Acta biochimica Polonica最新文献

{"title":"Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias.","authors":"Qiao-Hui Mou, Zhe Hu, Jing Zhang, Maurycy Daroch, Jie Tang","doi":"10.3389/abp.2024.13825","DOIUrl":"10.3389/abp.2024.13825","url":null,"abstract":"<p><p>Members of the families Thermosynechococcaceae and Thermostichaceae are well-known unicellular thermophilic cyanobacteria and a non-thermophilic genus <i>Pseudocalidococcus</i> was newly classified into the former. Analysis of the codon usage bias (CUB) of cyanobacterial species inhabiting different thermal and non-thermal niches will benefit the understanding of their genetic and evolutionary characteristics. Herein, the CUB and codon context patterns of protein-coding genes were systematically analyzed and compared between members of the two families. Overall, the nucleotide composition and CUB indices were found to differ between thermophiles and non-thermophiles. The thermophiles showed a higher G/C content in the codon base composition and tended to end with G/C compared to the non-thermophiles. Correlation analysis indicated significant associations between codon base composition and CUB indices. The results of the effective number of codons, parity-rule 2, neutral and correspondence analyses indicated that mutational pressure and natural selection primarily account for CUB in these cyanobacterial species, but the primary driving forces exhibit variation among genera. Moreover, the optimal codons identified based on relative synonymous codon usage values were found to differ among genera and even within genera. In addition, codon context pattern analysis revealed the specificity of the sequence context of start and stop codons among genera. Intriguingly, the clustering of codon context patterns appeared to be more related to thermotolerance than to phylogenomic relationships. In conclusion, this study facilitates the understanding of the characteristics and sources of variation of CUB and the evolution of the surveyed cyanobacterial clades with different thermotolerance and provides insights into their adaptation to different environments.</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"13825"},"PeriodicalIF":1.4,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimization of erythritol production through fermentation using molasses as carbon source.","authors":"Riahna Kembaren, Arli Aditya Parikesit, Jocelyn Nataniel, Nethania Angeline Dharmawan, Charlivo Mikaichi Dungus, Priscilla Angelique, Solmaz Aslanzadeh","doi":"10.3389/abp.2024.14000","DOIUrl":"10.3389/abp.2024.14000","url":null,"abstract":"<p><p>Erythritol is a beneficial sugar alcohol that can be used as a sugar substitute for diabetic patients. Erythritol is a bioproduct produced by microorganisms as a response to high osmotic pressure and stress in the growth medium. High concentrations of carbon source substrate can increase the osmotic pressure and provide more nutrient supply for yeast growth and metabolism. Aside from that, an optimal carbon-to-nitrogen (C/N) ratio can also make the erythritol conversion pathway more favorable. Therefore, this research aims to determine the optimal concentrations of molasses as the carbon source, yeast extract as the nitrogen source, and the optimal carbon-to-nitrogen (C/N) ratio to achieve the highest erythritol productivity. The research also seeks to optimize NaCl concentrations and pH while comparing batch and fed-batch fermentation systems to determine which produces a higher erythritol yield. One-Factor-at-A-Time (OFAT) method was used to identify optimal production conditions. The study found that the highest erythritol concentration, 17.48 ± 0.86 g/L, was achieved using 200 g/L of molasses, 7 g/L of yeast extract (200/7), and 25 g/L of NaCl, with a yield mass of 0.262 ± 0.00 g/g and a volumetric productivity of 0.095 ± 0.021 g/Lh. The pH optimization revealed that the best erythritol production occurred within a pH of 5. Furthermore, fed-batch fermentation significantly increased erythritol concentration to 26.52 ± 1.61 g/L, with a yield mass of 0.501 ± 0.032 g/g and a volumetric productivity of 0.158 ± 0.01 g/Lh. These findings emphasize the importance of optimizing carbon source, nitrogen source and NaCl concentration, pH, and fermentation systems, particularly highlighting the benefits of fed-batch fermentation in maximizing erythritol production. These findings provide a solid foundation for improving erythritol yields for industrial applications.