Signaling pathways for transduction of the initial message of the glycocode into cellular responses

The sugar units of glycan structures store information and establish an alphabet of life. The language of the oligosaccharide coding units is deciphered by receptors such as lectins and the decoded message can be transduced by multiple signaling pathways. Similar to glycoconjugates, these receptors can exhibit pronounced changes in quantitative and qualitative aspects of expression, as attested by a wealth of lectin and immunohistochemical studies. Since histochemistry provides a static picture, it is essential to shed light on the mechanisms of how a recognitive protein-carbohydrate interplay can be transduced into cellular responses. Their consequences for example for cell morphology will then be visible to the histochemist. Therefore, basic signaling routes will be graphically outlined and their trigger potential will be explained by selected examples from the realm of glycosciences

Dendritic glycopolymers based on dendritic polyamine scaffolds: view on their synthetic approaches, characteristics and potential for biomedical applications

In this review we highlight the potential for biomedical applications of dendritic glycopolymers based on polyamine scaffolds. The complex interplay of the molecular characteristics of the dendritic architectures and their specific interactions with various (bio)molecules are elucidated with various examples. A special role of the individual sugar units attached to the dendritic scaffolds and their density is identified, which govern ionic and H-bond interactions, and biological targeting, but to a large extent are also responsible for the significantly reduced toxicity of the dendritic glycopolymers compared to their polyamine scaffolds. Thus, the application of dendritic glycopolymers in drug delivery systems for gene transfection but also as therapeutics in neurodegenerative diseases has great promisePublikacja w ramach programu Royal Society of Chemistry "Gold for Gold" 2014 finansowanego przez Uniwersytet Łódzk

Nucleoside and Nucleotide Nomenclature

Current nomenclature in the area of nucleosides, nucleotides, and nucleic acids comprises a mixture of (1) common names that have gained official recognition, (2) guidelines that have been derived and officially recommended by the International Union of Pure and Applied Chemistry (IUPAC)/International Union of Biochemistry and Molecular Biology (IUBMB), and (3) evolving usage that is derived by individual scientists and laboratories and subjected to peer review through publication. A working group was commissioned in 1998 by IUBMB to review guidelines for nucleotide (including oligonucleotide) nomenclature. As those guidelines are developed and made available, they will be referenced in future updates of this appendix. The main purpose of this appendix is to provide pertinent references that will direct the reader to the relevant guidelines or evolving nomenclature as described in the literature. When additional suggestions or guidance are appropriate, those comments are included as well.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143595/1/cpnca01d.pd

XTHs from Fragaria vesca: Genomic structure and transcriptomic analysis in ripening fruit and other tissues

Indexación: Scopus.Background: Fragaria vesca or 'woodland strawberry' has emerged as an attractive model for the study of ripening of non-climacteric fruit. It has several advantages, such as its small genome and its diploidy. The recent availability of the complete sequence of its genome opens the possibility for further analysis and its use as a reference species. Fruit softening is a physiological event and involves many biochemical changes that take place at the final stages of fruit development; among them, the remodeling of cell walls by the action of a set of enzymes. Xyloglucan endotransglycosylase/hydrolase (XTH) is a cell wall-associated enzyme, which is encoded by a multigene family. Its action modifies the structure of xyloglucans, a diverse group of polysaccharides that crosslink with cellulose microfibrills, affecting therefore the functional structure of the cell wall. The aim of this work is to identify the XTH-encoding genes present in F. vesca and to determine its transcription level in ripening fruit. Results: The search resulted in identification of 26 XTH-encoding genes named as FvXTHs. Genetic structure and phylogenetic analyses were performed allowing the classification of FvXTH genes into three phylogenetic groups: 17 in group I/II, 2 in group IIIA and 4 in group IIIB. Two sequences were included into the ancestral group. Through a comparative analysis, characteristic structural protein domains were found in FvXTH protein sequences. In complement, expression analyses of FvXTHs by qPCR were performed in fruit at different developmental and ripening stages, as well as, in other tissues. The results showed a diverse expression pattern of FvXTHs in several tissues, although most of them are highly expressed in roots. Their expression patterns are not related to their respective phylogenetic groups. In addition, most FvXTHs are expressed in ripe fruit, and interestingly, some of them (FvXTH 18 and 20, belonging to phylogenic group I/II, and FvXTH 25 and 26 to group IIIB) display an increasing expression pattern as the fruit ripens. Conclusion: A discrete group of FvXTHs (18, 20, 25 and 26) increases their expression during softening of F. vesca fruit, and could take part in cell wall remodeling required for softening in collaboration with other cell wall degrading enzymes.https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4255-

