scholarly journals Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition

2021 ◽  
Vol 22 (16) ◽  
pp. 8595
Author(s):  
Dóra Papp ◽  
Imola Csilla Szigyártó ◽  
Bengt Nordén ◽  
András Perczel ◽  
Tamás Beke-Somfai
Keyword(s):  
Structural Changes ◽  
Biological Processes ◽  
Protein Assemblies ◽  
Isodesmic Reactions ◽  
Structural Water ◽  
Protein Motifs ◽  
State Preference ◽  
Β Sheets ◽  
The Difference ◽  
Liquid Liquid Phase Separation

Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol−1 per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol−1 per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol−1 per residue excess stabilization.

scholarly journals Observation of liquid-liquid phase separation of ataxin-3 and quantitative evaluation of its concentration in a single droplet using Raman microscopy

2021 ◽  
Author(s):  
Kazuki Murakami ◽  
Shinji Kajimoto ◽  
Daiki Shibata ◽  
Kunisato Kuroi ◽  
Fumihiko Fujii ◽  
...  
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Neurodegenerative Diseases ◽  
Protein Aggregation ◽  
Quantitative Evaluation ◽  
Raman Microscopy ◽  
Liquid Phase Separation ◽  
Biological Processes ◽  
Single Droplet ◽  
Liquid Liquid Phase Separation

Liquid–liquid phase separation (LLPS) plays an important role in a variety of biological processes and is also associated with protein aggregation in neurodegenerative diseases. Quantification of LLPS is necessary to...

scholarly journals Summertime canopy albedo is sensitive to forest thinning

2013 ◽  
Vol 10 (9) ◽  
pp. 15373-15414 ◽  
Author(s):  
J. Otto ◽  
D. Berveiller ◽  
F.-M. Bréon ◽  
N. Delpierre ◽  
G. Geppert ◽  
...  
Keyword(s):  
Forest Management ◽  
Tree Species ◽  
Structural Changes ◽  
Near Infrared ◽  
Canopy Structure ◽  
Model Parameters ◽  
Transfer Model ◽  
Forest Thinning ◽  
Crown Volume ◽  
The Difference

Abstract. Despite an emerging body of literature linking canopy albedo to forest management, understanding of the process is still fragmented. We combined a stand-level forest gap model with a canopy radiation transfer model and satellite-derived model parameters to quantify the effects of forest thinning, that is removing trees at a certain time during the forest rotation, on summertime canopy albedo. The effects of different forest species (pine, beech, oak) and four thinning strategies (light to intense thinning regimes) were examined. During stand establishment, summertime canopy albedo is driven by tree species. In the later stages of stand development, the effect of tree species on summertime canopy albedo decreases in favour of an increasing influence of forest thinning on summertime canopy albedo. These trends continue until the end of the rotation where thinning explains up to 50% of the variance in near-infrared canopy albedo and up to 70% of the variance in visible canopy albedo. More intense thinning lowers the summertime shortwave albedo in the canopy by as much as 0.02 compared to unthinned forest. The structural changes associated with forest thinning can be described by the change in LAI in combination with crown volume. However, forests with identical canopy structure can have different summertime albedo values due to their location: the further north a forest is situated, the more the solar zenith angle increases and thus the higher is the summertime canopy albedo, independent of the wavelength. Despite the increase of absolute summertime canopy albedo values with latitude, the difference in canopy albedo between managed and unmanaged forest decreases with increasing latitude. Forest management thus strongly altered summertime forest albedo.

