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Journal articles on the topic 'Imbalance of protein'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Yao, Yalin, Hao Chen, Jianxin Wang, and Yeru Wang. "Generative and Contrastive Self-Supervised Learning for Virulence Factor Identification Based on Protein–Protein Interaction Networks." Microorganisms 13, no. 7 (2025): 1635. https://doi.org/10.3390/microorganisms13071635.

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Virulence factors (VFs), produced by pathogens, facilitate pathogenic microorganisms to invade, colonize, and damage the host cells. Accurate VF identification advances pathogenic mechanism understanding and provides novel anti-virulence targets. Existing models primarily utilize protein sequence features while overlooking the systematic protein–protein interaction (PPI) information, despite pathogenesis typically resulting from coordinated protein–protein actions. Moreover, a severe imbalance exists between virulence and non-virulence proteins, which causes existing models trained on balanced

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Jensen, Kim, Stephen J. Simpson, Vivi H. Nielsen, John Hunt, David Raubenheimer, and David Mayntz. "Nutrient-specific compensatory feeding in a mammalian carnivore, the mink, Neovison vison." British Journal of Nutrition 112, no. 7 (2014): 1226–33. http://dx.doi.org/10.1017/s0007114514001664.

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Balancing of macronutrient intake has only recently been demonstrated in predators. In particular, the ability to regulate carbohydrate intake is little studied in obligate carnivores, as carbohydrate is present at very low concentrations in prey animal tissue. In the present study, we determined whether American mink (Neovison vison) would compensate for dietary nutritional imbalances by foraging for complementary macronutrients (protein, lipid and carbohydrate) when subsequently given a dietary choice. We used three food pairings, within which two macronutrients differed relative to each oth

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Derganc, Jure, Bruno Antonny, and Alenka Čopič. "Membrane bending: the power of protein imbalance." Trends in Biochemical Sciences 38, no. 11 (2013): 576–84. http://dx.doi.org/10.1016/j.tibs.2013.08.006.

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BATUWITA, RUKSHAN, and VASILE PALADE. "ADJUSTED GEOMETRIC-MEAN: A NOVEL PERFORMANCE MEASURE FOR IMBALANCED BIOINFORMATICS DATASETS LEARNING." Journal of Bioinformatics and Computational Biology 10, no. 04 (2012): 1250003. http://dx.doi.org/10.1142/s0219720012500035.

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One common and challenging problem faced by many bioinformatics applications, such as promoter recognition, splice site prediction, RNA gene prediction, drug discovery and protein classification, is the imbalance of the available datasets. In most of these applications, the positive data examples are largely outnumbered by the negative data examples, which often leads to the development of sub-optimal prediction models having high negative recognition rate (Specificity = SP) and low positive recognition rate (Sensitivity = SE). When class imbalance learning methods are applied, usually, the SE

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Mannucci, P. M., A. Tripodi, B. Bottasso, et al. "Markers of Procoagulant Imbalance in Patients with Inherited Thrombophilic Syndromes." Thrombosis and Haemostasis 67, no. 02 (1992): 200–202. http://dx.doi.org/10.1055/s-0038-1648412.

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SummaryIn 107 asymptomatic and untreated patients with inherited syndromes associated with thrombophilia (antithrombin III, protein C and protein S deficiencies), we compared in parallel two plasma peptides which reflect activation of the common coagulation pathway: the prothrombin fragment 1 + 2 (F1+2) and fibrinopeptide A (FPA). Both F1+2 and FPA were measured with simple, commercially available ELISA methods. High levels of F1+2 or FPA were found in about one fourth of the patients as a whole. When patients were divided according to the type of inherited thrombophilie syndrome, it appeared

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Squitti, Rosanna, Peter Faller, Christelle Hureau, Alberto Granzotto, Anthony R. White, and Kasper P. Kepp. "Copper Imbalance in Alzheimer’s Disease and Its Link with the Amyloid Hypothesis: Towards a Combined Clinical, Chemical, and Genetic Etiology." Journal of Alzheimer's Disease 83, no. 1 (2021): 23–41. http://dx.doi.org/10.3233/jad-201556.

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The cause of Alzheimer’s disease (AD) is incompletely defined. To date, no mono-causal treatment has so far reached its primary clinical endpoints, probably due to the complexity and diverse neuropathology contributing to the neurodegenerative process. In the present paper, we describe the plausible etiological role of copper (Cu) imbalance in the disease. Cu imbalance is strongly associated with neurodegeneration in dementia, but a complete biochemical etiology consistent with the clinical, chemical, and genetic data is required to support a causative association, rather than just correlation

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Karmazina, Irina, and Hady Al-Rihani. "Cytokines and C-Reactive Protein-Trigger of Imbalance of the Hemostasis System during Inflammation." Ukraïnsʹkij žurnal medicini, bìologìï ta sportu 2, no. 2 (2017): 21–25. http://dx.doi.org/10.26693/jmbs02.02.021.