A Step Forward to the Characterization of Secondary Effuents to Predict Membrane Fouling in a Subsequent Ultrafiltration

[EN] Nowadays, wastewater reuse in Mediterranean countries is necessary to cover the water demand. This contributes to the protection of the environment and encourages the circular economy. Due to increasingly strict regulation, the secondary effluent of a wastewater treatment plant requires further (tertiary) treatment to reach enough quality for its reuse in agriculture. Ultrafiltration is a membrane technique suitable for tertiary treatment. However, the most important drawback of ultrafiltration is membrane fouling. The aim of this work is to predict membrane fouling and ultrafiltered wastewater permeate quality for a particular membrane, using the information given by an exhaustive secondary effluent characterization. For this, ultrafiltration of real and simulated wastewaters and of their components after fractionation has been performed. In order to better characterize the secondary effluent, resin fractionation and further membrane ultrafiltration of the generated fractions and wastewater were performed. The results indicated that hydrophobic substances were lower than hydrophilic ones in the secondary effluent. Supelite DAX-8, Amberlite XAD-4 and Amberlite IRA-958 resins were found not to be specific for humic acids, proteins and carbohydrates, which are the main components of the effluent organic matter. Two models have been performed using statistics (partial least squares, PLS) and an artificial neural network (ANN), respectively. The results showed that the ANN model predicted permeate quality and membrane fouling with higher accuracy than PLS.This study was funded by Generalitat Valenciana (Project AICO 18/319).Anderson-Alejandro Benites-Zelaya; Soler Cabezas, JL.; Ferrer-Polonio, E.; Mendoza Roca, JA.; Vincent Vela, MC. (2020). A Step Forward to the Characterization of Secondary Effuents to Predict Membrane Fouling in a Subsequent Ultrafiltration. Water. 12(7):1-17. https://doi.org/10.3390/w12071975S117127European Commission—Environmenthttps://ec.europa.eu/environment/water/reuse.htmRippey, S. R., & Watkins, W. D. (1992). Comparative Rates of Disinfection of Microbial Indicator Organisms in Chlorinated Sewage Effluents. Water Science and Technology, 26(9-11), 2185-2189. doi:10.2166/wst.1992.0693Mounaouer, B., & Abdennaceur, H. (2016). Modeling and kinetic characterization of wastewater disinfection using chlorine and UV irradiation. Environmental Science and Pollution Research, 23(19), 19861-19875. doi:10.1007/s11356-016-7173-4Hijnen, W. A. M., Beerendonk, E. F., & Medema, G. J. (2006). Inactivation credit of UV radiation for viruses, bacteria and protozoan (oo)cysts in water: A review. 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Water Supply, 3(4), 161-168. doi:10.2166/ws.2003.0058Illueca-Muñoz, J., Mendoza-Roca, J. A., Iborra-Clar, A., Bes-Piá, A., Fajardo-Montañana, V., Martínez-Francisco, F. J., & Bernácer-Bonora, I. (2008). Study of different alternatives of tertiary treatments for wastewater reclamation to optimize the water quality for irrigation reuse. Desalination, 222(1-3), 222-229. doi:10.1016/j.desal.2007.01.157Delgado, S., Dı́az, F., Vera, L., Dı́az, R., & Elmaleh, S. (2004). Modelling hollow-fibre ultrafiltration of biologically treated wastewater with and without gas sparging. Journal of Membrane Science, 228(1), 55-63. doi:10.1016/j.memsci.2003.09.011Filloux, E., Labanowski, J., & Croue, J. P. (2012). Understanding the fouling of UF/MF hollow fibres of biologically treated wastewaters using advanced EfOM characterization and statistical tools. Bioresource Technology, 118, 460-468. doi:10.1016/j.biortech.2012.05.081Shon, H. K., Vigneswaran, S., & Snyder, S. A. (2006). Effluent Organic Matter (EfOM) in Wastewater: Constituents, Effects, and Treatment. Critical Reviews in Environmental Science and Technology, 36(4), 327-374. doi:10.1080/10643380600580011Wang, Z.-P., & Zhang, T. (2010). Characterization of soluble microbial products (SMP) under stressful conditions. Water Research, 44(18), 5499-5509. doi:10.1016/j.watres.2010.06.067Ferrer-Polonio, E., White, K., Mendoza-Roca, J. A., & Bes-Piá, A. (2018). The role of the operating parameters of SBR systems on the SMP production and on membrane fouling reduction. Journal of Environmental Management, 228, 205-212. doi:10.1016/j.jenvman.2018.09.036Ferrer-Polonio, E., Fernández-Navarro, J., Alonso-Molina, J. L., Bes-Piá, A., & Mendoza-Roca, J. A. (2018). Influence of organic matter type in wastewater on soluble microbial products production and on further ultrafiltration. Journal of Chemical Technology & Biotechnology, 93(11), 3284-3291. doi:10.1002/jctb.5689Leenheer, J. A. (1981). Comprehensive approach to preparative isolation and fractionation of dissolved organic carbon from natural waters and wastewaters. Environmental Science & Technology, 15(5), 578-587. doi:10.1021/es00087a010Imai, A., Fukushima, T., Matsushige, K., Kim, Y.-H., & Choi, K. (2002). Characterization of dissolved organic matter in effluents from wastewater treatment plants. Water Research, 36(4), 859-870. doi:10.1016/s0043-1354(01)00283-4Zheng, X., Khan, M. T., & Croué, J.-P. (2014). Contribution of effluent organic matter (EfOM) to ultrafiltration (UF) membrane fouling: Isolation, characterization, and fouling effect of EfOM fractions. Water Research, 65, 414-424. doi:10.1016/j.watres.2014.07.039Ferrer-Polonio, E., McCabe, M., Mendoza-Roca, J. A., & Vincent-Vela, M.