scholarly journals The Noisy and Marvelous Molecular World of Biology

Inventions ◽  
2019 ◽  
Vol 4 (2) ◽  
pp. 24
Author(s):  
Felix Ritort
Keyword(s):  
Single Molecule ◽  
Molecular Level ◽  
Second Law Of Thermodynamics ◽  
Physical World ◽  
Computational Studies ◽  
Biological Complexity ◽  
Concerted Action ◽  
Physical Information ◽  
Molecular Sequencing

At the molecular level biology is intrinsically noisy. The forces that regulate the myriad of molecular reactions in the cell are tiny, on the order of piconewtons (10−12 Newtons), yet they proceed in concerted action making life possible. Understanding how this is possible is one of the most fundamental questions biophysicists would like to understand. Single molecule experiments offer an opportunity to delve into the fundamental laws that make biological complexity surface in a physical world governed by the second law of thermodynamics. Techniques such as force spectroscopy, fluorescence, microfluidics, molecular sequencing, and computational studies project a view of the biomolecular world ruled by the conspiracy between the disorganizing forces due to thermal motion and the cosmic evolutionary drive. Here we will digress on some of the evidences in support of this view and the role of physical information in biology.

Can the Lewis basicity of an isolated solvent molecule be used for characterizing solvent effects?

2020 ◽  
Vol 16 ◽  
Author(s):  
Jean-François Gal ◽  
Pierre-Charles Maria
Keyword(s):  
Solvent Effects ◽  
Molecular Level ◽  
Solvent Molecule ◽  
Lewis Base ◽  
Bulk Liquid ◽  
Donor Number ◽  
Special Focus ◽  
Solution Processes ◽  
Inert Solvent

Background: The ubiquitous Lewis acid/base interactions are important in solution processes. Analytical chemistry may benefit of a better understanding of the role of Lewis basicity, at the molecular level or acting through a bulk solvent effect. Objective: To clearly delineate (i) the basicity at a molecular level, hereafter referred as solute basicity, and (ii) the solvent basicity, which is a bulk-liquid property. Method: The literature that relates Lewis basicity scales and solvent effects is analyzed. A special focus is placed on two extensive scales, the Donor Number, DN, and the BF3 affinity scale, BF3A, which were obtained by calorimetric measurement on molecules as solutes diluted in a quasi-inert solvent, and therefore define a molecular Lewis basicity. We discuss the validity of these solute scales when regarded as solvent scales, in particular when the basicity of strongly associated liquids is discussed. Results: We demonstrate the drawbacks of confusing the Lewis basicity of a solvent molecule, isolated as solute, and that of the bulk liquid solvent itself. Conclusion: Consequently, we recommend a reasoned use of the concept of Lewis basicity taking clearly into account the specificity of the process for which a Lewis basicity effect may be invoked. In particular, the action of the Lewis base, either as an isolated entity, or as a bulk liquid, must be distinguished.

Isolation of Natural Compounds from Syzygium densiflorum Fruits and Exploring its Chemical Property, Therapeutic Role in Diabetic Management

2020 ◽  
Vol 10 (2) ◽  
pp. 168-176
Author(s):  
Krishnasamy Gopinath ◽  
Nagarajan Subbiah ◽  
Muthusamy Karthikeyan
Keyword(s):  
Density Functional ◽  
Chemical Reactivity ◽  
Natural Compounds ◽  
Structure Activity Relationship ◽  
Activity Relationship ◽  
Computational Studies ◽  
Therapeutic Role ◽  
Relationship Analysis ◽  
Structure Activity

Background: Syzygium densiflorum Wall. ex Wight & Arn (Myrtaceae) has been traditionally used by the local tribes of the Nilgiris, Tamil Nadu, India, for the treatment of diabetes. Objective: This study aimed to isolate the major phytoconstituents from the S. densiflorum fruits and to perform computational studies for chemical reactivity and biological activity of the isolated compound. Materials and Methods: Two different compounds were isolated from ethanolic extract of S. densiflorum fruits and purified using HPLC. The structures of the compounds were elucidated on the basis of their 1H NMR, 13C NMR, 1H-1H COSY, HMBC, HRESIMS, and FT-IR data. Further, the chemical reactivity of the compounds was analyzed by density functional theory calculations and its therapeutic role in diabetic management was examined by comparing the structure of isolated compounds with previously reported bioactive compounds. Results: Of the two compounds ((6,6 & 1-kestopentaose (1) and 6-(hydroxymethyl)-3-[3,4,5- trihydroxy- 6-[(3,4,5-trihydroxyoxan-2-yl)oxymethyl]oxan-2-yl]oxyoxane-2,4,5-triol)(2)). β-glucosidase, β-galactosidase, α-glucosidase and β-amylase inhibition activity of the compounds were predicted by structure activity relationship. Conclusion: Structure-activity relationship analysis was performed to predict the therapeutic role of isolated compounds. These computational studies may be performed to minimize the efforts to determine the therapeutic role of natural compounds.

