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Journal articles on the topic 'Biomolecular manipulation'

Author: Grafiati

Published: 4 June 2021

Last updated: 7 February 2022

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1

Hook, A. L., N. H. Voelcker, and H. Thissen. "Patterned and switchable surfaces for biomolecular manipulation." Acta Biomaterialia 5, no. 7 (September 2009): 2350–70. http://dx.doi.org/10.1016/j.actbio.2009.03.040.

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2

Mogaki, Rina, P. K. Hashim, Kou Okuro, and Takuzo Aida. "Guanidinium-based “molecular glues” for modulation of biomolecular functions." Chem. Soc. Rev. 46, no. 21 (2017): 6480–91. http://dx.doi.org/10.1039/c7cs00647k.

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3

Takahashi, Shunsuke, Masahiko Oshige, and Shinji Katsura. "DNA Manipulation and Single-Molecule Imaging." Molecules 26, no. 4 (February 17, 2021): 1050. http://dx.doi.org/10.3390/molecules26041050.

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DNA replication, repair, and recombination in the cell play a significant role in the regulation of the inheritance, maintenance, and transfer of genetic information. To elucidate the biomolecular mechanism in the cell, some molecular models of DNA replication, repair, and recombination have been proposed. These biological studies have been conducted using bulk assays, such as gel electrophoresis. Because in bulk assays, several millions of biomolecules are subjected to analysis, the results of the biological analysis only reveal the average behavior of a large number of biomolecules. Therefore, revealing the elementary biological processes of a protein acting on DNA (e.g., the binding of protein to DNA, DNA synthesis, the pause of DNA synthesis, and the release of protein from DNA) is difficult. Single-molecule imaging allows the analysis of the dynamic behaviors of individual biomolecules that are hidden during bulk experiments. Thus, the methods for single-molecule imaging have provided new insights into almost all of the aspects of the elementary processes of DNA replication, repair, and recombination. However, in an aqueous solution, DNA molecules are in a randomly coiled state. Thus, the manipulation of the physical form of the single DNA molecules is important. In this review, we provide an overview of the unique studies on DNA manipulation and single-molecule imaging to analyze the dynamic interaction between DNA and protein.

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4

Soltani, Mohammad, Jun Lin, Robert A. Forties, James T. Inman, Summer N. Saraf, Robert M. Fulbright, Michal Lipson, and Michelle D. Wang. "Nanophotonic trapping for precise manipulation of biomolecular arrays." Nature Nanotechnology 9, no. 6 (April 28, 2014): 448–52. http://dx.doi.org/10.1038/nnano.2014.79.

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5

Baker, James E., Ryan P. Badman, and Michelle D. Wang. "Nanophotonic trapping: precise manipulation and measurement of biomolecular arrays." Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology 10, no. 1 (April 24, 2017): e1477. http://dx.doi.org/10.1002/wnan.1477.

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6

Okumura, Shu, Benediktus Nixon Hapsianto, Nicolas Lobato-Dauzier, Yuto Ohno, Seiju Benner, Yosuke Torii, Yuuka Tanabe, et al. "Morphological Manipulation of DNA Gel Microbeads with Biomolecular Stimuli." Nanomaterials 11, no. 2 (January 22, 2021): 293. http://dx.doi.org/10.3390/nano11020293.

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Hydrogels are essential in many fields ranging from tissue engineering and drug delivery to food sciences or cosmetics. Hydrogels that respond to specific biomolecular stimuli such as DNA, mRNA, miRNA and small molecules are highly desirable from the perspective of medical applications, however interfacing classical hydrogels with nucleic acids is still challenging. Here were demonstrate the generation of microbeads of DNA hydrogels with droplet microfluidic, and their morphological actuation with DNA strands. Using strand displacement and the specificity of DNA base pairing, we selectively dissolved gel beads, and reversibly changed their size on-the-fly with controlled swelling and shrinking. Lastly, we performed a complex computing primitive—A Winner-Takes-All competition between two populations of gel beads. Overall, these results show that strand responsive DNA gels have tantalizing potentials to enhance and expand traditional hydrogels, in particular for applications in sequencing and drug delivery.

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Cao, Lizhi, Zhengchun Peng, Wilbur Lam, and Thomas H. Barker. "A combined magnetophoresis/dielectrophoresis based microbead array as high-throughput biomolecular tweezers." TECHNOLOGY 02, no. 01 (March 2014): 23–27. http://dx.doi.org/10.1142/s2339547814500058.

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In this paper we describe a combined magnetophoresis (MAP) and dielectrophoresis (DEP) based platform for high throughput characterization of specific biomolecular interactions. The magnetic manipulation enables parallel loading of individual magnetic beads onto a magnetic pad array, while the combination of tightly controlled opposing magnetic and dielectrophoretic (DEP) forces is employed to produce characteristic out-of-plane (z-axial) bead displacement. We optimized design parameters to evenly load 2.8 μm biomolecule functionalized paramagnetic beads onto magnetic pads, and demonstrate the ability of our tweezers to discriminate between specific antibody-antigen bond from non-specific bond formed between bead and pad surface.

