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Journal articles on the topic 'Biomolecular analyses'

Author: Grafiati

Published: 3 June 2025

Last updated: 31 July 2025

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1

Raković, Dejan, Miroljub Dugić, Jasmina Jeknić-Dugić, Milenko Plavšić, Stevo Jaćimovski, and Jovan Šetrajčić. "On Macroscopic Quantum Phenomena in Biomolecules and Cells: From Levinthal to Hopfield." BioMed Research International 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/580491.

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In the context of the macroscopic quantum phenomena of the second kind, we hereby seek for a solution-in-principle of the long standing problem of the polymer folding, which was considered by Levinthal as (semi)classically intractable. To illuminate it, we applied quantum-chemical and quantum decoherence approaches to conformational transitions. Our analyses imply the existence of novel macroscopic quantum biomolecular phenomena, with biomolecular chain folding in an open environment considered as a subtle interplay between energy and conformation eigenstates of this biomolecule, governed by q

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Bates, Kathleen E., and Hang Lu. "Optics-Integrated Microfluidic Platforms for Biomolecular Analyses." Biophysical Journal 110, no. 8 (2016): 1684–97. http://dx.doi.org/10.1016/j.bpj.2016.03.018.

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Gopinath, Subash C. B., and Penmetcha K. R. Kumar. "Biomolecular discrimination analyses by surface plasmon resonance." Analyst 139, no. 11 (2014): 2678. http://dx.doi.org/10.1039/c3an02052e.

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Shinji, Seiichi, Zenya Naito, Toshiyuki Ishiwata, et al. "Pathological and Biomolecular Analyses of Colorectal Endocrine Carcinoma." Journal of Nippon Medical School 74, no. 1 (2007): 87–88. http://dx.doi.org/10.1272/jnms.74.87.

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Perlasca, Paolo, Marco Frasca, Cheick Tidiane Ba, et al. "Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools." PLOS ONE 15, no. 12 (2020): e0244241. http://dx.doi.org/10.1371/journal.pone.0244241.

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The visual exploration and analysis of biomolecular networks is of paramount importance for identifying hidden and complex interaction patterns among proteins. Although many tools have been proposed for this task, they are mainly focused on the query and visualization of a single protein with its neighborhood. The global exploration of the entire network and the interpretation of its underlying structure still remains difficult, mainly due to the excessively large size of the biomolecular networks. In this paper we propose a novel multi-resolution representation and exploration approach that e

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Etibor, Temitope Akhigbe, Aidan O’Riain, Marta Alenquer, Christian Diwo, Sílvia Vale-Costa, and Maria João Amorim. "Challenges in Imaging Analyses of Biomolecular Condensates in Cells Infected with Influenza A Virus." International Journal of Molecular Sciences 24, no. 20 (2023): 15253. http://dx.doi.org/10.3390/ijms242015253.

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Biomolecular condensates are crucial compartments within cells, relying on their material properties for function. They form and persist through weak, transient interactions, often undetectable by classical biochemical approaches. Hence, microscopy-based techniques have been the most reliable methods to detail the molecular mechanisms controlling their formation, material properties, and alterations, including dissolution or phase transitions due to cellular manipulation and disease, and to search for novel therapeutic strategies targeting biomolecular condensates. However, technical challenge

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Tsumoto, K. "1SE52 Experimental approaches for systematic analyses of biomolecular interactions." Seibutsu Butsuri 45, supplement (2005): S16. http://dx.doi.org/10.2142/biophys.45.s16_1.

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Ranjbar, Bijan, and Pooria Gill. "Circular Dichroism Techniques: Biomolecular and Nanostructural Analyses- A Review." Chemical Biology & Drug Design 74, no. 2 (2009): 101–20. http://dx.doi.org/10.1111/j.1747-0285.2009.00847.x.

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Rudden, Lucas S. P., Samuel C. Musson, Justin L. P. Benesch, and Matteo T. Degiacomi. "Biobox: a toolbox for biomolecular modelling." Bioinformatics 38, no. 4 (2021): 1149–51. http://dx.doi.org/10.1093/bioinformatics/btab785.