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Campbell, Katie M., Justin Saco, Egmidio Medina, et al. "Abstract 3818: Infrequent chromosomal loss and recurrent gains lead to imbalanced expression of HLA genes in melanoma." Cancer Research 82, no. 12_Supplement (2022): 3818. http://dx.doi.org/10.1158/1538-7445.am2022-3818.

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Abstract Introduction: Loss-of-heterozygosity (LOH) events in chromosome 6p, comprising the human leukocyte antigen (HLA) genes, have been reported in about 10% of cutaneous melanoma (compared to 20-40% of squamous cell carcinomas), while copy number gains in this region have been observed in over 50% of melanoma. Recent studies focused in HLA allelic loss have been restricted to DNA-based approaches, and have not been validated orthogonally at the RNA or protein levels. Here, using clinical melanoma biopsies and patient-derived melanoma cell lines, we show that genetic alterations in HLA gene

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Straznicka, Helena. "Protein requirement and amino acid imbalance in quail." British Poultry Science 31, no. 1 (1990): 139–45. http://dx.doi.org/10.1080/00071669008417239.

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10

Kimball, Scot R., and Charles H. Lang. "Mechanisms Underlying Muscle Protein Imbalance Induced by Alcohol." Annual Review of Nutrition 38, no. 1 (2018): 197–217. http://dx.doi.org/10.1146/annurev-nutr-071816-064642.

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Both acute intoxication and longer-term cumulative ingestion of alcohol negatively impact the metabolic phenotype of both skeletal and cardiac muscle, independent of overt protein calorie malnutrition, resulting in loss of skeletal muscle strength and cardiac contractility. In large part, these alcohol-induced changes are mediated by a decrease in protein synthesis that in turn is governed by impaired activity of a protein kinase, the mechanistic target of rapamycin (mTOR). Herein, we summarize recent advances in understanding mTOR signal transduction, similarities and differences between the

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Houtkooper, Riekelt H., Laurent Mouchiroud, Dongryeol Ryu, et al. "Mitonuclear protein imbalance as a conserved longevity mechanism." Nature 497, no. 7450 (2013): 451–57. http://dx.doi.org/10.1038/nature12188.

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12

Cordeiro, André V., Rafael S. Brícola, Renata R. Braga, et al. "Aerobic Exercise Training Induces the Mitonuclear Imbalance and UPRmt in the Skeletal Muscle of Aged Mice." Journals of Gerontology: Series A 75, no. 12 (2020): 2258–61. http://dx.doi.org/10.1093/gerona/glaa059.

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Abstract The impairment of the mitochondrial functions is a hallmark of aging. During aging, there is a downregulation of two mechanisms strictly associated with mitochondrial integrity, including the mitonuclear imbalance (eg, imbalance in mitochondrial- versus nuclear-encoded mitochondrial proteins) and the mitochondrial unfolded protein response (UPRmt). Here, we evaluated the effects of aerobic exercise in the mitonuclear imbalance and UPRmt markers in the skeletal muscle of old mice. We combined the physiological tests, molecular and bioinformatic analyzes to evaluate the effects of 4 wee

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Linovskaya, N. V., E. V. Mazukabzova, O. S. Rudenko, and T. V. Savenkova. "Justification of unconventional protein-containing raw materials for the construction of milk chocolate formulas with increased biological value." Vestnik MGTU 23, no. 3 (2020): 205–13. http://dx.doi.org/10.21443/1560-9278-2020-23-3-205-213.

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Milk chocolate is particularly popular with different age groups. It is characterized by low protein content with a large amount of fats and carbohydrates determining the food imbalance of the product. In conditions of high-grade animal proteins deficiency the selection of high-quality protein-containing ingredients for food production is very relevant. The aim of this work is to study the protein adequacy of various components of milk chocolate to enhance its biological value. The amino acid scale method has been used to assess the biological value of proteins; it is based on the determinatio

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Voloshchuk, O. N., Yu V. Stus, and G. P. Kopylchuk. "Features of free radical processes in the liver of rats with a nutrient imbalance." Biomeditsinskaya Khimiya 66, no. 5 (2020): 386–91. http://dx.doi.org/10.18097/pbmc20206605386.

