Journal articles on the topic '(Macro) molecular assemblies'
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1
HOTANI, Hirokazu. "Macro-and Bio-molecular Assemblies." Kobunshi 44, no. 1 (1995): 1. http://dx.doi.org/10.1295/kobunshi.44.1.
2
Agarwal, Gunjan, Adam W. Smith, and Blain Jones. "Discoidin domain receptors: Micro insights into macro assemblies." Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1866, no. 11 (November 2019): 118496. http://dx.doi.org/10.1016/j.bbamcr.2019.06.010.
3
Campbell, Jack, and Anna S. Vikulina. "Layer-By-Layer Assemblies of Biopolymers: Build-Up, Mechanical Stability and Molecular Dynamics." Polymers 12, no. 9 (August 28, 2020): 1949. http://dx.doi.org/10.3390/polym12091949.
Abstract:
Rapid development of versatile layer-by-layer technology has resulted in important breakthroughs in the understanding of the nature of molecular interactions in multilayer assemblies made of polyelectrolytes. Nowadays, polyelectrolyte multilayers (PEM) are considered to be non-equilibrium and highly dynamic structures. High interest in biomedical applications of PEMs has attracted attention to PEMs made of biopolymers. Recent studies suggest that biopolymer dynamics determines the fate and the properties of such PEMs; however, deciphering, predicting and controlling the dynamics of polymers remains a challenge. This review brings together the up-to-date knowledge of the role of molecular dynamics in multilayers assembled from biopolymers. We discuss how molecular dynamics determines the properties of these PEMs from the nano to the macro scale, focusing on its role in PEM formation and non-enzymatic degradation. We summarize the factors allowing the control of molecular dynamics within PEMs, and therefore to tailor polymer multilayers on demand.
4
Scott, Ridgway, Mercedes Boland, Kristina Rogale, and Ariel Fernández. "Continuum equations for dielectric response to macro-molecular assemblies at the nano scale." Journal of Physics A: Mathematical and General 37, no. 41 (September 30, 2004): 9791–803. http://dx.doi.org/10.1088/0305-4470/37/41/012.
5
De Graeve, Fabienne, and Florence Besse. "Neuronal RNP granules: from physiological to pathological assemblies." Biological Chemistry 399, no. 7 (June 27, 2018): 623–35. http://dx.doi.org/10.1515/hsz-2018-0141.
Abstract:
Abstract Neuronal cells rely on macro- and micro-cellular compartmentalization to rapidly process information, and respond locally to external stimuli. Such a cellular organization is achieved via the assembly of neuronal ribonucleoprotein (RNP) granules, dynamic membrane-less organelles enriched in RNAs and associated regulatory proteins. In this review, we discuss how these high-order structures transport mRNAs to dendrites and axons, and how they contribute to the spatio-temporal regulation of localized mRNA translation. We also highlight how recent biophysical studies have shed light on the mechanisms underlying neuronal RNP granule dynamic assembly, remodeling and maturation, in both physiological and pathological contexts.
6
Sorokin, A., Yu Kuzina, G. Sorokin, and N. Denisova. "MODELING OF HEAT AND MASS TRANSFER PROCESSES IN FUEL ASSEMBLIES OF FAST REACTORS AS PART OF THE CHANNEL-BY-CHANNEL CALCULATION METHOD. GENERALIZED EXCHANGE CHARACTERISTICS FOR SINGLE-PHASE FLOWS OF LIQUID METALS." PROBLEMS OF ATOMIC SCIENCE AND TECHNOLOGY. SERIES: NUCLEAR AND REACTOR CONSTANTS 2020, no. 2 (June 26, 2020): 104–30. http://dx.doi.org/10.55176/2414-1038-2020-2-104-130.
Abstract:
The results of experimental and computational-theoretical studies of the transverse interchannel molecular-turbulent and convective exchange of mass, momentum and energy are presented in the framework of the channel-by-channel model of thermohydraulic calculation of fuel assemblies of fuel elements of the fast reactors core with liquid metal coolants for nominal, non-nominal and accident conditions. A complete system of inter-channel exchange coefficients is obtained for closing the system of macro-transport equations in a wide range of parameters, taking into account the fuel assemblies deformation. It was shown that transverse convective exchange in fuel assemblies with spacing by wire wrapped is caused by a deficit of static pressure in the region behind winding at the surface of the rod, and the high intensity of molecular-turbulent exchange in tight bundles is explained by the appearance of secondary flows in cells. The heat exchange between cells due to the thermal conductivity of the fuel rods is determined by the thermal modeling parameter of the fuel rods for the first harmonic. The effect of wire wrapped on the flow can be modeled by periodically changing hydraulic resistance to the transverse coolant flow. The integral model of convective inter-channel exchange in fuel assemblies with distance wire wrap is substantiated. Taking into account the centrifugal effect and calculating the interchannel exchange coefficients taking into account the local distribution of parameters allows us to clarify the thermohydraulic characteristics in the shaped bundles. For the characteristic parameters of fuel assemblies of fast reactors (Pe ≥ 50; S/d ≥ 1,1; h/d ≤ 30; ε1 < 1) the predominant is convective inter-channel exchange due to the spacing of fuel rods by wire wrapped. For highly heat-conducting fuel compositions, a significant contribution to the inter-channel heat exchange can be made by the exchange due to the thermal conductivity of the fuel elements. At a low flow rate (Pe <50), the contribution of molecular-turbulent exchange and heat exchange increases due to the thermal conductivity of the fuel rods.
7
Sarikaya, Mehmet. "Organic-inorganic interfaces in biological composites." Proceedings, annual meeting, Electron Microscopy Society of America 52 (1994): 426–27. http://dx.doi.org/10.1017/s0424820100169869.
Abstract:
Biological hard tissues, such as bone, dentin, and mollusk shells, are composite materials incorporating an organic matrix and inorganic crystallites in a complex nano- and micro-architectural forms. The interest of physical sciences in biological composites stems from the fact that these materials are self assembled in an hierarchical fashion from molecular to macro scale, and that the resulting assemblies have properties that far exceed those of current synthetic materials of similar elemental or phase compositions. The objective of biomimetics is to either mimick structures of biological composites, biomimicking, or use the synthesis methodologies of organisms to produce new materials, bioduplication. In a biocomposite, substructure and crystallography of the inorganic component are highly ordered, its morphology and shape are species specific; these are all thought to be regulated by the organic matrix. The understanding of ructural relationship between the organic and ceramic components of a biological composite, therefore, is fundamental both to the understanding of mechanisms of biomineralization and to biomimetic design and synthesis of novel engineering materials. These issues will be addressed in the present paper.
8
Xin, Ting-Ting, Tongqi Yuan, Shu Xiao, and Jing He. "Synthesis of cellulose-graft-poly(methyl methacrylate) via homogeneous ATRP." BioResources 6, no. 3 (June 20, 2011): 2941–53. http://dx.doi.org/10.15376/biores.6.3.2941-2953.
Abstract:
Cellulose-graft-poly(methylmethacrylate) (cellulose-g-PMMA) copolymers were prepared by homogeneous atom transfer radical polymerization (ATRP) under mild conditions, in an attempt to develop an efficient way to modify the surface of cellulose. A cellulose macro-initiator was successfully synthesized by direct homogeneous acylation of cellulose with 2-bromopropionyl bromide in a room temperature ionic liquid (RTIL), 1-allyl-3-methylimidazolium chloride ([AMIM]Cl). Copolymers were obtained via ATRP of methyl methacrylate (MMA) with CuBr/penta-methyldiethylenetriamine (PMDETA) as catalyst and N,N-dimethyl-formamide (DMF) as solvent without homopolymer byproduct. The grafting copolymers were characterized by 1H-NMR, 13C-NMR, and FTIR. The grafted PMMA chain was obtained by the hydrolysis of the cellulose backbone and analyzed by GPC and TGA measurements. In addition, the assemblies or aggregates formed by cellulose-g-PMMA copolymers were studied by means of TEM and AFM. The results indicated that the graft polymerization occurred from the cellulose backbone and the obtained copolymers had grafted polymer chains with well-controlled molecular weight and polydispersity; the cellulose graft copolymer in solution could aggregate and self-assemble into sphere-like structures.