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Abstract Motivation The implementation of biomolecular modelling methods and analyses can be cumbersome, often carried out with in-house software reimplementing common tasks, and requiring the integration of diverse software libraries. Results We present Biobox, a Python-based toolbox facilitating the implementation of biomolecular modelling methods. Availability and implementation Biobox is freely available on https://github.com/degiacom/biobox, along with its API and interactive Jupyter notebook tutorials.

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Rembe, Julian-Dario, Waseem Garabet, Jan-Wilm Lackmann, et al. "Assessment and Monitoring of the Wound Micro-Environment in Chronic Wounds Using Standardized Wound Swabbing for Individualized Diagnostics and Targeted Interventions." Biomedicines 12, no. 10 (2024): 2187. http://dx.doi.org/10.3390/biomedicines12102187.

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Background/Objectives: Patient-specific diagnostic and therapeutic approaches are important in the care of people with chronic wounds. The heterogeneity of underlying disease profiles and the diversity of the wound micro-environment make generalized approaches difficult. While high-throughput molecular diagnostic methods are increasingly widespread and available, the analysis of objective biomolecular disease patterns has not found its way into everyday wound management. The aim of this study is to evaluate the use of wound swab samples for the analysis of biomarkers and disease patterns in pe

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Caffo, Maria, Giovanna Casili, Gerardo Caruso, et al. "DKK3 Expression in Glioblastoma: Correlations with Biomolecular Markers." International Journal of Molecular Sciences 25, no. 7 (2024): 4091. http://dx.doi.org/10.3390/ijms25074091.

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Glioblastoma is the most common malignant primary tumor of the CNS. The prognosis is dismal, with a median survival of 15 months. Surgical treatment followed by adjuvant therapies such as radiotherapy and chemotherapy characterize the classical strategy. The WNT pathway plays a key role in cellular proliferation, differentiation, and invasion. The DKK3 protein, capable of acting as a tumor suppressor, also appears to be able to modulate the WNT pathway. We performed, in a series of 40 patients, immunohistochemical and Western blot evaluations of DKK3 to better understand how the expression of

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Krylov, Sergey N. "Nonequilibrium Capillary Electrophoresis of Equilibrium Mixtures (NECEEM): A Novel Method for Biomolecular Screening." Journal of Biomolecular Screening 11, no. 2 (2005): 115–22. http://dx.doi.org/10.1177/1087057105284339.

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Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) is a new separation-based affinity method. It has kinetic capabilities exceeding those of surface plasmon resonance (SPR) and does not require immobilization of molecules on the surface. Another distinctive feature of NECEEM is that—if it is combined with an advanced method for the mixing solutions inside a capillary, termed transverse diffusion of laminar flow profiles (TDLFP)—it requires only nanoliter volumes of solutions. The proven applications of NECEEM to biomolecular screening include 1) measuring kinetic and the

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Barlow, D. J., and T. D. J. Perkins. "Applications of interactive computer graphics in analyses of biomolecular structures." Natural Product Reports 7, no. 4 (1990): 311. http://dx.doi.org/10.1039/np9900700311.

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Rodríguez-Galván, Andrés, and Flavio F. Contreras-Torres. "Scanning Tunneling Microscopy of Biological Structures: An Elusive Goal for Many Years." Nanomaterials 12, no. 17 (2022): 3013. http://dx.doi.org/10.3390/nano12173013.

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Scanning tunneling microscopy (STM) is a technique that can be used to directly observe individual biomolecules at near-molecular scale. Within this framework, STM is of crucial significance because of its role in the structural analysis, the understanding the imaging formation, and the development of relative techniques. Four decades after its invention, it is pertinent to ask how much of the early dream has come true. In this study, we aim to overview different analyses for DNA, lipids, proteins, and carbohydrates. The relevance of STM imaging is exhibited as an opportunity to assist measure

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Heylen, Dries, Jannes Peeters, Jan Aerts, Gökhan Ertaylan, and Jef Hooyberghs. "BioMOBS: A multi-omics visual analytics workflow for biomolecular insight generation." PLOS ONE 18, no. 12 (2023): e0295361. http://dx.doi.org/10.1371/journal.pone.0295361.

