Comprehensive structural overview of the C-terminal ligand-binding domains of the TetR family regulators.

TetR family regulators (TFRs) represent a large group of one-component bacterial signal transduction systems which recognize environmental signals, like the presence of antibiotics or other bactericidal compounds, and trigger the cell response by regulating the expression of genes that secure bacterial survival in harsh environmental conditions. TFRs act as homodimers, each protomer is composed of a conserved DNA-binding N-terminal domain (NTD) and a variable ligand-binding C-terminal domain (CTD). Currently, there are about 500 structures of TFRs available in the Protein Data Bank and one-fourth of them represent the structures of TFR-ligand complexes. In this review, we summarized information on the ligands interacting with TFRs and based on structural data, we compared the CTDs of the TFR family members, as well as their ligand-binding cavities. Additionally, we divided the whole TFR family, including more than half of a million sequences, into subfamilies according to calculated multiple sequence alignment and phylogenetic tree. We also highlighted structural elements characteristic of some of the subfamilies. The presented comprehensive overview of the TFR CTDs provides good bases and future directions for further studies on TFRs that are not only important targets for battling multidrug resistance but also good candidates for many biotechnological approaches, like TFR-based biosensors.

The Importance of Adverse Childhood Experiences in Depressive Symptoms and Their Biological Consequences in Healthy Adults: Results of a Polish University Student Study.

Adverse childhood experiences (ACEs) have a long-lasting effect on both physical and mental health. The aim of this study was to assess the consequences of ACEs and experienced stress on depression and the role of biological disturbances in this relationship in a student population. Potential participants filled out a screening questionnaire; 60 of 126 students met the inclusion criteria and were tested for the severity of stress and depressive symptoms, ACEs, dietary habits, and serum concentrations of biological markers. Depressive symptoms were related to a younger age (p = 0.012), a higher severity of stress (p = 0.001), ACEs (p = 0.007), and lower triglyceride (p = 0.01) and cortisol concentrations (p = 0.01). An inverse relationship between the triglyceride concentration and emotional abuse (R = -0.38) and emotional neglect (R = -0.33) was found. Occludin was positively associated with physical abuse (R = 0.31). Cortisol was inversely associated with emotional abuse (R = -0.35). Emotional neglect was associated with lipopolysaccharide binding protein (R = 0.38) and insulin levels (R = -0.31). The most promising multi-panel of biomarkers for recognizing mood symptoms included triglycerides, tight junction protein 1, and cortisol (cut-offs of ≤ 95.5 mg/dL, 0.72 ng/mL, and 134.63 ng/mL, respectively). This study confirmed the association between ACEs and depressive symptoms and the importance of psychological stress in developing mood disorders. ACEs could affect biological dysregulation. Some of the biological markers could be helpful in early detection of depression.

Structural analysis and molecular substrate recognition properties of Arabidopsis thaliana ornithine transcarbamylase, the molecular target of phaseolotoxin produced by Pseudomonas syringae.

Halo blight is a plant disease that leads to a significant decrease in the yield of common bean crops and kiwi fruits. The infection is caused by Pseudomonas syringae pathovars that produce phaseolotoxin, an antimetabolite which targets arginine metabolism, particularly by inhibition of ornithine transcarbamylase (OTC). OTC is responsible for production of citrulline from ornithine and carbamoyl phosphate. Here we present the first crystal structures of the plant OTC from Arabidopsis thaliana (AtOTC). Structural analysis of AtOTC complexed with ornithine and carbamoyl phosphate reveals that OTC undergoes a significant structural transition when ornithine enters the active site, from the opened to the closed state. In this study we discuss the mode of OTC inhibition by phaseolotoxin, which seems to be able to act only on the fully opened active site. Once the toxin is proteolytically cleaved, it mimics the reaction transition state analogue to fit inside the fully closed active site of OTC. Additionally, we indicate the differences around the gate loop region which rationally explain the resistance of some bacterial OTCs to phaseolotoxin.

How the Outliers Influence the Quality of Clustering?