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The activity of free radical processes in liver mitochondria was investigated in rats kept on high-sucrose and low protein/high-sucrose diets. Excess of dietary sucrose caused intensification of free radical processes in liver mitochondria as evidenced by increased hydroxyl radical generation, accumulation of primary (conjugated dienes, ketodienes) and secondary products (TBA-reactive products) of lipid peroxidation, increased cholesterol/phospholipids ratio and also accumulation of oxidative modification products of proteins (carbonyl derivatives). Additional nutritional protein deficiency (l

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Prado-Alcalá, Roberto A., Sofía González-Salinas, Anaid Antaramián, Gina L. Quirarte, Paola C. Bello-Medina, and Andrea C. Medina. "Imbalance in cerebral protein homeostasis: Effects on memory consolidation." Behavioural Brain Research 393 (September 2020): 112767. http://dx.doi.org/10.1016/j.bbr.2020.112767.

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Zeng, Mei, and Kang Zeng. "Soluble fibrinogen-like protein 2 in condyloma acuminatum lesions." Journal of Infection in Developing Countries 14, no. 06 (2020): 589–96. http://dx.doi.org/10.3855/jidc.12282.

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Introduction: An imbalance in type 1 (Th1) and type 2 (Th2) T helper cells is associated with the development and recurrence of condyloma acuminatum (CA); however, the mechanisms underlying this imbalance remain unknown. We investigated soluble fibrinogen-like protein 2 (sFGL2), which is an effector of regulatory T cells (Tregs), to determine its role in the Th1/Th2 imbalance of CA. Methodology: Lesion and blood samples were obtained from 30 CA patients, and these samples were compared with genital skin and blood samples from 20 control subjects. Serum sFGL2, mRNA, and protein levels wer

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Zhu, Yi-Heng, Jun Hu, Yong Qi, Xiao-Ning Song, and Dong-Jun Yu. "Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites." Combinatorial Chemistry & High Throughput Screening 22, no. 7 (2019): 455–69. http://dx.doi.org/10.2174/1386207322666190925125524.

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Aim and Objective: The accurate identification of protein-ligand binding sites helps elucidate protein function and facilitate the design of new drugs. Machine-learning-based methods have been widely used for the prediction of protein-ligand binding sites. Nevertheless, the severe class imbalance phenomenon, where the number of nonbinding (majority) residues is far greater than that of binding (minority) residues, has a negative impact on the performance of such machine-learning-based predictors. Materials and Methods: In this study, we aim to relieve the negative impact of class imbalance by

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Xia, Chun-Qiu, Xiaoyong Pan, and Hong-Bin Shen. "Protein–ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data." Bioinformatics 36, no. 10 (2020): 3018–27. http://dx.doi.org/10.1093/bioinformatics/btaa110.

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Abstract Motivation Knowledge of protein–ligand binding residues is important for understanding the functions of proteins and their interaction mechanisms. From experimentally solved protein structures, how to accurately identify its potential binding sites of a specific ligand on the protein is still a challenging problem. Compared with structure-alignment-based methods, machine learning algorithms provide an alternative flexible solution which is less dependent on annotated homogeneous protein structures. Several factors are important for an efficient protein–ligand prediction model, e.g. di

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Hasuda, A. L., K. K. M. C. Flaiban, J. A. N. Lisbôa, L. A. Gomes, I. G. Polizelli, and L. S. Santana. "Identifying hydric, electrolytic and acid-base imbalances through traditional and quantitative approaches in dogs with hemorrhagic gastroenteritis." Arquivo Brasileiro de Medicina Veterinária e Zootecnia 72, no. 1 (2020): 93–101. http://dx.doi.org/10.1590/1678-4162-11017.

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ABSTRACT Vomiting and diarrhea are two important clinical signs that can cause significant electrolytic and acid-base imbalances. The purposes of this study were to characterize hydric, electrolytic and acid-base disorders presented by puppies with hemorrhagic gastroenteritis and to compare the traditional and quantitative approaches to acid-base status interpretation. Sixty-one animals with a history of vomiting and/or diarrhea were used in this study and the following tests were performed: complete blood count, total plasma protein concentration and hemogasometry. Mean, standard deviation an

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Gadoth, Avi, Michal Nisnboym Ziv, Yifat Alcalay, et al. "Electrolyte Imbalance in Anti-LGI1 Encephalitis." Neurology - Neuroimmunology Neuroinflammation 10, no. 6 (2023): e200155. http://dx.doi.org/10.1212/nxi.0000000000200155.

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Background and ObjectivesAntileucine-rich glioma-inactivated 1 (anti-LGI1) autoimmune encephalitis was first described in 2010 and is today the most common type of limbic encephalitis. During the course of the disease, 60%–88% of the patients develop hyponatremia. The etiology of the sodium disorder is unclear, often presumed to be the result of the syndrome of inappropriate antidiuretic hormone secretion (SIADH). Other electrolyte abnormalities have not been reported in association with anti-LGI1 antibody encephalitis. Due to the presence of hypomagnesemia and hypophosphatemia in our patients

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Dong, Hongzhi, Bin Wang, and Li Pan. "Study on the interaction mechanism of phospholipid imbalance and endoplasmic reticulum protein secretion imbalance in Aspergillus niger." Biochimica et Biophysica Acta (BBA) - Biomembranes 1863, no. 3 (2021): 183530. http://dx.doi.org/10.1016/j.bbamem.2020.183530.

