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101.
In computational structural biology, structure comparison is fundamental for our understanding of proteins. Structure comparison is, e.g., algorithmically the starting point for computational studies of structural evolution and it guides our efforts to predict protein structures from their amino acid sequences. Most methods for structural alignment of protein structures optimize the distances between aligned and superimposed residue pairs, i.e., the distances traveled by the aligned and superimposed residues during linear interpolation. Considering such a linear interpolation, these methods do not differentiate if there is room for the interpolation, if it causes steric clashes, or more severely, if it changes the topology of the compared protein backbone curves. To distinguish such cases, we analyze the linear interpolation between two aligned and superimposed backbones. We quantify the amount of steric clashes and find all self-intersections in a linear backbone interpolation. To determine if the self-intersections alter the protein’s backbone curve significantly or not, we present a path-finding algorithm that checks if there exists a self-avoiding path in a neighborhood of the linear interpolation. A new path is constructed by altering the linear interpolation using a novel interpretation of Reidemeister moves from knot theory working on three-dimensional curves rather than on knot diagrams. Either the algorithm finds a self-avoiding path or it returns a smallest set of essential self-intersections. Each of these indicates a significant difference between the folds of the aligned protein structures. As expected, we find at least one essential self-intersection separating most unknotted structures from a knotted structure, and we find even larger motions in proteins connected by obstruction free linear interpolations. We also find examples of homologous proteins that are differently threaded, and we find many distinct folds connected by longer but simple deformations. TM-align is one of the most restrictive alignment programs. With standard parameters, it only aligns residues superimposed within 5 Ångström distance. We find 42165 topological obstructions between aligned parts in 142068 TM-alignments. Thus, this restrictive alignment procedure still allows topological dissimilarity of the aligned parts. Based on the data we conclude that our program ProteinAlignmentObstruction provides significant additional information to alignment scores based solely on distances between aligned and superimposed residue pairs. 相似文献
102.
Tim L. Springer 《Global Change Biology Bioenergy》2021,13(1):175-184
Ravenna grass, Tripidium ravennae (L.) H. Scholz, is known to produce an abundance of biomass, but how plant density affects its biomass potential remains unknown. The objectives were to determine the effects of plant density on biomass yield; plant growth traits; biomass?carbon, nitrogen, and ash concentrations; heating value; nitrogen removal; and sucrose concentration in leaves and culms. The treatments consisted of five plant densities (1,250; 2,500; 5,000; 10,000; and 20,000 plants per hectare) in a randomized complete block design with four blocks. Plots were nonirrigated, unfertilized, and harvested once during the dormant season each year. Data were collected from 2015?2019. Dependent variables that varied with plant population density (p < .05) were biomass yield, number of reproductive culms per plant, reproductive culm diameter, reproductive culm sucrose concentration, and nitrogen removal with biomass. Biomass yield ranged from 5.6 to 16.3 Mg/ha for plant densities of 1,250–20,000 plants per hectare, respectively. Combined over years, nonlinear regression of the data showed the equation for biomass yield to plateau at 16.2 Mg/ha at a plant density of 10,640 plants per hectare. As plant density increased, the number of reproductive culms per plant, culm diameter, and culm sucrose concentration significantly decreased. At 1,250 plants per hectare, the number of reproductive culms per plant, culm diameter, and culm sucrose averaged 70, 10.2 mm, and 63.2 g/kg, respectively. Nitrogen removed with biomass significantly increased as biomass yield increased with plant density. At a density of 10,000 and 20,000 plants per hectare, the amount of nitrogen removed annually in the harvested biomass averaged 88 kg/ha. The data suggest that 10,000 plants per hectare would produce the greatest annual biomass yields; however, research is needed to determine the nutrient requirement for Ravenna grass to sustain biomass production at that density. 相似文献
103.
