Effect of loop length variation on quadruplex-Watson Crick duplex competition

AbstractProtein folding is governed by non-covalent interactions under the benefits and constraints of the covalent linkage of the backbone chain. In the current work we investigate the influence of loop length variation on the free energies of folding and ligand binding in a small globular single-domain protein containing two EF-hand subdomains—calbindin D9k. We introduce a linker extension between the subdomains and vary its length between 1 to 16 glycine residues. We find a close to linear relationship between the linker length and the free energy of folding of the Ca2+-free protein. In contrast, the linker length has only a marginal effect on the Ca2+ affinity and cooperativity. The variant with a single-glycine extension displays slightly increased Ca2+ affinity, suggesting that the slightly extended linker allows optimized packing of the Ca2+-bound state. For the extreme case of disconnected subdomains, Ca2+ binding becomes coupled to folding and assembly. Still, a high affinity between the EF-hands causes the non-covalent pair to retain a relatively high apparent Ca2+ affinity. Our results imply that loop length variation could be an evolutionary option for modulating properties such as protein stability and turnover without compromising the energetics of the specific function of the protein.

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The intriguing dynamics of chromatin folding and assembly

10.1101/2020.02.18.953398 ◽

2020 ◽

Author(s):

Z. Yang ◽

W. Miao ◽

M. R.K. Mofrad

Keyword(s):

Transition Probabilities ◽

Research Work ◽

Dynamics Simulation ◽

Coarse Grained ◽

Length Variation ◽

Loop Length ◽

Wild Type ◽

Stable States ◽

Folding Process ◽

Chromatin Folding

ABSTRACTWe investigate the dynamics of chromatin folding based on the “strings and binders” (SBS) model with molecular dynamics simulation. SBS model is a coarse-grained model considering a self-avoiding chain interacting with diffusive binders. By introducing transition among different categories of beads with specific transition cycles and transition probabilities, our model is capable of introducing different dynamics quantitatively during the folding process, thus capturing variety of phenomena related to chromatin dynamics. Firstly, roles of dynamics in the process of chromatin folding were examined. We discovered that there is a minimum gyration of chromatin under varying characteristic times of transition which indicates neither dramatically dynamic nor static folding process is optimal for chromatin to reach stable states with relatively low free energy. Secondly, it is noticeable that when beads transit from or into others in distinct dynamics, the equilibrium concentrations are distinct as well. As a consequence, the distribution of chromatin loop length is relevant to the dynamics of binders which can be modified by complex such as Wings apart-like protein homolog (Wapl) and SCC2/SCC4 cohesin loader complex (SCC2/SCC4). Finally, our model is able to reproduce contact matrices of both wild type HAP1 cell and ΔWAPL HAP1 cell obtained from Hi-C technology with a relatively high accuracy. Our model recapitulate the accumulating contacts at the corners of TADs and vanishing short-range contacts along the diagonal, manifesting the difference of chromatin structures before and after eliminating WAPL.STATEMENT OF SIGNIFICANCEOur model includes reciprocal transition among beads in SBS model to introduce different dynamics in chromatin folding process. Our model is able to examine the roles of dynamics in chromatin folding, reveal the loop length variation due to the concentration imbalance caused by distinct dynamics and reproduce contact matrices of both wild type and WAPL-deficient cells. Our research work provides a model to investigate the dynamics of chromatin folding quantitatively and displays its significance of revealing multiple experimental results using computational tools.

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On the Crystal Chemistry of Inorganic Nitrides: Crystal-Chemical Parameters and Opportunities in the Exploration of Their Compositional Space

10.26434/chemrxiv.11626974.v2 ◽

2020 ◽

Author(s):

Olivier Charles Gagné

Keyword(s):