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Iino, Ryota, Tatsuya Iida, Akihiko Nakamura, Ei-ichiro Saita, Huijuan You, and Yasushi Sako. "Single-molecule imaging and manipulation of biomolecular machines and systems." Biochimica et Biophysica Acta (BBA) - General Subjects 1862, no. 2 (February 2018): 241–52. http://dx.doi.org/10.1016/j.bbagen.2017.08.008.

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9

CHEN, WEI-HUNG, JONATHAN D. WILSON, SITHARA S. WIJERATNE, SARAH A. SOUTHMAYD, KUAN-JIUH LIN, and CHING-HWA KIANG. "PRINCIPLES OF SINGLE-MOLECULE MANIPULATION AND ITS APPLICATION IN BIOLOGICAL PHYSICS." International Journal of Modern Physics B 26, no. 13 (May 5, 2012): 1230006. http://dx.doi.org/10.1142/s021797921230006x.

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Recent advances in nanoscale manipulation and piconewton force detection provide a unique tool for studying the mechanical and thermodynamic properties of biological molecules and complexes at the single-molecule level. Detailed equilibrium and dynamics information on proteins and DNA have been revealed by single-molecule manipulation and force detection techniques. The atomic force microscope (AFM) and optical tweezers have been widely used to quantify the intra- and inter-molecular interactions of many complex biomolecular systems. In this article, we describe the background, analysis, and applications of these novel techniques. Experimental procedures that can serve as a guide for setting up a single-molecule manipulation system using the AFM are also presented.

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10

Mahajan, Kalpesh D., Gang Ruan, Greg Vieira, Thomas Porter, Jeffrey J. Chalmers, R. Sooryakumar, and Jessica O. Winter. "Biomolecular detection, tracking, and manipulation using a magnetic nanoparticle-quantum dot platform." Journal of Materials Chemistry B 8, no. 16 (2020): 3534–41. http://dx.doi.org/10.1039/c9tb02481f.

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Fluorescent and magnetic materials play a significant role in biosensor technology, enabling sensitive quantification and separations with applications in diagnostics, purification, quality control, and therapeutics.

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11

Berezney, John P., and Omar A. Saleh. "Locked Nucleic Acid Biomolecular Handles Functionalize Double-Stranded DNA for Single Molecule Manipulation." Biophysical Journal 104, no. 2 (January 2013): 517a. http://dx.doi.org/10.1016/j.bpj.2012.11.2856.

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12

Taylor, Douglas Scott, James W. Chan, Theodore Zerdling, Stephen M. Lane, Ko Ihara, and Thomas Huser. "Laser Tweezers Raman Spectroscopy Detects Individual Neoplastic and Normal Hemotopoietic Cells." Blood 106, no. 11 (November 16, 2005): 4531. http://dx.doi.org/10.1182/blood.v106.11.4531.4531.

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Abstract Current methods for identifying neoplastic cells and discerning them from normal counterparts are often non-specific, slow, biologically perturbing, or a combination, thereof. Here, we show that single-cell, laser-tweezers Raman spectroscopy (LTRS) averts these shortcomings and also permits mechanical manipulation of the single cell under investigation. LTRS is used to characterize the biomolecular Raman signature of both normal human lymphocytes and transformed Jurkat and Raji lymphocyte cell lines from single, unfixed cells in suspension. We demonstrate that single-cell Raman spectra provide a highly reproducible biomolecular fingerprint. Characteristic peaks, mostly due to different DNA and protein concentrations, allow for discerning normal lymphocytes from transformed lymphocytes with high confidence (p << 0.05). Spectra are also compared and analyzed by principal component analysis (PCA) to demonstrate that normal and transformed cells form distinct clusters that can be defined using just two principal components. The method is shown to have a sensitivity of 98.3% for cancer detection, with 97.2% of the cells being correctly classified as being normal or transformed. These results demonstrate the potential application of LTRS as a clinical tool, research instrument, and for cell sorting based on its intrinsic biomolecular signature, therefore eliminating the need for exogenous fluorescent labeling.

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Cusano, Angela Maria, Filippo Causa, Raffaella Della Moglie, Nunzia Falco, Pasqualina Liana Scognamiglio, Anna Aliberti, Raffaele Vecchione, et al. "Integration of binding peptide selection and multifunctional particles as tool-box for capture of soluble proteins in serum." Journal of The Royal Society Interface 11, no. 99 (October 6, 2014): 20140718. http://dx.doi.org/10.1098/rsif.2014.0718.