9
Mongwaketsi, Nametso, Noluthando Mayedwa, Nolubabalo Matinise, Kasinathan Kaviyarasu, Raymond Sparrow, and Malik Maaza. "Polymer matrices for porphyrin nanorods incorporation. Artificial light harvesting applications." Journal of Porphyrins and Phthalocyanines 22, no. 04 (April 2018): 303–17. http://dx.doi.org/10.1142/s1088424618500268.
Abstract:
This contribution is focused on the supramolecular approach in exploration of aggregates formation by two different porphyrins wherein self-assembly plays an important role. Spectroscopic and microscopic studies usually provide information on investigations regarding the effects of various parameters on the fabrication of porphyrin aggregates by ionic self- assembly. Various properties of ionic self-assembled porphyrin nanorods have been investigated, including nonlinear optical (NLO) properties, and these studies were influenced by the fact that porphyrins have great thermal stability and extended [Formula: see text]conjugated macro cyclic rings which give them large nonlinear optical effects. The major reasons limiting porphyrin nanorods photonic applications include the difficulty of handling them in liquid solutions and their degradation with long exposure to light. This necessitates the use of appropriate solid matrices to host the nanorods. Inspired by the precise organization and orientation of the chromophores in natural systems, attention has been on the design of nanometer sized chromophoric assemblies, which may find applications in the field of molecular photonics. However, it is challenging to design multicomponent systems with controlled structural arrangement at the molecular level. A lack of precise arrangement may have a negative impact on the construction of an efficient artificial light harvesting system. This review is focused on exploring the possibility of incorporating nanorods into polymer matrices to overcome the limiting factors of applications of these materials in photonic devices.
10
Pérez-García, Lluïsa, and David B. Amabilino. "Spontaneous resolution, whence and whither: from enantiomorphic solids to chiral liquid crystals, monolayers and macro- and supra-molecular polymers and assemblies." Chem. Soc. Rev. 36, no. 6 (2007): 941–67. http://dx.doi.org/10.1039/b610714a.
11
Madhurapantula, Rama S., Gabriel Krell, Berenice Morfin, Rajarshi Roy, Kevin Lister, and Joseph P. R. O. Orgel. "Advanced Methodology and Preliminary Measurements of Molecular and Mechanical Properties of Heart Valves under Dynamic Strain." International Journal of Molecular Sciences 21, no. 3 (January 24, 2020): 763. http://dx.doi.org/10.3390/ijms21030763.
Abstract:
Mammalian heart valves are soft tissue assemblies with multi-scale material properties. This is because they are constructs comprising both muscle and non-contractile extracellular matrix proteins (such as collagens and proteoglycans) and transition regions where one form of tissue structure becomes another, significantly different form. The leaflets of the mitral and tricuspid valves are connected to chordae tendinae which, in turn, bind through papillary muscles to the cardiac wall of the ventricle. The transition regions between these tissue subsets are complex and diffuse. Their material composition and mechanical properties have not been previously described with both micro and nanoscopic data recorded simultaneously, as reported here. Annotating the mechanical characteristics of these tissue transitions will be of great value in developing novel implants, improving the state of the surgical simulators and advancing robot-assisted surgery. We present here developments in multi-scale methodology that produce data that can relate mechanical properties to molecular structure using scanning X-ray diffraction. We correlate these data to corresponding tissue level (macro and microscopic) stress and strain, with particular emphasis on the transition regions and present analyses to indicate points of possible failure in these tissues.
12
Griffin, Darren, Denis Larkin, Rebecca O’Connor, and Michael Romanov. "Dinosaurs: Comparative Cytogenomics of their Reptile Cousins and Avian Descendants." Animals 13, no. 1 (December 27, 2022): 106. http://dx.doi.org/10.3390/ani13010106.
Abstract:
Reptiles known as dinosaurs pervade scientific and popular culture, while interest in their genomics has increased since the 1990s. Birds (part of the crown group Reptilia) are living theropod dinosaurs. Chromosome-level genome assemblies cannot be made from long-extinct biological material, but dinosaur genome organization can be inferred through comparative genomics of related extant species. Most reptiles apart from crocodilians have both macro- and microchromosomes; comparative genomics involving molecular cytogenetics and bioinformatics has established chromosomal relationships between many species . The capacity of dinosaurs to survive multiple extinction events is now well established, and birds now have more species in comparison with any other terrestrial vertebrate. This may be due, in part, to their karyotypic features, including a distinctive karyotype of around n = 40 (~10 macro and 30 microchromosomes). Similarity in genome organization in distantly related species suggests that the common avian ancestor had a similar karyotype to e.g., the chicken/emu/zebra finch. The close karyotypic similarity to the soft-shelled turtle (n = 33) suggests that this basic pattern was mostly established before the Testudine–Archosaur divergence, ~255 MYA. That is, dinosaurs most likely had similar karyotypes and their extensive phenotypic variation may have been mediated by increased random chromosome segregation and genetic recombination, which is inherently higher in karyotypes with more and smaller chromosomes.
13
Kiazim, Lucas G., Rebecca E. O’Connor, Denis M. Larkin, Michael N. Romanov, Valery G. Narushin, Evgeni A. Brazhnik, and Darren K. Griffin. "Comparative Mapping of the Macrochromosomes of Eight Avian Species Provides Further Insight into Their Phylogenetic Relationships and Avian Karyotype Evolution." Cells 10, no. 2 (February 9, 2021): 362. http://dx.doi.org/10.3390/cells10020362.
Abstract:
Avian genomes typically consist of ~10 pairs of macro- and ~30 pairs of microchromosomes. While inter-chromosomally, a pattern emerges of very little change (with notable exceptions) throughout evolution, intrachromosomal changes remain relatively poorly studied. To rectify this, here we use a pan-avian universally hybridising set of 74 chicken bacterial artificial chromosome (BAC) probes on the macrochromosomes of eight bird species: common blackbird, Atlantic canary, Eurasian woodcock, helmeted guinea fowl, houbara bustard, mallard duck, and rock dove. A combination of molecular cytogenetic, bioinformatics, and mathematical analyses allowed the building of comparative cytogenetic maps, reconstruction of a putative Neognathae ancestor, and assessment of chromosome rearrangement patterns and phylogenetic relationships in the studied neognath lineages. We observe that, as with our previous studies, chicken appears to have the karyotype most similar to the ancestor; however, previous reports of an increased rate of intrachromosomal change in Passeriformes (songbirds) appear not to be the case in our dataset. The use of this universally hybridizing probe set is applicable not only for the re-tracing of avian karyotype evolution but, potentially, for reconstructing genome assemblies.
14
Marrero-Winkens, Cristóbal, Charu Sankaran, and Hermann Schätzl. "From Seeds to Fibrils and Back: Fragmentation as an Overlooked Step in the Propagation of Prions and Prion-Like Proteins." Biomolecules 10, no. 9 (September 10, 2020): 1305. http://dx.doi.org/10.3390/biom10091305.
Abstract:
Many devastating neurodegenerative diseases are driven by the misfolding of normal proteins into a pathogenic abnormal conformation. Examples of such protein misfolding diseases include Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, amyotrophic lateral sclerosis, and prion diseases. The misfolded proteins involved in these diseases form self-templating oligomeric assemblies that recruit further correctly folded protein and induce their conversion. Over time, this leads to the formation of high molecular and mostly fibrillar aggregates that are increasingly inefficient at converting normal protein. Evidence from a multitude of in vitro models suggests that fibrils are fragmented to form new seeds, which can convert further normal protein and also spread to neighboring cells as observed in vivo. While fragmentation and seed generation were suggested as crucial steps in aggregate formation decades ago, the biological pathways involved remain largely unknown. Here, we show that mechanisms of aggregate clearance—namely the mammalian Hsp70–Hsp40–Hsp110 tri-chaperone system, macro-autophagy, and the proteasome system—may not only be protective, but also play a role in fragmentation. We further review the challenges that exist in determining the precise contribution of these mechanisms to protein misfolding diseases and suggest future directions to resolve these issues.
