The Biopolymer Markup Language.

SUMMARY: An XML derived from a data model designed to be a hierarchical representation of an organism has been specified and a browser to use this language has been developed. AVAILABILITY: The language definition is available in HTML form at http://www.proteometrics.com/BIOML/. The BioML browser is available on request from the author.     

Mechanics,Structure and Function of Biopolymer Condensates

The spontaneous nature of biopolymer phase separation in cells entails that the resulting condensates can be thermodynamic machines, which, in the process of condensing, can take on distinct forms themselves and deform neighboring cellular structures. We introduce here general notions of material and mechanical properties of protein condensates with an emphasis on how molecular arrangements and intermolecular interaction within condensates determine their ability to do work on their surroundings. We further propose functional implications of these concepts to cellular and subcellular morphology and biogenesis.     

一种新型生物聚合物Ss的流变学性质及成胶特性

本文对一种新型生物聚合物Ss的流变学性质及成胶特性进行了研究。该聚合物的流变学性质与黄原胶类似, 具有高粘性、假塑性及耐盐性。0.6％以上的Ss溶液加热(≥75℃)并冷却至室温可形成凝胶, 加入金属离子可以改变其成胶所需的最低聚合物浓度及所成凝胶的性质。利用质构分析(TPA)方法, 研究了不同聚合物浓度和钙离子浓度下凝胶的质构性质。钙离子的加入能促进凝胶的形成, 凝胶的硬度、弹性、内聚性随聚合物浓度及钙离子浓度的增加而增大, 但大于最适钙离子浓度时, 硬度、弹性及内聚性均有所下降。     

Preparation of Biopolymer Aerogels Using Green Solvents

Although the first reports on aerogels made by Kistler¹ in the 1930s dealt with aerogels from both inorganic oxides (silica and others) and biopolymers (gelatin, agar, cellulose), only recently have biomasses been recognized as an abundant source of chemically diverse macromolecules for functional aerogel materials. Biopolymer aerogels (pectin, alginate, chitosan, cellulose, etc.) exhibit both specific inheritable functions of starting biopolymers and distinctive features of aerogels (80-99% porosity and specific surface up to 800 m²/g). This synergy of properties makes biopolymer aerogels promising candidates for a wide gamut of applications such as thermal insulation, tissue engineering and regenerative medicine, drug delivery systems, functional foods, catalysts, adsorbents and sensors. This work demonstrates the use of pressurized carbon dioxide (5 MPa) for the ionic cross linking of amidated pectin into hydrogels. Initially a biopolymer/salt dispersion is prepared in water. Under pressurized CO₂ conditions, the pH of the biopolymer solution is lowered to 3 which releases the crosslinking cations from the salt to bind with the biopolymer yielding hydrogels. Solvent exchange to ethanol and further supercritical CO₂ drying (10 - 12 MPa) yield aerogels. Obtained aerogels are ultra-porous with low density (as low as 0.02 g/cm³), high specific surface area (350 - 500 m²/g) and pore volume (3 - 7 cm³/g for pore sizes less than 150 nm).     

一种新型生物聚合物Ss的流变学性质及成胶特性

本文对一种新型生物聚合物ss的流变学性质及成胶特性进行了研究.该聚合物的流变学 性质与黄原胶类似,具有高粘性、假塑性及耐盐性.0.6%以上的Ss溶液加热(≥75℃)并冷却至室温可形成凝胶,加入金属离子可以改变其成胶所需的最低聚合物浓度及所成凝胶的性质.利用质构分析(TPA)方法,研究了不同聚合物浓度和钙离子浓度下凝胶的质构性质.钙离子的加入能促进凝胶的形成,凝胶的硬度、弹性、内聚性随聚合物浓度及钙离子浓度的增加而增大,但大于最适钙离子浓度时,硬度、弹性及内聚性均有所下降.     

Biopolymer flocculant produced by an Pseudomonas sp.

A biopolymer flocculant produced by Pseudomonas sp. A-99 had flocculating activity both in inorganic suspensions containing Ca2, Mg2 or Fe3 and in organic suspensions containing Fe2, Fe3 or Al3. The flocculant was an acidic protein and contained a small amount of an acidic polysaccharide consisting of galacturonic acid, glucose and galactose. Productivity of the flocculant was about 450 mg/l medium. © Rapid Science Ltd. 1998     

Biopolymer and water dynamics in microbial biofilm extracellular polymeric substance

Nuclear magnetic resonance (NMR) is a noninvasive and nondestructive tool able to access several observable quantities in biofilms such as chemical composition, diffusion, and macroscale structure and transport. Pulsed gradient spin echo (PGSE) NMR techniques were used to measure spectrally resolved biomacromolecular diffusion in biofilm biomass, extending previous research on spectrally resolved diffusion in biofilms. The dominant free water signal was nulled using an inversion recovery modification of the traditional PGSE technique in which the signal from free water is minimized in order to view the spectra of components such as the rotationally mobile carbohydrates, DNA, and proteins. Diffusion data for the major constituents obtained from each of these spectral peaks demonstrate that the biomass of the biofilm contains both a fast and slow diffusion component. The dependence of diffusion on antimicrobial and environmental challenges suggests the polymer molecular dynamics measured by NMR are a sensitive indicator of biofilm function.     