In this article, we evaluate the efficiency and performance of two clustering algorithms: AHC (Agglomerative Hierarchical Clustering) and K-Means. We are aware that there are various linkage options and distance measures that influence the clustering results. We assess the quality of clustering using the Davies-Bouldin and Dunn cluster validity indexes. The main contribution of this research is to verify whether the quality of clusters without outliers is higher than those with outliers in the data. To do this, we compare and analyze outlier detection algorithms depending on the applied clustering algorithm. In our research, we use and compare the LOF (Local Outlier Factor) and COF (Connectivity-based Outlier Factor) algorithms for detecting outliers before and after removing 1%, 5%, and 10% of outliers. Next, we analyze how the quality of clustering has improved. In the experiments, three real data sets were used with a different number of instances.

Characterization of the Putative Acylated Cellulose Synthase Operon in Komagataeibacter xylinus E25.

Bacterial cellulose is a natural polymer with an expanding array of applications. Because of this, the main cellulose producers of the Komagataeibacter genus have been extensively studied with the aim to increase its synthesis or to customize its physicochemical features. Up to now, the genetic studies in Komagataeibacter have focused on the first cellulose synthase operon (bcsI) encoding the main enzyme complex. However, the role of other accessory cellulose operons has been understudied. Here we aimed to fill this gap by performing a detailed analysis of the second cellulose synthase operon (bcsII), which is putatively linked with cellulose acylation. In this study we harnessed the genome sequence, gene expression and protein structure information of K. xylinus E25 and other Komagataeibacter species to discuss the probable features of bcsII and the biochemical function of its main protein products. The results of our study support the previous hypothesis that bcsII is involved in the synthesis of the acylated polymer and expand it by presenting the evidence that it may also function in the regulation of its attachment to the cell surface and to the crystalline cellulose fibers.

Crystal structure of the Escherichia coli CusS kinase core.

The CusS histidine kinase is a member of Escherichia coli two-component signal transduction system, engaged in a response to copper ions excess in the cell periplasm. The periplasmic sensor domain of CusS binds the free copper ions and the CusS kinase core phosphorylates the cognate CusR which regulates transcription of the efflux pomp CusCBA. A small amount of copper ions is indispensable for the aerobic cell metabolism. Nonetheless, its excess in the cytoplasm generates damaging and reactive hydroxyl radicals. For that reason, understanding the bacterial copper sensing mechanisms can contribute to reducing bacterial copper-resistance and developing bactericidal copper-based materials. The crystal structure of the CusS kinase core was solved at the resolution of 1.4 Å. The cytoplasmic catalytic core domains formed a homodimer. Based on the obtained structure, the intramolecular and intermolecular interactions crucial for the mechanism of CusS autophosphorylation were described.

Structures of the TetR-like transcription regulator RcdA alone and in complexes with ligands.

RcdA is a helix-turn-helix (HTH) transcriptional regulator belonging to the TetR family. The protein regulates the transcription of curlin subunit gene D, the master regulator of biofilm formation. Moreover, it was predicted that it might be involved in the regulation of up to 27 different genes. However, an effector of RcdA and the environmental conditions which trigger RcdA action remain unknown. Herein, we report the first crystal structures of RcdA in complexes with ligands, trimethylamine N-oxide (TMAO) and tris(hydroxymethyl)aminomethane (Tris), which might serve as RcdA effectors. Based on these structures, the ligand-binding pocket of RcdA was characterized in detail. The conservation of the amino acid residues forming the ligand-binding cavity was analyzed and the comprehensive search for RcdA structural homologs was performed. This analysis indicated that RcdA is structurally similar to multidrug-binding TetR family members, however, its ligand-binding cavity differs significantly from the pockets of its structural homologs. The interaction of RcdA with TMAO and Tris indicates that the protein might be involved in alkaline stress response.

Oxidative stress and soluble receptor for advanced glycation end-products play a role in the pathophysiology of delirium after cardiac surgery.