15
Renault, Ludovic, and Henning Stahlberg. "Three-Dimensional Electron Microscopy of Macro-molecular Assemblies: Visualization of Biological Molecules in Their Native State. By Joachim Frank. Oxford University Press, New York (2006). ISBN 0195182189; softback; 432 pages." Scanning 29, no. 1 (January 2007): 37. http://dx.doi.org/10.1002/sca.20031.
16
Traut, Walther, Virpi Ahola, David A. S. Smith, Ian J. Gordon, and Richard H. ffrench-Constant. "Karyotypes versus Genomes: The Nymphalid Butterflies Melitaea cinxia, Danaus plexippus, and D. chrysippus." Cytogenetic and Genome Research 153, no. 1 (2017): 46–53. http://dx.doi.org/10.1159/000484032.
Abstract:
The number of sequenced lepidopteran genomes is increasing rapidly. However, the corresponding assemblies rarely represent whole chromosomes and generally also lack the highly repetitive W sex chromosome. Knowledge of the karyotypes can facilitate genome assembly and further our understanding of sex chromosome evolution in Lepidoptera. Here, we describe the karyotypes of the Glanville fritillary Melitaea cinxia (n = 31), the monarch Danaus plexippus (n = 30), and the African queen D. chrysippus (2n = 60 or 59, depending on the source population). We show by FISH that the telomeres are of the (TTAGG)n type, as found in most insects. M. cinxia and D. plexippus have “conventional” W chromosomes which are heterochromatic in meiotic and somatic cells. In D. chrysippus, the W is inconspicuous. Neither telomeres nor W chromosomes are represented in the published genomes of M. cinxia and D. plexippus. Representation analysis in sequenced female and male D. chrysippus genomes detected an evolutionarily old autosome-Z chromosome fusion in Danaus. Conserved synteny of whole chromosomes, so called “macro synteny”, in Lepidoptera permitted us to identify the chromosomes involved in this fusion. An additional and more recent sex chromosome fusion was found in D. chrysippus by karyotype analysis and classical genetics. In a hybrid population between 2 subspecies, D. c. chrysippus and D. c. dorippus, the W chromosome was fused to an autosome that carries a wing colour locus. Thus, cytogenetics and the present state of genome data complement one another to reveal the evolutionary history of the species.
17
Southern, Emily J., Valentin Besnard, Bastien Lahaye, Andy M. Tyrrell, and Shuhei Miyashita. "Catalytic self-folding of 2D structures through cascading magnet reactions." Royal Society Open Science 6, no. 7 (July 2019): 182128. http://dx.doi.org/10.1098/rsos.182128.
Abstract:
While thousands of proteins involved in development of the human body are capable of self-assembling in a distributed manner from merely 20 types of amino acid, macroscopic products that can be assembled spontaneously from ‘alive’ components remains an aspiration in engineering. To attain such a mechanism, a major challenge lies in understanding which attributes from the bio-molecular realm must be leveraged at the macro-scale. Inspired by protein folding, we present a centimetre-size 1D tile chain whose self-folding processes are directed by structure-embedded magnetic interactions, which can theoretically self-assemble into convex 2D structures of any size or shape without the aid of a global ‘controller’. Each tile holds two magnets contained in paths designed to control their interactions. Once initiated by a magnetic unit (termed Catalyst), the chain self-reconfigures by consuming magnetic potential energy stored between magnet pairs, until the final 2D structure is reached at an energetic minimum. Both simulation and experimental results are presented to illustrate the method’s efficacy on chains of arbitrary length. Results demonstrate the promise of a physically implemented, bottom-up, and scalable self-assembly method for novel 2D structure manufacturing, bridging the bio-molecular and mechanical realms.
18
Shu, H. B., and H. C. Joshi. "Gamma-tubulin can both nucleate microtubule assembly and self-assemble into novel tubular structures in mammalian cells." Journal of Cell Biology 130, no. 5 (September 1, 1995): 1137–47. http://dx.doi.org/10.1083/jcb.130.5.1137.
Abstract:
alpha-, beta-, and gamma-tubulins are evolutionarily highly conserved members of the tubulin gene superfamily. While the abundant members, alpha- and beta-tubulins, constitute the building blocks of cellular microtubule polymers, gamma-tubulin is a low abundance protein which localized to the pericentriolar material and may play a role in microtubule assembly. To test whether gamma-tubulin mediates the nucleation of microtubule assembly in vivo, and co-assembles with alpha- and beta-tubulins into microtubules or self-assembles into macro-molecular structures, we experimentally elevated the expression of gamma-tubulin in the cell cytoplasm. In most cells, overexpression of gamma-tubulin causes a dramatic reorganization of the cellular microtubule network. Furthermore, we show that when overexpressed, gamma-tubulin causes ectopic nucleation of microtubules which are not associated with the centrosome. In a fraction of cells, gamma-tubulin self-assembles into novel tubular structures with a diameter of approximately 50 nm (named gamma-tubules). Furthermore, unlike microtubules, gamma-tubules are resistant to cold or drug induced depolymerization. These data provide evidence that gamma-tubulin can cause nucleation of microtubule assembly and can self-assemble into novel tubular structures.
19
Pradeesh, K., Nageswara Rao Kotla, Shahab Ahmad, Vindesh K. Dwivedi, and G. Vijaya Prakash. "Naturally Self-Assembled Nanosystems and Their Templated Structures for Photonic Applications." Journal of Nanoparticles 2013 (March 20, 2013): 1–13. http://dx.doi.org/10.1155/2013/531871.
Abstract:
Self-assembly has the advantage of fabricating structures of complex functionalities, from molecular levels to as big as macroscopic levels. Natural self-assembly involves self-aggregation of one or more materials (organic and/or inorganic) into desired structures while templated self-assembly involves interstitial space filling of diverse nature entities into self-assembled ordered/disordered templates (both from molecular to macro levels). These artificial and engineered new-generation materials offer many advantages over their individual counterparts. This paper reviews and explores the advantages of such naturally self-assembled hybrid molecular level systems and template-assisted macro-/microstructures targeting simple and low-cost device-oriented fabrication techniques, structural flexibility, and a wide range of photonic applications.
20
Drieu, Léa, Cédric Lepère, and Martine Regert. "The Missing Step of Pottery chaîne opératoire: Considering Post-firing Treatments on Ceramic Vessels Using Macro- and Microscopic Observation and Molecular Analysis." Journal of Archaeological Method and Theory 27, no. 2 (October 11, 2019): 302–26. http://dx.doi.org/10.1007/s10816-019-09428-8.
Abstract:
Abstract Post-firing treatments, produced by the interaction of an organic material with the hot surface of a ceramic, are frequently described in ethnographic literature, but have rarely been identified in archaeological ceramic assemblages. In order to address this question, this paper describes a methodology that combines macro- and microscopic observation and molecular analysis. The study of experimental ceramic vessels provided diagnostic tools to identify the type of substances, their liquid or solid state, and their mode of application and attested that the post-firing treatments do not completely waterproof the ceramics. The difficulty to observe macro- and microscopic evidence of post-firing treatments when pots are fired in reducing atmosphere suggests that these processes are probably underestimated in archaeological assemblages. Furthermore, the identification of molecular thermal transformation markers, such as ketones, calls into question their classical interpretation as markers for the cooking of fatty content. This pioneering work highlights the complexity of studying post-firing treatments, which leave small traces that are easily missed or misinterpreted. In order to address this issue, we propose a multi-analytical approach, which can serve as a basis for future studies to explore the full diversity of post-firing treatments mentioned in ethnoarchaeological literature.
21
Telegdi, J., G. Luciano, S. Mahanty, and T. Abohalkuma. "Inhibition of aluminum alloy corrosion in electrolytes by self-assembled fluorophosphonic acid molecular layer." Materials and Corrosion 67, no. 10 (February 16, 2016): 1027–33. http://dx.doi.org/10.1002/maco.201508792.
22
Sang, Yutao, and Minghua Liu. "Symmetry Breaking in Self-Assembled Nanoassemblies." Symmetry 11, no. 8 (July 25, 2019): 950. http://dx.doi.org/10.3390/sym11080950.