Identification of MdDof genes in apple and analysis of their response to biotic or abiotic stress

2018 ◽  
Vol 45 (5) ◽  
pp. 528 ◽  
Author(s):  
Qing Yang ◽  
Qiuju Chen ◽  
Yuandi Zhu ◽  
Tianzhong Li
Keyword(s):  
Abiotic Stress ◽  
Zinc Finger ◽  
Flower Development ◽  
Higher Plants ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Biological Processes ◽  
Protein Motifs ◽  
Gene Structures ◽  
Dof Transcription Factors

As a classic plant-specific transcription factor family – the Dof domain proteins – are involved in a variety of biological processes in organisms ranging from unicellular Chlamydomonas to higher plants. However, there are limited reports of MdDof (Malus domestica Borkh. DNA-binding One Zinc Finger) domain proteins in fruit trees, especially in apple. In this study we identified 54 putative Dof transcription factors in the apple genome. We analysed the gene structures, protein motifs, and chromosome locations of each of the MdDof genes. Next, we characterised all 54 MdDofs their expression patterns under different abiotic and biotic stress conditions. It was found that MdDof6,26 not only played an important role in the biotic/abiotic stress but may also be involved in many molecular functions. Further, both in flower development and pollen tube growth it was found that the relative expression of MdDof24 increased rapidly, also with gene ontology analysis it was indicated that MdDof24 was involved in the chemical reaction and flower development pathways. Taken together, our results provide useful clues as to the function of MdDof genes in apple and serve as a reference for studies of Dof zinc finger genes in other plants.

scholarly journals Genomic of the severe isolate of Maize chlorotic dwarf virus

2010 ◽  
Vol 40 (No. 4) ◽  
pp. 113-119 ◽  
Author(s):  
R. Chaouch ◽  
G. Redinbaugh M ◽  
M. Marrakchi ◽  
S.A. Hogenhout
Keyword(s):  
Type Strain ◽  
Dwarf Virus ◽  
Cdna Clones ◽  
Large Open Reading Frame ◽  
Reading Frame ◽  
Protein Motifs ◽  
Complete Sequences ◽  
The Difference ◽  
Maize Chlorotic Dwarf Virus ◽  
Severe Isolate

The complete sequences of the severe isolates of Maize chlorotic dwarf virus (MCDV-S) were obtained from cDNA clones of the viral RNA. The genome is 11 785 nucleotides (nt) in length and contains one large open reading frame between nt 455 and 10 825 that encodes a polyprotein of 3458 amino acids. Computer analysis revealed several conserved protein motifs similar to other plant picorna-like viruses. Comparison of the genome sequence of MCDV-S with that of the type strain of MCDV showed high similarities despite the difference in symptoms.  

A comparison of NH4/NO3 control strategies for alternating activated sludge processes

1999 ◽  
Vol 39 (4) ◽  
pp. 93-102 ◽  
Author(s):  
L. J. S. Lukasse ◽  
K. J. Keesman ◽  
A. Klapwijk ◽  
G. van Straten
Keyword(s):  
Activated Sludge ◽  
Time Delays ◽  
Control Strategies ◽  
Treatment Plant ◽  
Biological Processes ◽  
Effluent Quality ◽  
N Removal ◽  
Activated Sludge Reactor ◽  
The Difference ◽  
Activated Sludge Processes

Four control strategies for N-removal in alternating activated sludge plants (ASP's) are compared: 1. timer-based, 2. switching the aeration on/off when depletion of nitrate/ammonium is detected, 3. switching the aeration on/off when ammonium crosses an upper/lower-bound, 4. the newly developed adaptive receding horizon optimal controller (ARHOC) as presented in Lukasse et al. (1997). The comparison is made by simulating the controllers' application to an alternating continuously-mixed activated sludge reactor preceded by a small anoxic reactor for predenitrification. The biological processes in the reactors are modelled by the activated sludge model no. 1. Realistic influent patterns, measured at a full-scale wastewater treatment plant, are used. The results show that three totally different controllers (timer-based, NH4-bounds based and ARHOC) can achieve a more or less equal effluent quality, if tuned optimally. The difference mainly occurs in the sensitivity to suboptimal tunings. The timer-based strategy has a higher aeration demand. The sensitivity of the ARHOC controller to sub-optimal tuning, known measurement time delays and changing plant loads is significantly less than that of the other controllers. Also its tuning is more natural and explicit.

scholarly journals Liquid-liquid phase separation in particles containing secondary organic material free of inorganic salts