</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"14000"},"PeriodicalIF":1.4,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021719","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of uremic toxin removal between expanded hemodialysis and high volume online hemodiafiltrations in different modes.","authors":"Jan Biedunkiewicz, Agnieszka Zakrzewska, Sylwia Małgorzewicz, Michał Komorniczak, Katarzyna Jasiulewicz, Natalia Płonka, Agnieszka Tarasewicz, Magdalena Jankowska, Bogdan Biedunkiewicz, Alicja Dębska-Ślizień, Leszek Tylicki","doi":"10.3389/abp.2024.13715","DOIUrl":"10.3389/abp.2024.13715","url":null,"abstract":"<p><p>Various high-efficiency hemodialysis techniques exist, including different online high- volume hemodiafiltration (HDF) modes and expanded hemodialysis (HDx) utilizing dialyzers with medium cut-off (MCO) membranes. This study aimed to evaluate the efficacy of uremic toxin removal among four modalities: (I) HDx, (II) pre-dilution HDF (PRE-HDF), (III) mixed-dilution HDF (MIX-HDF), and (IV) post-dilution HDF (POST-HDF), each applied for 1 week in a randomized order. This research was a single-center, prospective, open-label, exploratory crossover study. The reduction ratio (RR) for small molecular toxins (urea and phosphate), a middle molecular toxin (beta-2-microglobulin, β2M), a large-middle molecular toxin (Chitinase-3-like protein 1, YKL-40), and a protein- bound uremic toxin (indoxyl sulfate, IS) was evaluated during a single mid-week dialysis session. Twelve patients were included, with an average age of 52.5 ± 15.47 years and an average dialysis duration of 42.05 ± 31.04 months. The dialysis parameters, including; post-dialysis weight, session duration, dialysate composition, blood and dialysate flow; rates, dialysate temperature, and anticoagulation dosage, were maintained consistently across all modalities. No significant differences in RR for urea, phosphate, β2M, YKL-40, and IS were observed between the treatments. Although the highest IS clearance, though not statistically significant, was observed with POST-HDF and HDx, the differences were not substantial enough to favor any particular modality as the most effective.</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"13715"},"PeriodicalIF":1.4,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11637868/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142827162","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of albumin and prealbumin in assessing nutritional status and predicting increased risk of infectious complications during childhood cancer treatment.","authors":"Anna Milaniuk, Katarzyna Drabko, Agnieszka Chojęta","doi":"10.3389/abp.2024.13693","DOIUrl":"https://doi.org/10.3389/abp.2024.13693","url":null,"abstract":"<p><strong>Introduction: </strong>Proper nutrition in patients with cancer is important for preventing treatment complications and achieving remission. Malnutrition in these patients leads to reduced production of essential structural proteins.</p><p><strong>Purpose: </strong>The aim of the study was to assess the role of albumin and prealbumin in assessing the nutritional status of cancer patients and in predicting an increased risk of infectious complications during treatment.</p><p><strong>Patients and methods: </strong>The study included 40 pediatric patients with newly diagnosed cancer and 30 healthy children serving as controls. Prealbumin, albumin, and C-reactive protein (CRP) levels and the upper arm muscle area (UAMA) were measured before and after treatment in children with cancer and compared with the control group to evaluate nutritional status. Additionally, we assessed associations between these parameters and the incidence of infectious complications during cancer treatment in patients with anthropometric malnutrition, as well as associations with an increased risk of malnutrition related to inflammation before treatment.</p><p><strong>Results: </strong>At baseline, patients with cancer had lower prealbumin and albumin levels (p< 0.001), higher CRP levels (p < 0.001), and lower UAMA percentiles (p = 0.0245) compared with controls. Cancer treatment resulted in an increase in prealbumin and albumin levels (p < 0.001) and a reduction in CRP levels (p < 0.001), with no change in UAMA (p = 1.000). Prealbumin deficiency was more common than albumin deficiency before and after cancer treatment. Median prealbumin and albumin levels tended to increase with an increasing UAMA percentile range, but these differences were not significant (p> 0.05). The incidence of infectious complications during treatment in patients with risk factors for inflammation-related malnutrition was similar to that in patients with pre-existing anthropometric malnutrition without inflammation (p = 1.000). In a univariable logistic regression model including prealbumin and albumin deficiency, as well as low UAMA percentile, albumin deficiency before treatment was shown to be a significant predictor of 3 or more infectious episodes during treatment (p = 0.02).</p><p><strong>Conclusion: </strong>Albumin and prealbumin deficiency may predict the risk of malnutrition associated with inflammation in patients with cancer. Hypoalbuminemia may predict an unfavorable course of treatment complicated by frequent infections in these patients.