Abstract:
The origin of biological homochirality, e.g., life selects the L-amino acids and D-sugar as molecular component, still remains a big mystery. It is suggested that mirror symmetry breaking plays an important role. Recent researches show that symmetry breaking can also occur at a supramolecular level, where the non-covalent bond was crucial. In these systems, equal or unequal amount of the enantiomeric nanoassemblies could be formed from achiral molecules. In this paper, we presented a brief overview regarding the symmetry breaking from dispersed system to gels, solids, and at interfaces. Then we discuss the rational manipulation of supramolecular chirality on how to induce and control the homochirality in the self-assembly system. Those physical control methods, such as Viedma ripening, hydrodynamic macro- and micro-vortex, superchiral light, and the combination of these technologies, are specifically discussed. It is hoped that the symmetry breaking at a supramolecular level could provide useful insights into the understanding of natural homochirality and further designing as well as controlling of functional chiral materials.
23
Cacabelos, Eva, Patrício Ramalhosa, João Canning-Clode, Jesús S. Troncoso, Celia Olabarria, Cristina Delgado, Sergey Dobretsov, and Ignacio Gestoso. "The Role of Biofilms Developed under Different Anthropogenic Pressure on Recruitment of Macro-Invertebrates." International Journal of Molecular Sciences 21, no. 6 (March 16, 2020): 2030. http://dx.doi.org/10.3390/ijms21062030.
Abstract:
Microbial biofilms can be key mediators for settlement of macrofoulers. The present study examines the coupled effects of microbial biofilms and local environmental conditions on the composition, structure and functioning of macrofouling assemblages. Settlement of invertebrates over a gradient of human-impacted sites was investigated on local biofilms and on biofilms developed in marine protected areas (MPAs). Special attention was given to the presence of non-indigenous species (NIS), a global problem that can cause important impacts on local assemblages. In general, the formation of macrofouling assemblages was influenced by the identity of the biofilm. However, these relationships varied across levels of anthropogenic pressure, possibly influenced by environmental conditions and the propagule pressure locally available. While the NIS Watersipora subatra seemed to be inhibited by the biofilm developed in the MPA, Diplosoma cf. listerianum seemed to be attracted by biofilm developed in the MPA only under mid anthropogenic pressure. The obtained information is critical for marine environmental management, urgently needed for the establishment of prevention and control mechanisms to minimize the settlement of NIS and mitigate their threats.
24
Tan, Hueyling. "Factors Affecting Molecular Self-Assembly and Its Mechanism." Scientific Research Journal 9, no. 1 (June 30, 2012): 43. http://dx.doi.org/10.24191/srj.v9i1.5385.
Abstract:
Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.
25
Tan, Huey Ling. "Factors Affecting Molecular Self-Assembly and Its Mechanism." Scientific Research Journal 9, no. 1 (June 1, 2012): 43. http://dx.doi.org/10.24191/srj.v9i1.9414.
Abstract:
Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use of peptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study of biological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries of existing disciplines. Many self-assembling systems are range from bi- and tri-block copolymers to DNA structures as well as simple and complex proteins and peptides. The ultimate goal is to harness molecular self-assembly such that design and control of bottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes of life and non-life science applications. Such aspirations can be achieved through understanding the fundamental principles behind the self organisation and self-synthesis processes exhibited by biological systems.
26
Cui, Lian Lai, Tao Yu, Xin Tan, Yue Zhao, Jian Ping Li, and Ling Zhang. "Preparation of Biocompatible Micelles as Drug Delivery via RAFT Polymerization." Advanced Materials Research 322 (August 2011): 219–23. http://dx.doi.org/10.4028/www.scientific.net/amr.322.219.
Abstract:
Block copolymers D,L-Polylactide-b-poly(poly(ethylene glycol) methyl ether acrylate) (D,L- P(LA)-b-P(PEGMA)) were prepared via ring-opening polymerization and reversible addition fragmentation chain transfer (RAFT) polymerization. The block polymers generated in the reaction reveal the living behavior with the molecular weight increasing with time. The copolymer D,L-P(LA)200-b-P(PEGMA)225 was synthesized successfully with D,L-P(LA) macro-RAFT agent, and was self-assembled in an aqueous environment, leading to the formation of self-assembly micelles. A distinct critical micelle concentration (CMC) was observed of the self-assembly system. The size of it was characterized by both DLS and TEM.
27
Mohamed, Mohamed Gamal, Wei-Shih Hung, Ahmed F. M. EL-Mahdy, Mahmoud M. M. Ahmed, Lizong Dai, Tao Chen, and Shiao-Wei Kuo. "High-Molecular-Weight PLA-b-PEO-b-PLA Triblock Copolymer Templated Large Mesoporous Carbons for Supercapacitors and CO2 Capture." Polymers 12, no. 5 (May 23, 2020): 1193. http://dx.doi.org/10.3390/polym12051193.
Abstract:
High-molecular-weight PLA440-b-PEO454-b-PLA440 (LEL) triblock copolymer was synthesized through simple ring-opening polymerization (ROP) by using the commercial homopolymer HO-PEO454-OH as the macro-initiator. The material acted as a single template to prepare the large mesoporous carbons by using resol-type phenolic resin as a carbon source. Self-assembled structures of phenolic/LEL blends mediated by hydrogen bonding interaction were determined by FTIR and SAXS analyses. Through thermal curing and carbonization procedures, large mesoporous carbons (>50 nm) with a cylindrical structure and high surface area (>600 m2/g) were obtained because the OH units of phenolics prefer to interact with PEO block rather than PLA block, as determined by FTIR spectroscopy. Furthermore, higher CO2 capture and good energy storage performance were observed for this large mesoporous carbon, confirming that the proposed approach provides an easy method for the preparation of large mesoporous materials.
28
Zhan, Yiqun, Hao Wu, Weimin Song, and Lin Zhu. "Molecular Dynamics Study of the Diffusion between Virgin and Aged Asphalt Binder." Coatings 12, no. 3 (March 18, 2022): 403. http://dx.doi.org/10.3390/coatings12030403.
Abstract:
The diffusion between the virgin and aged asphalt binder in the recycled asphalt mixture is a crucial factor affecting its macro-mechanical performance. In this study, a combined model of the virgin-aged layered asphalt structure was assembled based on the molecular dynamics (MD) method. A four-component and twelve-category molecule were used to model the asphalt. The diffusion behaviors of the virgin and aged asphalt were characterized by mean square displacement (MSD), diffusion coefficient, relative concentration and cohesive energy density (CED). Results indicated that at the same temperature, the diffusion coefficient of the virgin asphalt was the largest, followed by the virgin-aged asphalt and the aged asphalt. As the temperature increased, the relative concentration on both sides of the virgin-aged asphalt overlapped to a certain extent. The covered lengths of the virgin asphalt were larger than those of the aged asphalt, indicating the diffusion between the virgin asphalt and aged asphalt was mainly manifested as the diffusion from the virgin asphalt to the aged asphalt. The development of CED and the fraction of free volume (FFV) indicated the mutual attractive interactions among the molecules in virgin and aged asphalt layers became strong and the cohesion properties inside the model became better.
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Movilli, Jacopo, and Jurriaan Huskens. "Functionalized Polyelectrolytes for Bioengineered Interfaces and Biosensing Applications." Organic Materials 02, no. 02 (April 2020): 078–107. http://dx.doi.org/10.1055/s-0040-1708494.
Abstract:
The possibility of tuning the chemical moieties and their density plays a fundamental role in targeting surface-confined molecular structures and their functionalities at macro and nanoscale levels. Such interfacial control is crucial for engineered coating formation and biorecognition purposes, where the type and density of ligands/receptors at the surface affect the overall binding affinities and the device performance. Together with the well-established self-assembled monolayers, a surface modification approach based on polyelectrolytes (PEs) has gained importance to provide desired characteristics at the substrate interface. This review presents the innovations of functional PEs, modified in a preceding synthetic step, and their wide applicability in functional (a)biotic substrates. Examples of 2D and 3D architectures made by modified PEs are reviewed in relation with the reactive groups grafted to the PE backbones. The main focus lies on the strategy to use modified PEs to form bioengineered coatings for orthogonally anchoring biological entities, manufacturing biocidal/antifouling films, and their combinations in functional biosensing applications.
