Project description:Circulating protein biomarkers provide information regarding pathways in heart failure (HF) and can add important value to clinicians. Advancements in proteomics allow researchers to measure a multitude of proteins simultaneously with excellent sensitivity and selectivity to detect low abundance proteins. This helps identify previously unrecognized pathways in HF and discover biomarkers and potential targets for HF therapies. Although several proteomic methods exist, including mass spectrometry, protein microarray, aptamer, and proximity extension assay-based techniques, each have their unique advantages. This paper provides an overview of the various proteomic methods, with examples of how each has contributed to understanding the pathways in HF.
Project description:Aerobic life is based on numerous metabolic oxidation reactions as well as biosynthesis of oxygenated signaling compounds. Among the latter are the myriads of oxygenated lipids including a well-studied group of polyunsaturated fatty acids (PUFA) - octadecanoids, eicosanoids, and docosanoids. During the last two decades, remarkable progress in liquid-chromatography-mass spectrometry has led to significant progress in the characterization of oxygenated PUFA-containing phospholipids, thus designating the emergence of a new field of lipidomics, redox lipidomics. Although non-enzymatic free radical reactions of lipid peroxidation have been mostly associated with the aberrant metabolism typical of acute injury or chronic degenerative processes, newly accumulated evidence suggests that enzymatically catalyzed (phospho)lipid oxygenation reactions are essential mechanisms of many physiological pathways. In this review, we discuss a variety of contemporary protocols applicable for identification and quantitative characterization of different classes of peroxidized (phospho)lipids. We describe applications of different types of LCMS for analysis of peroxidized (phospho)lipids, particularly cardiolipins and phosphatidylethanolalmines, in two important types of programmed cell death - apoptosis and ferroptosis. We discuss the role of peroxidized phosphatidylserines in phagocytotic signaling. We exemplify the participation of peroxidized neutral lipids, particularly tri-acylglycerides, in immuno-suppressive signaling in cancer. We also consider new approaches to exploring the spatial distribution of phospholipids in the context of their oxidizability by MS imaging, including the latest achievements in high resolution imaging techniques. We present innovative approaches to the interpretation of LC-MS data, including audio-representation analysis. Overall, we emphasize the role of redox lipidomics as a communication language, unprecedented in diversity and richness, through the analysis of peroxidized (phospho)lipids.
Project description:An increasing number of peptides with specific binding affinity to various protein and even non-protein targets are being discovered from phage display libraries. The power of this method lies in its ability to efficiently and rapidly identify ligands with a desired target property from a large population of phage clones displaying diverse surface peptides. However, the search for the needle in the haystack does not always end successfully. False positive results may appear. Thus instead of specific binders phage with no actual affinity toward the target are recovered due to their propagation advantages or binding to other components of the screening system, such as the solid phase, capturing reagents, contaminants in the target sample or blocking agents, rather than the target. Biopanning experiments on different targets performed in our laboratory revealed some previously identified and many new target-unrelated peptide sequences, which have already been frequently described and published, but not yet recognized as target-unrelated. Distinguishing true binders from false positives is an important step toward phage display selections of greater integrity. This article thoroughly reviews and discusses already identified and new target-unrelated peptides and suggests strategies to avoid their isolation.
Project description:The classification codes granted by patent offices are useful instruments for simplifying the bewildering variety of patents in existence. They are singularly unhelpful, however, in locating a specific subgroup of patents such as that of drug-related pharmaceutical patents for which no classification codes exist. Taking advantage of advances in artificial intelligence and in natural language processing in particular, we offer a new method of identifying chemical drug-related patents in this article. The aim is primarily that of demonstrating how the proverbial needle in a haystack was identified, namely through leveraging the superb pattern-recognition abilities of the BERT (Bidirectional Encoder Representations from Transformers) algorithm. We build three different databases to train our algorithm and fine-tune its abilities to identify the patent group in question by exposing it to additional texts containing structures that are much more likely to be present in them, until we obtain the highest possible F1-score, combined with an accuracy of 94.40%. We also demonstrate some possible uses of the algorithm. Its application to the US patent office database enables the identification of potential chemical drug patents up to ten years before drug approval, whereas its application to the German patent office reveals the regional nature of drug R&D and patenting strategies. The hope is that both the method proposed and its applications will be further refined and expanded forthwith.
Project description:Ticks and tick-borne diseases are significant public health concerns. Bioactive molecules in tick saliva facilitate prolonged blood-feeding and transmission of tick-borne pathogens to the vertebrate host. Alpha-gal syndrome (AGS), a newly reported food allergy, is believed to be induced by saliva proteins decorated with a sugar molecule, the oligosaccharide galactose-⍺-1,3-galactose (α-gal). This syndrome is characterized by an IgE antibody-directed hypersensitivity against α-gal. The α-gal antigen was discovered in the salivary glands and saliva of various tick species including, the Lone Star tick (Amblyomma americanum). The underlying immune mechanisms linking tick bites with α-gal-specific IgE production are poorly understood and are crucial to identify and establish novel treatments for this disease. This article reviews the current understanding of AGS and its involvement with tick species.
Project description:Prediction of protein tertiary structures from amino acid sequence and understanding the mechanisms of how proteins fold, collectively known as "the protein folding problem," has been a grand challenge in molecular biology for over half a century. Theories have been developed that provide us with an unprecedented understanding of protein folding mechanisms. However, computational simulation of protein folding is still difficult, and prediction of protein tertiary structure from amino acid sequence is an unsolved problem. Progress toward a satisfying solution has been slow due to challenges in sampling the vast conformational space and deriving sufficiently accurate energy functions. Nevertheless, several techniques and algorithms have been adopted to overcome these challenges, and the last two decades have seen exciting advances in enhanced sampling algorithms, computational power and tertiary structure prediction methodologies. This review aims at summarizing these computational techniques, specifically conformational sampling algorithms and energy approximations that have been frequently used to study protein-folding mechanisms or to de novo predict protein tertiary structures. We hope that this review can serve as an overview on how the protein-folding problem can be studied computationally and, in cases where experimental approaches are prohibitive, help the researcher choose the most relevant computational approach for the problem at hand. We conclude with a summary of current challenges faced and an outlook on potential future directions.
Project description:Multi-grain crystallography, traditionally performed at synchrotron sources in association with high-pressure studies, has new relevance with respect to laboratory single-crystal X-ray diffraction, in which crystals can be grown rapidly in situ, and a preliminary dataset analysed and solved in a matter of minutes. Subsequently, a full-sphere of IUCr-quality data can then be collected in a few hours. To demonstrate the applicability of laboratory multi-grain crystallography with Cu Kα X-rays, co-crystals of hexafluorobenzene and pyrrole were grown rapidly by cooling a 1:1 liquid mixture in an X-ray capillary on the diffractometer. The software is able to identify a single unit cell from as few as 10% of the diffraction spots from a small number of diffraction frames. Once a unit cell is identified, a full crystal structure solution is rapidly obtained by collecting a small amount of data to a resolution of ca 1 Å. The co-crystal obtained from the 1:1 mixture showed that hexafluorobenzene and pyrrole crystallize in a 3:4 ratio, in contrast to the columnar 1:1 adduct structures typified by hexafluorobenzene and benzene. The generality of our multi-grain approach for samples that are liquid at room temperature (and form a polycrystalline solid mass on cooling) is further demonstrated by investigating and solving the 1:1 co-crystal formed between hexafluorobenzene and pyridine.