The Non-Causal Character of Renormalization Group Explanations

2018 ◽  
Author(s):  
Margaret Morrison
Keyword(s):  
Probability Theory ◽  
Renormalization Group ◽  
Dynamical Systems ◽  
Recent Literature ◽  
Mathematical Explanation ◽  
Causal Status ◽  
Physical Information ◽  
The Relationship ◽  
Structural Aspects

After reviewing some of the recent literature on non-causal and mathematical explanation, this chapter develops an argument as to why renormalization group (RG) methods should be seen as providing non-causal, yet physical, information about certain kinds of systems/phenomena. The argument centres on the structural character of RG explanations and the relationship between RG and probability theory. These features are crucial for the claim that the non-causal status of RG explanations involves something different from simply ignoring or “averaging over” microphysical details—the kind of explanations common to statistical mechanics. The chapter concludes with a discussion of the role of RG in treating dynamical systems and how that role exemplifies the structural aspects of RG explanations which in turn exemplifies the non-causal features.

The localized electron: magnetic properties

2018 ◽  
Author(s):  
Jean-Pierre Launay ◽  
Michel Verdaguer
Keyword(s):  
Single Molecule ◽  
Model Systems ◽  
Ferromagnetic Coupling ◽  
Single Chain ◽  
Single Molecule Magnets ◽  
Magnetic Systems ◽  
Orbital Interactions ◽  
Prussian Blue Analogues ◽  
Mononuclear Complexes

After preliminaries about electron properties, and definitions in magnetism, one treats the magnetism of mononuclear complexes, in particular spin cross-over, showing the role of cooperativity and the sensitivity to external perturbations. Orbital interactions and exchange interaction are explained in binuclear model systems, using orbital overlap and orthogonality concepts to explain antiferromagnetic or ferromagnetic coupling. The phenomenologically useful Spin Hamiltonian is defined. The concepts are then applied to extended molecular magnetic systems, leading to molecular magnetic materials of various dimensionalities exhibiting bulk ferro- or ferrimagnetism. An illustration is provided by Prussian Blue analogues. Magnetic anisotropy is introduced. It is shown that in some cases, a slow relaxation of magnetization arises and gives rise to appealing single-ion magnets, single-molecule magnets or single-chain magnets, a route to store information at the molecular level.

scholarly journals Sub-Inhibitory Concentrations of Ciprofloxacin Alone and Combinations with Plant-Derived Compounds against P. aeruginosa Biofilms and Their Effects on the Metabolomic Profile of P. aeruginosa Biofilms

Antibiotics ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 414
Author(s):  
Didem Kart ◽  
Tuba Reçber ◽  
Emirhan Nemutlu ◽  
Meral Sagiroglu
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Inhibitory Concentration ◽  
Molecular Level ◽  
Metabolomic Profile ◽  
Gene Expressions ◽  
New Agents ◽  
Qrt Pcr ◽  
Metabolomic Approach

Introduction: Alternative anti-biofilm agents are needed to combat Pseudomonas aeruginosa infections. The mechanisms behind these new agents also need to be revealed at a molecular level. Materials and methods: The anti-biofilm effects of 10 plant-derived compounds on P. aeruginosa biofilms were investigated using minimum biofilm eradication concentration (MBEC) and virulence assays. The effects of ciprofloxacin and compound combinations on P. aeruginosa in mono and triple biofilms were compared. A metabolomic approach and qRT-PCR were applied to the biofilms treated with ciprofloxacin in combination with baicalein, esculin hydrate, curcumin, and cinnamaldehyde at sub-minimal biofilm inhibitory concentration (MBIC) concentrations to highlight the specific metabolic shifts between the biofilms and to determine the quorum sensing gene expressions, respectively. Results: The combinations of ciprofloxacin with curcumin, baicalein, esculetin, and cinnamaldehyde showed more reduced MBICs than ciprofloxacin alone. The quorum sensing genes were downregulated in the presence of curcumin and cinnamaldehyde, while upregulated in the presence of baicalein and esculin hydrate rather than for ciprofloxacin alone. The combinations exhibited different killing effects on P. aeruginosa in mono and triple biofilms without affecting its virulence. The findings of the decreased metabolite levels related to pyrimidine and lipopolysaccharide synthesis and to down-regulated alginate and lasI expressions strongly indicate the role of multifactorial mechanisms for curcumin-mediated P. aeruginosa growth inhibition. Conclusions: The use of curcumin, baicalein, esculetin, and cinnamaldehyde with ciprofloxacin will help fight against P. aeruginosa biofilms. To the best of our knowledge, this is the first study of its kind to define the effect of plant-based compounds as possible anti-biofilm agents with low MBICs for the treatment of P. aeruginosa biofilms through metabolomic pathways.

scholarly journals Insights in the Role of Lipids, Oxidative Stress and Inflammation in Rheumatoid Arthritis Unveiled by New Trends in Lipidomic Investigations

Antioxidants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 45
Author(s):  
Helena Beatriz Ferreira ◽  
Tânia Melo ◽  
Artur Paiva ◽  
Maria do Rosário Domingues
Keyword(s):  
Rheumatoid Arthritis ◽  
Oxidative Stress ◽  
Lipid Peroxidation ◽  
Lipid Profile ◽  
Inflammatory Responses ◽  
Molecular Level ◽  
Lipid Hydroperoxides ◽  
Lipid Species ◽  
Inflammatory Autoimmune Disease