-C. (2018). Fractionation of secondary effluents of wastewater treatment plants in view of the evaluation of membrane fouling in a further ultrafiltration step. Journal of Chemical Technology & Biotechnology, 93(5), 1495-1501. doi:10.1002/jctb.5520Chaloulakou, A., Grivas, G., & Spyrellis, N. (2003). Neural Network and Multiple Regression Models for PM10 Prediction in Athens: A Comparative Assessment. Journal of the Air & Waste Management Association, 53(10), 1183-1190. doi:10.1080/10473289.2003.10466276Kalogirou, S. A. (2000). Applications of artificial neural-networks for energy systems. Applied Energy, 67(1-2), 17-35. doi:10.1016/s0306-2619(00)00005-2Hamed, M. M., Khalafallah, M. G., & Hassanien, E. A. (2004). Prediction of wastewater treatment plant performance using artificial neural networks. Environmental Modelling & Software, 19(10), 919-928. doi:10.1016/j.envsoft.2003.10.005Shon, H. K., Vigneswaran, S., Kim, I. S., Cho, J., & Ngo, H. H. (2006). Fouling of ultrafiltration membrane by effluent organic matter: A detailed characterization using different organic fractions in wastewater. Journal of Membrane Science, 278(1-2), 232-238. doi:10.1016/j.memsci.2005.11.006Marhaba, T. F. (2000). Fluorescence Technique for Rapid Identification of DOM Fractions. Journal of Environmental Engineering, 126(2), 145-152. doi:10.1061/(asce)0733-9372(2000)126:2(145)Teodosiu, C. (2000). Neural network models for ultrafiltration and backwashing. Water Research, 34(18), 4371-4380. doi:10.1016/s0043-1354(00)00217-7Delgrange-Vincent, N., Cabassud, C., Cabassud, M., Durand-Bourlier, L., & Laîné, J. M. (2000). Neural networks for long term prediction of fouling and backwash efficiency in ultrafiltration for drinking water production. Desalination, 131(1-3), 353-362. doi:10.1016/s0011-9164(00)90034-1Vincent Vela, M. C., Álvarez Blanco, S., Lora García, J., & Bergantiños Rodríguez, E. (2009). Analysis of membrane pore blocking models adapted to crossflow ultrafiltration in the ultrafiltration of PEG. Chemical Engineering Journal, 149(1-3), 232-241. doi:10.1016/j.cej.2008.10.027Zuriaga-Agustí, E., Bes-Piá, A., Mendoza-Roca, J. A., & Alonso-Molina, J. L. (2013). Influence of extraction methods on proteins and carbohydrates analysis from MBR activated sludge flocs in view of improving EPS determination. Separation and Purification Technology, 112, 1-10. doi:10.1016/j.seppur.2013.03.048Frølund, B., Palmgren, R., Keiding, K., & Nielsen, P. H. (1996). Extraction of extracellular polymers from activated sludge using a cation exchange resin. Water Research, 30(8), 1749-1758. doi:10.1016/0043-1354(95)00323-1Juang, L.-C., Tseng, D.-H., Chen, Y.-M., Semblante, G. U., & You, S.-J. (2013). The effect soluble microbial products (SMP) on the quality and fouling potential of MBR effluent. Desalination, 326, 96-102. doi:10.1016/j.desal.2013.07.005Ayache, C., Pidou, M., Croué, J. P., Labanowski, J., Poussade, Y., Tazi-Pain, A., … Gernjak, W. (2013). Impact of effluent organic matter on low-pressure membrane fouling in tertiary treatment. Water Research, 47(8), 2633-2642. doi:10.1016/j.watres.2013.01.043Barker, D. J., & Stuckey, D. C. (1999). A review of soluble microbial products (SMP) in wastewater treatment systems. Water Research, 33(14), 3063-3082. doi:10.1016/s0043-1354(99)00022-6Haberkamp, J., Ernst, M., Böckelmann, U., Szewzyk, U., & Jekel, M. (2008). Complexity of ultrafiltration membrane fouling caused by macromolecular dissolved organic compounds in secondary effluents. Water Research, 42(12), 3153-3161. doi:10.1016/j.watres.2008.03.007Yigit, N. O., Harman, I., Civelekoglu, G., Koseoglu, H., Cicek, N., & Kitis, M. (2008). Membrane fouling in a pilot-scale submerged membrane bioreactor operated under various conditions. Desalination, 231(1-3), 124-132. doi:10.1016/j.desal.2007.11.041Yammine, S., Rabagliato, R., Vitrac, X., Mietton Peuchot, M., & Ghidossi, R. (2019). Selecting ultrafiltration membranes for fractionation of high added value compounds from grape pomace extracts. OENO One, 53(3). doi:10.20870/oeno-one.2019.53.3.2343Babcock, J. J., & Brancaleon, L. (2013). Bovine serum albumin oligomers in the E- and B-forms at low protein concentration and ionic strength. International Journal of Biological Macromolecules, 53, 42-53. doi:10.1016/j.ijbiomac.2012.10.030Zirnsak, M. A., & Boger, D. V. (1998). Axisymmetric entry flow of semi-dilute xanthan gum solutions: prediction and experiment. Journal of Non-Newtonian Fluid Mechanics, 79(2-3), 105-136. doi:10.1016/s0377-0257(98)00104-9Corbatón-Báguena, M.-J., Álvarez-Blanco, S., & Vincent-Vela, M.-C. (2015). Fouling mechanisms of ultrafiltration membranes fouled with whey model solutions. Desalination, 360, 87-96. doi:10.1016/j.desal.2015.01.019Maruyama, T., Katoh, S., Nakajima, M., & Nabetani, H. (2001). Mechanism of bovine serum albumin aggregation during ultrafiltration. Biotechnology and Bioengineering, 75(2), 233-238. doi:10.1002/bit.10001Soler-Cabezas, J. L., Torà-Grau, M., Vincent-Vela, M. C., Mendoza-Roca, J. A., & Martínez-Francisco, F. J. (2014). Ultrafiltration of municipal wastewater: study on fouling models and fouling mechanisms. Desalination and Water Treatment, 56(13), 3427-3437. doi:10.1080/19443994.2014.969320Vela, M. C. V., Blanco, S. Á., García, J. L., & Rodríguez, E. B. (2008). Analysis of membrane pore blocking models applied to the ultrafiltration of PEG. Separation and Purification Technology, 62(3), 489-498. doi:10.1016/j.seppur.2008.02.028Mah, S.-K., Chuah, C.-K., Cathie Lee, W. P., & Chai, S.-P. (2012). Ultrafiltration of palm oil–oleic acid–glycerin solutions: Fouling mechanism identification, fouling mechanism analysis and membrane characterizations. Separation and Purification Technology, 98, 419-431. doi:10.1016/j.seppur.2012.07.020Saha, S., & Das, C. (2015). 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Guidelines to use tomato in experiments with a controlled environment