30
Liu, Ye, Catherine Dabrowska, Antranik Mavousian, Bernhard Strauss, Fanlong Meng, Corrado Mazzaglia, Karim Ouaras, et al. "Bio‐assembling Macro‐Scale, Lumenized Airway Tubes of Defined Shape via Multi‐Organoid Patterning and Fusion." Advanced Science 8, no. 9 (February 8, 2021): 2003332. http://dx.doi.org/10.1002/advs.202003332.
31
Al-Wedaei, Khalil, Humood Naser, Hashim Al-Sayed, and Abdulqader Khamis. "Assemblages of macro-fauna associated with two seagrass beds in Kingdom of Bahrain: Implications for conservation." Journal of the Association of Arab Universities for Basic and Applied Sciences 10, no. 1 (September 2011): 1–7. http://dx.doi.org/10.1016/j.jaubas.2011.06.004.
32
Putnam, Hollie M., Michael Stat, Xavier Pochon, and Ruth D. Gates. "Endosymbiotic flexibility associates with environmental sensitivity in scleractinian corals." Proceedings of the Royal Society B: Biological Sciences 279, no. 1746 (August 29, 2012): 4352–61. http://dx.doi.org/10.1098/rspb.2012.1454.
Abstract:
Flexibility in biological systems is seen as an important driver of macro-ecosystem function and stability. Spatially constrained endosymbiotic settings, however, are less studied, although environmental thresholds of symbiotic corals are linked to the function of their endosymbiotic dinoflagellate communities. Symbiotic flexibility is a hypothesized mechanism that corals may exploit to adapt to climate change. This study explores the flexibility of the coral– Symbiodinium symbiosis through quantification of Symbiodinium ITS2 sequence assemblages in a range of coral species and genera. Sequence assemblages are expressed as an index of flexibility incorporating phylogenetic divergence and relative abundance of Symbiodinium sequences recovered from the host. This comparative analysis reveals profound differences in the flexibility of corals for Symbiodinium , thereby classifying corals as generalists or specifists. Generalists such as Acropora and Pocillopora exhibit high intra- and inter-species flexibility in their Symbiodinium assemblages and are some of the most environmentally sensitive corals. Conversely, specifists such as massive Porites colonies exhibit low flexibility, harbour taxonomically narrow Symbiodinium assemblages, and are environmentally resistant corals. Collectively, these findings challenge the paradigm that symbiotic flexibility enhances holobiont resilience. This underscores the need for a deeper examination of the extent and duration of the functional benefits associated with endosymbiotic diversity and flexibility under environmental stress.
33
Malik, D. S., Ruchika Chauhan, and Prachi Rathi. "Factors affecting the ecological habitat of Benthic macro-invertebrate assemblages in Asan wetland, Dehradun in Garhwal Himalaya." Journal of Applied and Natural Science 15, no. 1 (March 19, 2023): 262–72. http://dx.doi.org/10.31018/jans.v15i1.4222.
Abstract:
The Himalayan region has several freshwater resources, such as rivers, lakes, and wetlands. These freshwater resources have been adversely affected by environmental factors. Freshwater biological systems are defenseless against outcomes of environmental changes that might prompt the irreversible disintegration of these natural surroundings. The present study aimed to investigate the effect of biotic and abiotic factors on the Benthic macro-invertebrate assemblages of the Asan wetland, Dehradun in Garhwal Himalaya. A determination of the physico-chemical health status of the Asan wetland viz., electrical conductivity (EC), total dissolved solids (TDS), biochemical oxygen demand (BOD), and nutrients parameters like nitrogen, potassium, and phosphorus were investigated during this study. Three sampling sites (Site 1, Site 2 and Site 3) of wetland were selected and the water samples were collected seasonally, i.e., summer, winter, and monsoon from April 2021-March 2022. Maximum values of EC(163.75 µS/cm), TDS (232.78 (mg/l), alkalinity (141.20 mg/l) and pH(7.8) were recorded in the monsoon season (June-September) and minimum values of EC( 135.80µS/cm), TDS (196.80 (mg/l), alkalinity (119.80mg/l) and pH(7.2) were recorded in the winter season (November–February). An overall total of 18 macrobenthos genera belonging to four classes was identified. Maximum communities of macrobenthos were observed during the winter and minimum communities during the monsoon season. Canonical correspondence analysis (CCA) was used to determine whether microbenthic genera and habitat ecological parameters and showed a positive or negative correlation. Thus, the present study contributed to the status of various factors and their impacts on the Benthic macro-invertebrate structure of the Asan wetland.
34
Jayaraman, Arthi, Christopher Price, Millicent O. Sullivan, and Kristi L. Kiick. "Collagen-Peptide-Based Drug Delivery Strategies." Technology & Innovation 21, no. 4 (December 1, 2020): 1–20. http://dx.doi.org/10.21300/21.4.2020.9.
Abstract:
Collagen-targeting strategies have proven to be an effective method for targeting drugs to pathological tissues for treatment of disease. The use of collagen-like peptides for controlling the assembly of drug delivery vehicles, as well as their integration into collagen-containing matrices, offers significant advantages for tuning the morphologies of assembled structures, their thermoresponsiveness, and the loading and release of both small-molecule and macro-molecular cargo. In this contribution, we summarize the design and development of collagen-peptide-based drug delivery systems introduced by the Kiick group and detail the expansion of our understanding and the application of these unique molecules through collaborations with experts in computational simulations (Jayaraman), osteoarthritis (Price), and gene delivery (Sullivan). Kiick was inducted as a Fellow of the National Academy of Inventors in 2019 and was to deliver an address describing the innovations of her research. Given the cancellation of the NAI Annual Meeting as a result of coronavirus travel restrictions, her work based on collagen-peptide-mediated assembly is instead summarized in this contribution.
35
Bellisario, Bruno, Federica Camisa, Chiara Abbattista, and Roberta Cimmaruta. "A network approach to identify bioregions in the distribution of Mediterranean amphipods associated with Posidonia oceanica meadows." PeerJ 7 (April 23, 2019): e6786. http://dx.doi.org/10.7717/peerj.6786.
Abstract:
Although amphipods are key components of the macro-fauna associated with Posidonia oceanica meadows, to date no studies focused on the structure and diversity of their assemblages across the whole Mediterranean Sea. Here, we applied a network approach based on modularity on a dataset mined from literature to identify biogeographic modules and to assess the biogeographic roles of associated localities. We also correlated the patterns evidenced with the biogeographic distribution of amphipod groups by means of a multivariate analysis. Modularity analysis highlighted four biogeographic modules bounded by the main Mediterranean biogeographic divides and evidenced a decrease in species diversity along a NW-SE gradient. Assemblages associated with Central-Western Mediterranean and, to a lesser extent, Tunisian modules showed the highest species richness and were identified as hubs, characterized by species with regional distributions that behave as source in a biogeographic context. The paleogeographic history of the host seagrass and the ecology of associated amphipods, both suggest the joint effect of species persistence and post-Last Glacial Maximum expansion in explaining the pattern of amphipod distribution in the Mediterranean Sea.
36
Sun, Limei, Junwu Liu, and Lin Zhang. "Evaluation of friction in different oral restoration materials and its influencing factors." Materials Express 10, no. 10 (October 31, 2020): 1746–52. http://dx.doi.org/10.1166/mex.2020.1790.
Abstract:
This research uses nanotechnology and molecular assembly technology, using biocompatible hydroxyapatite material as the inorganic filler, organically compound and assemble with the organic resin matrix to achieve the performance shear of the composite material, thus developing strength High-resistance, easy-to-process and good biocompatibility composite resin dental restoration materials, and the nano-composite resin material flexural strength, compressive strength and water absorption value were characterized in laboratory stage, the performance fully reached the current clinical use Various indicators of imported composite resin. This study analyzed the differences in the effects and friction properties of different prosthetic materials in oral repair. In order to better simulate the friction and wear performance of dental restoration materials in the oral environment, this paper studied under two conditions of oil lubrication and artificial saliva lubrication, and the wear mechanism from the macro aspects of friction coefficient, wear rate, wear resistance, etc. The research results show that the abrasion performance of the nanocomposite resin is closely related to its surface morphology and characteristics. The comparison with the performance of ceramic and composite resin restoration materials shows that nanocomposite resin materials have better mechanical properties and resistance than other dental restoration wear performance.
