scholarly journals Flow Induced Symmetry Breaking in a Conceptual Polarity Model

Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1524 ◽  
Author(s):  
Manon C. Wigbers ◽  
Fridtjof Brauns ◽  
Ching Yee Leung ◽  
Erwin Frey
Keyword(s):  
Pattern Formation ◽  
Protein Transport ◽  
Protein Pattern ◽  
Flow Speed ◽  
Flow Profile ◽  
Advective Transport ◽  
Protein Patterns ◽  
Lateral Instability ◽  
Protein Mass ◽  
Induce Pattern

Important cellular processes, such as cell motility and cell division, are coordinated by cell polarity, which is determined by the non-uniform distribution of certain proteins. Such protein patterns form via an interplay of protein reactions and protein transport. Since Turing’s seminal work, the formation of protein patterns resulting from the interplay between reactions and diffusive transport has been widely studied. Over the last few years, increasing evidence shows that also advective transport, resulting from cytosolic and cortical flows, is present in many cells. However, it remains unclear how and whether these flows contribute to protein-pattern formation. To address this question, we use a minimal model that conserves the total protein mass to characterize the effects of cytosolic flow on pattern formation. Combining a linear stability analysis with numerical simulations, we find that membrane-bound protein patterns propagate against the direction of cytoplasmic flow with a speed that is maximal for intermediate flow speed. We show that the mechanism underlying this pattern propagation relies on a higher protein influx on the upstream side of the pattern compared to the downstream side. Furthermore, we find that cytosolic flow can change the membrane pattern qualitatively from a peak pattern to a mesa pattern. Finally, our study shows that a non-uniform flow profile can induce pattern formation by triggering a regional lateral instability.

scholarly journals Geometry-induced protein pattern formation

2016 ◽  
Vol 113 (3) ◽  
pp. 548-553 ◽  
Author(s):  
Dominik Thalmeier ◽  
Jacob Halatek ◽  
Erwin Frey
Keyword(s):  
Pattern Formation ◽  
Protein Pattern ◽  
Dynamical Instability ◽  
Direct Result ◽  
Cell Geometry ◽  
Protein Patterns ◽  
Membrane Area ◽  
Local Ratio ◽  
Spatial Geometry ◽  
Protein Gradients

Protein patterns are known to adapt to cell shape and serve as spatial templates that choreograph downstream processes like cell polarity or cell division. However, how can pattern-forming proteins sense and respond to the geometry of a cell, and what mechanistic principles underlie pattern formation? Current models invoke mechanisms based on dynamic instabilities arising from nonlinear interactions between proteins but neglect the influence of the spatial geometry itself. Here, we show that patterns can emerge as a direct result of adaptation to cell geometry, in the absence of dynamical instability. We present a generic reaction module that allows protein densities robustly to adapt to the symmetry of the spatial geometry. The key component is an NTPase protein that cycles between nucleotide-dependent membrane-bound and cytosolic states. For elongated cells, we find that the protein dynamics generically leads to a bipolar pattern, which vanishes as the geometry becomes spherically symmetrical. We show that such a reaction module facilitates universal adaptation to cell geometry by sensing the local ratio of membrane area to cytosolic volume. This sensing mechanism is controlled by the membrane affinities of the different states. We apply the theory to explain AtMinD bipolar patterns in Δ EcMinDE Escherichia coli. Due to its generic nature, the mechanism could also serve as a hitherto-unrecognized spatial template in many other bacterial systems. Moreover, the robustness of the mechanism enables self-organized optimization of protein patterns by evolutionary processes. Finally, the proposed module can be used to establish geometry-sensitive protein gradients in synthetic biological systems.

scholarly journals Reverse and forward engineering of protein pattern formation

2018 ◽  
Vol 373 (1747) ◽  
pp. 20170104 ◽  
Author(s):  
Simon Kretschmer ◽  
Leon Harrington ◽  
Petra Schwille
Keyword(s):  
Pattern Formation ◽  
Reverse Engineering ◽  
De Novo ◽  
Protein Pattern ◽  
De Novo Design ◽  
Self Organization ◽  
Protein Networks ◽  
Protein Patterns ◽  
Forward Engineering ◽  
Self Organizing