Domesticated tomato (Solanum lycopersicum) is the most important horticultural crop worldwide. Low polymorphism at the DNA level conflicts with the wealth of morphological variation. Fruits vary widely in size, shape, and color. In contrast, genetic variation between the 16 wild relatives is tremendous. Several large seed banks provide tomato germplasm for both domesticated and wild accessions of tomato. Recently, the genomes of the inbred cultivar “Heinz 1706” (≈900 Mb), and S. pimpinellifolium (739 Mb) were sequenced. Genomic markers and genome re-sequencing data are available for >150 cultivars and accessions. Transformation of tomato is relatively easy and T-DNA insertion line collections are available. Tomato is widely used as a model crop for fruit development but also for diverse physiological, cellular, biochemical, molecular, and genetic studies. It can be easily grown in greenhouses or growth chambers. Plants grow, flower, and develop fruits well at daily light lengths between 8 and 16 h. The required daily light integral of an experiment depends on growth stage and temperature investigated. Temperature must be 10–35°C, relative humidity 30–90%, and, CO2 concentration 200–1500 μmol mol−1. Temperature determines the speed of the phenological development while daily light integral and CO2 concentration affect photosynthesis and biomass production. Seed to seed cultivation takes 100 days at 20°C and can be shortened or delayed by temperature. Tomato may be cultivated in soil, substrates, or aeroponically without any substrate. Root volume, and water uptake requirements are primarily determined by transpiration demands of the plants. Many nutrient supply recipes and strategies are available to ensure sufficient supply as well as specific nutrient deficits/surplus. Using appropriate cultivation techniques makes tomato a convenient model plant for researchers, even for beginners