Coronary-artery bypass graft (CABG) surgery is known to improve cardiac function and decrease mortality, albeit, this method of treatment is also associated with a neuropsychiatric complications including postoperative delirium. The pathophysiology of delirium after cardiac surgery remains poorly understood. Thus, the purpose of this study was to investigate whether oxidative stress reflected by decreased preoperative and postoperative plasma antioxidant activity is independently associated with delirium after cardiac surgery. The second aim was to assess whether decreased antioxidant activity is stress-related or mediated by other pathologies such as major depressive disorder (MDD), anxiety disorders, and cognitive impairment. Furthermore, the putative relationship between pre- and postoperative soluble receptor for advanced glycation end-products (sRAGE) overexpression and plasma antioxidant capacity was evaluated. The patients cognitive status was assessed 1 day preoperatively with the use of the Mini-Mental State Examination Test and the Clock Drawing Test. A diagnosis of MDD and anxiety disorders was established on the basis of DSM-5 criteria. Blood samples for antioxidant capacity and sRAGE levels were collected both preoperatively and postoperatively. The Confusion Assessment Method for the Intensive Care Unit was used within the first 5 days postoperatively to screen for a diagnosis of delirium. Postoperative delirium was diagnosed in 34% (61 of 177) of individuals. Multivariate logistic regression analysis revealed that low baseline antioxidant capacity was independently associated with postoperative delirium development. Moreover, increased risk of delirium was observed among patients with a preoperative diagnosis of MDD associated with antioxidant capacity decreased postoperatively. According to receiver operating characteristic analysis, the most optimal cutoff values of the preoperative and postoperative antioxidant capacity that predict the development of delirium were 1.72 mM and 1.89 mM, respectively. Pre- and postoperative antioxidant capacity levels were negatively correlated with postoperative sRAGE concentration (Spearman's Rank Correlation - 0.198 and - 0.158, p < 0.05, respectively). Patients with decreased preoperative antioxidant activity and those with depressive episodes complicated with lower postoperative antioxidant activity are at significantly higher risk of delirium after cardiac surgery development. sRAGE overexpression may be considered as protective mechanism against increased oxidative stress and subsequent cell damage.

Outliers in Covid 19 data based on Rule representation - the analysis of LOF algorithm.

The article concerns the detection of outliers in rule-based knowledge bases containing data on Covid 19 cases. The authors move from the automatic generation of a rule-based knowledge base from source data by clustering rules in the knowledge base to optimize inference processes and to detecting unusual rules allowing for the optimal structure of rule groups. The paper presents a two-phase procedure, wherein in the first phase, we look for the optimal structure of rule clusters when there are outlier rules in the knowledge base. In the second phase, we detect outliers in the rules using the LOF (Local Outlier Factor) algorithm. Then we eliminate the unusual rules from the database and check whether the selected cluster quality measures are responded positively to the elimination of outliers, which would indicate that the rules were rightly considered outliers. The performed experiments confirmed the effectiveness of the LOF algorithm and selected cluster quality measures in the context of detecting atypical rules. The detection of such rules can support knowledge engineers or domain experts in knowledge mining to improve the completeness of the knowledge base, which is usually the basis of the decision support system.

Qualitative Data Clustering to Detect Outliers.

Detecting outliers is a widely studied problem in many disciplines, including statistics, data mining, and machine learning. All anomaly detection activities are aimed at identifying cases of unusual behavior compared to most observations. There are many methods to deal with this issue, which are applicable depending on the size of the data set, the way it is stored, and the type of attributes and their values. Most of them focus on traditional datasets with a large number of quantitative attributes. The multitude of solutions related to detecting outliers in quantitative sets, a large and still has a small number of research solutions is a problem detecting outliers in data containing only qualitative variables. This article was designed to compare three different categorical data clustering algorithms: K-modes algorithm taken from MacQueen's K-means algorithm and the STIRR and ROCK algorithms. The comparison concerned the method of dividing the set into clusters and, in particular, the outliers detected by algorithms. During the research, the authors analyzed the clusters detected by the indicated algorithms, using several datasets that differ in terms of the number of objects and variables. They have conducted experiments on the parameters of the algorithms. The presented study made it possible to check whether the algorithms similarly detect outliers in the data and how much they depend on individual parameters and parameters of the set, such as the number of variables, tuples, and categories of a qualitative variable.

