journal
Journals Advances in Experimental Medic...

Advances in Experimental Medicine and Biology

https://read.qxmd.com/read/38429473/exploring-the-metabolic-response-of-pseudomonas-putida-to-l-arginine
#1
JOURNAL ARTICLE
Chiara Scribani-Rossi, María Antonia Molina-Henares, Manuel Espinosa-Urgel, Serena Rinaldo
Beyond their role as protein-building units, amino acids are modulators of multiple behaviours in different microorganisms. In the root-colonizing beneficial bacterium Pseudomonas putida (recently proposed to be reclassified as alloputida) KT2440, current evidence suggests that arginine functions both as a metabolic indicator and as an environmental signal molecule, modulating processes such as chemotactic responses, siderophore-mediated iron uptake or the levels of the intracellular second messenger cyclic diguanylate (c-di-GMP)...
March 2, 2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38418797/therapeutic-potential-of-stem-cells-in-natural-killer-like-b-cell-associated-diseases
#2
JOURNAL ARTICLE
Manali Rupareliya, Pravin Shende
Stem cells are undifferentiated cells possessing a remarkable capacity to develop into multiple cell types. NKB cells, referred to "natural killer-like B cells," are recently identified subtype of B lymphocytes possessing characteristics that are similar to both natural killer (NK) cells and regular B lymphocytes. NK cells are lymphocyte-like in structure and cytotoxic in nature participating in the immediate immune response to the infected or malignant cells, whereas B lymphocytes produce antibodies and participate in adaptive immune response by binding to the specific antigen...
February 29, 2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38353867/algae-in-biomedicine
#3
JOURNAL ARTICLE
Aysegul Inam, Tulay Oncu-Oner, Irem Deniz
Algae, which live in marine or freshwater, are photosynthetic organisms. They vary greatly in size, morphology, and degree of complexity of their body structures. Algae are generally divided into two main groups, microalgae, which are small in size, and macroalgae, which are larger in size. These aquatic organisms have rich and valuable compounds including sterols, polysaccharides, pigments, fatty acids, proteins, enzymes, minerals, and vitamins that could be used in different application fields due to their bioactive functions...
February 15, 2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38337088/antifungal-stewardship-in-invasive-fungal-infections-a-systematic-review
#4
JOURNAL ARTICLE
Cataldo Procacci, Luisa Marras, Leonarda Maurmo, Grazia Vivanet, Luca Scalone, Giacomo Bertolino
INTRODUCTION: Invasive fungal infections (IFI) are a group of life-threatening diseases associated with significant morbidity, mortality and high healthcare costs. Some modern management programs known as AFS (antifungal stewardship programs) have now been developed. The purpose of this systematic review is to evaluate the different declinations of antifungal stewardship programs (AFPs). METHODS: Articles were systematically reviewed using the PRISMA checklist 2020...
February 10, 2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38231346/roles-and-regulation-of-h3k4-methylation-during-mammalian-early-embryogenesis-and-embryonic-stem-cell-differentiation
#5
JOURNAL ARTICLE
Nihal Terzi Cizmecioglu
From generation of germ cells, fertilization, and throughout early mammalian embryonic development, the chromatin undergoes significant alterations to enable precise regulation of gene expression and genome use. Methylation of histone 3 lysine 4 (H3K4) correlates with active regions of the genome, and it has emerged as a dynamic mark throughout this timeline. The pattern and the level of H3K4 methylation are regulated by methyltransferases and demethylases. These enzymes, as well as their protein partners, play important roles in early embryonic development and show phenotypes in embryonic stem cell self-renewal and differentiation...
January 18, 2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507208/characterization-of-complexes-and-supramolecular-structures-by-electron-microscopy
#6
JOURNAL ARTICLE
José L Carrascosa
Recent advancements in cryo-electron microscopy (cryo-TEM) have enabled the determination of structures of macromolecular complexes at near-atomic resolution, establishing it as a pivotal tool in Structural Biology. This high resolution allows for the detection of ligands and substrates under physiological conditions. Enhancements in detectors and imaging devices, like phase plates, improve signal quality, facilitating the reconstruction of even smaller macromolecular complexes. The 100-kDa barrier has been surpassed, presenting new opportunities for pharmacological research and expanding the scope of crystallographic analyses in the pharmaceutical industry...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507207/sample-preparation-for-electron-cryo-microscopy-of-macromolecular-machines
#7
JOURNAL ARTICLE
Aurélien Deniaud, Burak V Kabasakal, Joshua C Bufton, Christiane Schaffitzel
High-resolution structure determination by electron cryo-microscopy underwent a step change in recent years. This now allows study of challenging samples which previously were inaccessible for structure determination, including membrane proteins. These developments shift the focus in the field to the next bottlenecks which are high-quality sample preparations. While the amounts of sample required for cryo-EM are relatively small, sample quality is the key challenge. Sample quality is influenced by the stability of complexes which depends on buffer composition, inherent flexibility of the sample, and the method of solubilization from the membrane for membrane proteins...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507206/small-angle-x-ray-scattering-for-macromolecular-complexes
