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Topic Review
G-quadruplexes and ligands: Biophysical methods
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized in structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and x-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In the last years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most used approaches to characterize the G4/ligand interactions, as well as the applications and type of information that can be obtained from the use of each technique.
  • 904
  • 03 Dec 2021
Topic Review
Surfactant and the Glycocalyx
Gas exchange in the lung takes place via the air-blood barrier in the septal walls of alveoli. The tissue elements that oxygen molecules have to cross are the alveolar epithelium, the interstitium and the capillary endothelium. The epithelium that lines the alveolar surface is covered by a thin and continuous liquid lining layer. Pulmonary surfactant acts at this air-liquid interface. By virtue of its biophysical and immunomodulatory functions, surfactant keeps alveoli open, dry and clean. What needs to be added to this picture is the glycocalyx of the alveolar epithelium. Here, we briefly review what is known about this glycocalyx and how it can be visualized using electron microscopy. The application of colloidal thorium dioxide as a staining agent reveals differences in the staining pattern between type I and type II alveolar epithelial cells and shows close associations of the glycocalyx with intraalveolar surfactant subtypes such as tubular myelin. These morphological findings indicate that specific spatial interactions between components of the surfactant system and those of the alveolar epithelial glycocalyx exist which may contribute to the maintenance of alveolar homeostasis, in particular to alveolar micromechanics, to the functional integrity of the air-blood barrier, to the regulation of the thickness and viscosity of the alveolar lining layer, and to the defence against inhaled pathogens. Exploring the alveolar epithelial glycocalyx in conjunction with the surfactant system opens novel physiological perspectives of potential clinical relevance for future research.
  • 904
  • 03 May 2021
Topic Review
Local Chicken Breeds and Varieties
Conservation of local breeds possessing genetic variations specific to the particular environment is essential for sustainable development. Although they exist as numerically small populations, local breeds are not only highly adapted to the natural environment, but are also an integral part of the lifestyle of the rural people. People, livestock and environment form a delicately balanced but sustainable ecosystem, and thus the potential impact of any intervention to improve production in the traditional system should be predetermined. The situation is less sensitive in periurban, industrial and small-scale intensive poultry production, in which rapid improvements can be achieved through well-designed development programmes. The intensive poultry production sector, however, is generally much smaller than the family poultry sector in virtually all developing countries. The present review evaluates twenty years (2001 to 2021) of the study of growth and performance in local chicken breeds worldwide. The assessment of methodological approaches and their constraints when intending to fit for data derived from often endangered autochthonous populations was performed. The evaluation of conditioning factors on the impact that publications reporting on research progresses in the field have on the scientific community and how such advances are valued suggests the need to seek new methodological alternatives or statistical strategies. Such strategies must meet the requirements of local populations which are characterized by reduced censuses, a lack of data structure, highly skewed sex ratios, and a large interbreed and variety variability. The sustainable conservation of these populations cannot be approached if scientific knowledge on their productive behaviour is not reinforced in a manner that allows distinctive products to be put on the market and be competitive. 
  • 903
  • 17 Sep 2021
Topic Review
Agrobacterium T−DNA Integration
Agrobacterium species transfer DNA (T−DNA) to plant cells where it may integrate into plant chromosomes. The process of integration is thought to involve invasion and ligation of T-DNA, or its copying, into nicks or breaks in the host genome. Integrated T−DNA often contains, at its junctions with plant DNA, deletions of T−DNA or plant DNA, filler DNA, and/or microhomology between T-DNA and plant DNA pre-integration sites. T−DNA integration is also often associated with major plant genome rearrangements, including inversions and translocations. These characteristics are similar to those often found after repair of DNA breaks, and thus DNA repair mechanisms have frequently been invoked to explain the mechanism of T−DNA integration. However, the involvement of specific plant DNA repair proteins and Agrobacterium proteins in integration remains controversial, with numerous contradictory results reported in the literature.
  • 903
  • 31 Aug 2021
Topic Review
Asian Carp, an Alternative Material for Surimi Production
Asian carp is a general designation for grass carp, silver carp, bighead carp, and black carp. These fish species belong to the family Cyprinidae. In 2018, more than 18.5 million tons of Asian carp were produced globally. Asian carp can be used for producing surimi, a stabilized myofibrillar protein concentrate that can be made into a wide variety of products such as imitation crab sticks, fish balls, fish cakes, fish tofu, and fish sausage. Surimi is usually made from marine fish, but Asian carp have been widely used for surimi production in China. The quality of surimi is affected by various factors, including the processing methods and food additives, such as polysaccharides, protein, salt, and cryoprotectant. With an impending shortage of marine fish due to overfishing and depletion of fish stocks, Asian carp have a potential to serve as an alternative raw material for surimi products thanks to their high abundancy, less emissions of greenhouse gases from farming, desirable flesh color, and sufficient gel forming ability.