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In this paper, we report on a general approach for the detection of a specific tumoural biomarker directly in serum. Such detection is made possible using a protein-binding peptide selected through an improved phage display technique and then conjugated to engineered microparticles (MPs). Protein biomarkers represent an unlimited source of information for non-invasive diagnostic and prognostic tests; MP-based assays are becoming largely used in manipulation of soluble biomarkers, but their direct use in serum is hampered by the complex biomolecular environment. Our technique overcomes the current limitations as it produces a selective MP—engineered with an antifouling layer—that ‘captures’ the relevant protein staying impervious to the background. Our system succeeds in fishing-out the human tumour necrosis factor alpha directly in serum with a high selectivity degree. Our method could have great impact in soluble protein manipulation and detection for a wide variety of diagnostic applications.

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Brut, Marie, Alain Estève, Georges Landa, and Mehdi Djafari Rouhani. "Toward in Silico Biomolecular Manipulation through Static Modes: Atomic Scale Characterization of HIV-1 Protease Flexibility." Journal of Physical Chemistry B 118, no. 11 (March 12, 2014): 2821–30. http://dx.doi.org/10.1021/jp4113156.

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15

Nersisyan, Lilit, Ruben Samsonyan, and Arsen Arakelyan. "CyKEGGParser: tailoring KEGG pathways to fit into systems biology analysis workflows." F1000Research 3 (August 14, 2014): 145. http://dx.doi.org/10.12688/f1000research.4410.2.

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The KEGG pathway database is a widely accepted source for biomolecular pathway maps. In this paper we present the CyKEGGParser app (http://apps.cytoscape.org/apps/cykeggparser) for Cytoscape 3 that allows manipulation with KEGG pathway maps. Along with basic functionalities for pathway retrieval, visualization and export in KGML and BioPAX formats, the app provides unique features for computer-assisted adjustment of inconsistencies in KEGG pathway KGML files and generation of tissue- and protein-protein interaction specific pathways. We demonstrate that using biological context-specific KEGG pathways created with CyKEGGParser makes systems biology analysis more sensitive and appropriate compared to original pathways.

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Yang, Fan, Xiaolei Zuo, Chunhai Fan, and Xian-En Zhang. "Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing." National Science Review 5, no. 5 (February 10, 2018): 740–55. http://dx.doi.org/10.1093/nsr/nwx134.

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Abstract Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.

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17

Vollmer, Frank, and Lan Yang. "Review Label-free detection with high-Q microcavities: a review of biosensing mechanisms for integrated devices." Nanophotonics 1, no. 3-4 (December 1, 2012): 267–91. http://dx.doi.org/10.1515/nanoph-2012-0021.

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AbstractOptical microcavities that confine light in high-Q resonance promise all of the capabilities required for a successful next-generation microsystem biodetection technology. Label-free detection down to single molecules as well as operation in aqueous environments can be integrated cost-effectively on microchips, together with other photonic components, as well as electronic ones. We provide a comprehensive review of the sensing mechanisms utilized in this emerging field, their physics, engineering and material science aspects, and their application to nanoparticle analysis and biomolecular detection. We survey the most recent developments such as the use of mode splitting for self-referenced measurements, plasmonic nanoantennas for signal enhancements, the use of optical force for nanoparticle manipulation as well as the design of active devices for ultra-sensitive detection. Furthermore, we provide an outlook on the exciting capabilities of functionalized high-Q microcavities in the life sciences.

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18

Polley, Anisha, Riffat Khanam, Arunima Sengupta, and Santanu Chakraborty. "Asporin Reduces Adult Aortic Valve Interstitial Cell Mineralization Induced by Osteogenic Media and Wnt Signaling Manipulation In Vitro." International Journal of Cell Biology 2020 (April 10, 2020): 1–19. http://dx.doi.org/10.1155/2020/2045969.

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Worldwide, calcific aortic valve disease is one of the leading causes of morbidity and mortality among patients with cardiac abnormalities. Aortic valve mineralization and calcification are the key events of adult calcific aortic valve disease manifestation and functional insufficiency. Due to heavy mineralization and calcification, adult aortic valvular cusps show disorganized and dispersed stratification concomitant with deposition of calcific nodules with severely compromised adult valve function. Interestingly, shared gene regulatory pathways are identified between bone-forming cells and heart valve cells during development. Asporin, a small leucine-rich proteoglycan (43 kDa), acts to inhibit mineralization in periodontal ligament cells and is also detected in normal murine adult aortic valve leaflets with unknown function. Therefore, to understand the Asporin function in aortic cusp mineralization and calcification, adult avian aortic valvular interstitial cell culture system is established and osteogenesis has been induced in these cells successfully. Upon induction of osteogenesis, reduced expression of Asporin mRNA and increased expression of bone and osteogenesis markers are detected compared to cells maintained without osteogenic induction. Importantly, treatment with human recombinant Asporin protein reduces the mineralization level in osteogenic media-induced aortic valvular interstitial cells with the concomitant decreased level of Wnt/β-catenin signaling. Overall, all these data are highly indicative that Asporin might be a novel biomolecular target to treat patients of calcific aortic valve disease over current cusp replacement surgery.