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Wójcik, Piotr, Agnieszka Gęgotek, Adam Wroński, Anna Jastrząb, Agnieszka Żebrowska, and Elżbieta Skrzydlewska. "Effect of redox imbalance on protein modifications in lymphocytes of psoriatic patients." Journal of Biochemistry 167, no. 3 (2019): 323–31. http://dx.doi.org/10.1093/jb/mvz096.

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Abstract Lymphocytes are one of the most important cells involved in the pathophysiology of psoriasis; therefore, the aim of this study was to assess the redox imbalance and protein modifications in the lymphocytes of patients with psoriasis vulgaris (PsV) or psoriatic arthritis (PsA). The results show a stronger shift in redox status to pro-oxidative conditions (observed as an increased reactive oxygen species level, a decrease in catalase activity and lower levels of glutathione peroxidase and vitamin E compared with healthy controls) in the lymphocytes of PsA than PsV patients. It is also f

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Ruan, Xiaoli, Dongming Zhou, Rencan Nie, and Yanbu Guo. "Predictions of Apoptosis Proteins by Integrating Different Features Based on Improving Pseudo-Position-Specific Scoring Matrix." BioMed Research International 2020 (January 14, 2020): 1–13. http://dx.doi.org/10.1155/2020/4071508.

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Apoptosis proteins are strongly related to many diseases and play an indispensable role in maintaining the dynamic balance between cell death and division in vivo. Obtaining localization information on apoptosis proteins is necessary in understanding their function. To date, few researchers have focused on the problem of apoptosis data imbalance before classification, while this data imbalance is prone to misclassification. Therefore, in this work, we introduce a method to resolve this problem and to enhance prediction accuracy. Firstly, the features of the protein sequence are captured by com

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Hussin, Sahar K., Salah M. Abdelmageid, Adel Alkhalil, Yasser M. Omar, Mahmoud I. Marie, and Rabie A. Ramadan. "Handling Imbalance Classification Virtual Screening Big Data Using Machine Learning Algorithms." Complexity 2021 (January 28, 2021): 1–15. http://dx.doi.org/10.1155/2021/6675279.

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Virtual screening is the most critical process in drug discovery, and it relies on machine learning to facilitate the screening process. It enables the discovery of molecules that bind to a specific protein to form a drug. Despite its benefits, virtual screening generates enormous data and suffers from drawbacks such as high dimensions and imbalance. This paper tackles data imbalance and aims to improve virtual screening accuracy, especially for a minority dataset. For a dataset identified without considering the data’s imbalanced nature, most classification methods tend to have high predictiv

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bio Klamt, Fá, Felipe Dal-Pizzol, Mario Luiz Conte da Frota, et al. "Imbalance of antioxidant defense in mice lacking cellular prion protein." Free Radical Biology and Medicine 30, no. 10 (2001): 1137–44. http://dx.doi.org/10.1016/s0891-5849(01)00512-3.

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Kim, Jong Min, Uk Lee, Jin Yong Kang, Seon Kyeong Park, Jong Cheol Kim, and Ho Jin Heo. "Matcha Improves Metabolic Imbalance-Induced Cognitive Dysfunction." Oxidative Medicine and Cellular Longevity 2020 (November 28, 2020): 1–19. http://dx.doi.org/10.1155/2020/8882763.

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This study was conducted to assess the protective effect of extract of match (EM) on high-fat diet- (HFD-) induced cognitive deficits in male C57BL/6 mice. It was found that EM improved glucose tolerance status by measuring OGTT and IPGTT with HFD-induced mice. EM protected behavioral and memory dysfunction in Y-maze, passive avoidance, and Morris water maze tests. Consumption of EM reduced fat mass, dyslipidemia, and inflammation in adipose tissue. Also, EM ameliorated hepatic and cerebral antioxidant systems. EM improved the cerebral cholinergic system by regulating ACh contents and expressi

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Voloshchuk, O. M., G. P. Kopylchuk, and М. S. Ursatyу. "THE RATIO OF UBIQUINON REDOX FORMS IN THE RAT LIVER MITOCHONDRIA UNDER CONDITIONS OF DIFFERENT NUTRIENT SUPPLY." Fiziolohichnyĭ zhurnal 66, no. 6 (2020): 82–87. http://dx.doi.org/10.15407/fz66.06.082.