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One of the challenges in multi-omics data analysis for precision medicine is the efficient exploration of undiscovered molecular interactions in disease processes. We present BioMOBS, a workflow consisting of two data visualization tools integrated with an open-source molecular information database to perform clinically relevant analyses (https://github.com/driesheylen123/BioMOBS). We performed exploratory pathway analysis with BioMOBS and demonstrate its ability to generate relevant molecular hypotheses, by reproducing recent findings in type 2 diabetes UK biobank data. The central visualisat

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Sarai, Akinori. "S04H2 Thermodynamic Databases and Analyses on Biomolecular Interactions(Thermodynamic Understanding of the Biomolecular Interactions Based on the Three-Dimensional Structures)." Seibutsu Butsuri 47, supplement (2007): S5. http://dx.doi.org/10.2142/biophys.47.s5_4.

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Hamada, Yuta, and Akira Kitamura. "Light-Induced Condensates Show Accumulation-Prone and Less Dynamic Properties in the Nucleus Compared to the Cytoplasm." Spectroscopy Journal 1, no. 2 (2023): 65–71. http://dx.doi.org/10.3390/spectroscj1020006.

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Biomolecular condensates, including membraneless organelles, are ubiquitously observed in subcellular compartments. However, the accumulation and dynamic properties of arbitrarily induced condensates remain elusive. Here, we show the size, amount, and dynamic properties of subcellular condensates using various fluorescence spectroscopic imaging analyses. Spatial image correlation spectroscopy showed that the size of blue-light-induced condensates of cryptochrome 2-derived oligomerization tag (CRY2olig) tagged with a red fluorescent protein in the nucleus was not different from that in the cyto

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Cui, Yanfang, Haiwang Wang, Su Liu, Yu Wang, and Jiadong Huang. "Target-activated DNA nanomachines for the ATP detection based on the SERS of plasmonic coupling from gold nanoparticle aggregation." Analyst 145, no. 2 (2020): 445–52. http://dx.doi.org/10.1039/c9an02051a.

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The self-assembly of plasmonic nanoparticles provides a powerful approach to generate surface-enhanced Raman scattering (SERS), which promotes the actual applications in chemical and biomolecular analyses.

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Di Zazzo, Antonio, Alessandra Micera, Marco Coassin, et al. "InflammAging at Ocular Surface: Clinical and Biomolecular Analyses in Healthy Volunteers." Investigative Opthalmology & Visual Science 60, no. 5 (2019): 1769. http://dx.doi.org/10.1167/iovs.18-25822.

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Edwards, H. G. M., R. Moeller, S. E. Jorge Villar, G. Horneck, and E. Stackebrandt. "Raman spectroscopic study of the photoprotection of extremophilic microbes against ultraviolet radiation." International Journal of Astrobiology 5, no. 4 (2006): 313–18. http://dx.doi.org/10.1017/s147355040600348x.

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Extremophiles use a range of pigments for protection against low-wavelength radiation in exposed terrestrial habitats and photoaccessory materials are synthesized for the effective harnessing of photosynthetically active radiation. Raman spectroscopy has been demonstrated to be a useful probe for information on the survival strategies employed by extremophilic bacteria through the identification of key biomolecular signatures of the suite of protective chemicals synthesized by the organisms in stressed environments. Raman spectroscopic analyses of Bacillus spp. spores, Bacillus atrophaeus (DSM

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Bada, Jeffrey L., Xueyun S. Wang, and Healy Hamilton. "Preservation of key biomolecules in the fossil record: current knowledge and future challenges." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354, no. 1379 (1999): 77–87. http://dx.doi.org/10.1098/rstb.1999.0361.

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We have developed a model based on the analyses of modern and Pleistocene eggshells and mammalian bones which can be used to understand the preservation of amino acids and other important biomolecules such as DNA in fossil specimens. The model is based on the following series of diagenetic reactions and processes involving amino acids: the hydrolysis of proteins and the subsequent loss of hydrolysis products from the fossil matrix with increasing geologic age; the racemization of amino acids which produces totally racemized amino acids in 10 5 –10 6 years in most environments on the Earth; the

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Kastritis, Panagiotis L., and Anne-Claude Gavin. "Enzymatic complexes across scales." Essays in Biochemistry 62, no. 4 (2018): 501–14. http://dx.doi.org/10.1042/ebc20180008.