Functional Properties ◽

A Priori ◽

Lone Pair ◽

Length Variation ◽

Electronic Effects ◽

Statistical Knowledge ◽

Redox Active ◽

Multiply Bonded ◽

Jahn Teller ◽

Compositional Space

The scarcity of nitrogen in Earth’s crust, combined with challenging synthesis, have made inorganic nitrides a relatively-unexplored class of compounds compared to their naturally-abundant oxide counterparts. To facilitate exploration of their compositional space via a priori modeling, and to help a posteriori structure verification not limited to inferring the oxidation state of redox-active cations, we derive a suite of bond-valence parameters and Lewis-acid strength values for 76 cations observed bonding to N3-, and further outline a baseline statistical knowledge of bond lengths for these compounds. We examine structural and electronic effects responsible for the functional properties and anomalous bonding behavior of inorganic nitrides, and identify promising venues for exploring uncharted compositional spaces beyond the reach of high-throughput computational methods. We find that many mechanisms of bond-length variation ubiquitous to oxide and oxysalt compounds (e.g., lone-pair stereoactivity, the Jahn-Teller and pseudo Jahn-Teller effects) are similarly pervasive in inorganic nitrides, and are occasionally observed to result in greater distortion magnitude than their oxide counterparts. We identify inorganic nitrides with multiply-bonded metal ions as a promising venue in heterogeneous catalysis, e.g. in the development of a post-Haber-Bosch process proceeding at milder reaction conditions, thus representing further opportunity in the thriving exploration of the functional properties of this emerging class of materials.

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Performance enhancement of Echo Cancellation Using a Combination of Partial Update ( PU) Methods and New Variable Length LMS (NVLLMS) Algorithm

Journal of Engineering ◽

10.31026/j.eng.2018.05.05 ◽

2018 ◽

Vol 24 (5) ◽

pp. 66

Author(s):

Thamer M. Jamel ◽

Faez Fawzi Hammood

Keyword(s):

Mean Square Error ◽

Return Loss ◽

Performance Enhancement ◽

Variable Length ◽

Echo Cancellation ◽

Convergence Time ◽

Length Variation ◽

Mean Square ◽

Step Size ◽

Echo Return Loss Enhancement

In this paper, several combination algorithms between Partial Update LMS (PU LMS) methods and previously proposed algorithm (New Variable Length LMS (NVLLMS)) have been developed. Then, the new sets of proposed algorithms were applied to an Acoustic Echo Cancellation system (AEC) in order to decrease the filter coefficients, decrease the convergence time, and enhance its performance in terms of Mean Square Error (MSE) and Echo Return Loss Enhancement (ERLE). These proposed algorithms will use the Echo Return Loss Enhancement (ERLE) to control the operation of filter's coefficient length variation. In addition, the time-varying step size is used.The total number of coefficients required was reduced by about 18% , 10% , 6%, and 16% using Periodic, Sequential, Stochastic, and M-max PU NVLLMS algorithms respectively, compared to that used by a full update method which is very important, especially in the application of mobile communication since the power consumption must be considered. In addition, the average ERLE and average Mean Square Error (MSE) for M-max PU NVLLMS are better than other proposed algorithms.

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Bone quality and quantity of the mandibular symphyseal region in autogenous bone grafting using cone-beam computed tomography: a cross-sectional study

Head & Face Medicine ◽

10.1186/s13005-021-00282-2 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Yaser Safi ◽

Reza Amid ◽

Mahdi Kadkhodazadeh ◽

Hamed Mortazavi ◽

Mohamad Payam Sharifi ◽

...

Keyword(s):

Computed Tomography ◽

Cross Sectional Study ◽

Cone Beam ◽

Autogenous Bone ◽

Loop Length ◽

Sectional Study ◽

Cross Sectional ◽

Anterior Loop ◽

Bone Graft Harvesting

Abstract Background Bone volume plays a pivotal role in the success of dental implant treatment. Autogenous bone grafts should be harvested from reliable sites in the maxillofacial region. This study sought to assess the quantity and quality of bone in the mandibular symphysis for autogenous bone graft harvesting using cone-beam computed tomography (CBCT). Methods This cross-sectional study evaluated the CBCT scans of 78 adults presenting to three oral and maxillofacial radiology centers. The vertical (VD) and horizontal (HD) alveolar bone dimensions, cortical thickness (CT), and cancellous to cortical bone ratio (C/C) were measured in the interforaminal region of the mandible at the sites of central incisor to first premolar teeth. The interforaminal distance (ID) and the anterior loop length were also measured. Nonparametric statistical tests were used to analyze the data with respect to sex, age, and tooth position. Results The median VD, HD, and CT of the symphysis were 20.21 (3.26), 4.13 (0.37), and 2.25 (0.23) mm, respectively. The median C/C was 1.51 (0.11). The median ID was 52.24 (8.24) mm, and the median anterior loop length was 1.82 (1.06) mm. Significant differences were observed in all parameters among different teeth. Most of the measured parameters were greater in males compared with females. There were significant differences in ID, VD, and CT between different age groups. Conclusions The quantity and quality of the available bone in the mandibular symphysis for bone graft harvesting vary by gender, age, and harvesting site, necessitating careful preoperative evaluation.