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The relationship between the quantitative ratio of redox forms of ubiquinone and the degree of free radical damage to mitochondrial proteins in rat liver against the background of nutritional imbalance was investigated. The animals were divided into the following experimental groups: I – animals receiving full-value semi-synthetic ration (control group); II – animals receiving high-sucrose diet; III – animals receiving low-protein high-sucrose diet. The content of total and oxidized ubiquinone was determined spectrophotometrically at 275 nm, the content of reduced ubiquinone was determined by

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Nie, Cunxi, Fei Xie, Ning Ma, Yueyu Bai, Wenju Zhang, and Xi Ma. "Nutrients Mediate Bioavailability and Turnover of Proteins in Mammals." Current Protein & Peptide Science 20, no. 7 (2019): 661–65. http://dx.doi.org/10.2174/1389203720666190125111235.

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As a major component of biologically active compounds in the body, proteins contribute to the synthesis of body tissues for the renewal and growth of the body. The high level of dietary protein and the imbalance of amino acid (AA) composition in mammals result in metabolic disorders, inefficient utilization of protein resources and increased nitrogen excretion. Fortunately, nutritional interventions can be an effective way of attenuating the nitrogen excretion and increasing protein utilization, which include, but are not limited to, formulating the AA balance and protein-restricted diet suppl

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Tripodi, Armando. "Detection of procoagulant imbalance." Thrombosis and Haemostasis 117, no. 05 (2017): 830–36. http://dx.doi.org/10.1160/th16-10-0806.

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SummaryEach individual possesses his/her own endogenous-thrombin-potential (ETP) (i. e. the ability to generate thrombin) which depends on the relative strength of the pro- and anticoagulant drivers operating in plasma. This ability depends in turn on the clinical conditions in which the balance between the two drivers is variably affected. One of the major determinants of this balance is the factor (F)VIII-protein C(PC) axis and its effect can be conveniently explored by the thrombin generation procedures with results expressed as ETP ratio with/without thrombomodulin (TM) (ETP-TM ratio). Fur

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Bevere, Michele, Caterina Morabito, Delia Verucci, Noemi Di Sinno, Maria A. Mariggiò, and Simone Guarnieri. "Growth-Associated Protein-43 Loss Promotes Ca2+ and ROS Imbalance in Cardiomyocytes." Antioxidants 14, no. 3 (2025): 361. https://doi.org/10.3390/antiox14030361.

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Growth-Associated Protein-43 (GAP-43) is a calmodulin-binding protein, originally found in neurons, that in skeletal muscle regulates the handling of intracellular Ca2+ dynamics. According to its role in Ca2+ regulation, myotubes from GAP-43 knockout (GAP-43−/−) mice display alterations in spontaneous Ca2+ oscillations and increased Ca2+ release. The emerging hypothesis is that GAP-43 regulates CaM interactions with RyR and DHPR Ca2+ channels. The loss of GAP-43 promotes cardiac hypertrophy in newborn GAP-43−/− mice, extending the physiological role of GAP-43 in cardiac muscle. We investigated

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Jing, Xiao-Yang, and Feng-Min Li. "Identifying Heat Shock Protein Families from Imbalanced Data by Using Combined Features." Computational and Mathematical Methods in Medicine 2020 (September 23, 2020): 1–11. http://dx.doi.org/10.1155/2020/8894478.

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Heat shock proteins (HSPs) are ubiquitous in living organisms. HSPs are an essential component for cell growth and survival; the main function of HSPs is controlling the folding and unfolding process of proteins. According to molecular function and mass, HSPs are categorized into six different families: HSP20 (small HSPS), HSP40 (J-proteins), HSP60, HSP70, HSP90, and HSP100. In this paper, improved methods for HSP prediction are proposed—the split amino acid composition (SAAC), the dipeptide composition (DC), the conjoint triad feature (CTF), and the pseudoaverage chemical shift (PseACS) were

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Sou, Yu-shin, Junji Yamaguchi, Keisuke Masuda, Yasuo Uchiyama, Yusuke Maeda, and Masato Koike. "Golgi pH homeostasis stabilizes the lysosomal membrane throughN-glycosylation of membrane proteins." Life Science Alliance 7, no. 10 (2024): e202402677. http://dx.doi.org/10.26508/lsa.202402677.