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An unprecedented opportunity to integrate ~100 years of meticulous in vitro biomolecular research is currently provided in the light of recent advances in methods to visualize closer-to-native architectures of biomolecular machines, and metabolic enzymes in particular. Traditional views of enzymes, namely biomolecular machines, only partially explain their role, organization and kinetics in the cellular milieu. Enzymes self- or hetero-associate, form fibers, may bind to membranes or cytoskeletal elements, have regulatory roles, associate into higher order assemblies (metabolons) or even active

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Peters, Joshua M., Sydney L. Solomon, Christopher Y. Itoh, and Bryan D. Bryson. "Uncovering complex molecular networks in host–pathogen interactions using systems biology." Emerging Topics in Life Sciences 3, no. 4 (2019): 371–78. http://dx.doi.org/10.1042/etls20180174.

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Abstract Interactions between pathogens and their hosts can induce complex changes in both host and pathogen states to privilege pathogen survival or host clearance of the pathogen. To determine the consequences of specific host–pathogen interactions, a variety of techniques in microbiology, cell biology, and immunology are available to researchers. Systems biology that enables unbiased measurements of transcriptomes, proteomes, and other biomolecules has become increasingly common in the study of host–pathogen interactions. These approaches can be used to generate novel hypotheses or to chara

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Hintzen, Jordi C. J., Jordi Poater, Kiran Kumar, et al. "Comparison of Molecular Recognition of Trimethyllysine and Trimethylthialysine by Epigenetic Reader Proteins." Molecules 25, no. 8 (2020): 1918. http://dx.doi.org/10.3390/molecules25081918.

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Gaining a fundamental insight into the biomolecular recognition of posttranslationally modified histones by epigenetic reader proteins is of crucial importance to understanding the regulation of the activity of human genes. Here, we seek to establish whether trimethylthialysine, a simple trimethyllysine analogue generated through cysteine alkylation, is a good trimethyllysine mimic for studies on molecular recognition by reader proteins. Histone peptides bearing trimethylthialysine and trimethyllysine were examined for binding with five human reader proteins employing a combination of thermody

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Richter, Merle, Yannik Loth, Christian Weisenstein, et al. "Ultrasensitive marker-free biomolecular THz-detection for tumor-related analytics." Frequenz 76, no. 11-12 (2022): 627–37. http://dx.doi.org/10.1515/freq-2022-0092.

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Abstract Terahertz (THz) biosensing has emerged as an important research field, mainly driven by the resonant behavior of many biomolecules in this spectral range which holds potential for highly sensitive analyses. In this work, we present a detailed overview of our current research on THz biosensing, focusing on the development and analysis of THz biosensors based on frequency selective surfaces (FSS) for two different measurement scenarios: i) label-free, highly sensitive and selective analysis of dried biomolecules, and ii) sensitive and selective analysis in an aqueous environment. With o

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Greco, Enrico, Ola El-Aguizy, Mona Fouad Ali, et al. "Proteomic Analyses on an Ancient Egyptian Cheese and Biomolecular Evidence of Brucellosis." Analytical Chemistry 90, no. 16 (2018): 9673–76. http://dx.doi.org/10.1021/acs.analchem.8b02535.

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Šebela, Marek. "Biomolecular Profiling by MALDI-TOF Mass Spectrometry in Food and Beverage Analyses." International Journal of Molecular Sciences 23, no. 21 (2022): 13631. http://dx.doi.org/10.3390/ijms232113631.

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Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has frequently been applied to the analysis of biomolecules. Its strength resides not only in compound identification but particularly in acquiring molecular profiles providing a high discriminating power. The main advantages include its speed, simplicity, versatility, minimum sample preparation needs, and a relatively high tolerance to salts. Other benefits are represented by the possibility of automation, high throughput, sensitivity, accuracy, and good reproducibility, allowing quantitative studies.

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Si, Haiyang, Claudia Maria Tucciarone, Mattia Cecchinato, Matteo Legnardi, Sandro Mazzariol, and Cinzia Centelleghe. "Comparison between Sampling Techniques for Virological Molecular Analyses: Dolphin Morbillivirus and Herpesvirus Detection from FTA® Card and Frozen Tissue." Viruses 15, no. 12 (2023): 2422. http://dx.doi.org/10.3390/v15122422.