Khoo Kelvin H. P. Sheedy Jason G. Taylor Julian D. Croser Janine S. Hayes Julie E. Sutton Tim Thompson John P. Mather Diane E. 《Molecular breeding : new strategies in plant improvement》2021,41(12):1-13
Molecular Breeding - Plant height is vital for crop yield by influencing plant architecture and resistance to lodging. Although lots of quantitative trait loci (QTLs) controlling plant height had... 相似文献
104.
Ecosystems - Native biodiversity often depends on remnant vegetation for survival in agricultural landscapes. However, the size and shape of remnant patches can affect their conservation values... 相似文献
105.
Tim G. Ashlin Nicholas J. Blunsom Shamshad Cockcroft 《Biochimica et Biophysica Acta (BBA)/Molecular and Cell Biology of Lipids》2021,1866(9):158985
Phosphatidylinositol is the parent lipid for the synthesis of seven phosphorylated inositol lipids and each of them play specific roles in numerous processes including receptor-mediated signalling, actin cytoskeleton dynamics and membrane trafficking. PI synthesis is localised to the endoplasmic reticulum (ER) whilst its phosphorylated derivatives are found in other organelles where the lipid kinases also reside. Phosphorylation of PI to phosphatidylinositol (4,5) bisphosphate (PI(4,5)P2) at the plasma membrane and to phosphatidylinositol 4-phosphate (PI4P) at the Golgi are key events in lipid signalling and Golgi function respectively. Here we review a family of proteins, phosphatidylinositol transfer proteins (PITPs), that can mobilise PI from the ER to provide the substrate to the resident kinases for phosphorylation. Recent studies identify specific and overlapping functions for the three soluble PITPs (PITPα, PITPβ and PITPNC1) in phospholipase C signalling, neuronal function, membrane trafficking, viral replication and in cancer metastases. 相似文献
106.
Tim Coulson 《Ecology letters》2021,24(1):3-5
Ecological systems are no longer at equilibrium, but over much of the history of the Earth, the natural world has been in stationary states, that are punctuated by periods of transience. Just because we have knocked our planet away from a stable state, doesn't mean we have to abandon the concept of equilibrium when we strive to understand the dynamics of the natural world. 相似文献
107.
Rucha Karnik Christopher Grefen Robert Bayne Annegret Honsbein Tim K?hler Dimitrios Kioumourtzoglou Mary Williams Nia J. Bryant Michael R. Blatt 《The Plant cell》2013,25(4):1368-1382
The Arabidopsis thaliana Qa-SNARE SYP121 (=SYR1/PEN1) drives vesicle traffic at the plasma membrane of cells throughout the vegetative plant. It facilitates responses to drought, to the water stress hormone abscisic acid, and to pathogen attack, and it is essential for recovery from so-called programmed stomatal closure. How SYP121-mediated traffic is regulated is largely unknown, although it is thought to depend on formation of a fusion-competent SNARE core complex with the cognate partners VAMP721 and SNAP33. Like SYP121, the Arabidopsis Sec1/Munc18 protein SEC11 (=KEULE) is expressed throughout the vegetative plant. We find that SEC11 binds directly with SYP121 both in vitro and in vivo to affect secretory traffic. Binding occurs through two distinct modes, one requiring only SEC11 and SYP121 and the second dependent on assembly of a complex with VAMP721 and SNAP33. SEC11 competes dynamically for SYP121 binding with SNAP33 and VAMP721, and this competition is predicated by SEC11 association with the N terminus of SYP121. These and additional data are consistent with a model in which SYP121-mediated vesicle fusion is regulated by an unusual “handshaking” mechanism of concerted SEC11 debinding and rebinding. They also implicate one or more factors that alter or disrupt SEC11 association with the SYP121 N terminus as an early step initiating SNARE complex formation. 相似文献
108.
Sponsored by Waters Corporation organized by the Education Committee: Dr. Kevin L. Knudtson Dr. Allis S. Chien Dr Natalia G. Reyero Vinas Dr LeRoy Martin Dr. Janet M Murray Dr. Paul A Rudnick Brian C. Searle Michael Zianni Tim C Hunter James Van Ee David Needleman Elke Kuster-Schock 《Journal of biomolecular techniques》2013,24(2):112
109.
