Enzyme co-localization in pea leaf chloroplasts: glyceraldehyde-3-P dehydrogenase,triose-P isomerase,aldolase and sedoheptulose bisphosphatase

Nearest neighbor analysis of immunocytolocalization experiments indicates that the enzymes glyceraldehyde-3-P dehydrogenase, triose-P isomerase and aldolase are located close to one another in the pea leaf chloroplast stroma, and that aldolase is located close to sedoheptulose bisphosphatase. Direct transfer of the triose phosphates between glyceraldehyde-3-P dehydrogenase and triose-P isomerase, and from glyceraldehyde-3-P dehydrogenase and triose-P isomerase to aldolase, is then a possibility, as is direct transfer of sedoheptulose bisphosphate from aldolase to sedoheptulose bisphosphatase. Spatial organization of these enzymes may be important for efficient CO₂ fixation in photosynthetic organisms. In contrast, there is no indication that fructose bisphosphatase is co-localized with aldolase, and direct transfer of fructose bisphosphate from aldolase to fructose bisphosphatase seems unlikely.     

Long‐term temporal and spatial trends in eutrophication status of the Baltic Sea

Much of the Baltic Sea is currently classified as ‘affected by eutrophication’. The causes for this are twofold. First, current levels of nutrient inputs (nitrogen and phosphorus) from human activities exceed the natural processing capacity with an accumulation of nutrients in the Baltic Sea over the last 50–100 years. Secondly, the Baltic Sea is naturally susceptible to nutrient enrichment due to a combination of long retention times and stratification restricting ventilation of deep waters. Here, based on a unique data set collated from research activities and long‐term monitoring programs, we report on the temporal and spatial trends of eutrophication status for the open Baltic Sea over a 112‐year period using the HELCOM Eutrophication Assessment Tool (HEAT 3.0). Further, we analyse variation in the confidence of the eutrophication status assessment based on a systematic quantitative approach using coefficients of variation in the observations. The classifications in our assessment indicate that the first signs of eutrophication emerged in the mid‐1950s and the central parts of the Baltic Sea changed from being unaffected by eutrophication to being affected. We document improvements in eutrophication status that are direct consequences of long‐term efforts to reduce the inputs of nutrients. The reductions in both nitrogen and phosphorus loads have led to large‐scale alleviation of eutrophication and to a healthier Baltic Sea. Reduced confidence in our assessment is seen more recently due to reductions in the scope of monitoring programs. Our study sets a baseline for implementation of the ecosystem‐based management strategies and policies currently in place including the EU Marine Strategy Framework Directives and the HELCOM Baltic Sea Action Plan.     

Short‐term harvesting of biomass from conservation grasslands maintains plant diversity

High yields are a priority in managing biomass for renewable energy, but the environmental impacts of various feedstocks and production systems should be equally considered. Mixed‐species, perennial grasslands enrolled in conservation programs are being considered as a source of biomass for renewable energy. Conservation grasslands are crucial in sustaining native biodiversity throughout the US Upper Midwest, and the effects of biomass harvest on biodiversity are largely unknown. We measured the effect of late‐season biomass harvest on plant community composition in conservation grasslands in three regions of Minnesota, USA from 2009 to 2012. Temporal trends in plant species composition within harvested grasslands were compared to unharvested grasslands using mixed effects models. A before‐after control‐impact approach using effect sizes was applied to focus on pre‐ and postharvest conditions. Production‐scale biomass harvest did not affect plant species richness, species or functional group diversity, nor change the relative abundance of the main plant functional groups. Differences in the relative abundances of plant functional groups were observed across locations; and at some locations, changed through time. The proportion of non‐native species remained constant, while the proportion of noxious weeds decreased through time in both harvested and unharvested grasslands at the central location. Ordination revealed patterns in species composition due to location, but not due to harvest treatment. Therefore, habitat and bioenergy characteristics related to grassland plant communities are not expected to change due to short‐term or intermittent late‐season biomass harvest.     

Limited influence of local and landscape factors on finescale gene flow in two pond‐breeding amphibians

Dispersal and gene flow within animal populations are influenced by the composition and configuration of the landscape. In this study, we evaluated hypotheses about the impact of natural and anthropogenic factors on genetic differentiation in two amphibian species, the spotted salamander (Ambystoma maculatum) and the wood frog (Lithobates sylvaticus) in a commercial forest in central Maine. We conducted this analysis at two scales: a local level, focused on factors measured at each breeding pond, and a landscape level, focused on factors measured between ponds. We investigated the effects of a number of environmental factors in six categories including Productivity, Physical, Land Composition, Land Configuration, Isolation and Location. Embryos were sampled from 56 spotted salamander breeding ponds and 39 wood frog breeding ponds. We used a hierarchical Bayesian approach in the program GESTE at each breeding pond and a random forest algorithm in conjunction with a network analysis between the ponds. We found overall high genetic connectivity across distances up to 17 km for both species and a limited effect of natural and anthropogenic factors on gene flow. We found the null models best explained patterns of genetic differentiation at a local level and found several factors at the landscape level that weakly influenced gene flow. This research indicates multiscale investigations that incorporate local and landscape factors are valuable for understanding patterns of gene flow. Our findings suggest that dispersal rates in this system are high enough to minimize genetic structuring and that current forestry practices do not significantly impede dispersal.     