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Stranded animals offer valuable information on marine mammal physiology and pathology; however, the decomposition state of the carcasses and lack of a rigorous cold chain for sample preservation can sometimes discourage diagnostic analyses based on nucleic acid detection. The present paper aims at evaluating the reliability of FTA® card tissue imprints as an alternative matrix to frozen tissues for virological analyses based on biomolecular methods. Given the contribution of Cetacean morbillivirus (CeMV) to strandings and the increase of herpesvirus detection in cetaceans, these two pathogens

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Al-Maawi, Sarah, Priscilia Valenzuela, Eva Dohle, Anja Heselich, Robert Sader, and Shahram Ghanaati. "Comparison of Different Fixation Methods for Combined Histological and Biomolecular Analysis of Fixed and Decalcified Bone Samples." Methods and Protocols 5, no. 4 (2022): 64. http://dx.doi.org/10.3390/mps5040064.

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The combination of histological and biomolecular analyses provides deep understanding of different biological processes and is of high interest for basic and applied research. However, the available analytical methods are still limited, especially when considering bone samples. This study compared different fixation media to identify a sufficient analytical method for the combination of histological, immuno-histological and biomolecular analyses of the same fixed, processed and paraffin embedded bone sample. Bone core biopsies of rats’ femurs were fixed in different media (RNAlater + formaldeh

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Carducci, A., B. Casini, A. Bani, et al. "Virological control of groundwater quality using biomolecular tests." Water Science and Technology 47, no. 3 (2003): 261–66. http://dx.doi.org/10.2166/wst.2003.0205.

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Deep groundwater, even if generally protected, could be contaminated by surface or rain water infiltration through soil fractures, septic tanks, cesspits, land irrigation, disposal of wastewater and disposal of muds from depuration systems. The sanitary importance of such possible contamination is related to the different uses of the water and it is at the maximum level when it is intended for human use. Routine microbiological analyses do not consider viruses, only bacterial parameters, as contamination indicators. However, it is known that enteric viruses can survive a long time in deep aqui

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Stojanovski, Darko, Ivana Živaljević, Vesna Dimitrijević, et al. "Living off the land: Terrestrial-based diet and dairying in the Neolithic Balkans." PLOS ONE 15, no. 8 (2020): e0237608. https://doi.org/10.1371/journal.pone.0237608.

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The application of biomolecular techniques to archaeological materials from the Balkans is providing valuable new information on the prehistory of the region. This is especially relevant for the study of the neolithisation process in SE Europe, which gradually affected the rest of the continent. Here, to answer questions regarding diet and subsistence practices in early farming societies in the central Balkans, we combine organic residue analyses of archaeological pottery, taxonomic and isotopic study of domestic animal remains and biomolecular analyses of human dental calculus. The results fr

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Florenzano, Assunta, Eleonora Clò, and Jérémy Jacob. "Pollen and Molecular Biomarkers from Sedimentary Archives in the Central Po Plain (N Italy): Assessing Their Potential to Deepen Changes in Natural and Agricultural Systems." Sustainability 15, no. 13 (2023): 10408. http://dx.doi.org/10.3390/su151310408.

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This paper proposes to improve the information provided by biological indicators from sedimentary archives by integrating biomolecular techniques and botanical skills. This study represents a first proposal for combining pollen and biomolecular markers to detect land use and improve knowledge of past environmental change drivers. The specific aim of the research is to verify the relationship between miliacin (a pentacyclic triterpene methyl ether, usually interpreted as a broomcorn millet biomarker) and Panicum pollen in three near-site stratigraphic sequences of the Terramara S. Rosa di Povig

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Budja, Mihael. "THE NEOLITHISATION OF EURASIA: ARCHAEOLOGICAL, ARCHAEOGENTIC AND BIOMOLECULAR PERSPECTIVES." Samara Journal of Science 3, no. 3 (2014): 23–34. http://dx.doi.org/10.17816/snv20143204.