#8
JOURNAL ARTICLE
Stephanie Hutin, Mark D Tully, Martha Brennich
Small angle X-ray scattering (SAXS) is a versatile technique that can provide unique insights in the solution structure of macromolecules and their complexes, covering the size range from small peptides to complete viral assemblies. Technological and conceptual advances in the last two decades have tremendously improved the accessibility of the technique and transformed it into an indispensable tool for structural biology. In this chapter we introduce and discuss several approaches to collecting SAXS data on macromolecular complexes, including several approaches to online chromatography...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507205/characterization-of-biological-samples-using-ultra-short-and-ultra-bright-xfel-pulses
#9
JOURNAL ARTICLE
Adam Round, E Jungcheng, Carsten Fortmann-Grote, Klaus Giewekemeyer, Rita Graceffa, Chan Kim, Henry Kirkwood, Grant Mills, Ekaterina Round, Tokushi Sato, Sakura Pascarelli, Adrian Mancuso
The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507204/x-ray-crystallography-for-macromolecular-complexes
#10
JOURNAL ARTICLE
Francisco J Fernández, Javier Querol-García, Sergio Navas-Yuste, Fabrizio Martino, M Cristina Vega
X-ray crystallography has for most of the last century been the standard technique to determine the high-resolution structure of biological macromolecules, including multi-subunit protein-protein and protein-nucleic acids as large as the ribosome and viruses. As such, the successful application of X-ray crystallography to many biological problems revolutionized biology and biomedicine by solving the structures of small molecules and vitamins, peptides and proteins, DNA and RNA molecules, and many complexes-affording a detailed knowledge of the structures that clarified biological and chemical mechanisms, conformational changes, interactions, catalysis and the biological processes underlying DNA replication, translation, and protein synthesis...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507203/the-complementarity-of-nuclear-magnetic-resonance-and-native-mass-spectrometry-in-probing-protein-protein-interactions
#11
JOURNAL ARTICLE
Elisabetta Boeri Erba, Annalisa Pastore
Nuclear magnetic resonance (NMR) and native mass spectrometry (MS) are mature physicochemical techniques with long histories and important applications. NMR spectroscopy provides detailed information about the structure, dynamics, interactions, and chemical environment of biomolecules. MS is an effective approach for determining the mass of biomolecules with high accuracy, sensitivity, and speed. The two techniques offer unique advantages and provide solid tools for structural biology. In the present review, we discuss their individual merits in the context of their applications to structural studies in biology with specific focus on protein interactions and evaluate their limitations...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507202/studying-macromolecular-interactions-of-cellular-machines-by-the-combined-use-of-analytical-ultracentrifugation-light-scattering-and-fluorescence-spectroscopy-methods
#12
JOURNAL ARTICLE
Carlos Alfonso, Marta Sobrinos-Sanguino, Juan Román Luque-Ortega, Silvia Zorrilla, Begoña Monterroso, Oscar M Nuero, Germán Rivas
Cellular machines formed by the interaction and assembly of macromolecules are essential in many processes of the living cell. These assemblies involve homo- and hetero-associations, including protein-protein, protein-DNA, protein-RNA, and protein-polysaccharide associations, most of which are reversible. This chapter describes the use of analytical ultracentrifugation, light scattering, and fluorescence-based methods, well-established biophysical techniques, to characterize interactions leading to the formation of macromolecular complexes and their modulation in response to specific or unspecific factors...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507201/protein-protein-binding-kinetics-by-biolayer-interferometry
#13
JOURNAL ARTICLE
Jorge Santos-López, Sara Gómez, Francisco J Fernández, M Cristina Vega
The specific kinetics and thermodynamics of protein-protein interactions underlie the molecular mechanisms of cellular functions; hence the characterization of these interaction parameters is central to the quantitative understanding of physiological and pathological processes. Many methods have been developed to study protein-protein interactions, which differ in various features including the interaction detection principle, the sensitivity, whether the method operates in vivo, in vitro, or in silico, the temperature control, the use of labels, immobilization, the amount of sample required, the number of measurements that can be accomplished simultaneously, or the cost...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507200/discovery-and-characterization-of-linear-motif-mediated-protein-protein-complexes
#14
JOURNAL ARTICLE
András Zeke, Anita Alexa, Attila Reményi
There are myriads of protein-protein complexes that form within the cell. In addition to classical binding events between globular domains, many protein-protein interactions involve short disordered protein regions. The latter contain so-called linear motifs binding specifically to ordered protein domain surfaces. Linear binding motifs are classified based on their consensus sequence, where only a few amino acids are conserved. In this chapter we will review experimental and in silico techniques that can be used for the discovery and characterization of linear motif mediated protein-protein complexes involved in cellular signaling, protein level and gene expression regulation...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507199/probing-protein-complexes-composition-stoichiometry-and-interactions-by-peptide-based-mass-spectrometry
