Dicodon-based measures for modeling gene expression.

MOTIVATION: Codon usage preference patterns have been associated with modulation of translation efficiency, protein folding, and mRNA decay. However, new studies support that codon pair usage has also a remarkable effect at the gene expression level. Here, we expand the concept of CAI to answer if codon pair usage patterns can be understood in terms of codon usage bias, or if they offer new information regarding coding translation efficiency. RESULTS: Through the implementation of a weighting strategy to consider the dicodon contributions, we observe that the dicodon-based measure has greater correlations with gene expression level than CAI. Interestingly, we have noted that dicodons associated with a low value of adaptiveness are related to dicodons which mediate strong translational inhibition in yeast. We have also noticed that some codon-pairs have a smaller dicodon contribution than estimated by the product of the respective codon contributions. AVAILABILITY AND IMPLEMENTATION: Scripts, implemented in Python, are freely available for download at https://zenodo.org/record/7738276#.ZBIDBtLMIdU.

PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders.

Mutations in the adaptor protein PSTPIP1 cause a spectrum of autoinflammatory diseases, including PAPA and PAMI; however, the mechanism underlying these diseases remains unknown. Most of these mutations lie in PSTPIP1 F-BAR domain, which binds to LYP, a protein tyrosine phosphatase associated with arthritis and lupus. To shed light on the mechanism by which these mutations generate autoinflammatory disorders, we solved the structure of the F-BAR domain of PSTPIP1 alone and bound to the C-terminal homology segment of LYP, revealing a novel mechanism of recognition of Pro-rich motifs by proteins in which a single LYP molecule binds to the PSTPIP1 F-BAR dimer. The residues R228, D246, E250, and E257 of PSTPIP1 that are mutated in immunological diseases directly interact with LYP. These findings link the disruption of the PSTPIP1/LYP interaction to these diseases, and support a critical role for LYP phosphatase in their pathogenesis.

Triclabendazole and clofazimine reduce replication and spermine uptake in vitro in Toxoplasma gondii.

Toxoplasmosis is a worldwide zoonosis caused by the protozoan parasite Toxoplasma gondii. Although this infection is generally asymptomatic in immunocompetent individuals, it can cause serious clinical manifestations in newborns with congenital infection or in immunocompromised patients. As current treatments are not always well tolerated, there is an urgent need to find new drugs against human toxoplasmosis. Drug repurposing has gained considerable momentum in the last decade and is a particularly attractive approach for the search of therapeutic alternatives to treat rare and neglected diseases. Thus, in this study, we investigated the antiproliferative effect of several repurposed drugs. Of these, clofazimine and triclabendazole displayed a higher selectivity against T. gondii, affecting its replication. Furthermore, both compounds inhibited spermine incorporation into the parasite, which is necessary for the formation of other polyamines. The data reported here indicate that clofazimine and triclabendazole could be used for the treatment of human toxoplasmosis and confirms that drug repurposing is an excellent strategy to find new therapeutic targets of intervention.

[Moyamoya disease in children] / Moyamoya hos barn.

Moyamoya is a rare condition that affects the blood vessels of the brain in children and young adults. It can cause both ischaemic stroke and cerebral haemorrhage. Although established diagnostic criteria and examinations exist, limited knowledge of the condition often leads to a mistaken or delayed diagnosis. Treatment consists of antiplatelet drugs and surgical revascularisation. Prognosis after successful surgery is good, but the disease requires a dedicated medical team.

Soils from abandoned shooting range facilities as contamination source of potentially toxic elements: distribution among soil geochemical fractions.

Civilian and military shooting range facilities cause environmental issues in several countries due to the accumulation of Potentially Toxic Elements; as a result of weathering of ammunitions accumulated into the soils. The contents and distribution of Cu, Ni, Pb and Zn were analyzed in 12 soils in an abandoned clay target shooting range at two different depths (0-15 and 15-30 cm). Single extractions (CaCl2 and DTPA) and Tessier sequential extraction were conducted to assess the PTE mobility and the PTE distribution in the different soil geochemical fractions at both depths. High total contents of Pb were found at both soil depths, while Cu, Ni and Zn showed lower significance levels. Copper, Ni and Zn are mainly associated with the residual fraction (> 95% of total content in all cases). However, Pb was highly associated with exchangeable fractions (21-52%), showing a high mobility at both depths. With moderate-high contents of organic matter (6-12%), the studied soils have acidic values and low levels of Al, Fe and Mn oxides that favors the migration of Pb through the soil profile and potential transformation to more mobile forms (Pb0 to Pb2+ and Pb4+). Although Pb reduced downward mobility in soils, due to the specific conditions of these facilities and the lead source (weathering of ammunition), risk assessment studies on clay-target shooting and firing range facilities should study the potential migration of Pb through the soil profile.

Understanding Pediatric Neuroimmune Disorder Conflicts: A Neuroradiologic Approach in the Molecular Era.