Living systems employ protein pattern formation to regulate important life processes in space and time. Although pattern-forming protein networks have been identified in various prokaryotes and eukaryotes, their systematic experimental characterization is challenging owing to the complex environment of living cells. In turn, cell-free systems are ideally suited for this goal, as they offer defined molecular environments that can be precisely controlled and manipulated. Towards revealing the molecular basis of protein pattern formation, we outline two complementary approaches: the biochemical reverse engineering of reconstituted networks and the de novo design, or forward engineering, of artificial self-organizing systems. We first illustrate the reverse engineering approach by the example of the Escherichia coli Min system, a model system for protein self-organization based on the reversible and energy-dependent interaction of the ATPase MinD and its activating protein MinE with a lipid membrane. By reconstituting MinE mutants impaired in ATPase stimulation, we demonstrate how large-scale Min protein patterns are modulated by MinE activity and concentration. We then provide a perspective on the de novo design of self-organizing protein networks. Tightly integrated reverse and forward engineering approaches will be key to understanding and engineering the intriguing phenomenon of protein pattern formation. This article is part of the theme issue ‘Self-organization in cell biology’.

scholarly journals Enhancement of drought tolerance in Triticum aestivum L. seedlings using Azospirillum brasilense NO40 and Stenotrophomonas maltophilia B11

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Wedad A. Kasim ◽  
Mohamed E. H. Osman ◽  
Mohamed N. Omar ◽  
Samar Salama
Keyword(s):  
Triticum Aestivum ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Azospirillum Brasilense ◽  
Stenotrophomonas Maltophilia ◽  
Protein Pattern ◽  
Triticum Aestivum L ◽  
Protein Patterns ◽  
Wheat Seedlings ◽  
Enhanced Production

Abstract Background The effectiveness of two PGPB; Azospirillum brasilense NO40 and Stenotrophomonas maltophilia B11 was investigated in enhancing the drought tolerance of wheat (Triticum aestivum L.) seedlings cultivar Gemiza9. The inoculated or uninoculated grains were sown in unsterilized sandy soil and watered normally untill the 8th day. Drought stress was initiated by completely withholding water for 7 days (until wilting). Samples were collected after 15 days from sowing to evaluate some growth criteria, damage and defense indicators and to analyze the roots’ protein pattern. Results The results showed that inoculating wheat seedlings with these strains significantly diminished the inhibitory effects of drought stress on the relative water content of roots, shoots and leaves; area of leaves; contents of pigments (chlorophyll a and b) and ascorbic acid; and on the protein patterns of roots. Moreover, the bacterial inoculation notably reduced the drought-induced damage indicated by lower leakage of electrolytes and less accumulation of Malondialdehyde and hydrogen peroxide, surprisingly with less enhanced production of proline and activities of catalase and peroxidase than their uninoculated counterparts. Under normal conditions, inoculating wheat plants with these PGPB resulted in significantly promoted growth and elevated contents of pigments and altered protein patterns of roots. Conclusion Overall, we can say that both Azospirillum brasilense NO40 and Stenotrophomonas maltophilia B11 were able to deactivate the growth inhibition in wheat seedlings to some extent, while maintaining a certain level of efficient protection against damage under drought stress.

scholarly journals Para Protein Pattern Formation Drives Bacterial Plasmid Segregation

2014 ◽  
Vol 106 (2) ◽  
pp. 362a
Author(s):  
Ling Chin Hwang ◽  
Anthony G. Vecchiarelli ◽  
Yong Woon Han ◽  
Michiyo Mizuuchi ◽  
Yoshie Harada ◽  
...  
Keyword(s):  
Pattern Formation ◽  
Protein Pattern ◽  
Plasmid Segregation ◽  
Bacterial Plasmid

Structure of the insect head as revealed by the EN protein pattern in developing embryos

