Three-dimensional geometry and topology effects in viscous streaming

Recent studies on viscous streaming flows in two dimensions have elucidated the impact of body curvature variations on resulting flow topology and dynamics, with opportunities for microfluidic applications. Following that, we present here a three-dimensional characterization of streaming flows as functions of changes in body geometry and topology, starting from the well-known case of a sphere to progressively arrive at toroidal shapes. We leverage direct numerical simulations and dynamical systems theory to systematically analyse the reorganization of streaming flows into a dynamically rich set of regimes, the origins of which are explained using bifurcation theory.

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Susceptibility of protein therapeutics to spontaneous chemical modifications by oxidation, cyclization, and elimination reactions

Amino Acids ◽

10.1007/s00726-019-02787-2 ◽

2019 ◽

Vol 51 (10-12) ◽

pp. 1409-1431 ◽

Cited By ~ 5

Author(s):

Luigi Grassi ◽

Chiara Cabrele

Keyword(s):

Small Molecules ◽

Three Dimensional ◽

Drug Market ◽

Structure And Function ◽

Dimensional Structure ◽

Chemical Modifications ◽

Small Molecule Drugs ◽

And Function ◽

The Impact

Abstract Peptides and proteins are preponderantly emerging in the drug market, as shown by the increasing number of biopharmaceutics already approved or under development. Biomolecules like recombinant monoclonal antibodies have high therapeutic efficacy and offer a valuable alternative to small-molecule drugs. However, due to their complex three-dimensional structure and the presence of many functional groups, the occurrence of spontaneous conformational and chemical changes is much higher for peptides and proteins than for small molecules. The characterization of biotherapeutics with modern and sophisticated analytical methods has revealed the presence of contaminants that mainly arise from oxidation- and elimination-prone amino-acid side chains. This review focuses on protein chemical modifications that may take place during storage due to (1) oxidation (methionine, cysteine, histidine, tyrosine, tryptophan, and phenylalanine), (2) intra- and inter-residue cyclization (aspartic and glutamic acid, asparagine, glutamine, N-terminal dipeptidyl motifs), and (3) β-elimination (serine, threonine, cysteine, cystine) reactions. It also includes some examples of the impact of such modifications on protein structure and function.

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The impact of contrast-enhanced spectral mammogram (CESM) and three-dimensional breast ultrasound (3DUS) on the characterization of the disease extend in cancer patients

British Journal of Radiology ◽

10.1259/bjr.20170977 ◽

2018 ◽

pp. 20170977 ◽

Cited By ~ 4

Author(s):

Maha Hussien Helal ◽

Sahar Mahmoud Mansour ◽

Lamia Adel Salaleldin ◽

Basma Mohamed Alkalaawy ◽

Dorria Saleh Salem ◽

...

Keyword(s):

Cancer Patients ◽

Three Dimensional ◽

Breast Ultrasound ◽

Contrast Enhanced ◽

The Impact

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Expression, purification and crystallization of a protein resulting from the inversion of the amino-acid sequence of a helical bundle

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x16020173 ◽

2017 ◽

Vol 73 (1) ◽

pp. 51-53

Author(s):

Aikaterini Kefala ◽

Dina Kotsifaki ◽

Mary Providaki ◽

Maria Amprazi ◽

Michael Kokkinidis

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Three Dimensional ◽

Unfolded Proteins ◽

Unit Cell Parameters ◽

Cell Parameters ◽

Helical Bundle ◽

Sequence Inversion ◽

The Impact

Earlier studies have found that the occurrence of inverse sequence identity in proteins is not indicative of three-dimensional similarity, but rather leads to different folds or unfolded proteins. Short helices, however, frequently keep their conformations when their sequences are inverted. To explore the impact of sequence inversion on long helices, revRM6, with the inverse amino-acid sequence relative to RM6, a highly stable variant of the ColE1 Rop protein, was engineered. RM6 is a highly regular four-α-helical bundle that serves as a model system for protein-folding studies. Here, the crystallization and preliminary crystallographic characterization of revRM6 are reported. The protein was overexpressed inEscherichia coli, purified to homogeneity and crystallized. The crystals belonged to space groupP41212, with unit-cell parametersa=b= 44.98,c= 159.74 Å, and diffracted to a resolution of 3.45 Å.

