Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae).

Rafflesia is a genus of holoparasitic plants endemic to Southeast Asia that has lost the ability to undertake photosynthesis. With short-read sequencing technology, we assembled a draft sequence of the mitochondrial genome of Rafflesia lagascae Blanco, a species endemic to the Philippine island of Luzon, with ∼350× sequencing depth coverage. Using multiple approaches, however, we were only able to identify small fragments of plastid sequences at low coverage depth (<2×) and could not recover any substantial portion of a chloroplast genome. The gene fragments we identified included photosynthesis and energy production genes (atp, ndh, pet, psa, psb, rbcL), ribosomal RNA genes (rrn16, rrn23), ribosomal protein genes (rps7, rps11, rps16), transfer RNA genes, as well as matK, accD, ycf2, and multiple nongenic regions from the inverted repeats. None of the identified plastid gene sequences had intact reading frames. Phylogenetic analysis suggests that ∼33% of these remnant plastid genes may have been horizontally transferred from the host plant genus Tetrastigma with the rest having ambiguous phylogenetic positions (<50% bootstrap support), except for psaB that was strongly allied with the plastid homolog in Nicotiana. Our inability to identify substantial plastid genome sequences from R. lagascae using multiple approaches--despite success in identifying and developing a draft assembly of the much larger mitochondrial genome--suggests that the parasitic plant genus Rafflesia may be the first plant group for which there is no recognizable plastid genome, or if present is found in cryptic form at very low levels.

Gene Expression During Early Folliculogenesis in Goats Using Microarray Analysis.

Understanding of gene expression and metabolic, biological and physiological pathways in ovarian follicular development can have a significant impact on the dynamics of follicular atresia or survival. In fact, some oocyte loss occurs during the transition from secondary to early tertiary follicles. This study aimed to understand, by microarray analysis, the temporal changes in transcriptional profiles of secondary and early antral (tertiary) follicles in caprine ovaries. Ovarian follicles were microdissected and pooled to extract total RNA. The RNA was cross hybridized with the bovine array. Among 23,987 bovine genes, a total of 14,323 genes were hybridized with goat mRNAs while 9,664 genes were not. Of all the hybridized genes, 2,466 were stage-specific, up- and down-regulated in the transition from secondary to early tertiary follicles. Gene expression profiles showed that three major metabolic pathways (lipid metabolism, cell death, and hematological system) were significantly differentiated between the two follicle stages. In conclusion, this study has identified important genes and pathways which may potentially be involved in the transition from secondary to early tertiary follicles in goats.

Effects of environmentally relevant concentrations of mixtures of TiO2, ZnO and Ag ENPs on a river bacterial community.

Effluent from wastewater treatment plants contains a wide variety of engineered nanoparticles (ENPs) released from different sources. Although single type ENPs have been studied extensively with respect to their environmental impact, ENPs in mixed forms have not been investigated much at environmentally relevant concentrations. This study was designed to test the effect of mixed ENPs at three combinations and concentrations on an aquatic bacterial community. After mixing artificial treated wastewater with river water and exposing the microbial community to ENPs for three days, the ENPs were characterized by SP-ICP-MS. Results from this study showed that: 1) the size distribution of Ti and Zn at the beginning and end of the experiment did not vary much among all tested conditions. For Ag, the most frequent size increased more than 2-fold when the highest Ag ENPs were added; 2) particle concentrations of ENPs generally correlated positively with added concentrations; 3) dissolved Zn and Ag increased significantly as a result of spike; and 4) the bacterial community structure was shifted significantly as a consequence of ENPs' addition. With the dominant population being suppressed, the community exposed to ENPs became more diverse and even. Surprisingly, further increase of the doses of the three ENPs did not bring significant change to the microbial community. These results revealed that ENPs could bring significant impacts to prokaryotes even at low concentrations. But these impacts do not necessarily correlate positively with doses.

Impact of TiO2 and ZnO nanoparticles on an aquatic microbial community: effect at environmentally relevant concentrations.

To investigate effects of engineered nanoparticles (ENPs) at environmentally relevant concentrations to aquatic microbial communities, TiO2 at 700 µg/L and ZnO at 70 µg/L were spiked to river water samples either separately or combined. Compared to controls where no ENPs were added, the addition of TiO2 ENPs alone at the tested concentration had no statistically significant effect on both the bacterial and eukaryotic communities. The presence of added ENPs: ZnO or ZnO + TiO2 led to significant shift of the microbial community structure and genus distribution. This shift was more obvious for the bacteria than the eukaryotes. Based on results from single particle - inductively coupled plasma - mass spectrometry (SP-ICP-MS), all ENPs aggregated rapidly in water and resulted in much larger particles sizes than the original counterparts. "Dissolved" (including particles smaller than the size detection limits and dissolved ions) concentrations of Ti and Zn increased, too in treatment groups vs. the controls.