Development ◽  
1996 ◽  
Vol 122 (11) ◽  
pp. 3419-3432 ◽  
Author(s):  
B.T. Rogers ◽  
T.C. Kaufman
Keyword(s):  
Drosophila Melanogaster ◽  
Pattern Formation ◽  
Protein Pattern ◽  
Related Protein ◽  
Specific Expression ◽  
Tissue Specific Expression ◽  
Single Segment ◽  
Dorsal Ridge ◽  
Insect Embryos ◽  
Comparative Embryology

The structure of the insect head has long been a topic of enjoyable yet endless debate among entomologists. More recently geneticists and molecular biologists trying to better understand the structure of the head of the Dipteran Drosophila melanogaster have joined the discourse extrapolating from what they have learned about Drosophila to insects in general. Here we present the results of an investigation into the structure of the insect head as revealed by the distribution of engrailed related protein (Engrailed) in the insect orders Diptera, Siphonaptera, Orthoptera and Hemiptera. The results of this comparative embryology in conjunction with genetic experiments on Drosophila melanogaster lead us to conclude: (1) The insect head is composed of six Engrailed accumulating segments, four postoral and two preoral. The potential seventh and eighth segments (clypeus or labrum) do not accumulate Engrailed. (2) The structure known as the dorsal ridge is not specific to the Diptera but is homologous to structures found in other insect orders. (3) A part of this structure is a single segment-like entity composed of labial and maxillary segment derivatives which produce the most anterior cuticle capable of taking a dorsal fate. The segments anterior to the maxillary segment produce only ventral structures. (4) As in Drosophila, the process of segmentation of the insect head is fundamentally different from the process of segmentation in the trunk. (5) The pattern of Engrailed accumulation and its presumed role in the specification and development of head segments appears to be highly conserved while its role in other pattern formation events and tissue-specific expression is variable. An overview of the pattern of Engrailed accumulation in developing insect embryos provides a basis for discussion of the generality of the parasegment and the evolution of Engrailed patterns.

scholarly journals Salicylic acid and potassium nitrate promote flowering through modulating the hormonal levels and protein pattern of date palm Phoenix dactylifera ‘Sayer’ offshoot

2019 ◽  
Vol 114 (2) ◽  
pp. 231 ◽  
Author(s):  
Hussein Jasim SHAREEF
Keyword(s):  
Salicylic Acid ◽  
Molecular Mass ◽  
Date Palm ◽  
Salt Water ◽  
Protein Pattern ◽  
Phoenix Dactylifera ◽  
Potassium Nitrate ◽  
Protein Patterns ◽  
Nitrate Treatment

<p>Salicylic acid enhances the flowering process in the plant by creating new proteins under salinity stress. The study was to determine the role of salicylic acid (500 ppm) and potassium nitrate (1500 ppm), on flowering of date palm ‘Sayer’ offshoots under salinity effect. Application of salicylic acid increased the number of clusters, the number of new leaves, the content of carbohydrates, ascorbic acid, indoleacetic acid, zeatin, gibberellin, and abscisic acid significantly under salinity compared with control. Although the measured parameters were the highest in plants treated with salicylic acid, there was no distinction among potassium nitrate treatment under saltwater, and salicylic acid treatment with saltwater. Salicylic acid and potassium nitrate treatment demonstrated some amazing contrasts in protein patterns in light of gel electrophoresis. Plants treated with salicylic acid with fresh water and with saltwater showed five and six protein bands, respectively, that differed in the molecular mass of one polypeptide compared to control with freshwater. However, there was a difference in the molecular mass of two polypeptides compared to control with salt water, which showed six bands. In contrast, potassium nitrate application showed five protein bands, whether with freshwater or with saltwater. The findings could facilitate to elucidate the flowering mechanisms in date palm.<br /><strong></strong></p>

scholarly journals Local flow sensing on helical microrobots for semi-automatic motion adaptation