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Jarukanont, Daungruthai, João T. S. Coimbra, Bernd Bauerhenne, Pedro A. Fernandes, Shekhar Patel, Maria J. Ramos, and Martin E. Garcia. "Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase." Phys. Chem. Chem. Phys. 16, no. 39 (2014): 21768–77. http://dx.doi.org/10.1039/c4cp02289k.

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20

Conde, João, João Rosa, João C. Lima, and Pedro V. Baptista. "Nanophotonics for Molecular Diagnostics and Therapy Applications." International Journal of Photoenergy 2012 (2012): 1–11. http://dx.doi.org/10.1155/2012/619530.

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Light has always fascinated mankind and since the beginning of recorded history it has been both a subject of research and a tool for investigation of other phenomena. Today, with the advent of nanotechnology, the use of light has reached its own dimension where light-matter interactions take place at wavelength and subwavelength scales and where the physical/chemical nature of nanostructures controls the interactions. This is the field of nanophotonics which allows for the exploration and manipulation of light in and around nanostructures, single molecules, and molecular complexes. What is more is the use of nanophotonics in biomolecular interactions—nanobiophotonics—has prompt for a plethora of molecular diagnostics and therapeutics making use of the remarkable nanoscale properties. In this paper, we shall focus on the uses of nanobiophotonics for molecular diagnostics involving specific sequence characterization of nucleic acids and for gene delivery systems of relevance for therapy strategies. The use of nanobiophotonics for the combined diagnostics/therapeutics (theranostics) will also be addressed, with particular focus on those systems enabling the development of safer, more efficient, and specific platforms. Finally, the translation of nanophotonics for theranostics into the clinical setting will be discussed.

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Kinosita, Yoshiaki, Nagisa Mikami, Zhengqun Li, Frank Braun, Tessa E. F. Quax, Chris van der Does, Robert Ishmukhametov, Sonja-Verena Albers, and Richard M. Berry. "Motile ghosts of the halophilic archaeon, Haloferax volcanii." Proceedings of the National Academy of Sciences 117, no. 43 (October 13, 2020): 26766–72. http://dx.doi.org/10.1073/pnas.2009814117.

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Archaea swim using the archaellum (archaeal flagellum), a reversible rotary motor consisting of a torque-generating motor and a helical filament, which acts as a propeller. Unlike the bacterial flagellar motor (BFM), ATP (adenosine-5′-triphosphate) hydrolysis probably drives both motor rotation and filamentous assembly in the archaellum. However, direct evidence is still lacking due to the lack of a versatile model system. Here, we present a membrane-permeabilized ghost system that enables the manipulation of intracellular contents, analogous to the triton model in eukaryotic flagella and gliding Mycoplasma. We observed high nucleotide selectivity for ATP driving motor rotation, negative cooperativity in ATP hydrolysis, and the energetic requirement for at least 12 ATP molecules to be hydrolyzed per revolution of the motor. The response regulator CheY increased motor switching from counterclockwise (CCW) to clockwise (CW) rotation. Finally, we constructed the torque–speed curve at various [ATP]s and discuss rotary models in which the archaellum has characteristics of both the BFM and F1-ATPase. Because archaea share similar cell division and chemotaxis machinery with other domains of life, our ghost model will be an important tool for the exploration of the universality, diversity, and evolution of biomolecular machinery.

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Borg, Yanika, Aurelija Marija Grigonyte, Philipp Boeing, Bethan Wolfenden, Patrick Smith, William Beaufoy, Simon Rose, Tonderai Ratisai, Alexey Zaikin, and Darren N. Nesbeth. "Open source approaches to establishingRoseobacterclade bacteria as synthetic biology chassis for biogeoengineering." PeerJ 4 (July 7, 2016): e2031. http://dx.doi.org/10.7717/peerj.2031.

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Aim.The nascent field of bio-geoengineering stands to benefit from synthetic biologists’ efforts to standardise, and in so doing democratise, biomolecular research methods.Roseobacterclade bacteria comprise 15–20% of oceanic bacterio-plankton communities, making them a prime candidate for establishment of synthetic biology chassis for bio-geoengineering activities such as bioremediation of oceanic waste plastic. Developments such as the increasing affordability of DNA synthesis and laboratory automation continue to foster the establishment of a global ‘do-it-yourself’ research community alongside the more traditional arenas of academe and industry. As a collaborative group of citizen, student and professional scientists we sought to test the following hypotheses: (i) that an incubator capable of cultivating bacterial cells can be constructed entirely from non-laboratory items, (ii) that marine bacteria from theRoseobacterclade can be established as a genetically tractable synthetic biology chassis using plasmids conforming to the BioBrickTMstandard and finally, (iii) that identifying and subcloning genes from aRoseobacterclade species can readily by achieved by citizen scientists using open source cloning and bioinformatic tools.Method.We cultivated threeRoseobacterspecies,Roseobacter denitrificans,Oceanobulbus indolifexandDinoroseobacter shibae. For each species we measured chloramphenicol sensitivity, viability over 11 weeks of glycerol-based cryopreservation and tested the effectiveness of a series of electroporation and heat shock protocols for transformation using a variety of plasmid types. We also attempted construction of an incubator-shaker device using only publicly available components. Finally, a subgroup comprising citizen scientists designed and attempted a procedure for isolating the cold resistanceanf1gene fromOceanobulbus indolifexcells and subcloning it into a BioBrickTMformatted plasmid.Results.All species were stable over 11 weeks of glycerol cryopreservation, sensitive to 17 µg/mL chloramphenicol and resistant to transformation using the conditions and plasmids tested. An incubator-shaker device, ‘UCLHack-12’ was assembled and used to cultivate sufficient quantity ofOceanobulbus indolifexcells to enable isolation of theanf1gene and its subcloning into a plasmid to generate the BioBrickTMBBa_K729016.Conclusion.The process of ‘de-skilling’ biomolecular techniques, particularly for relatively under-investigated organisms, is still on-going. However, our successful cell growth and DNA manipulation experiments serve to indicate the types of capabilities that are now available to citizen scientists. Science democratised in this way can make a positive contribution to the debate around the use of bio-geoengineering to address oceanic pollution or climate change.