A theoretical study of Ru(II) polypyridyl DNA intercalators: Structure and electronic absorption spectroscopy of [Ru(phen)2(dppz)] and [Ru(tap)2(dppz)] complexes intercalated in guanine-cytosine base pairs

The structural and spectroscopic properties of [Ru(phen)₂(dppz)]²⁺ and [Ru(tap)₂(dppz)]²⁺ (phen = 1,10-phenanthroline; tap = 1,4,5,8-tetraazaphenanthrene; dppz = dipyridophenazine ) have been investigated by means of density functional theory (DFT), time-dependent DFT (TD-DFT) within the polarized continuum model (IEF-PCM) and quantum mechanics/molecular mechanics (QM/MM) calculations. The model of the Δ and Λ enantiomers of Ru(II) intercalated in DNA in the minor and major grooves is limited to the metal complexes intercalated in two guanine-cytosine base pairs. The main experimental spectral features of these complexes reported in DNA or synthetic polynucleotides are better reproduced by the theoretical absorption spectra of the Δ enantiomers regardless of intercalation mode (major or minor groove). This is especially true for [Ru(phen)₂(dppz)]²⁺. The visible absorption of [Ru(tap)₂(dppz)]²⁺ is governed by the MLCT_tap transitions regardless of the environment (water, acetonitrile or bases pair), the visible absorption of [Ru(phen)₂(dppz)]²⁺ is characterized by transitions to metal-to-ligand-charge-transfer MLCT_dppz in water and acetonitrile and to MLCT_phen when intercalated in DNA. The response of the IL_dppz state to the environment is very sensitive. In vacuum, water and acetonitrile these transitions are characterized by significant oscillator strengths and their positions depend significantly on the medium with blue shifts of about 80 nm when going from vacuum to solvent. When the complex is intercalated in the guanine-cytosine base pairs the ¹IL_dppz transition contributes mainly to the band at 370 nm observed in the spectrum of [Ru(phen)₂(dppz)]²⁺ and to the band at 362 nm observed in the spectrum of [Ru(tap)₂(dppz)]²⁺.     

Genome-wide survey of prokaryotic O-protein phosphatases

Complex and diverse signal transduction circuits are responsible for the efficient functioning of cellular network. Protein kinases and O-protein phosphatases are primarily responsible for propagating such stimuli within a eukaryotic cell. However, there is limited understanding of O-protein phosphatases in the prokaryotic genomes. The availability of complete genome sequence information for several prokaryotes permits a genome-wide survey of O-protein phosphatases. The distribution of the various protein phosphatase families has been observed to be mosaic, with the exception of the members of the phospho protein family P (PPP), which is consistent with previous studies. The PPP family is ubiquitous in the prokaryotic world and undergoes the highest sequence divergence within a genome amongst phosphatases studied. The co-occurrence of low molecular mass tyrosine phosphatase (LMWPc) and PPP domain in a single polypeptide suggests that the protein present in Archaeoglobus fulgidus might represent the progenitor for all protein phosphatases. The curation of data on prokaryotic protein phosphatases provides a convenient framework for the analysis of domain architectures and for characterising structural and functional properties of this important family of signalling proteins.     

Adsorption of CO on Cu (110) and (100) surfaces using COSMO-based DFT

Density functional theory (DFT) combined with the conductor-like solvent model (COSMO) can provide valuable atomistic level insights into CO adsorption on Cu surface interactions in liquid paraffin. The objective of this research was to investigate the solvent effect of liquid paraffin. It was found that both structural parameters and relative energies are very sensitive to the COSMO solvent model. Solvent effects can improve the stability of CO adsorption on Cu (110) and (100) surfaces and the extent of CO activation.     

Escherichia coli TolA tolerates multiple amino-acid substitutions as revealed by screening randomized variants for membrane integrity and phage receptor function

Escherichia coli TolA is a cytoplasmic membrane protein required for outer membrane integrity and the translocation of F-specific filamentous (Ff) bacteriophage DNA. Both phage infection and membrane integrity depend on several TolA interactions, e.g. those of the TolA C-terminal domain (TolAIII). Membrane integrity involves interaction with two host proteins and phage translocation requires direct interaction with the N-terminal domain (N1) of Ff phage protein g3p. Although cocrystallization of TolAIII and N1g3p has identified several contact points, it is still uncertain which residues are selectively involved in the different TolA functions. Thus, four different limited substitution libraries of TolA were created, targeting contacts at positions 415-420. These libraries were introduced into the tolA strain K17DE3tolA/F(+) and several variants, containing complementing, multiple amino-acid substitutions, were identified. However, most randomized variants did not complement the tolA strain K17DE3tolA/F(+). The TolA variants that restored sensitivity to phage infection displayed a considerable sequence variation, while the few variants that restored tolerance to detergent were from the same library. A comparison of the generated residue variation and natural variation, suggests that structural dependence overrides contact residue dependence. Thus, library screening can be efficient in identifying TolA variants with different functionally associated characteristics.     

小麦的比较基因组学和功能基因组学

小麦是异源多倍体植物,具有大的染色体组,并且基因组中重复序列所占比例较高,这些特征限制了小麦基因组研究的进展。比较基因组学方法为运用模式植物进行小麦基因组学研究提供了一个操作平台。功能基因组学的研究集中于基因组中转录表达的部分,基因功能的确定是功能基因组学研究的主要内容。对比较基因组学在小麦基因组研究中的应用和小麦功能基因组学的研究内容和方法进行了综述。     

Trio Haploinsufficiency Causes Neurodevelopmental Disease-Associated Deficits

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