Screening of promoters from metagenomic DNA and their use for the construction of expression vectors

This study was focused on the screening of valuable genetic resources, such as promoters from metagenome, and describes a promoter trapping system with a bidirectional probe concept, which can select promoters or operons from various biological resources including metagenomic DNA. A pair of reporters, GFP and DsRed, facing the opposite direction without promoters, is an effective system that can function regardless of the direction of inserted promoters. The feasibility of this system was tested for the isolation of constitutively expressed promoters in E. coli from a soil metagenome, resulting in a potential pool of various promoters for practical application. The analyses of structural organization of the trapped genes demonstrated that constitutively expressible promoters in E. coli were broadly distributed within the metagenome, and suggested that some promoters were useful for the construction of expression vectors. Based on these observations, three constitutive promoters were employed in the expression vector system and their potentials for practical application were evaluated in terms of expression level, protein solubility, and effects on host growth.     

Effects of fish introduction on the length of the tail of cryptomonads in mesocosm experiments

Two different morphs of the small cryptomonad, Plagioselmis prolonga var. nordica with a posterior tail, were observed during summer and fall in the hypertrophic lake, Lake Kasumigaura, Japan. The tail shortened in mesocosms stocked with planktivorous silver carp ( Hypophthalmichthys molitrix Val.) and elongated by more than 50% in mesocosms from which silver carp were removed. The density of Plagioselmis cells increased significantly upon fish stocking and decreased upon fish removal. The tail length was negatively correlated with algal abundance and positively correlated with crustacean densities, but there was no correlation with nutrient levels or physical environmental parameters in the mesocosms. The variation in tail length was induced by the presence/absence of fish, but was not related to their density. However, silver carp manipulation strongly affected the density of the majority of zooplankters and, interestingly, there was a strong correlation between zooplankton density and tail-length change in Plagioselmis. We propose a possible herbivore-induced defense mechanism triggered by the top predator, silver carp.     

Antiemetic Role of Thalidomide in a Rat Model of Cisplatin-Induced Emesis

The efficacy of thalidomide to attenuate cisplatin-induced emesis was evaluated in a rat model. Four groups were utilized: control group (peritoneal injection and gastric lavage with normal saline), cisplatin group (peritoneal injection of cisplatin at 10 mg/kg and gastric lavage with normal saline), thalidomide group (cisplatin as above and gastric lavage with thalidomide at 10 mg/kg), and granisetron group (positive control for antiemetic effects; cisplatin given as above and gastric lavage done with granisetron at 0.5 mg/kg). The cisplatin-induced kaolin consumption (pica behavior) was used as a model of emesis in patients. The animals’ kaolin and food intakes were measured. Further, medulla and gastric tissues were obtained 5 and 33 h after peritoneal injections to quantify the levels of Substance P and Neurokinin-1 receptor (NK-1R). The cisplatin-induced kaolin consumption was significantly (p < 0.05 vs. cisplatin group) attenuated by thalidomide 72 h after the injection. The levels of Substance P in the medulla and gastric tissue were increased 5 h after the injection in both cisplatin and thalidomide groups, however, returned faster to normal levels in the thalidomide group (p < 0.05 vs. cisplatin group). Further, levels of NK-1R in the cisplatin, thalidomide, and granisetron group were significantly increased at both 5 and 33 h (p < 0.05 vs. control group), with no obvious difference among these three groups. In conclusion, thalidomide attenuates animal equivalent of cisplatin-induced emesis, and this beneficial effect is associated with decreased levels of Substance P levels in the medulla and gastric tissue.     

Toward Long‐Term Stable and Highly Efficient Perovskite Solar Cells via Effective Charge Transporting Materials

Perovskite solar cells (PSCs) have advanced quickly with their power conversion efficiency approaching the record of silicon solar cells. However, there is still a big challenge to obtain both high efficiency and long‐term stability for future commercialization of PSCs. The major instability issue is associated with the decomposition or phase transition of perovskite materials that are believed to be intrinsically unstable under outdoor working conditions. Herein, the authors review the approaches that marked important progress in developing new functional electron/hole transporting materials that enabled highly efficient and stable PSCs. The findings that accelerate charge diffusion and that suppress the irrevocable loss of ions diffusing out of perovskite materials and other diffusion processes are highlighted. In addition, derivative interface engineering methods to control the diffusion process of charges/ions/molecules are also reviewed. Finally, the authors propose key research issues in charge transporting materials and interface engineering with regard to the important diffusion processes that will be one of the keys to realize highly efficient and long‐term stable PSCs.     

Overlapping motifs (PTAP and PPEY) within the Ebola virus VP40 protein function independently as late budding domains: involvement of host proteins TSG101 and VPS-4

The VP40 protein of Ebola virus can bud from mammalian cells in the form of lipid-bound, virus-like particles (VLPs), and late budding domains (L-domains) are conserved motifs (PTAP, PPxY, or YxxL; where "x" is any amino acid) that facilitate the budding of VP40-containing VLPs. VP40 is unique in that potential overlapping L-domains with the sequences PTAP and PPEY are present at amino acids 7 to 13 of VP40 (PTAPPEY). L-domains are thought to function by interacting with specific cellular proteins, such as the ubiquitin ligase Nedd4, and a component of the vacuolar protein sorting (vps) pathway, tsg101. Mutational analysis of the PTAPPEY sequence of VP40 was performed to understand further the contribution of each individual motif in promoting VP40 budding. In addition, the contribution of tsg101 and a second member of the vps pathway, vps4, in facilitating budding was addressed. Our results indicate that (i) both the PTAP and PPEY motifs contribute to efficient budding of VP40-containing VLPs; (ii) PTAP and PPEY can function as L-domains when separated and moved from the N terminus (amino acid position 7) to the C terminus (amino acid position 316) of full-length VP40; (iii) A VP40-PTAP/tsg101 interaction recruits tsg101 into budding VLPs; (iv) a VP40-PTAP/tsg101 interaction recruits VP40 into lipid raft microdomains; and (v) a dominant-negative mutant of vps4 (E228Q), but not wild-type vps4, significantly inhibited the budding of Ebola virus (Zaire). These results provide important insights into the complex interplay between viral and host proteins during the late stages of Ebola virus budding.     

Improving transmembrane protein consensus topology prediction using inter-helical interaction

Alpha helix transmembrane proteins (αTMPs) represent roughly 30% of all open reading frames (ORFs) in a typical genome and are involved in many critical biological processes. Due to the special physicochemical properties, it is hard to crystallize and obtain high resolution structures experimentally, thus, sequence-based topology prediction is highly desirable for the study of transmembrane proteins (TMPs), both in structure prediction and function prediction. Various model-based topology prediction methods have been developed, but the accuracy of those individual predictors remain poor due to the limitation of the methods or the features they used. Thus, the consensus topology prediction method becomes practical for high accuracy applications by combining the advances of the individual predictors. Here, based on the observation that inter-helical interactions are commonly found within the transmembrane helixes (TMHs) and strongly indicate the existence of them, we present a novel consensus topology prediction method for αTMPs, CNTOP, which incorporates four top leading individual topology predictors, and further improves the prediction accuracy by using the predicted inter-helical interactions. The method achieved 87% prediction accuracy based on a benchmark dataset and 78% accuracy based on a non-redundant dataset which is composed of polytopic αTMPs. Our method derives the highest topology accuracy than any other individual predictors and consensus predictors, at the same time, the TMHs are more accurately predicted in their length and locations, where both the false positives (FPs) and the false negatives (FNs) decreased dramatically. The CNTOP is available at: http://ccst.jlu.edu.cn/JCSB/cntop/CNTOP.html.