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Xian, Yuejiao, Chitra B. Karki, Sebastian Miki Silva, Lin Li, and Chuan Xiao. "The Roles of Electrostatic Interactions in Capsid Assembly Mechanisms of Giant Viruses." International Journal of Molecular Sciences 20, no. 8 (April 16, 2019): 1876. http://dx.doi.org/10.3390/ijms20081876.

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In the last three decades, many giant DNA viruses have been discovered. Giant viruses present a unique and essential research frontier for studies of self-assembly and regulation of supramolecular assemblies. The question on how these giant DNA viruses assemble thousands of proteins so accurately to form their protein shells, the capsids, remains largely unanswered. Revealing the mechanisms of giant virus assembly will help to discover the mysteries of many self-assembly biology problems. Paramecium bursaria Chlorella virus-1 (PBCV-1) is one of the most intensively studied giant viruses. Here, we implemented a multi-scale approach to investigate the interactions among PBCV-1 capsid building units called capsomers. Three binding modes with different strengths are found between capsomers around the relatively flat area of the virion surface at the icosahedral 2-fold axis. Furthermore, a capsomer structure manipulation package is developed to simulate the capsid assembly process. Using these tools, binding forces among capsomers were investigated and binding funnels were observed that were consistent with the final assembled capsid. In addition, total binding free energies of each binding mode were calculated. The results helped to explain previous experimental observations. Results and tools generated in this work established an initial computational approach to answer current unresolved questions regarding giant virus assembly mechanisms. Results will pave the way for studying more complicated process in other biomolecular structures.

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Uvebrant, Kristina, Dorthe Da Graça Thrige, Anna Rosén, Mats Åkesson, Helena Berg, Björn Walse, and Per Björk. "Discovery of Selective Small-Molecule CD80 Inhibitors." Journal of Biomolecular Screening 12, no. 4 (March 22, 2007): 464–72. http://dx.doi.org/10.1177/1087057107300464.

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Protein-protein interactions are widely found in biological systems controlling diverse cellular events. Because these interactions are implicated in many diseases such as autoimmunity and cancer, regulation of protein-protein interactions provides ideal targets for drug intervention. The CD80-CD28 costimulatory pathway plays a critical role in regulation of the immune response and thus constitutes an attractive target for therapeutic manipulation of autoimmune diseases. The objective of this study is to identify small compounds disrupting these pivotal protein-protein interactions. Compounds that specifically blocked binding of CD80 to CD28 were identified using a strategy involving a cell-based scintillation proximity assay as the initial step. Secondary screening (e.g., by analyzing the direct binding of these compounds to the target immobilized on a biosensor surface) revealed that these compounds are highly selective CD80 binders. Screening of structurally related derivatives led to the identification of the chemical features required for inhibition of the CD80-CD28 interaction. In addition, the optimization process led to a 10-fold increase in binding affinity of the CD80 inhibitors. Using this approach, the authors identify low-molecular-weight compounds that specifically and with high potency inhibit the interaction between CD80 and CD28. These compounds serve as promising starting points for further development of CD80 inhibitors as potential immunomodulatory drugs. ( Journal of Biomolecular Screening 2007:464-472)

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Strick, Terence, Jean-François Allemand, Vincent Croquette, and David Bensimon. "The Manipulation of Single Biomolecules." Physics Today 54, no. 10 (October 2001): 46–51. http://dx.doi.org/10.1063/1.1420553.

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Allemand, Jean-François, Gilles Charvin, Vincent Croquette, Giuseppe Lia, and David Bensimon. "The manipulation of single biomolecules." Interdisciplinary Science Reviews 32, no. 2 (June 2007): 149–61. http://dx.doi.org/10.1179/030801807x163625.

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Miralles, I., C. Capel Ferrón, V. Hernández, J. T. López-Navarrete, and S. E. Jorge-Villar. "Lichen biomarkers upon heating: a Raman spectroscopic study with implications for extra-terrestrial exploration." International Journal of Astrobiology 16, no. 1 (February 17, 2016): 74–81. http://dx.doi.org/10.1017/s147355041500052x.