2017 ◽  
Author(s):  
Mijung Song ◽  
Pengfei Liu ◽  
Scot T. Martin ◽  
Allan K. Bertram
Keyword(s):  
Phase Separation ◽  
Liquid Phase ◽  
Organic Material ◽  
Water Saturation ◽  
Liquid Phase Separation ◽  
Inorganic Salts ◽  
Photo Oxidation ◽  
Condensation Nucleation ◽  
The Difference ◽  
Liquid Liquid Phase Separation

Abstract. Particles containing secondary organic material (SOM) are ubiquitous in the atmosphere and play a role in climate and air quality. Recently, research has shown that liquid-liquid phase separation (LLPS) occurs at high relative humidities (RH) (greater than ~ 95 %) in α-pinene-derived SOM particles free of inorganic salts while LLPS does not occur in isoprene-derived SOM particles free of inorganic salts. We expand on these findings by investigating LLPS in SOM particles free of inorganic salts produced from ozonolysis of β-caryophyllene, ozonolysis of limonene, and photo-oxidation of toluene. LLPS was observed at greater than ~ 95 % RH in the biogenic SOM particles derived from β-caryophyllene and limonene while LLPS was not observed in the anthropogenic SOM particles derived from toluene at 290 ± 1 K. This work combined with the earlier work on LLPS in SOM particles free of inorganic salts suggests that the occurrence of LLPS in SOM particles free of inorganic salts is related to the average oxygen-to-carbon elemental ratio (O : C) of the organic material. When the average O : C is between 0.25 and 0.60, LLPS was observed, but when the average O : C was between 0.52 and 1.3, LLPS was not observed. These results help explain the difference between the hygroscopic parameter k of SOM particles measured above and below water saturation in the laboratory and field, and have implications for predicting the cloud condensation nucleation properties of SOM particles.

Thermophysical Properties of Cement Based Composites with Addition of Plastic Fibers and Horse Manure

2018 ◽  
Vol 776 ◽  
pp. 92-97
Author(s):  
Gabriela Pavlendová ◽  
Peter Šín ◽  
Jozefa Lukovičová ◽  
Michal Kopčok
Keyword(s):  
Water Uptake ◽  
Thermophysical Properties ◽  
Structural Changes ◽  
Natural Fiber ◽  
Horse Manure ◽  
The Difference

Effect of different amount of plastic fiber and horse manure addition on thermophysical properties of cement based composite is studied. 1-D process of water uptake, and porosity measurement were carried out to understand the structural changes. Horse manure has high microfiber content, so that the difference between plastic and natural fiber was compared.

scholarly journals Transcriptome Sequencing and Comparative Analysis of Amphoteric ESCs and PGCs in Chicken (Gallus gallus)

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2228
Author(s):  
Kai Jin ◽  
Jing Zhou ◽  
Qisheng Zuo ◽  
Jiuzhou Song ◽  
Yani Zhang ◽  
...  
Keyword(s):  
Primordial Germ Cells ◽  
Embryonic Stem ◽  
Gallus Gallus ◽  
Future Research ◽  
Biological Processes ◽  
Rna Seq ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
The Difference ◽  
Go Terms

Chicken (Gallus gallus) pluripotent embryonic stem cells (ESCs) and primordial germ cells (PGCs) can be broadly applied in the research of developmental and embryonic biology, but the difference between amphoteric ESCs and PGCs is still elusive. This study determined the sex of collected samples by identifying specific sex markers via polymerase chain reaction (PCR) and fluorescence activated cell sorter (FACS). RNA-seq was utilized to investigate the transcriptomic profile of amphoteric ESCs and PGCs in chicken. The results showed no significant differentially expressed genes (DEGs) in amphoteric ESCs and 227 DEGs exhibited in amphoteric PGCs. Moreover, those 227 DEGs were mainly enriched in 17 gene ontology (GO) terms and 27 pathways according to Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Furthermore, qRT-PCR was performed to verify RNA-seq results, and the results demonstrated that Notch1 was highly expressed in male PGCs. In summary, our results provided a knowledge base of chicken amphoteric ESCs and PGCs, which is helpful for future research in relevant biological processes.