</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"13693"},"PeriodicalIF":1.4,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variability of plant transcriptomic responses under stress acclimation: a review from high throughput studies.","authors":"Michał Rurek, Mikołaj Smolibowski","doi":"10.3389/abp.2024.13585","DOIUrl":"https://doi.org/10.3389/abp.2024.13585","url":null,"abstract":"<p><p>Plant transcriptomes are complex entities shaped spatially and temporally by a multitude of stressors. The aim of this review was to summarize the most relevant transcriptomic responses to selected abiotic (UV radiation, chemical compounds, drought, suboptimal temperature) and biotic (bacteria, fungi, viruses, viroids) stress conditions in a variety of plant species, including model species, crops, and medicinal plants. Selected basic and applicative studies employing RNA-seq from various sequencing platforms and single-cell RNA-seq were involved. The transcriptomic responsiveness of various plant species and the diversity of affected gene families were discussed. Under stress acclimation, plant transcriptomes respond particularly dynamically. Stress response involved both distinct, but also similar gene families, depending on the species, tissue, and the quality and dosage of the stressor. We also noted the over-representation of transcriptomic data for some plant organs. Studies on plant transcriptomes allow for a better understanding of response strategies to environmental conditions. Functional analyses reveal the multitude of stress-affected genes as well as acclimatory mechanisms and suggest metabolome diversity, particularly among medicinal species. Extensive characterization of transcriptomic responses to stress would result in the development of new cultivars that would cope with stress more efficiently. These actions would include modern methodological tools, including advanced genetic engineering, as well as gene editing, especially for the expression of selected stress proteins <i>in planta</i> and for metabolic modifications that allow more efficient synthesis of secondary metabolites.</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"13585"},"PeriodicalIF":1.4,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11543463/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611940","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>In situ</i> oxidative stress in patients with epiretinal membrane.","authors":"Tomasz Wilczyński, Jolanta Zalejska-Fiolka, Sabina Sapeta-Wieckowska, Monika Sarnat-Kucharczyk, Wojciech Rokicki","doi":"10.3389/abp.2024.13581","DOIUrl":"10.3389/abp.2024.13581","url":null,"abstract":"<p><strong>Context: </strong>Oxidative stress is an important factor for vitreomacular interface disease development in a theoretical model.</p><p><strong>Purpose: </strong>The aim of the study was to evaluate the correlation between oxidative stress in the human epiretinal membrane (ERM) and retinal morphological changes.</p><p><strong>Material and methods: </strong>The study included patients scheduled for vitrectomy with epiretinal membrane removal. LogMAR best corrected visual acuity was assessed and optical coherence tomography was performed. Patients were divided into three groups: Type 1 - epiretinal membrane with premacular fibrosis; type 2 - epiretinal membrane with co-existing layer hole; and type 3 - ERM with co-existing full-thickness macular hole. During vitrectomy, epiretinal membranes were collected. Total oxidant status was determined by an automated colorimetric method in homogenates of epiretinal membrane.</p><p><strong>Statistical analysis: </strong>The Mann-Whitney U test, Kruskal-Wallis test and Spearman linear correlation analysis were used. Statistical significance was set with a level of α = 0.05.</p><p><strong>Results: </strong>Twenty-one Caucasian women (60%) and 14 men (40%) were included in the study. The average age of participants was 74.7 years (95% CI: 71.13-75.45). The mean best corrected visual acuity LogMAR value in the group was 0.8 (95% CI: 0.9-0.7). The mean ratio of total oxidant status to protein level in the collected samples was 0.161 (95% CI: 0.08-0.23) µmol/mg of protein. No correlation was found between total oxidant status and the degree of morphological retinal changes.</p><p><strong>Conclusion: </strong>The study found no significant correlation between the level of oxidative stress in epiretinal membrane and retinal morphological changes.</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"13581"},"PeriodicalIF":1.4,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11528693/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142567185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retraction: Dynamic changes of serum miR-105-3p expression and prognostic value evaluation of postoperative thyroid cancer.","authors":"","doi":"10.3389/abp.2024.13857","DOIUrl":"10.3389/abp.2024.13857","url":null,"abstract":"<p><p>[This retracts the article DOI: 10.18388/abp.2023_6398.].