37
Cilluffo, Danilo, Roberta Flavia Chiavetta, Serena Bivona, Flavia Contino, Claudia Coronnello, Salvatore Feo, Aldo Di Leonardo, and Viviana Barra. "Transcriptomic Changes Following Partial Depletion of CENP-E in Normal Human Fibroblasts." Genes 12, no. 9 (August 26, 2021): 1322. http://dx.doi.org/10.3390/genes12091322.
Abstract:
The centromere is a fundamental chromosome structure in which the macro-molecular kinetochore assembles and is bound by spindle microtubules, allowing the segregation of sister chromatids during mitosis. Any alterations in kinetochore assembly or functioning or kinetochore–microtubule attachments jeopardize chromosome stability, leading to aneuploidy, a common feature of cancer cells. The spindle assembly checkpoint (SAC) supervises this process, ensuring a faithful segregation of chromosomes. CENP-E is both a protein of the kinetochore and a crucial component of the SAC required for kinetochore–microtubule capture and stable attachment, as well as congression of chromosomes to the metaphase plate. As the function of CENP-E is restricted to mitosis, its haploinsufficiency has been used to study the induced cell aneuploidy; however, the gene expression profile triggered by CENP-E reduction in normal cells has never been explored. To fill this gap, here we investigated whether a gene network exists that is associated with an siRNA-induced 50% reduction in CENP-E and consequent aneuploidy. Gene expression microarray analyses were performed at early and late timepoints after transfection. Initially, cell cycle regulation and stress response pathways were downregulated, while afterwards pathways involved in epithelial–mesenchymal transition, hypoxia and xenobiotic metabolism were altered. Collectively, our results suggest that CENP-E reduction triggers a gene expression program that recapitulates some features of tumor cells.
38
von Gratowski, Svetlana, Victor Koledov, Zoya Kosakowskiya, Peter Lega, Andrey Orlov, and Monica A. Cotta. "Mechanical Bottom-up Nano-Assembling and Nano-Manipulation Using Shape Memory Alloy Nano-Gripper." Solid State Phenomena 323 (August 30, 2021): 130–39. http://dx.doi.org/10.4028/www.scientific.net/ssp.323.130.
Abstract:
The numerous 1-D and 2-D nanomaterials: nanotubes, nanowires (NWs), graphene, etc. were discovered, synthesized and intensively studied in the past decades. These nanomaterials had appeared to reveal the unique physical and functional properties allowing constructing the large number of nanodevice based on single nanoobjects. Recently many studies have led to a wide range of proof-of-concept of individual nanoscale devices including nanolasers, nanosensors, field-effect transistors (nanoFETs) and many others based on NWs, carbon nanotubes (CNT) and many other nanoobjects. Such nanodevices represent attractive building blocks for hierarchical assembly of microscale and macroscopic devices which are attractive for creating of micro-and –macro-devices and arrays by the bottom-up and hybrid paradigm. In this paper the conceptual survey is given of nowadays achievements in the field of mechanical bottom-up nanoassembling. We emphasize on the system based on smallest and the fastest in the World nanotweezer developed on the base of the new smart materials with shape memory effect for nanomanipulation of real nanoobjects. We discuss the recent experiments on nanomanipulation, nanoassembling and nanomanufacturing of nanoand micro-devices using this method, which in many cases can replaced very expensive “top-down” technologies.
39
Oppong, Samuel K., Collins Ayine Nsor, and Gabriel Kwabena Buabeng. "Response of benthic invertebrate assemblages to seasonal and habitat condition in the Wewe River, Ashanti region (Ghana)." Open Life Sciences 16, no. 1 (January 1, 2021): 336–53. http://dx.doi.org/10.1515/biol-2021-0040.
Abstract:
Abstract Aquatic macro-invertebrates play a vital role in the food chain of river ecosystem at several trophic guilds and consumer levels, and are used as biomonitoring tools for aquatic ecosystem health. However, hydrologic conditions of these ecosystems have been severely altered because of the increase in urban development and agricultural expansion. This study examined benthic invertebrate response to processes that structure their community in the Wewe River, segmented into intact, medium, and severe condition zones. We sampled in 100 stations in a period of 4 months in the wet (June–September, 2019) and 3 months in the dry (January–March, 2020) seasons. Geometric series, rarefaction, and Hill numbers models were used to quantify invertebrate assemblages, while ordination technique, canonical correspondence analysis, was used to evaluate the influence of predictive factors on their assemblages. A total of 2,075 individuals belonging to 20 family taxa were registered. There was no significant difference in benthic assemblages between the dry and wet seasons. Predictive factors accounted for 47.04 and 50.84% variances, respectively. Taxa distribution patterns differed significantly only in the severely disturbed zone during the wet season. Neptidae, Libellulidae, and Chironomidae were the most abundant taxa, indicating their broad range habitat preference and their ability to adapt to seasonal changes. Asellidae and Perlidae were the least detected, suggesting their sensitivity to elevated levels of some water quality parameters. The findings highlight the threats to the benthic community and overall functional state of the Wewe River, with the need to consider the proposed conservation interventions indicated in this study.
40
Laroche, Olivier, Susanna A. Wood, Louis A. Tremblay, Gavin Lear, Joanne I. Ellis, and Xavier Pochon. "Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities." PeerJ 5 (May 17, 2017): e3347. http://dx.doi.org/10.7717/peerj.3347.
Abstract:
Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.
41
Selkoe, Kimberly A., Oscar E. Gaggiotti, Eric A. Treml, Johanna L. K. Wren, Mary K. Donovan, and Robert J. Toonen. "The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages." Proceedings of the Royal Society B: Biological Sciences 283, no. 1829 (April 27, 2016): 20160354. http://dx.doi.org/10.1098/rspb.2016.0354.
Abstract:
Conservation of ecological communities requires deepening our understanding of genetic diversity patterns and drivers at community-wide scales. Here, we use seascape genetic analysis of a diversity metric, allelic richness (AR), for 47 reef species sampled across 13 Hawaiian Islands to empirically demonstrate that large reefs high in coral cover harbour the greatest genetic diversity on average. We found that a species's life history (e.g. depth range and herbivory) mediates response of genetic diversity to seascape drivers in logical ways. Furthermore, a metric of combined multi-species AR showed strong coupling to species richness and habitat area, quality and stability that few species showed individually. We hypothesize that macro-ecological forces and species interactions, by mediating species turnover and occupancy (and thus a site's mean effective population size), influence the aggregate genetic diversity of a site, potentially allowing it to behave as an apparent emergent trait that is shaped by the dominant seascape drivers. The results highlight inherent feedbacks between ecology and genetics, raise concern that genetic resilience of entire reef communities is compromised by factors that reduce coral cover or available habitat, including thermal stress, and provide a foundation for new strategies for monitoring and preserving biodiversity of entire reef ecosystems.
42
Cheeseman, Samuel, Z. L. Shaw, Jitraporn Vongsvivut, Russell J. Crawford, Madeleine F. Dupont, Kylie J. Boyce, Sheeana Gangadoo, et al. "Analysis of Pathogenic Bacterial and Yeast Biofilms Using the Combination of Synchrotron ATR-FTIR Microspectroscopy and Chemometric Approaches." Molecules 26, no. 13 (June 25, 2021): 3890. http://dx.doi.org/10.3390/molecules26133890.
Abstract:
Biofilms are assemblages of microbial cells, extracellular polymeric substances (EPS), and other components extracted from the environment in which they develop. Within biofilms, the spatial distribution of these components can vary. Here we present a fundamental characterization study to show differences between biofilms formed by Gram-positive methicillin-resistant Staphylococcus aureus (MRSA), Gram-negative Pseudomonas aeruginosa, and the yeast-type Candida albicans using synchrotron macro attenuated total reflectance-Fourier transform infrared (ATR-FTIR) microspectroscopy. We were able to characterise the pathogenic biofilms’ heterogeneous distribution, which is challenging to do using traditional techniques. Multivariate analyses revealed that the polysaccharides area (1200–950 cm−1) accounted for the most significant variance between biofilm samples, and other spectral regions corresponding to amides, lipids, and polysaccharides all contributed to sample variation. In general, this study will advance our understanding of microbial biofilms and serve as a model for future research on how to use synchrotron source ATR-FTIR microspectroscopy to analyse their variations and spatial arrangements.