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AbstractLithopanspermia Theory has suggested that life was transferred among planets by meteorites and other rocky bodies. If the planet had an atmosphere, this transfer of life had to survive drastic temperature changes in a very short time in its entry or exit. Only organisms able to endure such a temperature range could colonize a planet from outer space. Many experiments are being carried out by NASA and European Space Agency to understand which organisms were able to survive and how. Among the suite of instruments designed for extraplanetary exploration, particularly for Mars surface exploration, a Raman spectrometer was selected with the main objective of looking for life signals. Among all attributes, Raman spectroscopy is able to identify organic and inorganic compounds, either pure or in admixture, without requiring sample manipulation. In this study, we used Raman spectroscopy to examine the lichen Squamarina lentigera biomarkers. We analyse spectral signature changes after sample heating under different experimental situations, such as (a) laser, (b) analysis accumulations over the same spot and (c) environmental temperature increase. Our goal is to evaluate the capability of Raman spectroscopy to identify unambiguously life markers even if heating has induced spectral changes, reflecting biomolecular transformations. Usnic acid, chlorophyll, carotene and calcium oxalates were identified by the Raman spectra. From our experiments, we have seen that usnic acid, carotene and calcium oxalates (the last two have been suggested to be good biomarkers) respond in a different way to environmental heating. Our main conclusion is that despite their abundance in nature or their inorganic composition the resistance to heat makes some molecules more suitable than others as biomarkers.

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Hwang, Hyundoo, and Je-Kyun Park. "Optoelectrofluidic Manipulation of Nanoparticles and Biomolecules." Advances in OptoElectronics 2011 (November 15, 2011): 1–13. http://dx.doi.org/10.1155/2011/482483.

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This paper presents optoelectrofluidic technologies for manipulation of nanoparticles and biomolecules. Optoelectrofluidics provides an elegant scheme for the programmable manipulation of particles or fluids in microenvironments based on optically induced electrokinetics. Recent progress on the optoelectrofluidic manipulation of nanoobjects, which include nanospheres, nanowires, nanotubes, and biomolecules, is introduced. Some potential applications of the optoelectrofluidic nanoparticle manipulation, such as nanoparticles separation, nanostructures manufacturing, molecular physics, and clinical diagnostics, and their future directions are also discussed.

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Enea, Ramona, Ana-Maria Resmeriţă, Laura Petraru, Cristian Grigoraş, Dan Scutaru, Cristofor Simionescu, and Nicolae Hurduc. "Synthesis and photochromic behavior of some azo-polysiloxanes modified with nucleobases or donor-acceptor groups." Open Chemistry 5, no. 4 (December 1, 2007): 981–95. http://dx.doi.org/10.2478/s11532-007-0042-8.

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AbstractThis paper presents the syntheses, characterization and photochromic behavior of some new azo-polysiloxanes modified with uracil, cytosine or nitro-phenolic groups. Taking into consideration the possibility of generating H-bonds or donor/acceptor interactions, this class of materials present a potential applicability in the immobilization of biomolecules and their nano-manipulations. Also, such compounds are capable of producing a fluid phase, with directional flowing capacity. For all these polymers, the molecular modeling simulations have shown disordered structures, which would generate amorphous phases, a very important aspect for molecules’ nano-manipulation. The photochromic behavior in the presence of UV irradiation was also evaluated.

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Ronchi, Giulia, Michele Cillino, Giovanna Gambarotta, Benedetta Elena Fornasari, Stefania Raimondo, Pierfrancesco Pugliese, Pierluigi Tos, Adriana Cordova, Francesco Moschella, and Stefano Geuna. "Irreversible changes occurring in long-term denervated Schwann cells affect delayed nerve repair." Journal of Neurosurgery 127, no. 4 (October 2017): 843–56. http://dx.doi.org/10.3171/2016.9.jns16140.

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OBJECTIVEMultiple factors may affect functional recovery after peripheral nerve injury, among them the lesion site and the interval between the injury and the surgical repair. When the nerve segment distal to the lesion site undergoes chronic degeneration, the ensuing regeneration (when allowed) is often poor. The aims of the current study were as follows: 1) to examine the expression changes of the neuregulin 1/ErbB system during long-term nerve degeneration; and 2) to investigate whether a chronically denervated distal nerve stump can sustain nerve regeneration of freshly axotomized axons.METHODSThis study used a rat surgical model of delayed nerve repair consisting of a cross suture between the chronically degenerated median nerve distal stump and the freshly axotomized ulnar proximal stump. Before the suture, a segment of long-term degenerated median nerve stump was harvested for analysis. Functional, morphological, morphometric, and biomolecular analyses were performed.RESULTSThe results showed that neuregulin 1 is highly downregulated after chronic degeneration, as well as some Schwann cell markers, demonstrating that these cells undergo atrophy, which was also confirmed by ultrastructural analysis. After delayed nerve repair, it was observed that chronic degeneration of the distal nerve stump compromises nerve regeneration in terms of functional recovery, as well as the number and size of regenerated myelinated fibers. Moreover, neuregulin 1 is still downregulated after delayed regeneration.CONCLUSIONSThe poor outcome after delayed nerve regeneration might be explained by Schwann cell impairment and the consequent ineffective support for nerve regeneration. Understanding the molecular and biological changes occurring both in the chronically degenerating nerve and in the delayed nerve repair may be useful to the development of new strategies to promote nerve regeneration. The results suggest that neuregulin 1 has an important role in Schwann cell activity after denervation, indicating that its manipulation might be a good strategy for improving outcome after delayed nerve repair.