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Protein glycosylation plays a vital role in various cellular functions, many of which occur within the Golgi apparatus. The Golgi pH regulator (GPHR) is essential for the proper functioning of the Golgi apparatus. The lysosomal membrane contains highly glycosylated membrane proteins in abundance. This study investigated the role of the Golgi luminal pH inN-glycosylation of lysosomal membrane proteins and the effect of this protein modification on membrane stability usingGphr-deficient MEFs. We showed thatGphrdeficiency causes an imbalance in the Golgi luminal pH, resulting in abnormal proteinN

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Avenatti, R. C. "The intersection of inflammation, insulin resistance and ageing: implications for the study of molecular signalling pathways in horses." Comparative Exercise Physiology 8, no. 3-4 (2012): 153–71. http://dx.doi.org/10.3920/cep12018.

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Inflammation-associated insulin resistance contributes to chronic disease in humans and other long-lived species, such as horses. Insulin resistance arises due to an imbalance among molecular signalling mediators in response to pro-inflammatory cytokines in the aged and obese. The mammalian heat shock protein response has received much attention as an avenue for attenuating inflammatory mediator signalling and for contributing to preservation and restoration of insulin signalling in metabolically important tissues. Data on heat shock proteins and inflammatory signalling mediators in untrained

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Heropolitanska-Pliszka, Edyta, Klaudia Berk, Mateusz Maciejczyk, et al. "Systemic Redox Imbalance in Patients with Chronic Granulomatous Disease." Journal of Clinical Medicine 9, no. 5 (2020): 1397. http://dx.doi.org/10.3390/jcm9051397.

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The aim of our study was to evaluate redox status, enzymatic and non-enzymatic antioxidant barriers, oxidative damage of proteins, lipids and DNA, as well as concentration of coenzyme Q10 and vitamins A and E in patients with chronic granulomatous disease (CGD). The study was performed on fifteen Caucasian individuals (median age 24 years and seven months) diagnosed with CGD. The mutation in the NCF1 gene was confirmed in ten patients, and in the CYBB gene in five patients. We demonstrated high levels of total oxidant status (TOS) and oxidative stress index (OSI), lipids (↑8-isoprostanes (8-is

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Wang, Xiaoying, Bin Yu, Anjun Ma, Cheng Chen, Bingqiang Liu, and Qin Ma. "Protein–protein interaction sites prediction by ensemble random forests with synthetic minority oversampling technique." Bioinformatics 35, no. 14 (2018): 2395–402. http://dx.doi.org/10.1093/bioinformatics/bty995.

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Abstract Motivation The prediction of protein–protein interaction (PPI) sites is a key to mutation design, catalytic reaction and the reconstruction of PPI networks. It is a challenging task considering the significant abundant sequences and the imbalance issue in samples. Results A new ensemble learning-based method, Ensemble Learning of synthetic minority oversampling technique (SMOTE) for Unbalancing samples and RF algorithm (EL-SMURF), was proposed for PPI sites prediction in this study. The sequence profile feature and the residue evolution rates were combined for feature extraction of ne

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Monção, Caio C. D., Carlos A. Scrideli, Augusto F. Andrade, et al. "Indisulam Reduces Viability and Regulates Apoptotic Gene Expression in Pediatric High-Grade Glioma Cells." Biomedicines 11, no. 1 (2022): 68. http://dx.doi.org/10.3390/biomedicines11010068.

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Pediatric high-grade glioma (pHGG) is one of the most aggressive brain tumors. Treatment includes surgery, radiotherapy, chemotherapy, or combination therapy in children older than 3–5 years of age. These devastating tumors are influenced by the hypoxic microenvironment that coordinatively increases the expression of carbonic anhydrases (CA9 and CA12) that are involved in pH regulation, metabolism, cell invasion, and resistance to therapy. The synthetic sulphonamide Indisulam is a potent inhibitor of CAs. The aim of this study was to evaluate the effects of Indisulam on CA9 and CA12 enzymes in

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Lachén-Montes, Mercedes, Naroa Mendizuri, Domitille Schvartz, Joaquín Fernández-Irigoyen, Jean Charles Sánchez, and Enrique Santamaría. "Proteomic Characterization of the Olfactory Molecular Imbalance in Dementia with Lewy Bodies." International Journal of Molecular Sciences 21, no. 17 (2020): 6371. http://dx.doi.org/10.3390/ijms21176371.

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Olfactory dysfunction is one of the prodromal symptoms in dementia with Lewy bodies (DLB). However, the molecular pathogenesis associated with decreased smell function remains largely undeciphered. We generated quantitative proteome maps to detect molecular alterations in olfactory bulbs (OB) derived from DLB subjects compared to neurologically intact controls. A total of 3214 olfactory proteins were quantified, and 99 proteins showed significant alterations in DLB cases. Protein interaction networks disrupted in DLB indicated an imbalance in translation and the synaptic vesicle cycle. These a

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Wen, Jun-Hao, Xiang-Hong He, Ze-Sen Feng, Dong-Yi Li, Ji-Xin Tang, and Hua-Feng Liu. "Cellular Protein Aggregates: Formation, Biological Effects, and Ways of Elimination." International Journal of Molecular Sciences 24, no. 10 (2023): 8593. http://dx.doi.org/10.3390/ijms24108593.