43
Quinn, Robert A., Mark J. A. Vermeij, Aaron C. Hartmann, Ines Galtier d'Auriac, Sean Benler, Andreas Haas, Steven D. Quistad, et al. "Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence." Proceedings of the Royal Society B: Biological Sciences 283, no. 1829 (April 27, 2016): 20160469. http://dx.doi.org/10.1098/rspb.2016.0469.
Abstract:
Holobionts are assemblages of microbial symbionts and their macrobial host. As extant representatives of some of the oldest macro-organisms, corals and algae are important for understanding how holobionts develop and interact with one another. Using untargeted metabolomics, we show that non-self interactions altered the coral metabolome more than self-interactions (i.e. different or same genus, respectively). Platelet activating factor (PAF) and Lyso-PAF, central inflammatory modulators in mammals, were major lipid components of the coral holobionts. When corals were damaged during competitive interactions with algae, PAF increased along with expression of the gene encoding Lyso-PAF acetyltransferase; the protein responsible for converting Lyso-PAF to PAF. This shows that self and non-self recognition among some of the oldest extant holobionts involve bioactive lipids identical to those in highly derived taxa like humans. This further strengthens the hypothesis that major players of the immune response evolved during the pre-Cambrian.
44
Liu, Ye, Catherine Dabrowska, Antranik Mavousian, Bernhard Strauss, Fanlong Meng, Corrado Mazzaglia, Karim Ouaras, et al. "Multi‐Tissue Organoid Engineering: Bio‐assembling Macro‐Scale, Lumenized Airway Tubes of Defined Shape via Multi‐Organoid Patterning and Fusion (Adv. Sci. 9/2021)." Advanced Science 8, no. 9 (May 2021): 2170046. http://dx.doi.org/10.1002/advs.202170046.
45
Kalinova, Radostina, and Ivaylo Dimitrov. "Functional Polyion Complex Micelles for Potential Targeted Hydrophobic Drug Delivery." Molecules 27, no. 7 (March 28, 2022): 2178. http://dx.doi.org/10.3390/molecules27072178.
Abstract:
Polyion complex (PIC) micelles have gained an increasing interest, mainly as promising nano-vehicles for the delivery of various hydrophilic charged (macro)molecules such as DNA or drugs to the body. The aim of the present study is to construct novel functional PIC micelles bearing cell targeting ligands on the surface and to evaluate the possibility of a hydrophobic drug encapsulation. Initially, a pair of functional oppositely charged peptide-based hybrid diblock copolymers were synthesized and characterized. The copolymers spontaneously co-assembled in water into nanosized PIC micelles comprising a core of a polyelectrolyte complex between poly(L-aspartic acid) and poly(L-lysine) and a biocompatible mixed shell of disaccharide-modified poly(ethylene glycol) and poly(2-hydroxyethyl methacrylate). Depending on the molar ratio between the oppositely charged groups, PIC micelles varying in surface charge were obtained and loaded with the natural hydrophobic drug curcumin. PIC micelles’ drug loading efficiency, in vitro drug release profiles and antioxidant activity were evaluated. The preliminary results indicate that PIC micelles can be successfully used as carriers of hydrophobic drugs, thus expanding their potential application in nanomedicine.
46
Alvino, E. R., R. L. Robker, and D. L. Russell. "269. CD44 signaling in mouse ovulatory cumulus - oocyte complexes." Reproduction, Fertility and Development 20, no. 9 (2008): 69. http://dx.doi.org/10.1071/srb08abs269.
Abstract:
Oocytes grow and develop within ovarian follicles, providing a nurturing environment before their release (ovulation) into the oviduct for fertilisation. For ovulation to occur the ovarian follicle responds to LH from the pituitary, leading to a cascade of regulated gene expression and formation of the hyaluronan rich cumulus matrix around the oocyte. This COC (cumulus oocyte complex) matrix is composed of high concentrations of the ECM glycosaminoglycan hyaluronan (HA) cross-linked by several HA-binding proteins. Several of the COC matrix components are essential for ovulation, since null gene mutations in mice lead to ovulation defects. Mechanisms by which the COC matrix controls ovulation however, are unknown. We have investigated cellular signalling and cellular phenotypes that occur as part of the formation of the COC matrix. The transmembrane HA receptor CD44 was significantly upregulated in cumulus cells from 6 h after hCG (LH analogue) treatment (9.8 ± 1.5 fold) until ovulation at 12 h post hCG (11.8 ± 2.9-fold). In many cell types CD44 activates the intracellular Rho-family GTPase Rac1 and its activator, the guanine exchange factor Tiam1, pleiotropic regulators of cytoskeletal function, cell-cell adhesion and migration. We found both Rac1 and Tiam1 were strongly detected in cumulus cells, but not regulated by hCG. These observations show that at the time of ovulation a macro-molecular complex associated with cell motility is assembled through the extracellular interaction of the COC matrix and cell surface proteins. We investigated the migratory and invasive activity of COCs from hormonally stimulated mice. Migration of cumulus cells from hCG treated mice was significantly increased compared with untreated COCs. Furthermore the hCG-stimulated cumulus cells were able to invade a range of ECM substrates including collagen and laminin. These results suggest the cumulus cells in the expanded COC transition to a motile cell phenotype that may play a key role in promoting ovulation.
47
Casey, Jordan M., Tracy D. Ainsworth, J. Howard Choat, and Sean R. Connolly. "Farming behaviour of reef fishes increases the prevalence of coral disease associated microbes and black band disease." Proceedings of the Royal Society B: Biological Sciences 281, no. 1788 (August 7, 2014): 20141032. http://dx.doi.org/10.1098/rspb.2014.1032.
Abstract:
Microbial community structure on coral reefs is strongly influenced by coral–algae interactions; however, the extent to which this influence is mediated by fishes is unknown. By excluding fleshy macroalgae, cultivating palatable filamentous algae and engaging in frequent aggression to protect resources, territorial damselfish (f. Pomacentridae), such as Stegastes , mediate macro-benthic dynamics on coral reefs and may significantly influence microbial communities. To elucidate how Stegastes apicalis and Stegastes nigricans may alter benthic microbial assemblages and coral health, we determined the benthic community composition (epilithic algal matrix and prokaryotes) and coral disease prevalence inside and outside of damselfish territories in the Great Barrier Reef, Australia. 16S rDNA sequencing revealed distinct bacterial communities associated with turf algae and a two to three times greater relative abundance of phylotypes with high sequence similarity to potential coral pathogens inside Stegastes 's territories. These potentially pathogenic phylotypes (totalling 30.04% of the community) were found to have high sequence similarity to those amplified from black band disease (BBD) and disease affected corals worldwide. Disease surveys further revealed a significantly higher occurrence of BBD inside S. nigricans 's territories. These findings demonstrate the first link between fish behaviour, reservoirs of potential coral disease pathogens and the prevalence of coral disease.
48
Franks, Nigel R., Alan Worley, Katherine A. J. Grant, Alice R. Gorman, Victoria Vizard, Harriet Plackett, Carolina Doran, Margaret L. Gamble, Martin C. Stumpe, and Ana B. Sendova-Franks. "Social behaviour and collective motion in plant-animal worms." Proceedings of the Royal Society B: Biological Sciences 283, no. 1825 (February 24, 2016): 20152946. http://dx.doi.org/10.1098/rspb.2015.2946.
Abstract:
Social behaviour may enable organisms to occupy ecological niches that would otherwise be unavailable to them. Here, we test this major evolutionary principle by demonstrating self-organizing social behaviour in the plant-animal, Symsagittifera roscoffensis . These marine aceol flat worms rely for all of their nutrition on the algae within their bodies: hence their common name. We show that individual worms interact with one another to coordinate their movements so that even at low densities they begin to swim in small polarized groups and at increasing densities such flotillas turn into circular mills. We use computer simulations to: (i) determine if real worms interact socially by comparing them with virtual worms that do not interact and (ii) show that the social phase transitions of the real worms can occur based only on local interactions between and among them. We hypothesize that such social behaviour helps the worms to form the dense biofilms or mats observed on certain sun-exposed sandy beaches in the upper intertidal of the East Atlantic and to become in effect a super-organismic seaweed in a habitat where macro-algal seaweeds cannot anchor themselves. Symsagittifera roscoffensis , a model organism in many other areas in biology (including stem cell regeneration), also seems to be an ideal model for understanding how individual behaviours can lead, through collective movement, to social assemblages.