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Bifurcations of Invariant Torus and Knotted Periodic Orbits in Generalized Hopf-Langford Type Equations

10.21203/rs.3.rs-364736/v1 ◽

2021 ◽

Author(s):

Yanggeng Fu ◽

Jibin Li

Keyword(s):

Dynamical Systems ◽

Periodic Orbits ◽

Invariant Torus ◽

Bifurcation Theory ◽

Three Dimensional ◽

Heteroclinic Orbits ◽

Stable Limit ◽

Planar System ◽

Perturbed System ◽

Stable Limit Cycles

Abstract In this paper, we study the bifurcations of invariant torus and knotted periodic orbits for generalized Hopf-Langford type equations. By using bifurcation theory of dynamical systems, we obtain the exact explicit form of the heteroclinic orbits and knot periodic orbits. Moreover, under small perturbation, we prove that the perturbed planar system has two symmetric stable limit cycles created by Poincare bifurcations. Therefore, the corresponding three-dimensional perturbed system has an attractive invariant rotation torus.

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Super Secondary Structures of Proteins with Post-Translational Modifications in Colon Cancer

Molecules ◽

10.3390/molecules25143144 ◽

2020 ◽

Vol 25 (14) ◽

pp. 3144

Author(s):

Dmitry Tikhonov ◽

Liudmila Kulikova ◽

Arthur Kopylov ◽

Kristina Malsagova ◽

Alexander Stepanov ◽

...

Keyword(s):

Colorectal Cancer ◽

Control Cell ◽

Three Dimensional ◽

Vitamin D Binding Protein ◽

High Throughput Analysis ◽

Post Translational Modifications ◽

New Strategy ◽

The Impact ◽

Identification And Characterization

New advances in protein post-translational modifications (PTMs) have revealed a complex layer of regulatory mechanisms through which PTMs control cell signaling and metabolic pathways, contributing to the diverse metabolic phenotypes found in cancer. Using conformational templates and the three-dimensional (3D) environment investigation of proteins in patients with colorectal cancer, it was demonstrated that most PTMs (phosphorylation, acetylation, and ubiquitination) are localized in the supersecondary structures (helical pairs). We showed that such helical pairs are represented on the outer surface of protein molecules and characterized by a largely accessible area for the surrounding solvent. Most promising and meaningful modifications were observed on the surface of vitamin D-binding protein (VDBP), complement C4-A (CO4A), X-ray repair cross-complementing protein 6 (XRCC6), Plasma protease C1 inhibitor (IC1), and albumin (ALBU), which are related to colorectal cancer developing. Based on the presented data, we propose the impact of the observed modifications in immune response, inflammatory reaction, regulation of cell migration, and promotion of tumor growth. Here, we suggest a computational approach in which high-throughput analysis for identification and characterization of PTM signature, associated with cancer metabolic reprograming, can be improved to prognostic value and bring a new strategy to the targeted therapy.

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DYNAMICS OF CREMONA MAPS FROM PHYSICAL MODELS

International Journal of Modern Physics B ◽

10.1142/s0217979201007622 ◽

2001 ◽

Vol 15 (24n25) ◽

pp. 3279-3286

Author(s):

W. SCHWALM ◽

B. MORITZ ◽

M. SCHWALM

Keyword(s):