Structural Evidence of Active Site Adaptability towards Different Sized Substrates of Aromatic Amino Acid Aminotransferase from Psychrobacter Sp. B6.

Aromatic amino acid aminotransferases present a special potential in the production of drugs and synthons, thanks to their ability to accommodate a wider range of substrates in their active site, in contrast to aliphatic amino acid aminotransferases. The mechanism of active site adjustment toward substrates of psychrophilic aromatic amino acid aminotransferase (PsyArAT) from Psychrobacter sp. B6 is discussed based on crystal structures of complexes with four hydroxy-analogs of substrates: phenylalanine, tyrosine, tryptophan and aspartic acid. These competitive inhibitors are bound in the active center of PsyArAT but do not undergo transamination reaction, which makes them an outstanding tool for examination of the enzyme catalytic center. The use of hydroxy-acids enabled insight into substrate binding by native PsyArAT, without mutating the catalytic lysine and modifying cofactor interactions. Thus, the binding mode of substrates and the resulting analysis of the volume of the catalytic site is close to a native condition. Observation of these inhibitors' binding allows for explanation of the enzyme's adaptability to process various sizes of substrates and to gain knowledge about its potential biotechnological application. Depending on the character and size of the used inhibitors, the enzyme crystallized in different space groups and showed conformational changes of the active site upon ligand binding.

Elevated Monocyte Chemoattractant Protein-1 as the Independent Risk Factor of Delirium after Cardiac Surgery. A Prospective Cohort Study.

BACKGROUND: The pathogenesis of postoperative delirium is largely unknown. The primary objective of this study is to assess whether increased levels of monocyte chemoattractant protein-1 (MCP-1) and high-sensitivity C-reactive protein (hsCRP) are associated with postoperative delirium in patients who have undergone cardiac surgery. The secondary objective is to investigate whether any association between raised inflammatory biomarkers levels and delirium is related to surgical and anesthetic procedures or mediated by pre-existing psychiatric conditions associated with raised pro-inflammatory markers levels. METHODS: The patients were screened for cognitive impairment one day preoperatively with the use of the Mini-Mental State Examination Test and the Clock Drawing Test. A diagnosis of major depressive disorder (MDD) and anxiety disorders was established on the basis of Diagnostic and Statistical Manual of Mental Disorders (DSM-5) criteria. Blood samples were collected pre- and postoperatively for hsCRP and chemokine levels. RESULTS: Postoperative delirium developed in 34% (61 of 177) of patients. Both pre- and postoperative hsCRP, and preoperative MCP-1 levels were associated with postoperative delirium in univariate comparisons; p = 0.001; p < 0.001; p < 0.001, respectively. However, according to a multivariable logistic regression analysis, only a raised MCP-1 concentration before surgery was independently associated with postoperative delirium, and related to advancing age, preoperative anxiety disorders and prolonged intubation. CONCLUSIONS: The present study suggests that an elevated preoperative MCP-1 concentration is associated with delirium after cardiac surgery. Monitoring of this inflammatory marker may reveal the cardiovascular disease (CVD) patients who are at risk of neuropsychiatric syndromes development.

Exploration of Outliers in If-Then Rule-Based Knowledge Bases.

The article presents both methods of clustering and outlier detection in complex data, such as rule-based knowledge bases. What distinguishes this work from others is, first, the application of clustering algorithms to rules in domain knowledge bases, and secondly, the use of outlier detection algorithms to detect unusual rules in knowledge bases. The aim of the paper is the analysis of using four algorithms for outlier detection in rule-based knowledge bases: Local Outlier Factor (LOF), Connectivity-based Outlier Factor (COF), K-MEANS, and SMALLCLUSTERS. The subject of outlier mining is very important nowadays. Outliers in rules If-Then mean unusual rules, which are rare in comparing to others and should be explored by the domain expert as soon as possible. In the research, the authors use the outlier detection methods to find a given number of outliers in rules (1%, 5%, 10%), while in small groups, the number of outliers covers no more than 5% of the rule cluster. Subsequently, the authors analyze which of seven various quality indices, which they use for all rules and after removing selected outliers, improve the quality of rule clusters. In the experimental stage, the authors use six different knowledge bases. The best results (the most often the clusters quality was improved) are achieved for two outlier detection algorithms LOF and COF.