Epigenetics in the Remission of Anorexia Nervosa: A Follow-up Study of Whole-genome Methylation Profiles

2017 ◽  
Vol 41 (S1) ◽  
pp. S102-S102 ◽  
Author(s):  
N. Ramoz ◽  
S. Guillaume ◽  
P. Courtet ◽  
P. Gorwood
Keyword(s):  
Anorexia Nervosa ◽  
Whole Genome ◽  
Biological Processes ◽  
Methylation Of Dna ◽  
Genome Methylation ◽  
The Difference ◽  
Competing Interest ◽  
One Year ◽  
Epigenetic Signatures

IntroductionAnorexia nervosa (AN) is a severe psychiatric disorder. The epigenetic regulations are strongly suggested in AN. We and other groups have performed a whole-genome methylation study (methylome) in AN. We found that the differentially methylated CpG sites are located around genes involved in biological processes in link with embryonic morphogenesis, brain development and its plasticity, in particular adhesion and axon guidance. Here, we study an independent group of 40 AN patients. Furthermore, we have done a follow-up during more than one year, to compare the methylation profiles in subjects that evolve to the remission.ObjectivesOur work is to replicate the methylome study in an independent AN cohort and to characterize profiles of methylation at two times for the same subjects to compare the AN patients that convert to remitters.AimsOur goal is to identify diagnostic and prognostic epigenetic signatures for AN.MethodsOf the 40 AN patients, 18 evolved to remission. Furthermore, the blood samples of the subjects from the 2 times will be investigated, like this, each subject is its own control. Methylation of DNA is measured by using the Infinium HumanMethylation450 BeadChip technology.ResultsComparisons of AN to controls showed similar profiles of methylation involving the same biological processes as previously identified. We are comparing now the difference of methylation between the 18 remitters and the 18 actual AN, taking into account of the two times of samples.ConclusionsWe expect to characterize specific methylation signature of the prognostic of the AN remission.Disclosure of interestThe authors have not supplied their declaration of competing interest.

scholarly journals Impacts Assessments without True Baselines: Assessing the Relative Effects of Training on the Performance of Water User Associations in Southern Tajikistan

2018 ◽  
Vol 04 (03) ◽  
pp. 1850007 ◽  
Author(s):  
Soumya Balasubramanya ◽  
Joseph P. G. Price ◽  
Theodore M. Horbulyk
Keyword(s):  
Structural Changes ◽  
Propensity Scores ◽  
Single Point ◽  
Water User Associations ◽  
Water User ◽  
The Difference ◽  
Synthetic Controls ◽  
New Institutions ◽  
Time Invariant ◽  
The Impact

Conducting rigorous evaluations of whether the process of creating new institutions affects their performance of mandated duties presents several challenges. Not only is assignment to process often not random, but when the process of creating new institutions starts, outcomes and other performance-influencing covariates are not measurable because the yet-to-be created institutions are not functioning at baseline. This paper compares the performance of 74 ‘treated’ water user associations (WUAs) in Tajikistan that were created using a longer training process with 67 ‘control’ WUAs that were created using shorter training, to assess the impact of training on WUA performance of mandated duties. First, propensity scores were constructed to estimate the probabilities of being ‘treated’ by treatment status. These results guided the application of the difference-in-difference technique with right-hand side covariates in a context where field measures of outcomes and other performance-influencing covariates were made after the new institutions were created and functioning. The first measures were taken within 12–18 months of the new institutions being functional and the second measures were taken 24 months after the first. This choice of methods introduces a bias due to measurement error causing an underestimate of the treatment effects, while controlling for biases due to time-invariant and time-varying unobservables. An alternative method that only compared the differences in outcomes at a single point in time after the new institutions were created would have provided an inaccurate estimate of the effects of the intervention. This is a context in which methods such as synthetic controls are impossible to employ due to the nature of the intervention, other macroeconomic structural changes, and severe data restrictions. The methodology employed here generates evidence that, while biased toward generating an underestimate of effect, can still be useful and informative for policy and management purposes, and for evaluating the impact of process on the functioning of new institutions in transition settings.

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