  • 903
  • 06 Jun 2022
Topic Review
Porphyrins/Chlorins for Viruses Inactivation
The problem of treating viral infections is extremely important both in connection with the emergence of new viral diseases and in connection with the low efficiency of existing approaches to the treatment of known viral infections. This entry is devoted to the use of porphyrins, chlorins, and phthalocyanines for the fight against viral infections using chemical and photochemical inactivation methods. The purpose of this work is to summarize the main approaches developed to date to chemical and photodynamic inactivation of human and animal viruses using porphyrins and their analogs, as well as to analyze and discuss information on viral targets and antiviral activity of porphyrins, chlorins and their derivatives obtained in the last 10-15 years, in order to identify the most promising areas.
  • 903
  • 23 Jun 2021
Topic Review
Seaweeds
Seaweeds have a long history of use as food, as flavouring agents, and also used in traditional folk medicine. Seaweed products range from food, feed, and dietary supplements to pharmaceuticals, and from bioenergy intermediates to materials. At present, 98% of the seaweed required by the seaweed industry is provided by five genera and only ten species. The two brown kelp seaweeds Laminaria digitata, a native Irish species, and Macrocystis pyrifera, a native New Zealand species, are not included in these eleven species, although they have been used as dietary supplements and as animal and fish feed. The properties associated with the polysaccharides and proteins from these two species have resulted in increased interest in them, enabling their use as functional foods. Improvements and optimisations in aquaculture methods and bioproduct extractions are essential to realise the commercial potential of these seaweeds.
  • 903
  • 16 Jan 2022
Topic Review
Allotetraploid Cotton
Allotetraploid cotton (Gossypium hirsutum and Gossypium barbadense) are cultivated worldwide for its white fiber. Since centuries, conventional breeding approaches increase cotton yield at the cost of extensive erosion of natural genetic variability. Sea Island cotton (G. barbadense) is known for its superior fiber quality, but show poor adaptability as compared to Upland cotton. Hence, there is a dire need to improve the current germplasm resources of Sea Island cotton to develop diverse breeding lines with improved adaptability and excellent agronomic and economic traits. Ethyl methanesulfonate (EMS) is an excellent mutagenic agent that induces genome-wide point mutations to activate the mutagenic potential of plants. In current study, we determined the optimal EMS experimental procedure suitable for construction of cotton mutant library. At M6 generation, mutant library comprised of lines with distinguished phenotypes of the plant architecture, leaf, flower, boll and fiber. Genome wide analysis of SNP distribution and density in yellow leaf mutants reflected the better quality of mutant library. Our mutant collection will serve as the valuable resource for basic research on cotton functional genomics, as well as cotton breeding.
  • 903
  • 09 Nov 2020
Biography
Alex Halderman
J. Alex Halderman (born c. January 1981) is professor of Computer Science and Engineering at the University of Michigan, where he is also director of the Center for Computer Security & Society. Halderman's research focuses on computer security and privacy, with an emphasis on problems that broadly impact society and public policy. Halderman was awarded the A.B. summa cum laude in June 2003, t
  • 903
  • 01 Dec 2022
Topic Review
Enterococci in Dairy Products
Enterococci are part of the subdominant microbiota of many artisanal cheeses. As a genus that has evolved for resistance against adverse environmental factors and that readily exchanges genetic elements, enterococci are well adapted to the cheese environment and may reach high numbers in artisanal cheeses. Their metabolites impact cheese flavor, texture, and rheological properties, thus contributing to the development of its typical sensorial properties. Due to their antimicrobial activity, enterococci modulate the cheese microbiota, stimulate autolysis of other lactic acid bacteria (LAB), control pathogens and deterioration microorganisms, and may offer beneficial effects to the health of their hosts. They could in principle be employed as adjunct/protective/probiotic cultures; however, due to their propensity to acquire genetic determinants of virulence and antibiotic resistance, together with the opportunistic character of some of its members, this genus does not possess Qualified Presumption of Safety (QPS) status. It is, however, noteworthy that some putative virulence factors described in foodborne enterococci may simply reflect adaptation to the food environment and to the human host as commensal. Further research is needed to help distinguish friend from foe among enterococci, eventually enabling exploitation of the beneficial aspects of specific cheese-associated strains. 
  • 903
  • 15 Mar 2022
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