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The Mesolithic-Neolithic transformation was far more complex and variable process than previously hypothesised. The introduction of ceramic technology and initial pottery distributions in Eurasia show a wide-spread appearance of different pottery-making techniques and ornamental principles in different cultural and chronological contexts. The pattern cannot be explained by way of a narrow and gradual southeast - north west oriented spread of both people and vessels across Europe in the context of demic diffusion migratory model. The data indicate that ceramic technology was invented and reinve

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Rahman, Md Ashiqur, Abdullah Aman Tutul, Sifat Muhammad Abdullah, and Md Shamsuzzoha Bayzid. "CHAPAO: Likelihood and hierarchical reference-based representation of biomolecular sequences and applications to compressing multiple sequence alignments." PLOS ONE 17, no. 4 (2022): e0265360. http://dx.doi.org/10.1371/journal.pone.0265360.

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Background High-throughput experimental technologies are generating tremendous amounts of genomic data, offering valuable resources to answer important questions and extract biological insights. Storing this sheer amount of genomic data has become a major concern in bioinformatics. General purpose compression techniques (e.g. gzip, bzip2, 7-zip) are being widely used due to their pervasiveness and relatively good speed. However, they are not customized for genomic data and may fail to leverage special characteristics and redundancy of the biomolecular sequences. Results We present a new lossle

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Reddy, Tyler, and Jan K. Rainey. "Interpretation of biomolecular NMR spin relaxation parametersThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 88, no. 2 (2010): 131–42. http://dx.doi.org/10.1139/o09-152.

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Biomolecular nuclear magnetic resonance (NMR) spin relaxation experiments provide exquisite information on the picosecond to nanosecond timescale motions of bond vectors. Spin–lattice (T1) and spin–spin (T2) relaxation times and the steady-state nuclear Overhauser effect (NOE) are the first set of parameters extracted from typical 15N or 13C NMR relaxation experiments. Therefore, verifying that T1, T2, and NOE are consistent with theoretical predictions is an important step before carrying out the more detailed model-free and reduced spectral density mapping analyses commonly employed. In this

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Voegele, Kristyn K., Zachary M. Boles, Paul V. Ullmann, Elena R. Schroeter, Wenxia Zheng, and Kenneth J. Lacovara. "Soft Tissue and Biomolecular Preservation in Vertebrate Fossils from Glauconitic, Shallow Marine Sediments of the Hornerstown Formation, Edelman Fossil Park, New Jersey." Biology 11, no. 8 (2022): 1161. http://dx.doi.org/10.3390/biology11081161.

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Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted paleomolecular analyses of shallow marine vertebrate fossils from the Cretaceous–Paleogene Hornerstown Formation, an 80–90% glauconitic greensand from Jean and Ric Edelman Fossil Park in Mantua Township, NJ. Twelve samples were demineralized and found to yield products morphologically co

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Terabe, Shigeru, Maria Rowena N. Monton, Thomas Le Saux, and Koshi Imami. "Applications of capillary electrophoresis to high-sensitivity analyses of biomolecules." Pure and Applied Chemistry 78, no. 5 (2006): 1057–67. http://dx.doi.org/10.1351/pac200678051057.

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To increase the detection sensitivity of capillary electrophoresis (CE) and thereby widen its application to biomolecular analyses, we have developed a number of on-line preconcentration strategies, i.e., techniques to increase sample loading without compromising resolution and efficiency. Two such techniques, namely, dynamic pH junction and field-enhanced sample injection (FESI) are covered in this work. Dynamic pH junction is predicated on a sharp reduction in an analyte's migration velocity following a reversal of its electrophoretic direction from the acidic sample zone to the basic backgr

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Hermon, L., J. Denonfoux, J. Hellal, et al. "Dichloromethane biodegradation in multi-contaminated groundwater: Insights from biomolecular and compound-specific isotope analyses." Water Research 142 (October 2018): 217–26. http://dx.doi.org/10.1016/j.watres.2018.05.057.

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Balzamino, Bijorn Omar, Lucia Dinice, Andrea Cacciamani, et al. "Short-Term In Vitro ROS Detection and Oxidative Stress Regulators in Epiretinal Membranes and Vitreous from Idiopathic Vitreoretinal Diseases." BioMed Research International 2022 (December 16, 2022): 1–12. http://dx.doi.org/10.1155/2022/7497816.