Biopolymer nanoparticle production for controlled release of biopharmaceuticals

Abstract

For drug applications, nanoparticles, used as drug carriers, offer the advantage of controlled release, therapeutic impact and targeted delivery. In drug delivery applications, biodegradable polymers can be extracted from natural sources or prepared synthetically by polymerization. Natural polymers typically have varying compositions and physiochemical properties. As a result, methods which utilize natural polymers to encapsulate drugs are more varied and polymer dependent. The following polymers are discussed in this review article: alginate, chitosan, gelatin, albumin, gliadin, pullulan, and dextran. Specialized encapsulation nanotechnologies will be discussed such as ionotropic gelation, complexation, the reverse microemulsion technique, cross-linking methods, emulsion-dependent methods, desolvation methods and self-assembly methods. For each biopolymer an overview of the structure is presented with the corresponding encapsulation techniques. Understanding the structure of the biopolymer is important as to not only understand the rational for current encapsulation techniques but to continue to develop new encapsulation techniques in pursuit of the ideal drug carrier for application in therapeutic treatments.     

Cyclic‐di‐GMP and cyclic‐di‐AMP activate the NLRP3 inflammasome

The cyclic dinucleotides 3'‐5'diadenylate (c‐diAMP) and 3'‐5' diguanylate (c‐diGMP) are important bacterial second messengers that have recently been shown to stimulate the secretion of type I Interferons (IFN‐Is) through the c‐diGMP‐binding protein MPYS/STING. Here, we show that physiologically relevant levels of cyclic dinucleotides also stimulate a robust secretion of IL‐1β through the NLRP3 inflammasome. Intriguingly, this response is independent of MPYS/STING. Consistent with most NLRP3 inflammasome activators, the response to c‐diGMP is dependent on the mobilization of potassium and calcium ions. However, in contrast to other NLRP3 inflammasome activators, this response is not associated with significant changes in mitochondrial potential or the generation of mitochondrial reactive oxygen species. Thus, cyclic dinucleotides activate the NLRP3 inflammasome through a unique pathway that could have evolved to detect pervasive bacterial pathogen‐associated molecular patterns associated with intracellular infections.     

Biopolymer flocculant produced by an Enterobacter sp.

A new biopolymer flocculant was produced by Enterobacter sp. BY-29. Flocculating activity increased in the presence of Al , Fe or Fe . The flocculant had flocculating activity not only in inorganic suspensions of kaolin and active carbon but also in organic suspensions of cellulose and yeast. The flocculant was an acidic polysaccharide consisting of glucose, galactose, xylose and galacturonic acid, and its MW was about 2.5 ¥ 10 6 Da.     

Regulation of the sperm‐to‐oocyte transition in Caenorhabditis briggsae hermaphrodites by the Cbr‐met‐2 and Cbr‐fem‐3 genes

In Caenorhabditis briggsae hermaphrodites, spermatogenesis begins in the L4 larval stage and persists into early adulthood. Oogenesis begins after spermatogenesis; the sperm‐to‐oocyte transition is irreversible. The timing of this transition is believed to have evolved in response to selection to maximize the intrinsic growth rate. Sperm‐to‐oocyte transitions occurred early in Cbr‐met‐2 and Cbr‐fem‐3 mutants. These early transitions resulted in reduced brood sizes, but had little or no impact on the intrinsic growth rate. In Cbr‐met‐2; Cbr‐fem‐3 doubly mutant hermaphrodites, the transition to oogenesis occurred even earlier and brood size was further reduced, indicating that Cbr‐met‐2 and Cbr‐fem‐3 regulate the sperm‐to‐oocyte transition through separate pathways. Mutations in Cbr‐met‐2 also resulted in an increase in the frequency of males in mutant populations. These increased male frequencies were not caused by increased rates of X nondisjunction during oogenesis in mutant hermaphrodites. Rather, increases in the rates of outcrossing in mutant populations likely were an indirect effect of reduced brood sizes derived from self‐fertilization. Based on these observations, it is possible that the timing of the sperm‐to‐oocyte transition in C. briggsae evolved in response to sexual selection on hermaphrodites to limit rates of outcrossing. Mutations in the orthologous Caenorhabditis elegans gene, Cel‐met‐2, did not impact the timing of the sperm‐to‐oocyte transition, consistent with the independent evolution of hermaphroditic reproduction in these species. Although brood sizes were reduced in Cel‐met‐2 mutant strains, increased male frequencies were not observed. Cbr‐ and Cel‐met‐2 mutations also differed in terms of germline mortality, observed in C. elegans, but not in C. briggsae.