Blocking the flow of propionate into TCA cycle through a mutB knockout leads to a significant increase of erythromycin production by an industrial strain of Saccharopolyspora erythraea

Bioprocess and Biosystems Engineering - A high erythromycin producing mutant strain Saccharopolyspora erythraea HL3168 E3-ΔmutB was constructed by deleting mutB (SACE_5639) gene encoding the...     

Net primary production in three bioenergy crop systems following land conversion

Aims Identifying the amount of production and the partitioning to above- and belowground biomass is generally the first step toward selecting bioenergy systems. There are very few existing studies on the dynamics of production following land conversion. The objectives of this study were to (i) determine the differences in aboveground net primary production (ANPP), belowground net primary production (BNPP), shoot-to-root ratio (S:R) and leaf area index in three bioenergy crop systems and (ii) evaluate the production of these three systems in two different land use conversions.Methods This investigation included biometric analysis of NPP on three agricultural sites converted from conservation reserve program (CRP) management to bioenergy crop production (corn, switchgrass and prairie mix) and three sites converted from traditional agriculture production to bioenergy crop production.Important findings The site converted from conventional agriculture produced smaller ANPP in corn (19.03±1.90 standard error [SE] Mg ha^-1 year^-1) than the site converted from CRP to corn (24.54±1.43 SE Mg ha^-1 year^-1). The two land conversions were similar in terms of ANPP for switchgrass (4.88±0.43 SE for CRP and 2.04±0.23 SE Mg ha^-1 year^-1 for agriculture) and ANPP for prairie mix (4.70±0.50 SE for CRP and 3.38±0.33 SE Mg ha^-1 year^-1 for agriculture). The BNPP at the end of the growing season in all the bioenergy crop systems was not significantly different (P = 0.75, N = 8).     

多裂紫菊(菊科-菊苣族)后选模式的指定

指定了多裂紫菊Prenanthes henryi Dunn (=Notoseris henryi (Dunn) Shih)的后选模式。     

Potent RNAi by short RNA triggers

RNA interference (RNAi) is a gene-silencing mechanism by which a ribonucleoprotein complex, the RNA-induced silencing complex (RISC) and a double-stranded (ds) short-interfering RNA (siRNA), targets a complementary mRNA for site-specific cleavage and subsequent degradation. While longer dsRNA are endogenously processed into 21- to 24-nucleotide (nt) siRNAs or miRNAs to induce gene silencing, RNAi studies in human cells typically use synthetic 19- to 20-nt siRNA duplexes with 2-nt overhangs at the 3′-end of both strands. Here, we report that systematic synthesis and analysis of siRNAs with deletions at the passenger and/or guide strand revealed a short RNAi trigger, 16-nt siRNA, which induces potent RNAi in human cells. Our results indicate that the minimal requirement for dsRNA to trigger RNAi is an ~42 Å A-form helix with ~1.5 helical turns. The 16-nt siRNA more effectively knocked down mRNA and protein levels than 19-nt siRNA when targeting the endogenous CDK9 gene, suggesting that 16-nt siRNA is a more potent RNAi trigger. In vitro kinetic analysis of RNA-induced silencing complex (RISC) programmed in HeLa cells indicates that 16-nt siRNA has a higher RISC-loading capacity than 19-nt siRNA. These results suggest that RISC assembly and activation during RNAi does not necessarily require a 19-nt duplex siRNA and that 16-nt duplexes can be designed as more potent triggers to induce RNAi.     