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The accumulation of protein aggregates is the hallmark of many neurodegenerative diseases. The dysregulation of protein homeostasis (or proteostasis) caused by acute proteotoxic stresses or chronic expression of mutant proteins can lead to protein aggregation. Protein aggregates can interfere with a variety of cellular biological processes and consume factors essential for maintaining proteostasis, leading to a further imbalance of proteostasis and further accumulation of protein aggregates, creating a vicious cycle that ultimately leads to aging and the progression of age-related neurodegener

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Diansyah, Mohammad Romano, Annisa Annisa, and Wisnu Ananta Kusuma. "Analysis using top‐k skyline query of protein‐protein interaction reveals alpha‐synuclein as the most important protein in Parkinson’s disease." Indonesian Journal of Biotechnology 26, no. 4 (2021): 197. http://dx.doi.org/10.22146/ijbiotech.63023.

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Parkinson’s disease is the second‐most‐common neurodegenerative disorder and can reduce patients’ quality of life. The disease is caused by abnormalities in dopaminergic neurons, such as reactive oxygen species (ROS) imbalance leading to programmed cell death, protein misfolding, and vesicle trafficking. Protein‐protein interaction (PPI) analysis has been demonstrated to understand better candidate proteins that might contribute to multifactorial neurodegenerative diseases, particularly in Parkinson’s disease. PPI analysis can be obtained from experiments and computational predictions. However

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D’Egidio, Francesco, Vanessa Castelli, Annamaria Cimini, and Michele d’Angelo. "Cell Rearrangement and Oxidant/Antioxidant Imbalance in Huntington’s Disease." Antioxidants 12, no. 3 (2023): 571. http://dx.doi.org/10.3390/antiox12030571.

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Huntington’s Disease (HD) is a hereditary neurodegenerative disorder caused by the expansion of a CAG triplet repeat in the HTT gene, resulting in the production of an aberrant huntingtin (Htt) protein. The mutant protein accumulation is responsible for neuronal dysfunction and cell death. This is due to the involvement of oxidative damage, excitotoxicity, inflammation, and mitochondrial impairment. Neurons naturally adapt to bioenergetic alteration and oxidative stress in physiological conditions. However, this dynamic system is compromised when a neurodegenerative disorder occurs, resulting

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Doni, Davide, Marta Meggiolaro, Javier Santos, et al. "A Combined Spectroscopic and In Silico Approach to Evaluate the Interaction of Human Frataxin with Mitochondrial Superoxide Dismutase." Biomedicines 9, no. 12 (2021): 1763. http://dx.doi.org/10.3390/biomedicines9121763.

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Frataxin (FXN) is a highly conserved mitochondrial protein whose deficiency causes Friedreich’s ataxia, a neurodegenerative disease. The precise physiological function of FXN is still unclear; however, there is experimental evidence that the protein is involved in biosynthetic iron–sulfur cluster machinery, redox imbalance, and iron homeostasis. FXN is synthesized in the cytosol and imported into the mitochondria, where it is proteolytically cleaved to the mature form. Its involvement in the redox imbalance suggests that FXN could interact with mitochondrial superoxide dismutase (SOD2), a key

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Bohush, Anastasiia, Paweł Bieganowski, and Anna Filipek. "Hsp90 and Its Co-Chaperones in Neurodegenerative Diseases." International Journal of Molecular Sciences 20, no. 20 (2019): 4976. http://dx.doi.org/10.3390/ijms20204976.

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Proper folding is crucial for proteins to achieve functional activity in the cell. However, it often occurs that proteins are improperly folded (misfolded) and form aggregates, which are the main hallmark of many diseases including cancers, neurodegenerative diseases and many others. Proteins that assist other proteins in proper folding into three-dimensional structures are chaperones and co-chaperones. The key role of chaperones/co-chaperones is to prevent protein aggregation, especially under stress. An imbalance between chaperone/co-chaperone levels has been documented in neurons, and sugge

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Di Nisio, Valentina, Sevastiani Antonouli, Sabrina Colafarina, et al. "Repeated Rounds of Gonadotropin Stimulation Induce Imbalance in the Antioxidant Machinery and Activation of Pro-Survival Proteins in Mouse Oviducts." International Journal of Molecular Sciences 24, no. 11 (2023): 9294. http://dx.doi.org/10.3390/ijms24119294.