The interaction of DNA repair factors ASCC2 and ASCC3 is affected by somatic cancer mutations.

The ASCC3 subunit of the activating signal co-integrator complex is a dual-cassette Ski2-like nucleic acid helicase that provides single-stranded DNA for alkylation damage repair by the α-ketoglutarate-dependent dioxygenase AlkBH3. Other ASCC components integrate ASCC3/AlkBH3 into a complex DNA repair pathway. We mapped and structurally analyzed interacting ASCC2 and ASCC3 regions. The ASCC3 fragment comprises a central helical domain and terminal, extended arms that clasp the compact ASCC2 unit. ASCC2-ASCC3 interfaces are evolutionarily highly conserved and comprise a large number of residues affected by somatic cancer mutations. We quantified contributions of protein regions to the ASCC2-ASCC3 interaction, observing that changes found in cancers lead to reduced ASCC2-ASCC3 affinity. Functional dissection of ASCC3 revealed similar organization and regulation as in the spliceosomal RNA helicase Brr2. Our results delineate functional regions in an important DNA repair complex and suggest possible molecular disease principles.

H-type lectins - Structural characteristics and their applications in diagnostics, analytics and drug delivery.

Lectins are ubiquitous carbohydrate-binding proteins that interact with sugar moieties in a highly specific manner. H-type lectins represent a new group of lectins that were identified in invertebrates. These lectins share structural homology and bind mainly to N-acetylgalactosamine (GalNAc). Recent structural studies on the H-type lectins provided a detailed description of the GalNAc-lectin interaction that is already exploited in a number of biomedical applications. Two members of the H-type lectin family, Helix pomatia agglutinin (HPA) and Helix aspersa agglutinin (HAA), have already been extensively used in many diagnostic tests due their ability to specifically recognize GalNAc. This ability is especially important because aberrant glycosylation patterns of proteins expressed by cancer cells contain GalNAc. In addition, H-type lectins were utilized in diagnostics of other non-cancer diseases and represent great potential as components of drug delivery systems. Here, we present an overview of the H-type lectins and their applications in diagnostics, analytics and drug delivery.

Depression in Dementia or Dementia in Depression? Systematic Review of Studies and Hypotheses.

The majority of research works to date suggest that Major Depressive Disorder (MDD) is a risk factor for dementia and may predispose to cognitive decline in both early and late onset variants. The presence of depression may not, however, reflect the cause, rather, an effect: it may be a response to cognitive impairment or alters the threshold at which cognitive impairment might manifest or be detected. An alternative hypothesis is that depression may be part of a prodrome to Alzheimer's Disease (AD), suggesting a neurobiological association rather than one of psychological response alone. Genetic polymorphisms may explain some of the variances in shared phenomenology between the diagnoses, the instance, when the conditions arise comorbidly, the order in which they are detected that may depend on individual cognitive and physical reserves, as well as the medical history and individual vulnerability. This hypothesis is biologically sound but has not been systematically investigated to date. The current review highlights how genetic variations are involved in the development of both AD and MDD, and the risk conferred by these variations on the expression of these two disorders comorbidly is an important consideration for future studies of pathoaetiological mechanisms and in the stratification of study samples for randomised controlled trials.

Redox regulation by reversible protein S-thiolation in Gram-positive bacteria.