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HONG, Seok-Cheol, and Hyeon-Min MOON. "Mechanical Manipulation of a Single Biomolecule." Physics and High Technology 22, no. 11 (November 30, 2013): 16. http://dx.doi.org/10.3938/phit.22.050.

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Rostaing, Hervé, Hichem Chetouani, Marin Gheorghe, and Paul Galvin. "A micromagnetic actuator for biomolecule manipulation." Sensors and Actuators A: Physical 135, no. 2 (April 2007): 776–81. http://dx.doi.org/10.1016/j.sna.2006.08.012.

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Funatsu, Takashi, Yoshie Harada, Hideo Higuchi, Makio Tokunaga, Kiwamu Saito, Yoshiharu Ishii, Ronald D. Vale, and Toshio Yanagida. "Imaging and nano-manipulation of single biomolecules." Biophysical Chemistry 68, no. 1-3 (October 1997): 63–72. http://dx.doi.org/10.1016/s0301-4622(97)00008-2.

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Mahdjour Firouzi, M. A., H. Nejat Pishkenari, S. H. Mahboobi, and A. Meghdari. "Manipulation of biomolecules: A molecular dynamics study." Current Applied Physics 14, no. 9 (September 2014): 1216–27. http://dx.doi.org/10.1016/j.cap.2014.06.014.

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Yu, Yue, and Eijiro Miyako. "Manipulation of Biomolecule-Modified Liquid-Metal Blobs." Angewandte Chemie International Edition 56, no. 44 (October 2, 2017): 13606–11. http://dx.doi.org/10.1002/anie.201705996.

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Yu, Yue, and Eijiro Miyako. "Manipulation of Biomolecule-Modified Liquid-Metal Blobs." Angewandte Chemie 129, no. 44 (October 2, 2017): 13794–99. http://dx.doi.org/10.1002/ange.201705996.

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Luo, Tao, Lei Fan, Rong Zhu, and Dong Sun. "Microfluidic Single-Cell Manipulation and Analysis: Methods and Applications." Micromachines 10, no. 2 (February 1, 2019): 104. http://dx.doi.org/10.3390/mi10020104.

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In a forest of a hundred thousand trees, no two leaves are alike. Similarly, no two cells in a genetically identical group are the same. This heterogeneity at the single-cell level has been recognized to be vital for the correct interpretation of diagnostic and therapeutic results of diseases, but has been masked for a long time by studying average responses from a population. To comprehensively understand cell heterogeneity, diverse manipulation and comprehensive analysis of cells at the single-cell level are demanded. However, using traditional biological tools, such as petri-dishes and well-plates, is technically challengeable for manipulating and analyzing single-cells with small size and low concentration of target biomolecules. With the development of microfluidics, which is a technology of manipulating and controlling fluids in the range of micro- to pico-liters in networks of channels with dimensions from tens to hundreds of microns, single-cell study has been blooming for almost two decades. Comparing to conventional petri-dish or well-plate experiments, microfluidic single-cell analysis offers advantages of higher throughput, smaller sample volume, automatic sample processing, and lower contamination risk, etc., which made microfluidics an ideal technology for conducting statically meaningful single-cell research. In this review, we will summarize the advances of microfluidics for single-cell manipulation and analysis from the aspects of methods and applications. First, various methods, such as hydrodynamic and electrical approaches, for microfluidic single-cell manipulation will be summarized. Second, single-cell analysis ranging from cellular to genetic level by using microfluidic technology is summarized. Last, we will also discuss the advantages and disadvantages of various microfluidic methods for single-cell manipulation, and then outlook the trend of microfluidic single-cell analysis.

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Hook, Andrew L., Helmut Thissen, and Nicolas H. Voelcker. "Surface manipulation of biomolecules for cell microarray applications." Trends in Biotechnology 24, no. 10 (October 2006): 471–77. http://dx.doi.org/10.1016/j.tibtech.2006.08.001.

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Smith, Alastair. "Mechanical manipulation of biomolecules: pulling back the frontiers!" Physics Education 37, no. 1 (January 2002): 34–36. http://dx.doi.org/10.1088/0031-9120/37/1/304.