Dynamical Systems ◽

Three Dimensional ◽

Two Dimensions ◽

Physical Models ◽

Invariant Curves ◽

Chiral Potts Model ◽

Cremona Transformation ◽

Rational Mapping ◽

Area Preserving Maps ◽

The Matrix

A Cremona transformation X=f(x, y), Y=g(x, y) is a rational mapping (meaning that f and g are ratios of polynomials) with rational inverse x=F(X, Y), y=G(X, Y). Discrete dynamical systems defined by such transformations are well studied. They include symmetries of the Yang-Baxter equations and their generalizations. In this paper we comment on two types of dynamical systems based on Cremona transformations. The first is the P1 case of Bellon et al. which pertains to the inversion relation for the matrix of Boltzmann weights of the 4-state chiral Potts model. The resulting dynamical system decouples completely to one in a single variable. The sub case z=x corresponds to the symmetric Ashkin-Teller model. We solve this case explicitly giving orbits as closed formulas in the number n of iterations. The second type of system treated is an extension from the famous example due to McMillan of invariant curves of area preserving maps in two dimensions to the case of invariant curves and surfaces of three dimensional Cremona maps that preserve volume. The trace map of the renormalization of transmission through a Fibonacci chain, first introduced by Kohmoto, Kadanoff and Tang, is considered as an example of such a system.

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Preparation and Characterization of Water Absorbing and Anti-Fogging Coatings

Materials Science Forum ◽

10.4028/www.scientific.net/msf.848.722 ◽

2016 ◽

Vol 848 ◽

pp. 722-725

Author(s):

Kai Wang ◽

Min Huang ◽

Yue Huang ◽

Zhong Hua Zhou ◽

Shirley Shen

Keyword(s):

Three Dimensional ◽

Steam Bath ◽

Structure Characterization ◽

Hydroxyl Groups ◽

Functional Coatings ◽

Cure Reaction ◽

Water Steam ◽

Dimensional Network ◽

The Impact

Anti-fogging functional coatings have a broad application prospective in the fields of construction and transportation vehicles. In this study, superior water absorbing and anti-fogging coatings were prepared by a cure reaction using epoxy resins as water absorbent resins, hydroxyethyl ethylenediamine as a curing agent, γ-ammonia propyl triethoxy silane as a coupling agent, organic silicon sol as filler. The impact of additional polyethylene glycol (PEG) on the properties of water absorbing and antifogging coating has also been studied. The anti-fogging experiments were conducted in a 40 °C water steam bath, and the result shows that the sample with additional 4.0 % PEG has an anti-fogging time of 315 seconds (s), which is better than that without PEG (the anti-fogging time being 240s). Infrared spectroscopy and scanning electron microscope structure characterization indicate that the sample with additional PEG has an obvious three-dimensional network structure with hydroxyl groups, which leads to a great saturated water quantity and a superior anti-fogging performance.

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Quantitative Classification of Cerebellar Foliation in Cartilaginous Fishes (Class: Chondrichthyes) Using Three-Dimensional Shape Analysis and Its Implications for Evolutionary Biology

Brain Behavior and Evolution ◽

10.1159/000446904 ◽

2016 ◽

Vol 87 (4) ◽

pp. 252-264 ◽

Cited By ~ 2

Author(s):

Kara E. Yopak ◽

Vitaly L. Galinsky ◽

Rachel M. Berquist ◽

Lawrence R. Frank

Keyword(s):