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Background. A plethora of inflammatory, angiogenic, and tissue remodeling factors has been reported in idiopathic epiretinal membranes (ERMs). Herein we focused on the expression of a few mediators (oxidative, inflammatory, and angiogenic/vascular factors) by means of short-term vitreal cell cultures and biomolecular analysis. Methods. Thirty-nine (39) ERMs and vitreal samples were collected at the time of vitreoretinal surgery and biomolecular analyses were performed in clear vitreous, vitreal cell pellets, and ERMs. ROS products and iNOS were investigated in adherent vitreal cells and/or ERM

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Xie, Jiang, Dongfang Lu, Jiaxin Li, et al. "Kernel differential subgraph reveals dynamic changes in biomolecular networks." Journal of Bioinformatics and Computational Biology 16, no. 01 (2018): 1750027. http://dx.doi.org/10.1142/s0219720017500275.

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Many major diseases, including various types of cancer, are increasingly threatening human health. However, the mechanisms of the dynamic processes underlying these diseases remain ambiguous. From the holistic perspective of systems science, complex biological networks can reveal biological phenomena. Changes among networks in different states influence the direction of living organisms. The identification of the kernel differential subgraph (KDS) that leads to drastic changes is critical. The existing studies contribute to the identification of a KDS in networks with the same nodes; however,

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Moen, Birgitte, Astrid Oust Janbu, Solveig Langsrud, et al. "Global responses ofEscherichia colito adverse conditions determined by microarrays and FT-IR spectroscopy." Canadian Journal of Microbiology 55, no. 6 (2009): 714–28. http://dx.doi.org/10.1139/w09-016.

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The global gene expression and biomolecular composition in an Escherichia coli model strain exposed to 10 adverse conditions (sodium chloride, ethanol, glycerol, hydrochloric and acetic acid, sodium hydroxide, heat (46 °C), and cold (15 °C), as well as ethidium bromide and the disinfectant benzalkonium chloride) were determined using DNA microarrays and Fourier transform infrared (FT-IR) spectroscopy. In total, approximately 40% of all investigated genes (1682/4279 genes) significantly changed expression, compared with a nonstressed control. There were, however, only 3 genes (ygaW (unknown fun

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Llido, John Paul, Giorgia Valerio, David Křepelka, et al. "Transcriptomic and Proteomic Changes in the Brain Along with Increasing Phenotypic Severity in a Rat Model of Neonatal Hyperbilirubinemia." International Journal of Molecular Sciences 26, no. 13 (2025): 6262. https://doi.org/10.3390/ijms26136262.

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Kernicterus spectrum disorder is the permanent and highly disabling neurologic sequel of neonatal exposure to hyperbilirubinemia, presenting, among other symptoms, variable and untreatable motor disabilities. To search for potential biomolecular explanations, we used a Gunn rat colony exhibiting spontaneous hyperbilirubinemia and a large variability of motor deficits on a beam-walking test. Histological and microscopic analyses confirmed worsening damage in the cerebellum (Cll; hypoplasia, increased death of neurons, and disrupted astroglial structures) and parietal motor cortex (hCtx; increas

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Cardillo, Lorena, Claudio de Martinis, Sergio Brandi, et al. "SARS-CoV-2 Serological and Biomolecular Analyses among Companion Animals in Campania Region (2020–2021)." Microorganisms 10, no. 2 (2022): 263. http://dx.doi.org/10.3390/microorganisms10020263.

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The first reports of SARS-CoV-2 among domestic and wild animals, together with the rapid emergence of new variants, have created serious concerns regarding a possible spillback from animal hosts, which could accelerate the evolution of new viral strains. The present study aimed to investigate the prevalence and the transmission of SARS-CoV-2 among both owned and stray pets. A total of 182 dogs and 313 cats were tested for SARS-CoV-2. Specimens collected among owned and stray pets were subjected to RT-PCR and serological examinations. No viral RNA was detected, while anti-N antibodies were obse

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Johansen, Knut, Ingemar Lundström, and Bo Liedberg. "Sensitivity deviation: instrumental linearity errors that influence concentration analyses and kinetic evaluation of biomolecular interactions." Biosensors and Bioelectronics 15, no. 9-10 (2000): 503–9. http://dx.doi.org/10.1016/s0956-5663(00)00109-3.