49
Armitage, Lindsey, Sarah Gibson, Pedro S. de Carvalho, Lee Wisner, Joo Y. Song, Wing C. Chan, Jennifer R. Chapman-Fredricks, et al. "Genomic Stability, DNA Repair and the SKP1-CUL1-F-Box Complex in HIV Associated Diffuse Large B-Cell Lymphoma." Blood 142, Supplement 1 (November 28, 2023): 2991. http://dx.doi.org/10.1182/blood-2023-182953.
Abstract:
Introduction: Previously we demonstrated that HIV associated diffuse large B-cell lymphomas (DLBCL) of Germinal Center B-cell subtype (GCB) are more proliferative, with enhanced genomic stability and increased expression of DNA repair genes, particularly Fanconi anemia (FA) and homologous recombination (HR) genes compared to their HIV negative counterparts (Maguire et al, 2019). It is unknown if this signature is unique to the GCB subtype or if it is also observed in Activated B-cell (ABC) and Unclassified (UNC) DLBCL. Herein we validate our HIV associated GCB DLBCL findings in a larger independent cohort and report for the first time the aberrational profile of molecularly profiled HIV associated ABC DLBCL compared to their HIV negative counterparts respectively. Methods: An independent cohort of 353 DLBCL FFPE cases was assembled, including 125 HIV-DLBCL samples. All samples underwent hematopathological review to confirm diagnosis and determine tumor content. Samples with <60% tumor content were macro-dissected before they were RNA/DNA extracted. Cell of origin (COO) profiles were assessed using the Lymph3Cx molecular assay which can distinguish primary mediastinal B-cell lymphoma (PMBL) like from GCB, ABC and UNC DLBCL (Mottok et al 2018). Copy number (CN) analyses were performed on samples with sufficient DNA (41 HIV neg, 32 HIV pos) using the OncoScan FFPE assay kit and the resulting data analyzed using Chromosome Analysis Suite (ChAS) v4.1 and the multisample viewer module of Reproductive Health Research Analysis Software (RHAS) v1.1. Additional digital gene expression profiling was performed using the Pan-Cancer panel (NanoString, Seattle, WA) customized to include 9 BCL2 family genes for a total of 739 genes and analyzed using the NanoString nSolver Advanced Analysis module. Results: GCB, ABC, UNC and PMBL-like proportions were 50%, 30%, 14% and 6% in HIV unassociated (HIV neg) and 50%, 23%, 25% and 2% in HIV pos tumors respectively, confirming both cohorts were GCB-enriched by molecular profiling. PMBL-like cases were excluded from further analyses. OncoScan CN analyses showed that HIV pos DLBCL were significantly less aberrant than HIV neg DLBCL (median CN per sample 0.56 vs 1.01, p<0.001). HIV pos GCB tumors were significantly less aberrant than both HIV neg GCB tumors (median CN per sample 0.50 vs 1.11, p<0.001), and HIV pos ABC tumors (median CN per sample 0.50 vs 0.81, p=0.009). HIV pos ABC tumors were also less aberrant than HIV neg ABC tumors, however, the difference was not significant overall (median CN per sample 0.81 vs 1.03, p=0.162) or for gain/amplifications (median CN per sample 0.38 vs 0.42, p=0.814), but was borderline significant for loss/deletions (median CN per sample 0.31 vs 0.47, p=0.06). GEP analyses identified Cell Cycle and DNA repair as the top two upregulated pathways in HIV pos GCB tumors compared to HIV neg GCB tumors. In contrast, Cell Cycle and DNA repair were downregulated in HIV pos ABC tumors compared to HIV neg ABC tumors. However, one gene ( RBX1) was identified as significantly upregulated in both pathways in HIV pos GCB (adjusted p-value 0.0215) and HIV pos ABC (adjusted p-value 0.0046) tumors compared to their HIV neg counterparts. A second gene ( SKP1) was also significantly upregulated in HIV pos GCB (adjusted p-value 3.94E-5) and HIV pos ABC (adjusted p-value 0.0031) tumors. Together RBX1 and SKP1 encode the two principal functional subunits of the SKP1, CUL1, F-box protein (SCF) complex which is part of the ubiquitin proteasome system (UPS) and has been reported as essential for maintaining genome and chromosome stability (Thompson et al 2021). Conclusions: These results demonstrate that HIV pos DLBCL tumors are less aberrant than their HIV neg counterparts irrespective of COO subtype. However, the degree of genomic stability differs by COO, with HIV pos GCB tumors being more genomically stable than HIV pos ABC tumors. Although both have enhanced expression of UPS related SCF genes ( RBX1, SKP1), only HIV pos GCB tumors have enhanced expression of key DNA repair genes as well including Fanconi Anemia ( BRCA2/FANCD1, FANCL) and mismatch repair ( MSH2, MSH6) genes (adjusted p-values of ≤ 0.0263). Given the reported role of SCF in genomic stability maintenance, the HIV pos COO CN differences could be due to the contributions of both DNA repair and SCF mechanisms in HIV pos GCB and mainly SCF mechanisms in HIV pos ABC tumors.
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Thome, Patricia E., Jacqueline Rivera-Ortega, Jenny C. Rodríguez-Villalobos, Daniel Cerqueda-García, Edgar O. Guzmán-Urieta, José Q. García-Maldonado, Natalia Carabantes, and Eric Jordán-Dahlgren. "Local dynamics of a white syndrome outbreak and changes in the microbial community associated with colonies of the scleractinian brain coral Pseudodiploria strigosa." PeerJ 9 (February 2, 2021): e10695. http://dx.doi.org/10.7717/peerj.10695.
Abstract:
Reef corals in the Mexican Reef System have been severely affected by the emergence of a white syndrome that resembles both White Plague II and SCTLD descriptions. Meandroid scleractinian coral species are among the most severely affected. To gain insight into this affliction we conducted a broad study in the brain coral Pseudodiploria strigosa at a rear reef site in the NE Mexican Caribbean. We describe macro and microscopical signals of the disease, characterize the outbreak dynamics, the tissue histopathology, explore immunological responses in the individuals, and compare microbial assemblages associated with the surface mucus layer of healthy and unhealthy colonies. At the study site, the white syndrome outbreak on P. strigosa showed a high incidence rate in summer-fall and a low one in winter, as well as low survival expectation of diseased colonies at the end of the study. After 306 days of observation, out of 96 tracked colonies, eight remained apparently healthy and seven were diseased. No effective resistance to colony disease progression was observed once white syndrome signs developed. Tissue loss rate during the study varied among colonies (mean = 10.8 cm2, s.d. = 7.8 cm2) suggesting a complex relation between causal agents and colony resistance. The deterioration of tissues was evidenced from the basal to the surface body wall of polyps (up to 66% hypertrophy and liquefactive necrosis in unhealthy colonies), implying that microscopic alterations begin before macroscopic signals develop, suggesting this may be a systemic disease. We measured high levels of phenoloxidase (two orders of magnitude higher PO activity than P. strigosa affected by BBD) and antibacterial activity without significant reduction in unhealthy samples from the mucus layer, indicative of an enhanced immunological response. Results showed that opportunistic bacteria dominated damaged colonies, where six genera of the Bacteroidia class were found with significant changes in unhealthy colonies after DeSeq2 analysis. Nevertheless, histological observations did not support infection of the tissues. The opportunistic overload seems to be contained within the mucus layer but may be associated with the mortality of tissues in a yet unclear way. Future research should focus on experimental infections, the tracking of natural infections, and the immunocompetence of corals in the face of environmental pressures due to local, regional, and global impacts. If environmental deterioration is the primary cause of the continuing emergence and re-emergence of lethal coral diseases, as has been proposed by many authors, the only true option to effectively help preserve the coral reef biodiversity and services, is to restore the environmental quality of reef waters at the local scale and reduce greenhouse gases at the global scale.