Evolutionary Biology ◽

Spherical Wave ◽

Three Dimensional ◽

Evolutionary Process ◽

Two Dimensions ◽

Statistical Criterion ◽

Quantitative Classification ◽

Cartilaginous Fishes ◽

High Degree

A true cerebellum appeared at the onset of the chondrichthyan (sharks, batoids, and chimaerids) radiation and is known to be essential for executing fast, accurate, and efficient movement. In addition to a high degree of variation in size, the corpus cerebellum in this group has a high degree of variation in convolution (or foliation) and symmetry, which ranges from a smooth cerebellar surface to deep, branched convexities and folds, although the functional significance of this trait is unclear. As variation in the degree of foliation similarly exists throughout vertebrate evolution, it becomes critical to understand this evolutionary process in a wide variety of species. However, current methods are either qualitative and lack numerical rigor or they are restricted to two dimensions. In this paper, a recently developed method for the characterization of shapes embedded within noisy, three-dimensional data called spherical wave decomposition (SWD) is applied to the problem of characterizing cerebellar foliation in cartilaginous fishes. The SWD method provides a quantitative characterization of shapes in terms of well-defined mathematical functions. An additional feature of the SWD method is the construction of a statistical criterion for the optimal fit, which represents the most parsimonious choice of parameters that fits to the data without overfitting to background noise. We propose that this optimal fit can replace a previously described qualitative visual foliation index (VFI) in cartilaginous fishes with a quantitative analog, i.e. the cerebellar foliation index (CFI). The capability of the SWD method is demonstrated in a series of volumetric images of brains from different chondrichthyan species that span the range of foliation gradings currently described for this group. The CFI is consistent with the qualitative grading provided by the VFI, delivers a robust measure of cerebellar foliation, and can provide a quantitative basis for brain shape characterization across taxa.

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Impact of Cubic Symmetry on Optical Activity of Dielectric 8-srs Networks

Applied Sciences ◽

10.3390/app8112104 ◽

2018 ◽

Vol 8 (11) ◽

pp. 2104 ◽

Cited By ~ 1

Author(s):

Elena Goi ◽

Benjamin Cumming ◽

Min Gu

Keyword(s):

Photonic Crystals ◽

Optical Activity ◽

Three Dimensional ◽

Interesting Case ◽

Optical Components ◽

Cubic Symmetry ◽

Light Manipulation ◽

Engineered Structures ◽

The Impact

Photonic crystals are engineered structures able to control the propagation and properties of light. Due to this ability, they can be fashioned into optical components for advanced light manipulation and sensing. For these applications, a particularly interesting case study is the gyroid srs-network, a three-dimensional periodic network with both cubic symmetry and chirality. In this work we present the fabrication and characterization of three-dimensional cubically symmetric 8-srs photonic crystals derived from combination of eight individual gyroid srs-networks. We numerically and experimentally investigate optical properties of these photonic crystals and study in particular, the impact of cubic symmetry on transmission and optical activity (OA). Gyroid photonic crystals fabricated in this work can lead to the development of smaller, cheaper, and more efficient optical components with functionalities that go beyond the concept of lenses.

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Collagen hydroxylysine glycosylation: non-conventional substrates for atypical glycosyltransferase enzymes

Biochemical Society Transactions ◽

10.1042/bst20200767 ◽

2021 ◽

Author(s):

Francesca De Giorgi ◽

Marco Fumagalli ◽

Luigi Scietti ◽

Federico Forneris

Keyword(s):

Current Knowledge ◽

Three Dimensional ◽

Major Constituent ◽

Post Translational Modifications ◽

Current State ◽

Lysine Residues ◽

Collagen Molecules ◽

Triple Helices ◽

The Impact

Collagen is a major constituent of the extracellular matrix (ECM) that confers fundamental mechanical properties to tissues. To allow proper folding in triple-helices and organization in quaternary super-structures, collagen molecules require essential post-translational modifications (PTMs), including hydroxylation of proline and lysine residues, and subsequent attachment of glycan moieties (galactose and glucose) to specific hydroxylysine residues on procollagen alpha chains. The resulting galactosyl-hydroxylysine (Gal-Hyl) and less abundant glucosyl-galactosyl-hydroxylysine (Glc-Gal-Hyl) are amongst the simplest glycosylation patterns found in nature and are essential for collagen and ECM homeostasis. These collagen PTMs depend on the activity of specialized glycosyltransferase enzymes. Although their biochemical reactions have been widely studied, several key biological questions about the possible functions of these essential PTMs are still missing. In addition, the lack of three-dimensional structures of collagen glycosyltransferase enzymes hinders our understanding of the catalytic mechanisms producing this modification, as well as the impact of genetic mutations causing severe connective tissue pathologies. In this mini-review, we summarize the current knowledge on the biochemical features of the enzymes involved in the production of collagen glycosylations and the current state-of-the-art methods for the identification and characterization of this important PTM.

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