homology between recombining DNA sequences on double-strand break repair in Saccharomyces cerevisiae

In this paper we study the influence of non-homology between plasmid and chromosomal DNA on the efficiency of recombinational repair of plasmid double-strand breaks and gaps in yeast. For this purpose we used different combinations of plasmids and yeast strains carrying various deletions within the yeast LYS2 gene. A 400 by deletion in plasmid DNA had no effect on recombinational plasmid repair. However, a 400 by deletion in chromosomal DNA dramatically reduced the efficiency of this repair mechanism, but recombinational repair of plasmids linearized by a double-strand break with cohesive ends still remained the dominant repair process. We have also studied the competition between recombination and ligation in the repair of linearized plasmids. Our experimental evidence suggests that recombinational repair is attempted but aborted if only one recombinogenic end with homology to chromosomal DNA is present in plasmid DNA. This situation results in a decreased probability of non-recombinational (i.e. ligation) repair of linearized plasmid DNA.     

Simulations of chlorophyll fluorescence incorporated into the Community Land Model version 4

Several studies have shown that satellite retrievals of solar‐induced chlorophyll fluorescence (SIF) provide useful information on terrestrial photosynthesis or gross primary production (GPP). Here, we have incorporated equations coupling SIF to photosynthesis in a land surface model, the National Center for Atmospheric Research Community Land Model version 4 (NCAR CLM4), and have demonstrated its use as a diagnostic tool for evaluating the calculation of photosynthesis, a key process in a land surface model that strongly influences the carbon, water, and energy cycles. By comparing forward simulations of SIF, essentially as a byproduct of photosynthesis, in CLM4 with observations of actual SIF, it is possible to check whether the model is accurately representing photosynthesis and the processes coupled to it. We provide some background on how SIF is coupled to photosynthesis, describe how SIF was incorporated into CLM4, and demonstrate that our simulated relationship between SIF and GPP values are reasonable when compared with satellite (Greenhouse gases Observing SATellite; GOSAT) and in situ flux‐tower measurements. CLM4 overestimates SIF in tropical forests, and we show that this error can be corrected by adjusting the maximum carboxylation rate (V_max) specified for tropical forests in CLM4. Our study confirms that SIF has the potential to improve photosynthesis simulation and thereby can play a critical role in improving land surface and carbon cycle models.     

An ultrastructural study of the role of an extracellular matrix during normal cleavage in a marsupial,the brushtail possum

In marsupials, the mechanisms of lineage allocation into pluriblast and trophoblast are related to conceptus polarity and polarized discharge of extracellular matrix (ECM). The brushtail possum, Trichosurus vulpecula, a major pest species in New Zealand, is being intensively studied to develop an immunocontraceptive control method. Of 23 specimens examined, 11 were examined by electron microscopy to study the presence and role of the ECM in lineage allocation in the possum. A number of polarized features in the zygote identified the future embryonic and abembryonic poles. Pronuclei, in a broad band of mitochondrion-rich cortical cytoplasm, lay in the embryonic hemisphere, and numerous electron-lucent vesicles characterized the abembryonic cytoplasm. These vesicles seemed to contribute to the ECM. During cleavage, cells lay near the zona in the embryonic hemisphere, and ECM accumulated chiefly in the abembryonic hemisphere. Cell-zona adhesion facilitated by microvillous and club processes occurred at the early 4-cell stage, and cell-cell adhesion commenced at the late 4-cell stage. The first two cleavages were meridional, equal, and accompanied by elimination into the cleavage cavity of much of the electron-lucent vesicular material in the form of several membrane-bound yolk masses. The third cleavage was unequal, with both meridional and latitudinal planes. The first differences between trophoblast and pluriblast lineages appeared at the 8-cell stage. Later cleavage planes were latitudinal or oblique. Conceptus polarity, polarized discharge of ECM, and localized cell-zona adhesion were related to the first lineage allocation in the possum. Mol. Reprod. Dev. 50:420–433, 1998. © 1998 Wiley-Liss, Inc.