Low molecular weight (LMW) thiols play an important role as thiol-cofactors for many enzymes and are crucial to maintain the reduced state of the cytoplasm. Most Gram-negative bacteria utilize glutathione (GSH) as major LMW thiol. However, in Gram-positive Actinomycetes and Firmicutes alternative LMW thiols, such as mycothiol (MSH) and bacillithiol (BSH) play related roles as GSH surrogates, respectively. Under conditions of hypochlorite stress, MSH and BSH are known to form mixed disulfides with protein thiols, termed as S-mycothiolation or S-bacillithiolation that function in thiol-protection and redox regulation. Protein S-thiolations are widespread redox-modifications discovered in different Gram-positive bacteria, such as Bacillus and Staphylococcus species, Mycobacterium smegmatis, Corynebacterium glutamicum and Corynebacterium diphtheriae. S-thiolated proteins are mainly involved in cellular metabolism, protein translation, redox regulation and antioxidant functions with some conserved targets across bacteria. The reduction of protein S-mycothiolations and S-bacillithiolations requires glutaredoxin-related mycoredoxin and bacilliredoxin pathways to regenerate protein functions. In this review, we present an overview of the functions of mycothiol and bacillithiol and their physiological roles in protein S-bacillithiolations and S-mycothiolations in Gram-positive bacteria. Significant progress has been made to characterize the role of protein S-thiolation in redox-regulation and thiol protection of main metabolic and antioxidant enzymes. However, the physiological roles of the pathways for regeneration are only beginning to emerge as well as their interactions with other cellular redox systems. Future studies should be also directed to explore the roles of protein S-thiolations and their redox pathways in pathogenic bacteria under infection conditions to discover new drug targets and treatment options against multiple antibiotic resistant bacteria.

The influence of p02, BE, BB parameters of perinatally obtained cord blood on quantity of obtained cells and focus on the perfect donor criteria.

The aim of the study was to analyze the influence of oxygene partial pressure (p02), base excess (BE) and buffer base (BB) parameters of cord blood obtained perinatally on quantity of obtained cells and focus on the perfect donor criteria. The study included 50 pregnant women aged between 18 and 38 years in which spontaneous labors and elective cesarean sections were performed. Umbilical cord blood was collected immediately after the women were delivered of newborns. The cells were analyzed in the Polish Stem Cells Bank in Warsaw. In the study group of patients different stem cells viability levels did not differ significantly in terms of pO2, BB and BE level, however, there was a trend that the higher the viability the lower BE value. The experiment showed also that the cord blood (CB) oxygenation scope is vitally important for the CB cells viability.

Crystal Structure of the Escherichia coli DExH-Box NTPase HrpB.

Eukaryotic DExH-box proteins are important post-transcriptional gene regulators, many of which employ RNA-stimulated nucleoside triphosphatase activity to remodel RNAs or ribonucleoprotein complexes. However, bacterial DExH-box proteins are structurally and functionally poorly characterized. We report the crystal structure of the Escherichia coli DExH-box protein HrpB. A globular head is composed of dual RecA, winged-helix, helical bundle and oligonucleotide/oligosaccharide-binding domains, resembling a compact version of eukaryotic DExH-box proteins. Additionally, HrpB harbors a C-terminal region not found in proteins with known structure, which bestows the protein with unique interaction potential. Interaction and activity assays showed that the protein binds RNA but not DNA, hydrolyzes all nucleoside triphosphates in an RNA-stimulated manner, but does not unwind diverse model RNAs in vitro. These observations can be rationalized by detailed comparisons with structurally characterized eukaryotic DExH-box proteins. Comparative phenotypic analyses of an E. coli hrpB knockout mutant suggested diverse functions of HrpB homologs in different bacteria.

Predictive model of pollutant loads discharged by combined sewer overflows.

Effective protection of receiving waters on urbanized areas requires knowledge about the amount of pollutants contained in discharged wastewater, inter alia by combined sewer overflows (CSOs). This involves the need to conduct long-lasting, costly and technically complex studies on the quantity and quality of discharged sewage. Loads of pollutants emitted by CSOs depend on many factors, inter alia on very variable characteristics of precipitations. This paper attempts to develop a simplified predictive model of pollutant loads for two basic parameters: total suspended solids (TSS) and chemical oxygen demand (COD). Studies were conducted in Lodz (Poland) between 2012 and 2015 on an urban catchment. Obtained data were analysed using the Pearson's correlation and principal component analysis method which enabled selection of the key parameters forming the model (depth and maximum intensity of rainfall and CSO volume). A good fit for the developed model was obtained (R2 = 0.79 for TSS and R2 = 0.80 for COD). The model was verified for two other catchments in the same city. Results indicate that the load of TSS and COD can be sufficiently precisely determined by using the proposed model for the studied city without the need to perform long-term continuous quality research of wastewater.