Carbohydrate structure: : the rocky road to automation

With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to ‘protein standards’ will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most

<em>Blastococcus carthaginiensis</em> sp. nov., isolated from a monument sampled in Carthage, Tunisia

A comprehensive polyphasic investigation was conducted to elucidate the taxonomic position of an actinobacterium, designated BMG 814T, which was isolated from the historic ruins of Carthage city in Tunisia. It grew as pink-orange pigmented colonies and displayed versatile growth capabilities, thriving within a temperature range of 20-40 \ub0C, across a pH spectrum ranging from pH 5.5 to 10 and in the presence of up to 4 % NaCl. Chemotaxonomic investigations unveiled specific cell components, including diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, glycophosphatidylinositol, an unidentified aminoglycophospholipid, six unidentified aminolipids, two unidentified phospholipids and one unidentified lipid in its polar lipid profile. Furthermore, galactose, glucose and ribose were identified as the primary cell-wall sugars. Major menaquinones identified were MK-9(H4), MK-9(H2) and MK-9, while major fatty acids comprised iso-C15 : 0, iso-C16 : 0, C17 : 1 ω8c and C18 : 1 ω9c. Through phylogenetic analysis based on the 16S rRNA gene sequence, the strain was positioned within the genus Blastococcus, with Blastococcus capsiensis BMG 804T showing the closest relationship (99.1 %). In light of this, draft genomes for both strains, BMG 814T and BMG 804T, were sequenced in this study, and comparative analysis revealed that strain BMG 814T exhibited digital DNA-DNA hybridization and average nucleotide identity values below the recommended thresholds for demarcating new species with all available genomes of type strains of validly names species. Based on the polyphasic taxonomy assessment, strain BMG 814T (=DSM 46848T=CECT 8878T) was proposed as the type strain of a novel species named Blastococcus carthaginiensis sp. nov

Mass Spectrometry in the Elucidation of the Glycoproteome of Bacterial Pathogens

Presently some three hundred post-translational modifications are known to occur in bacteria in vivo. Many of these modifications play critical roles in the regulation of proteins and control key biological processes. One of the most predominant modifications, N- and O-glycosylations are now known to be present in bacteria (and archaea) although they were long believed to be limited to eukaryotes. In a number of human pathogens these glycans have been found attached to the surfaces of pilin, flagellin and other surface and secreted proteins where it has been demonstrated that they play a role in the virulence of these bacteria. Mass spectrometry characterization of these glycosylation events has been the enabling key technology for these findings. This review will look at the use of mass spectrometry as a key technology for the detection and mapping of these modifications within microorganisms, with particular reference to the human pathogens, Campylobacter jejuni and Mycobacterium tuberculosis. The overall aim of this review will be to give a basic understanding of the current ‘state-of-the-art’ of the key techniques, principles and technologies, including bioinformatics tools, involved in the analysis of the glycosylation modifications

Strategies for carbohydrate model building, refinement and validation

Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein-sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade