The purpose of this article is to provide a compendium of major histocompatibility complex (MHC) peptide motifs and MHC ligands known to date, together with a discussion of the methods used to gain this information. A problem here is the exponential growth of information in this field over the recent years. The number of known MHC ligands was zero in 1989 and three in 1990. This article, written in 1994, lists a couple of hundred such ligands, plus a large number of likely ligands. By the time this work is published, we expect a lot more ligands to be known. On the other hand, the peptide motifs of many of the more important MHC class I molecules are known already, so that this article will still be useful as a source of information. For class II, the situation is a bit different. Only a few allele-specific motifs have been reported, and the data from different authors are partially conflicting. The principles of allele-specific ligand motifs, however, have emerged recently by the combination of information on MHC class II structure, ligand sequencing, and peptide binding assays. Thus, these principles can be applied to further ligands to be identified.

/pdf/mhc-ligands-and-peptide-motifs-first-listing-3wmk826w0h.pdf

MHC ligands and peptide motifs: first listing.

Extracellular polymeric substances (EPS) produced by microorganisms are a complex mixture of biopolymers primarily consisting of polysaccharides, as well as proteins, nucleic acids, lipids and humic substances. EPS make up the intercellular space of microbial aggregates and form the structure and architecture of the biofilm matrix. The key functions of EPS comprise the mediation of the initial attachment of cells to different substrata and protection against environmental stress and dehydration. The aim of this review is to present a summary of the current status of the research into the role of EPS in bacterial attachment followed by biofilm formation. The latter has a profound impact on an array of biomedical, biotechnology and industrial fields including pharmaceutical and surgical applications, food engineering, bioremediation and biohydrometallurgy. The diverse structural variations of EPS produced by bacteria of different taxonomic lineages, together with examples of biotechnological applications, are discussed. Finally, a range of novel techniques that can be used in studies involving biofilm-specific polysaccharides is discussed.

https://www.mdpi.com/1420-3049/14/7/2535/pdf

Bacterial extracellular polysaccharides involved in biofilm formation.

Peptide antigens bound to molecules encoded by the major histocompatibility complex (MHC) and presented on the cell surface form the targets of T lymphocytes. This critical arm of the adaptive immune system facilitates the eradication of pathogen-infected and cancerous cells, as well as the production of antibodies. Methods to identify these peptide antigens are critical to the development of new vaccines, for which the goal is the generation of effective adaptive immune responses and long-lasting immune memory. Here, we describe a robust protocol for the identification of MHC-bound peptides from cell lines and tissues, using nano-ultra-performance liquid chromatography coupled to high-resolution mass spectrometry (nUPLC–MS/MS) and recent improvements in methods for isolation and characterization of these peptides. The protocol starts with the immunoaffinity capture of naturally processed MHC-peptide complexes. The peptides dissociate from the class I human leukocyte antigens (HLAs) upon acid denaturation. This peptide cargo is then extracted and separated into fractions by HPLC, and the peptides in these fractions are identified using nUPLC–MS/MS. With this protocol, several thousand peptides can be identified from a wide variety of cell types, including cancerous and infected cells and those from tissues, with a turnaround time of 2–3 d. Peptide antigens are bound to molecules encoded by the major histocompatibility complex (MHC) and presented on the cell surface as targets for T lymphocytes. This protocol uses nUPLC–MS/MS to identify MHC-bound peptides from cell lines and tissues.

Mass spectrometry-based identification of MHC-bound peptides for immunopeptidomics.

Preface Section I - Fundamentals, microorganisms and mechanisms Microorganisms involved in bioleaching and nucleic acid-based molecular methods for their identification and quantification Axel Schippers Mechanisms and biochemical fundamentals of bacterial metal sulfide oxidation Thore Rodwerder and Wolfgang Sand Electrochemical techniques used to study bacterial-metal sulfides interactions Denise Bevilaqua, Heloisa A. Acciari, Assis V. Benedetti and Oswaldo Garcia Jr Electrochemical mechanism of leaching. Influence of the presence of catalytic ions and bacteria Antonio Ballester, Maria Luisa Blazquez, Felisa Gonzalez and Jesus A. Munoz Recovery of zinc, nickel, cobalt and other metals by bioleaching Marisa R. Viera, Cristina M. Pogliani and Edgardo R. Donati Bioleaching of metals in neutral and slightly alkaline environment Aleksandra Sklodowska and Renata Matlakowska Section II - Bioreactors and Bioheaps Bioleaching of sulfide minerals in continuous stirred tanks Dominique Henri Roger Morin Bioreactor design fundamentals and their application to gold mining Fernando Acevedo and Juan Carlos Gentina Air-lift reactors: characterization and applications in biohydrometallurgy Alejandra Giaveno, Laura Lavalle, Patricia Chiacchiarini and Edgardo R. Donati Principles, mechanisms and dynamics of chalcocite heap bioleaching Jochen Petersen and David G. Dixon Section III - Genetics and Molecular Biology The use of bioinformatics and genome biology to advance our understanding of bioleaching microorganisms Raquel Quatrini, Jorge Valdes, Eugenia Jedlicki and David S. Holmes Proteomics and metaproteomics applied to biomining microorganisms Carlos A. Jerez Cell-cell communication in bacteria: A promising new approach to improve bioleaching efficiency? Susana Valenzuela,Alvaro Banderas, Carlos A. Jerez and Nicolas Guiliani Section IV - Other Applications Bioflotation and bioflocculation of relevance to minerals Bioprocessing K. Hanumantha Rao and S. Subramanian Desulphurization of gaseous emissions containing hydrogen sulfide Jose Manuel Gomez and Domingo Cantero Index

Microbial Processing of Metal Sulfides

Microorganisms capable of actively solubilizing and precipitating gold appear to play a larger role in the biogeochemical cycling of gold than previously believed. Recent research suggests that bacteria and archaea are involved in every step of the biogeochemical cycle of gold, from the formation of primary mineralization in hydrothermal and deep subsurface systems to its solubilization, dispersion and re-concentration as secondary gold under surface conditions. Enzymatically catalysed precipitation of gold has been observed in thermophilic and hyperthermophilic bacteria and archaea (for example, Thermotoga maritime, Pyrobaculum islandicum), and their activity led to the formation of gold- and silver-bearing sinters in New Zealand's hot spring systems. Sulphate-reducing bacteria (SRB), for example, Desulfovibrio sp., may be involved in the formation of gold-bearing sulphide minerals in deep subsurface environments; over geological timescales this may contribute to the formation of economic deposits. Iron- and sulphur-oxidizing bacteria (for example, Acidothiobacillus ferrooxidans, A. thiooxidans) are known to breakdown gold-hosting sulphide minerals in zones of primary mineralization, and release associated gold in the process. These and other bacteria (for example, actinobacteria) produce thiosulphate, which is known to oxidize gold and form stable, transportable complexes. Other microbial processes, for example, excretion of amino acids and cyanide, may control gold solubilization in auriferous top- and rhizosphere soils. A number of bacteria and archaea are capable of actively catalysing the precipitation of toxic gold(I/III) complexes. Reductive precipitation of these complexes may improve survival rates of bacterial populations that are capable of (1) detoxifying the immediate cell environment by detecting, excreting and reducing gold complexes, possibly using P-type ATPase efflux pumps as well as membrane vesicles (for example, Salmonella enterica, Cupriavidus (Ralstonia) metallidurans, Plectonema boryanum); (2) gaining metabolic energy by utilizing gold-complexing ligands (for example, thiosulphate by A. ferrooxidans) or (3) using gold as metal centre in enzymes (Micrococcus luteus). C. metallidurans containing biofilms were detected on gold grains from two Australian sites, indicating that gold bioaccumulation may lead to gold biomineralization by forming secondary 'bacterioform' gold. Formation of secondary octahedral gold crystals from gold(III) chloride solution, was promoted by a cyanobacterium (P. boryanum) via an amorphous gold(I) sulphide intermediate. 'Bacterioform' gold and secondary gold crystals are common in quartz pebble conglomerates (QPC), where they are often associated with bituminous organic matter possibly derived from cyanobacteria. This may suggest that cyanobacteria have played a role in the formation of the Witwatersrand QPC, the world's largest gold deposit.

The geomicrobiology of gold

Genomics, metagenomics and proteomics in biomining microorganisms

Mass Spectrometric Analysis of Peptides Associated with the Human Class I MHC Molecules HLA-A2.1 and HLA-B7 and Identification of Structural Features that Determine Binding

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Genomics, metagenomics and proteomics in biomining microorganisms

Mass Spectrometric Analysis of Peptides Associated with the Human Class I MHC Molecules HLA-A2.1 and HLA-B7 and Identification of Structural Features that Determine Binding