Rheumatoid arthritis (RA) is a highly debilitating chronic inflammatory autoimmune disease most prevalent in women. The true etiology of this disease is complex, multifactorial, and is yet to be completely elucidated. However, oxidative stress and lipid peroxidation are associated with the development and pathogenesis of RA. In this case, oxidative damage biomarkers have been found to be significantly higher in RA patients, associated with the oxidation of biomolecules and the stimulation of inflammatory responses. Lipid peroxidation is one of the major consequences of oxidative stress, with the formation of deleterious lipid hydroperoxides and electrophilic reactive lipid species. Additionally, changes in the lipoprotein profile seem to be common in RA, contributing to cardiovascular diseases and a chronic inflammatory environment. Nevertheless, changes in the lipid profile at a molecular level in RA are still poorly understood. Therefore, the goal of this review was to gather all the information regarding lipid alterations in RA analyzed by mass spectrometry. Studies on the variation of lipid profile in RA using lipidomics showed that fatty acid and phospholipid metabolisms, especially in phosphatidylcholine and phosphatidylethanolamine, are affected in this disease. These promising results could lead to the discovery of new diagnostic lipid biomarkers for early diagnosis of RA and targets for personalized medicine.

scholarly journals Sex-Specific Differences in Glioblastoma

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1783
Author(s):  
Anna Carrano ◽  
Juan Jose Juarez ◽  
Diego Incontri ◽  
Antonio Ibarra ◽  
Hugo Guerrero Cazares
Keyword(s):  
Sex Differences ◽  
Immune System ◽  
Molecular Level ◽  
Deep Understanding ◽  
Protective Role ◽  
Men And Women ◽  
Individualized Approach ◽  
Male Patients ◽  
Outcome Differences

Sex differences have been well identified in many brain tumors. Even though glioblastoma (GBM) is the most common primary malignant brain tumor in adults and has the worst outcome, well-established differences between men and women are limited to incidence and outcome. Little is known about sex differences in GBM at the disease phenotype and genetical/molecular level. This review focuses on a deep understanding of the pathophysiology of GBM, including hormones, metabolic pathways, the immune system, and molecular changes, along with differences between men and women and how these dimorphisms affect disease outcome. The information analyzed in this review shows a greater incidence and worse outcome in male patients with GBM compared with female patients. We highlight the protective role of estrogen and the upregulation of androgen receptors and testosterone having detrimental effects on GBM. Moreover, hormones and the immune system work in synergy to directly affect the GBM microenvironment. Genetic and molecular differences have also recently been identified. Specific genes and molecular pathways, either upregulated or downregulated depending on sex, could potentially directly dictate GBM outcome differences. It appears that sexual dimorphism in GBM affects patient outcome and requires an individualized approach to management considering the sex of the patient, especially in relation to differences at the molecular level.

scholarly journals Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

2021 ◽  
Vol 22 (3) ◽  
pp. 1018
Author(s):  
Hiroaki Yokota
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Underlying Mechanism ◽  
Amino Acid Sequences ◽  
E Coli ◽  
X Ray Crystallography ◽  
Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

Welcome to AI Matters 7(1)

AI Matters ◽  
2021 ◽  
Vol 7 (1) ◽  
pp. 4-4
Author(s):  
Iolanda Leite ◽  
Anuj Karpatne
Keyword(s):  
High School Students ◽  
Regular Education ◽  
Physical World ◽  
School Students ◽  
Social Good ◽  
The Third ◽  
Ai Ethics ◽  
K 12 ◽  
Applications Of Ai

Welcome to the first issue of this year's AI Matters Newsletter! We start with a report on upcoming SIGAI Events by Dilini Samarasinghe and Conference reports by Louise Dennis, our conference coordination officers. In our regular Education column, Duri Long, Jonathan Moon, and Brian Magerko introduce two "unplugged" activities (i.e., no technology needed) to learn about AI focussed on K-12 AI Education. We then bring you our regular Policy column, where Larry Medsker covers several topics on AI policy, including the role of Big Tech on AI Ethics and an interview with Dr. Eric Daimler who is the CEO of the MIT-spinout Conexus.com. Finally, we close with four article contributions. The first article discusses emerging applications of AI in analyzing source code and its implications to several industries. The second article discusses topics in the area of physical scene understanding that are necessary for machines to perceive, interact, and reason about the physical world. The third article presents novel practices and highlights from the Fourth Workshop on Mechanism Design for Social Good. The fourth article provides a report on the "Decoding AI" event that was conducted online by ViSER for high school students and adults sponsored by ACM SIGAI.

scholarly journals Role of the ribosomal protein L27 revealed by single-molecule FRET study

2012 ◽  
Vol 21 (11) ◽  
pp. 1696-1704 ◽  
Author(s):  
Yuhong Wang ◽  
Ming Xiao
Keyword(s):  
Ribosomal Protein ◽  
Single Molecule ◽  
Single Molecule Fret
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