2019 ◽  
Vol 39 (4) ◽  
pp. 476-489 ◽  
Author(s):  
Antoine Barbot ◽  
Dominique Decanini ◽  
Gilgueng Hwang
Keyword(s):  
Closed Loop ◽  
Flow Speed ◽  
Closed Loop Control ◽  
Flow Profile ◽  
Microfluidic Chips ◽  
Level Control ◽  
Local Flow ◽  
Loop Control ◽  
Flow Sensing ◽  
Swimming Motion

Helical microrobots with dimensions below 100 µm could serve many applications for manipulation and sensing in small, closed environments such as blood vessels or inside microfluidic chips. However, environmental conditions such as surface stiction from the channel wall or local flow can quickly result in the loss of control of the microrobot, especially for untrained users. Therefore, to automatically adapt to changing conditions, we propose an algorithm that switches between a surface-based motion of the microrobot and a 3D swimming motion depending on the local flow value. Indeed swimming is better for avoiding obstacles and difficult surface stiction areas but it is more sensitive to the flow than surface motion such as rolling or spintop motion. First, we prove the flow sensing ability of helical microrobots based on the difference between the tracked and theoretical speed. For this, a 50 µm long and 5 µm diameter helical microrobot measures the flow profile shape in two different microchannels. These measurements are then compared with simulation results. Then, we demonstrate both swimming and surface-based motion using closed-loop control. Finally, we test our algorithm by following a 2D path using closed-loop control, and adapting the type of motion depending on the flow speed measured by the microrobot. Such results could enable simple high-level control that could expand the development of microrobots toward applications in complex microfluidic environments.

scholarly journals Protein Pattern Formation

2018 ◽  
pp. 229-260 ◽  
Author(s):  
Erwin Frey ◽  
Jacob Halatek ◽  
Simon Kretschmer ◽  
Petra Schwille
Keyword(s):  
Pattern Formation ◽  
Protein Pattern

Rapid Fish Species Identification by Agarose Gel Isoelectric Focusing of Sarcoplasmic Proteins

1981 ◽  
Vol 64 (1) ◽  
pp. 38-43
Author(s):  
Ronald C Lundstrom
Keyword(s):  
Species Identification ◽  
Isoelectric Focusing ◽  
Fish Species ◽  
Protein Pattern ◽  
Agarose Gel ◽  
Tissue Fluid ◽  
Protein Patterns ◽  
Fish Species Identification ◽  
Species Specific ◽  
Gel Isoelectric Focusing

Abstract A rapid method is described for fish species identification by agarose gel isoelectric focusing (AGIEF). The AGIEF method can be completed in less than 2 h and gives reproducible species-specific sarcoplasmic protein patterns. Protein patterns are similar using either centrifuged tissue fluid or muscle tissue as the sample. One species, monkfish (Lophius americanus), has a polymorphic protein pattern. A predominant pattern was found in 66.7% of the individuals; 2 variant patterns were equally distributed among the remaining 33.3%. AGIEF offers a more rapid, less expensive alternative to the current AOAC official first action method for fish species identification based on polyacrylamide gel isoelectric focusing.

Restriction fragment analysis of hordein genes in western Canadian two-rowed barleys

1995 ◽  
Vol 75 (1) ◽  
pp. 191-193
Author(s):  
S. J. Molnar ◽  
A. McKay
Keyword(s):  
Restriction Fragment ◽  
Cultivar Identification ◽  
Protein Pattern ◽  
Gene Families ◽  
Protein Patterns ◽  
Fragment Analysis ◽  
Banding Patterns ◽  
Barley Cultivars ◽  
Length Polymorphisms ◽  
Restriction Fragment Length

Restriction fragment length polymorphisms (RFLP) at the hordein loci were compared with hordein protein patterns for discrimination of barley cultivars. RFLP banding patterns documented extensive polymorphism for B and C hordein gene families in eight closely related western Canadian two-rowed barley cultivars, five parental cultivars and a U.K. cultivar. RFLP results were compared with published protein pattern data on the same cultivars. The power to discriminate cultivars by the two methods is similar. Key words: RFLP, hordein, barley, Hordeum vulgare, cultivar identification

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