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Song, Min Ok, Jianying Li, and Jonathan H. Freedman. "Physiological and toxicological transcriptome changes in HepG2 cells exposed to copper." Physiological Genomics 38, no. 3 (2009): 386–401. http://dx.doi.org/10.1152/physiolgenomics.00083.2009.

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Copper is an essential trace element; however, at supraphysiological levels, it can be extremely toxic. Microarray data from HepG2 cells exposed to 100, 200, 400, and 600 μM copper for 4, 8, 12 and 24 h were generated and analyzed. Principal components, K-means, and hierarchical clustering, interactome, and pathway mapping analyses indicated that these exposure conditions induce physiological and toxicological changes in the HepG2 transcriptome. As a general trend, when the level of toxicity increases, the number and diversity of affected genes, Gene Ontology categories, regulatory pathways, a

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Power, Karen, Manuela Martano, Nadia Piscopo, et al. "Prevalence of Eucoleus garfiai in Wild Boars Hunted at Different Altitudes in the Campania and Latium Regions (Italy)." Animals 13, no. 4 (2023): 706. http://dx.doi.org/10.3390/ani13040706.

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Recent reports of Eucoleus garfiai in wild boars in southern Italy have highlighted the need for collecting epidemiological data on the presence of this parasite and understanding the role of possible interactions between wild boars, E. garfiai, and the environment. This study analyses, using histopathological and biomolecular techniques, the presence of E. garfiai in tongue samples of wild boars hunted in four provinces of the Campania and Latium regions (Italy), in areas located above and below 900 m above sea level (asl). Histopathological examinations revealed the presence of adults and eg

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Guler, Adil. "Thermodynamic and Structural Signatures of Arginine Self-Assembly Across Concentration Regimes." Processes 13, no. 7 (2025): 1998. https://doi.org/10.3390/pr13071998.

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Arginine plays a critical role in biomolecular interactions due to its guanidinium side chain, which enables multivalent electrostatic and hydrogen bonding contacts. In this study, atomistic molecular dynamics simulations were conducted across a broad concentration range (26–605 mM) to investigate the thermodynamic and structural features of arginine self-assembly in aqueous solution. Key observables—including hydrogen bond count, radius of gyration, contact number, and isobaric heat capacity—were analyzed to characterize emergent behavior. A three-regime aggregation pattern (dilute, cooperati

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Baud, A., L. Aymé, F. Gonnet, et al. "SOLEIL shining on the solution-state structure of biomacromolecules by synchrotron X-ray footprinting at the Metrology beamline." Journal of Synchrotron Radiation 24, no. 3 (2017): 576–85. http://dx.doi.org/10.1107/s1600577517002478.

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Synchrotron X-ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small-angle X-ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X-ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France. This work presents X-ray footp

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Helliwell, John R., Alice Brink, Surasak Kaenket, Victoria Laurina Starkey, and Simon W. M. Tanley. "X-ray diffraction in temporally and spatially resolved biomolecular science." Faraday Discussions 177 (2015): 429–41. http://dx.doi.org/10.1039/c4fd00166d.

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Time-resolved Laue protein crystallography at the European Synchrotron Radiation Facility (ESRF) opened up the field of sub-nanosecond protein crystal structure analyses. There are a limited number of such time-resolved studies in the literature. Why is this? The X-ray laser now gives us femtosecond (fs) duration pulses, typically 10 fs up to ∼50 fs. Their use is attractive for the fastest time-resolved protein crystallography studies. It has been proposed that single molecules could even be studied with the advantage of being able to measure X-ray diffraction from a ‘crystal lattice free’ sin

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Okuwaki, Koji, Kazuki Akisawa, Ryo Hatada, et al. "Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method." Applied Physics Express 15, no. 1 (2021): 017001. http://dx.doi.org/10.35848/1882-0786/ac4300.

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Abstract In large biomolecular systems such as protein complexes, there are huge numbers of combinations of inter-residue interactions whose comprehensive analyses are often beyond the intuitive processing by researchers. Here we propose a computational method to allow for a systematic analysis of these interactions based on the fragment molecular orbital calculations, in which the inter-fragment interaction energies are comprehensively processed by the singular value decomposition. For a trimer complex of SARS-CoV-2 spike protein, three-body interactions among residues belonging to three chai

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