Tuula Larmola Jill L. Bubier Christine Kobyljanec Nathan Basiliko Sari Juutinen Elyn Humphreys Michael Preston Tim R. Moore 《Global Change Biology》2013,19(12):3729-3739
To study vegetation feedbacks of nutrient addition on carbon sequestration capacity, we investigated vegetation and ecosystem CO2 exchange at Mer Bleue Bog, Canada in plots that had been fertilized with nitrogen (N) or with N plus phosphorus (P) and potassium (K) for 7–12 years. Gross photosynthesis, ecosystem respiration, and net CO2 exchange were measured weekly during May–September 2011 using climate‐controlled chambers. A substrate‐induced respiration technique was used to determine the functional ability of the microbial community. The highest N and NPK additions were associated with 40% less net CO2 uptake than the control. In the NPK additions, a diminished C sink potential was due to a 20–30% increase in ecosystem respiration, while gross photosynthesis rates did not change as greater vascular plant biomass compensated for the decrease in Sphagnum mosses. In the highest N‐only treatment, small reductions in gross photosynthesis and no change in ecosystem respiration led to the reduced C sink. Substrate‐induced microbial respiration was significantly higher in all levels of NPK additions compared with control. The temperature sensitivity of respiration in the plots was lower with increasing cumulative N load, suggesting more labile sources of respired CO2. The weaker C sink potential could be explained by changes in nutrient availability, higher woody : foliar ratio, moss loss, and enhanced decomposition. Stronger responses to NPK fertilization than to N‐only fertilization for both shrub biomass production and decomposition suggest that the bog ecosystem is N‐P/K colimited rather than N‐limited. Negative effects of further N‐only deposition were indicated by delayed spring CO2 uptake. In contrast to forests, increased wood formation and surface litter accumulation in bogs seem to reduce the C sink potential owing to the loss of peat‐forming Sphagnum. 相似文献
110.
Tim S. Jessop Michael R. Kearney Joslin L. Moore Tim Lockwood Michael Johnston 《Biological invasions》2013,15(8):1653-1663
Control of introduced predators to mitigate biodiversity impacts is a pressing conservation challenge. Across Australia feral cats (Felis catus) are a major threat to terrestrial biodiversity. Currently feral cat control is hindered by the limited utility of existing predator baiting methods. Further proposed control methods include use of the novel poison para-aminopropiophenone (PAPP) which may present a hazard to some native animal populations. Here we used experimental and predictive approaches to evaluate feral cat bait take by a large native Australian predatory reptile the Lace monitor (Varanus varius). These lizards would be expected to readily detect, ingest and consume a lethal dose (depending on toxin) from surface-laid baits intended for feral cat control if a precautionary approach was not adopted when baiting. We modelled V. varius bait take using experimental and predictive biophysical modelling approaches to evaluate temporal effects of climate variables on V. varius activity and hence potential for bait removal. Finally we conducted a pre-PAPP baiting site occupancy assessment of V. varius within Wilson Promontory National Park (WPNP) to provide a basis for monitoring any longer term population effects of cat baiting. V. varius removed 7 % of deployed baits from 73 % of bait stations across another study area in Far Eastern Victoria. Daily bait removal was positively correlated with maximum temperature and solar radiation. Biophysical modelling for Far Eastern Victoria predicted that maximum temperatures <19.5 °C prevented V. varius activity and hence opportunity for bait removal. V. varius in WPNP was undetectable suggesting aerial baiting posed limited hazard to this species at this location. Depending how climate influences annual activity patterns and the specific poison, surface-laid baits could pose a significant mortality risk to V. varius. However, use of biophysical models to predict periods of V. varius inactivity may provide a novel means to reduce non-target bait take by this predator. 相似文献