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Brzeska, M., M. Panhorst, P. B. Kamp, J. Schotter, G. Reiss, A. Pühler, A. Becker, and H. Brückl. "Detection and manipulation of biomolecules by magnetic carriers." Journal of Biotechnology 112, no. 1-2 (August 2004): 25–33. http://dx.doi.org/10.1016/j.jbiotec.2004.04.018.

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Dinu, Cerasela Zoica, Tania Chakrabarty, Elaine Lunsford, Christopher Mauer, Joseph Plewa, Jonathan S. Dordick, and Douglas B. Chrisey. "Optical manipulation of microtubules for directed biomolecule assembly." Soft Matter 5, no. 20 (2009): 3818. http://dx.doi.org/10.1039/b904639a.

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Sitters, Gerrit, Niels Laurens, Emile de Rijk, Holger Kress, Erwin J. G. Peterman, and Gijs J. L. Wuite. "Optical Pushing: A Tool for Parallelized Biomolecule Manipulation." Biophysical Journal 110, no. 1 (January 2016): 44–50. http://dx.doi.org/10.1016/j.bpj.2015.11.028.

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Sitters, G., N. Laurens, E. de Rijk, H. Kress, E. J. G. Peterman, and G. J. L. Wuite. "Optical Pushing: A Tool for Parallelized Biomolecule Manipulation." Biophysical Journal 111, no. 2 (July 2016): 463. http://dx.doi.org/10.1016/j.bpj.2016.07.007.

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Oh, Kwang W. "Microfluidic Devices for Biomedical Applications: Biomedical Microfluidic Devices 2019." Micromachines 11, no. 4 (April 1, 2020): 370. http://dx.doi.org/10.3390/mi11040370.

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Wallace, G. G., and L. A. P. Kane-Maguire. "Manipulating and Monitoring Biomolecular Interactions with Conducting Electroactive Polymers." Advanced Materials 14, no. 13-14 (July 5, 2002): 953–60. http://dx.doi.org/10.1002/1521-4095(20020705)14:13/14<953::aid-adma953>3.0.co;2-t.

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Wallace, G. G., and L. A. P. Kane-Maguire. "Manipulating and Monitoring Biomolecular Interactions with Conducting Electroactive Polymers." Advanced Materials 14, no. 13-14 (July 4, 2002): 953–60. http://dx.doi.org/10.1002/1521-4095(20020704)14:13/14<953::aid-adma953>3.0.co;2-w.

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Oh, Myungkeun, Vidura Jayasooriya, Sung Oh Woo, Dharmakeerthi Nawarathna, and Yongki Choi. "Selective Manipulation of Biomolecules with Insulator-Based Dielectrophoretic Tweezers." ACS Applied Nano Materials 3, no. 1 (January 3, 2020): 797–805. http://dx.doi.org/10.1021/acsanm.9b02302.

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Li, Na, Zijuan Liao, Shupeng He, Xiao Chen, Shenhao Huang, Yanwei Wang, and Guangcan Yang. "Demonstration of pH-controlled DNA–surfactant manipulation for biomolecules." RSC Advances 11, no. 25 (2021): 15099–105. http://dx.doi.org/10.1039/d1ra01420j.

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Fahad, Ruan, and Chen. "A Wideband Terahertz Transmissive Polarization Manipulator Based on Metasurfaces." Electronics 8, no. 10 (September 20, 2019): 1068. http://dx.doi.org/10.3390/electronics8101068.

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Wideband and multifunction operation for THz polarization manipulating devices has been desired for a wide range of applications. In this paper, a novel wideband transmissive type polarization manipulator based on metasurfaces is proposed in the THz region. The designed metasurface acts as a multifunctional polarization manipulator, performing linear to circular polarization conversion (LCPC) for relative bandwidth 43.9% (0.94 THz to 1.47 THz) for incident x/y polarizations and a wideband bandpass filter with relative bandwidth 67% (0.713 THz to 1.4346 THz) for incident slant (xy) polarizations. Wideband LCPC operation is achieved using a unique diagonal symmetric structure based on a bilayered metasurface. In order to confirm the validation of proposed results, electromagnetic simulation was carried out in two industry-standard software packages, HFSS and CST, using frequency domain and time domain solvers, respectively. Close agreement between numerical results depicts the validity and reliability of the proposed design. Polarized wave trajectory, equivalent microscopic circuit, physical mechanisms, and impact of different geometrical parameters on the performance is investigated. To the best of our knowledge, this is the first polarization manipulator based on bilayered metasurfaces. The same structure can be used as for LCPC and the transmit reject filter for THz wireless communication, including THz satellite communications, the future of communication. Moreover, they can be used in THz imaging and biomolecular control devices.

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Kim, Yun-Soung, Brian M. Dincau, Young-Tae Kwon, Jong-Hoon Kim, and Woon-Hong Yeo. "Directly Accessible and Transferrable Nanofluidic Systems for Biomolecule Manipulation." ACS Sensors 4, no. 5 (May 7, 2019): 1417–23. http://dx.doi.org/10.1021/acssensors.9b00470.

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