#15
JOURNAL ARTICLE
Gianluca Degliesposti
The characterization of a protein complex by mass spectrometry can be conducted at different levels. Initial steps regard the qualitative composition of the complex and subunit identification. After that, quantitative information such as stoichiometric ratios and copy numbers for each subunit in a complex or super-complex is acquired. Peptide-based LC-MS/MS offers a wide number of methods and protocols for the characterization of protein complexes. This chapter concentrates on the applications of peptide-based LC-MS/MS for the qualitative, quantitative, and structural characterization of protein complexes focusing on subunit identification, determination of stoichiometric ratio and number of subunits per complex as well as on cross-linking mass spectrometry and hydrogen/deuterium exchange as methods for the structural investigation of the biological assemblies...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507198/peptide-based-mass-spectrometry-for-the-investigation-of-protein-complexes
#16
JOURNAL ARTICLE
Gianluca Degliesposti
In the last two decades, biological mass spectrometry has become the gold standard for the identification of proteins in biological samples. The technological advancement of mass spectrometers and the development of methods for ionization, gas phase transfer, peptide fragmentation as well as for acquisition of high-resolution mass spectrometric data marked the success of the technique. This chapter introduces peptide-based mass spectrometry as a tool for the investigation of protein complexes. It provides an overview of the main steps for sample preparation starting from protein fractionation, reduction, alkylation and focus on the final step of protein digestion...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507197/purification-of-in-vivo-or-in-vitro-assembled-rna-protein-complexes-by-rna-centric-methods
#17
JOURNAL ARTICLE
Aurélie Janvier, Hassan Hayek, Fatima Alghoul, Lauriane Gross, Christine Allmang, Franck Martin, Gilbert Eriani
Throughout their entire life cycle, RNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions and very diverse functions in RNA metabolism, including splicing, translational regulation, ribosome assembly. Many RNPs remain poorly characterized due to the challenges inherent in their purification and subsequent biochemical characterization. Therefore, developing methods to isolate specific RNA-protein complexes is an important initial step toward understanding their function...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38507196/immunoprecipitation-methods-to-isolate-messenger-ribonucleoprotein-complexes-mrnp
#18
JOURNAL ARTICLE
Hassan Hayek, Lauriane Gross, Fatima Alghoul, Franck Martin, Gilbert Eriani, Christine Allmang
Throughout their life cycle, messenger RNAs (mRNAs) associate with proteins to form ribonucleoproteins (mRNPs). Each mRNA is part of multiple successive mRNP complexes that participate in their biogenesis, cellular localization, translation and decay. The dynamic composition of mRNP complexes and their structural remodelling play crucial roles in the control of gene expression. Studying the endogenous composition of different mRNP complexes is a major challenge. In this chapter, we describe the variety of protein-centric immunoprecipitation methods available for the identification of mRNP complexes and the requirements for their experimental settings...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38467984/hla-genetics-for-the-human-diseases
#19
JOURNAL ARTICLE
Takashi Shiina, Jerzy K Kulski
Highly polymorphic human leukocyte antigen (HLA) molecules (alleles) expressed by different classical HLA class I and class II genes have crucial roles in the regulation of innate and adaptive immune responses, transplant rejection and in the pathogenesis of numerous infectious and autoimmune diseases. To date, over 35,000 HLA alleles have been published from the IPD-IMGT/HLA database, and specific HLA alleles and HLA haplotypes have been reported to be associated with more than 100 different diseases and phenotypes...
2024: Advances in Experimental Medicine and Biology
https://read.qxmd.com/read/38467983/dissecting-the-immune-system%C3%A2-through%C3%A2-gene-regulation
#20
JOURNAL ARTICLE
Hideyuki Yoshida
The immune system plays a dual role in human health, functioning both as a protector against pathogens and, at times, as a contributor to disease. This feature emphasizes the importance to uncover the underlying causes of its malfunctions, necessitating an in-depth analysis in both pathological and physiological conditions to better understand the immune system and immune disorders. Recent advances in scientific technology have enabled extensive investigations into gene regulation, a crucial mechanism governing cellular functionality...
2024: Advances in Experimental Medicine and Biology
journal
journal
21742
1
2
Fetch more papers »
Fetching more papers... Fetching...
Remove bar
Read by QxMD icon Read
×

Save your favorite articles in one place with a free QxMD account.

×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"

We want to hear from doctors like you!

Take a second to answer a survey question.