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FGF5 missense mutation is associated with dromedary hair length variation

Animal Genetics ◽

10.1111/age.13132 ◽

2021 ◽

Author(s):

T. Maraqa ◽

B. H. Alhajeri ◽

H. Alhaddad

Keyword(s):

Missense Mutation ◽

Length Variation ◽

Hair Length

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Natural variation in plant telomere length is associated with flowering time

The Plant Cell ◽

10.1093/plcell/koab022 ◽

2021 ◽

Author(s):

Jae Young Choi ◽

Liliia R Abdulkina ◽

Jun Yin ◽

Inna B Chastukhina ◽

John T Lovell ◽

...

Keyword(s):

Life History ◽

Telomere Length ◽

Flowering Time ◽

Dna Sequences ◽

Genome Wide Association Study ◽

Genomic Analysis ◽

Life History Strategies ◽

Length Variation ◽

Chromosomal Structure ◽

Chromosome Integrity

Abstract Telomeres are highly repetitive DNA sequences found at the ends of chromosomes that protect the chromosomes from deterioration during cell division. Here, using whole genome re-sequencing and terminal restriction fragment assays, we found substantial natural intraspecific variation in telomere length in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). Genome-wide association study (GWAS) mapping in A. thaliana identified 13 regions with GWAS-significant associations underlying telomere length variation, including a region that harbors the telomerase reverse transcriptase (TERT) gene. Population genomic analysis provided evidence for a selective sweep at the TERT region associated with longer telomeres. We found that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life history traits and chromosome integrity. Our results point to several possible reasons for this correlation, including the possibility that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier). Our work suggests that chromosomal structure itself might be an adaptive trait associated with plant life history strategies.

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Predicting the Impact of Describing New Species on Phylogenetic Patterns

Integrative Organismal Biology ◽

10.1093/iob/obz028 ◽

2019 ◽

Vol 1 (1) ◽

Cited By ~ 1

Author(s):

D C Blackburn ◽

G Giribet ◽

D E Soltis ◽

E L Stanley

Keyword(s):

New Species ◽

Phylogenetic Trees ◽

Branch Length ◽

Length Variation ◽

Tree Shape ◽

Branch Lengths ◽

Taxonomic History ◽

Ecological Patterns ◽

The Impact ◽

Incomplete Sampling

Abstract Although our inventory of Earth’s biodiversity remains incomplete, we still require analyses using the Tree of Life to understand evolutionary and ecological patterns. Because incomplete sampling may bias our inferences, we must evaluate how future additions of newly discovered species might impact analyses performed today. We describe an approach that uses taxonomic history and phylogenetic trees to characterize the impact of past species discoveries on phylogenetic knowledge using patterns of branch-length variation, tree shape, and phylogenetic diversity. This provides a framework for assessing the relative completeness of taxonomic knowledge of lineages within a phylogeny. To demonstrate this approach, we use recent large phylogenies for amphibians, reptiles, flowering plants, and invertebrates. Well-known clades exhibit a decline in the mean and range of branch lengths that are added each year as new species are described. With increased taxonomic knowledge over time, deep lineages of well-known clades become known such that most recently described new species are added close to the tips of the tree, reflecting changing tree shape over the course of taxonomic history. The same analyses reveal other clades to be candidates for future discoveries that could dramatically impact our phylogenetic knowledge. Our work reveals that species are often added non-randomly to the phylogeny over multiyear time-scales in a predictable pattern of taxonomic maturation. Our results suggest that we can make informed predictions about how new species will be added across the phylogeny of a given clade, thus providing a framework for accommodating unsampled undescribed species in evolutionary analyses.

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