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Controlled ovarian stimulation (COS) through gonadotropin administration has become a common procedure in assisted reproductive technologies. COS’s drawback is the formation of an unbalanced hormonal and molecular environment that could alter several cellular mechanisms. On this basis, we detected the presence of mitochondrial DNA (mtDNA) fragmentation, antioxidant enzymes (catalase; superoxide dismutases 1 and 2, SOD-1 and -2; glutathione peroxidase 1, GPx1) and apoptotic (Bcl-2-associated X protein, Bax; cleaved caspases 3 and 7; phosphorylated (p)-heat shock protein 27, p-HSP27) and cell-cy

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Vajrychova, Marie, Barbora Salovska, Kristyna Pimkova, et al. "Quantification of cellular protein and redox imbalance using SILAC-iodoTMT methodology." Redox Biology 24 (June 2019): 101227. http://dx.doi.org/10.1016/j.redox.2019.101227.

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Brawley, L., C. Torrens, F. W. Anthony, et al. "Glycine rectifies vascular dysfunction induced by dietary protein imbalance during pregnancy." Journal of Physiology 554, no. 2 (2004): 497–504. http://dx.doi.org/10.1113/jphysiol.2003.052068.

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Bakhoum, Samuel F. "Targeting RNA and Protein Turnover in Aneuploid Cancers." Cancer Discovery 14, no. 12 (2024): 2315–16. https://doi.org/10.1158/2159-8290.cd-24-1350.

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Summary:Aneuploidy, an imbalance in chromosome number, is a hallmark of human cancers with chromosomal instability, and it remains a major therapeutic challenge. In this issue, Ippolito and colleagues identify RNA and protein turnover as targetable therapeutic vulnerabilities in aneuploid cancers.See related article by Ippolito et al., p. 2532

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Tiwari, Anoop Kumar, Abhigyan Nath, Karthikeyan Subbiah, and Kaushal Kumar Shukla. "Enhanced Prediction for Observed Peptide Count in Protein Mass Spectrometry Data by Optimally Balancing the Training Dataset." International Journal of Pattern Recognition and Artificial Intelligence 31, no. 12 (2017): 1750040. http://dx.doi.org/10.1142/s0218001417500409.

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Imbalanced dataset affects the learning of classifiers. This imbalance problem is almost ubiquitous in biological datasets. Resampling is one of the common methods to deal with the imbalanced dataset problem. In this study, we explore the learning performance by varying the balancing ratios of training datasets, consisting of the observed peptides and absent peptides in the Mass Spectrometry experiment on the different machine learning algorithms. It has been observed that the ideal balancing ratio has yielded better performance than the imbalanced dataset, but it was not the best as compared

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Hsu, Yu-Wen, Wen-Kang Chen, and Chia-Fang Tsai. "Senescence-Mediated Redox Imbalance in Liver and Kidney: Antioxidant Rejuvenating Potential of Green Tea Extract." International Journal of Environmental Research and Public Health 19, no. 1 (2021): 260. http://dx.doi.org/10.3390/ijerph19010260.

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This study investigates the catechin composition and protective effect of green tea extract on senescence-mediated redox imbalance in the livers and kidneys of aged mice. The results showed that the seven catechins in the green tea extract analyzed in this study could be completely separated within 30 min and the main components of catechins in green tea extract were EGCG, EGC and ECG. In terms of the anti-senescence effects of green tea extract, green tea extract supplementation at doses of 125, 625 and 1250 mg/kg for 4 weeks significantly alleviated the senescence-mediated redox imbalance, a

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Moriya, Hisao. "Quantitative nature of overexpression experiments." Molecular Biology of the Cell 26, no. 22 (2015): 3932–39. http://dx.doi.org/10.1091/mbc.e15-07-0512.

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Overexpression experiments are sometimes considered as qualitative experiments designed to identify novel proteins and study their function. However, in order to draw conclusions regarding protein overexpression through association analyses using large-scale biological data sets, we need to recognize the quantitative nature of overexpression experiments. Here I discuss the quantitative features of two different types of overexpression experiment: absolute and relative. I also introduce the four primary mechanisms involved in growth defects caused by protein overexpression: resource overload, s

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Yang, Yanfang, Yu He, Xixi Wang, et al. "Protein SUMOylation modification and its associations with disease." Open Biology 7, no. 10 (2017): 170167. http://dx.doi.org/10.1098/rsob.170167.

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SUMOylation, as a post-translational modification, plays essential roles in various biological functions including cell growth, migration, cellular responses to stress and tumorigenesis. The imbalance of SUMOylation and deSUMOylation has been associated with the occurrence and progression of various diseases. Herein, we summarize and discuss the signal crosstalk between SUMOylation and ubiquitination of proteins, protein SUMOylation relations with several diseases, and the identification approaches for SUMOylation site. With the continuous development of bioinformatics and mass spectrometry, s

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