</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"13857"},"PeriodicalIF":1.4,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11513583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The role of TGF-β in the electrotactic reaction of mouse 3T3 fibroblasts <i>in vitro</i>.","authors":"Patrycja Ciesielska, Slawomir Lasota, Sylwia Bobis-Wozowicz, Zbigniew Madeja","doi":"10.3389/abp.2024.12993","DOIUrl":"10.3389/abp.2024.12993","url":null,"abstract":"<p><p>Endogenous electric fields (EFs) serve as a crucial signal to guide cell movement in processes such as wound healing, embryonic development, and cancer metastasis. However, the mechanism underlying cell electrotaxis remains poorly understood. A plausible hypothesis suggests that electrophoretic or electroosmotic forces may rearrange charged components of the cell membrane, including receptors for chemoattractants which induce asymmetric signaling and directional motility. This study aimed to explore the role of Transforming Growth Factor Beta (TGFβ) signaling in the electrotactic reaction of 3T3 fibroblasts. Our findings indicate that inhibiting canonical and several non-canonical signaling pathways originating from the activated TGF-β receptor does not hinder the directed migration of 3T3 cells to the cathode. Furthermore, suppression of TGF-β receptor expression does not eliminate the directional migration effect of 3T3 cells in the electric field. Additionally, there is no observed redistribution of the TGF-β receptor in the electric field. However, our studies affirm the significant involvement of Phosphoinositide 3-Kinase (PI3K) in electrotaxis, suggesting that in our model, its activation is likely associated with factors independent of TGFβ action.</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"12993"},"PeriodicalIF":1.4,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11231101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141562389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding mitochondrial potassium channels: 33 years after discovery.","authors":"Adam Szewczyk","doi":"10.3389/abp.2024.13126","DOIUrl":"10.3389/abp.2024.13126","url":null,"abstract":"<p><p>Mitochondrial investigations have extended beyond their traditional functions, covering areas such as ATP synthesis and metabolism. Mitochondria are now implicated in new functional areas such as cytoprotection, cellular senescence, tumor function and inflammation. The basis of these new areas still relies on fundamental biochemical/biophysical mitochondrial functions such as synthesis of reactive oxygen species, mitochondrial membrane potential, and the integrity of the inner mitochondrial membrane i.e., the passage of various molecules through the mitochondrial membranes. In this view transport of potassium cations, known as the potassium cycle, plays an important role. It is believed that K⁺ influx is mediated by various potassium channels present in the inner mitochondrial membrane. In this article, we present an overview of the key findings and characteristics of mitochondrial potassium channels derived from research of many groups conducted over the past 33 years. We propose a list of six fundamental observations and most important ideas dealing with mitochondrial potassium channels. We also discuss the contemporary challenges and future prospects associated with research on mitochondrial potassium channels.</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"13126"},"PeriodicalIF":1.7,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11165062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141305070","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Marine natural products: potential agents for depression treatment.","authors":"Xunqiang Wang, Cece Yang, Xing Zhang, Caiping Ye, Wenping Liu, Chengmin Wang","doi":"10.3389/abp.2024.12569","DOIUrl":"10.3389/abp.2024.12569","url":null,"abstract":"<p><p>Depression is a common psychiatric disorder. Due to the disadvantages of current clinical drugs, including poor efficacy and unnecessary side effects, research has shifted to novel natural products with minimal or no adverse effects as therapeutic alternatives. The ocean is a vast ecological home, with a wide variety of organisms that can produce a large number of natural products with unique structures, some of which have neuroprotective effects and are a valuable source for the development of new drugs for depression. In this review, we analyzed preclinical and clinical studies of natural products derived from marine organisms with antidepressant potential, including the effects on the pathophysiology of depression, and the underlying mechanisms of these effects. It is expected to provide a reference for the development of new antidepressant drugs.</p>","PeriodicalId":6984,"journal":{"name":"Acta biochimica Polonica","volume":"71 ","pages":"12569"},"PeriodicalIF":1.7,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11135343/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141174126","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}