Whole genome mapping in a wheat doubled haploid population using SSRs and TRAPs and the identification of QTL for agronomic traits

Genetic maps are useful for detecting quantitative trait loci (QTL) associated with quantitative traits and for marker-assisted selection (MAS) in breeding. In this research, we used the wheat × maize method to develop a doubled haploid (DH) population derived from the synthetic hexaploid wheat (SHW) line TA4152-60 and the North Dakota hard red spring wheat line ND495. The population consisted of 213 lines, of which a subset of 120 lines was randomly selected and used to construct linkage maps of all 21 chromosomes and for QTL detection. The whole genome maps consisted of 632 markers including 410 SSRs, 218 TRAPs, 1 RFLP, and 3 phenotypic markers, and spanned 3,811.5 cM with an average density of one marker per 6.03 cM. Telomere sequence-based TRAPs allowed us to define the ends of seven linkage groups. Analysis revealed major QTLs associated with the traits of days to heading on chromosomes 5A and 5B, plant height on chromosomes 4D and 5A, and spike characteristics on chromosomes 3D, 4A, 4D, 5A and 5B. The DH population and genetic map will be a useful tool for the identification of disease resistance QTL and agronomically important loci, and will aid in the identification and development of markers for MAS. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.     

A combined computational-experimental analyses of selected metabolic enzymes in Pseudomonas species

Comparative genomic analysis has revolutionized our ability to predict the metabolic subsystems that occur in newly sequenced genomes, and to explore the functional roles of the set of genes within each subsystem. These computational predictions can considerably reduce the volume of experimental studies required to assess basic metabolic properties of multiple bacterial species. However, experimental validations are still required to resolve the apparent inconsistencies in the predictions by multiple resources. Here, we present combined computational-experimental analyses on eight completely sequenced Pseudomonas species. Comparative pathway analyses reveal that several pathways within the Pseudomonas species show high plasticity and versatility. Potential bypasses in 11 metabolic pathways were identified. We further confirmed the presence of the enzyme O-acetyl homoserine (thiol) lyase (EC: 2.5.1.49) in P. syringae pv. tomato that revealed inconsistent annotations in KEGG and in the recently published SYSTOMONAS database. These analyses connect and integrate systematic data generation, computational data interpretation, and experimental validation and represent a synergistic and powerful means for conducting biological research.     

Challenges and opportunities for photochemists on the verge of solar energy conversion.

Has photochemistry missed the boat on solar energy conversion? Certainly not, but it is time to reach out and make a difference if we do not want to have to choose between feeding our families or our thirst for fuel. Compared to other initiatives, such as biofuels or nuclear fusion, direct conversion of solar energy into electricity or fuels is lagging behind in terms of funding, and this is slowing progress on overcoming critical bottlenecks. This perspective outlines some of the key fundamental issues in solar energy conversion based on organic photovoltaic devices or artificial photosynthesis where being a photochemist can make a difference.     

Cellular conditioning with trichostatin A enhances the anti-stress response through up-regulation of HDAC4 and down-regulation of the IGF/Akt pathway

Evidence is accumulating that chromatin plays a major role in the control of cellular response to stress. This is best illustrated by the recent findings that chromatin-modifying factors of class III histone deacetylases (sirtuins) are capable of protecting cells from oxidative and genotoxic stress. In particular, Sirt1 has been shown to mimic the action of caloric restriction for the prevention of aging-associated diseases. In the present study, we have investigated the potential role of class I and II histone deacetylases (HDACs) in cellular protection against various stresses, including those caused by nutrient deprivation. For this, we utilized a cellular model in which expression of class I and II HDACs was altered as a result of cellular adaptation to trichostatin A (TSA), a selective inhibitor of these deacetylases. Our results indicated that TSA-resistant cells also developed resistance to H₂O₂, DNA-damaging agents, and to nutrient deprivation. Interestingly, the insulin signaling pathway mediated by Akt was inhibited in the TSA-resistant cells, mirroring the effect of glucose deprivation on this pathway. Since expression of HDAC4 was consistently enhanced in the TSA-resistant cell lines, we suggest that this enzyme may contribute to their anti-stress response. In agreement with this, siRNA-mediated knockdown of HDAC4 in stress-resistant cells enhanced their sensitivity to the DNA-damaging drug doxorubicin and also to glucose deprivation. Akt phosphorylation was also up-regulated in response to HDC4 knockdown. Together, these findings suggest that cellular conditioning with TSA may represent a useful approach to mimic the effects of caloric restriction.