Neuroimmune disorders in children are a complex group of inflammatory conditions of the central nervous system with diverse pathophysiologic mechanisms and clinical manifestations. Improvements in antibody analysis, genetics, neuroradiology, and different clinical phenotyping have expanded knowledge of the different neuroimmune disorders. The authors focus on pediatric-onset myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease, which is a new entity in the spectrum of inflammatory demyelinating diseases, distinct from both multiple sclerosis (MS) and anti-aquaporin-4 (AQP4) antibody neuromyelitis optica spectrum disorders (NMOSDs). The authors review the importance of an optimized antibody-detection assay, the frequency of MOG antibodies in children with acquired demyelinating syndrome (ADS), the disease course, the clinical spectrum, proposed diagnostic criteria, and neuroimaging of MOG antibody-associated disease. Also, they outline differential diagnosis from other neuroimmune disorders in children according to the putative primary immune mechanism. Finally, they recommend a diagnostic algorithm for the first manifestation of ADS or relapsing ADS that leads to four demyelinating syndromes: MOG antibody-associated disease, AQP4 antibody NMOSDs, MS, and seronegative relapsing ADS. This diagnostic approach provides a framework for the strategic role of neuroradiology in diagnosis of ADS and decision making, to optimize patient care and treatment outcome in concert with clinicians. Online supplemental material is available for this article. ©RSNA, 2020.

A new pattern in hepatitis A virus infection in an urban population.

INTRODUCTION: hepatitis A virus (HAV) infection is a common cause of acute hepatitis worldwide. Since the generalization of vaccination, its incidence had markedly declined. Nevertheless, several HAV-outbreaks have been described in the last decade, mainly related to contaminated alimentary products. In recent years, a new pattern of acute HAV infection has been described with changes in the demographic profile of the infected population, which is more common in healthy young men. PATIENTS AND METHODS: a retrospective case series study was performed to evaluate this possible change in the pattern of HAV infection. The case series included all patients with a diagnosis of HAV acute infection in our hospital between January 2005 and May 2017. RESULTS: a total of 196 cases were diagnosed which were comprised of two probable outbreaks: one starting in November 2008 of 26 cases and one starting in 2016 with 69 cases at the time of data collection. The two outbreak populations were comparable. While the sporadic cases group was predominantly formed by pediatric and third-age patients with a slight male tendency, the outbreak related cases showed a clear predominance for young males (proportion of males: 63.2% vs 85.3%, p < 0.001). A possible chronological relationship with the national gay festivity celebrated in Madrid was observed. Outbreak related cases had higher bilirubin, alanine aminotransferase and longer APPT at diagnosis as well as a lower albumin concentration. The clinical relevance was minimal with a similar hospitalization rate and clinical outcome in both groups. There were no related deaths, acute liver failure or need for liver transplantation in our cohort. CONCLUSION: these epidemiological findings emphasize the importance of implementing preventive measures as well as social awareness campaigns.

Serological diagnosis of Toxoplasmosis disease using a fluorescent immunosensor with chitosan-ZnO-nanoparticles.

This article describes a microfluidic LIF immunosensor for the quantitative determination of anti-Toxoplasma gondii IgG (anti-T. gondii) specific antibodies. The serological detection of these antibodies plays a crucial role in the clinical diagnosis of toxoplasmosis. Zinc oxide nanoparticles (ZnO-NPs) obtained by wet chemical procedure were covered with chitosan and then used to conjugate T-gondii antigens into the central microfluidic channel. Serum samples containing anti-T-gondii IgG antibodies were injected into the immunosensor where they interact immunologically with T. gondii antigens. Bound antibodies were quantified by the addition of anti-IgG antibodies labeled whit alkaline phosphatase (ALP). ALP enzymatically converts the non-fluorescent 4-methylumbelliferyl phosphate (4-MUP) to soluble fluorescent methylumbelliferone that was measured using excitation at 355 nm and emission at 440 nm. The relative fluorescent response of methylumbelliferone is proportional to the concentration of anti-T. gondii IgG antibodies. The coefficients of variation are less than 4.73% for within-day assays and less than 6.34% for between-day assays. Results acquired by LIF immunosensor agree with those obtained by enzyme-linked immunosorbent assay method, suggesting that the designed sensor represents a promising tool for the quantitative determination of anti-T. gondii IgG antibodies of clinical samples.

Exploring protein myristoylation in Toxoplasma gondii.

Toxoplasma gondii is an important human and veterinary pathogen and the causative agent of toxoplasmosis, a potentially severe disease especially in immunocompromised or congenitally infected humans. Current therapeutic compounds are not well-tolerated, present increasing resistance, limited efficacy and require long periods of treatment. On this context, searching for new therapeutic targets is crucial to drug discovery. In this sense, recent works suggest that N-myristoyltransferase (NMT), the enzyme responsible for protein myristoylation that is essential in some parasites, could be the target of new anti-parasitic compounds. However, up to date there is no information on NMT and the extent of this modification in T. gondii. In this work, we decided to explore T. gondii genome in search of elements related with the N-myristoylation process. By a bioinformatics approach it was possible to identify a putative T. gondii NMT (TgNMT). This enzyme that is homologous to other parasitic NMTs, presents activity in vitro, is expressed in both intra- and extracellular parasites and interacts with predicted TgNMT substrates. Additionally, NMT activity seems to be important for the lytic cycle of Toxoplasma gondii. In parallel, an in silico myristoylome predicts 157 proteins to be affected by this modification. Myristoylated proteins would be affecting several metabolic functions with some of them being critical for the life cycle of this parasite. Together, these data indicate that TgNMT could be an interesting target of intervention for the treatment of toxoplasmosis.

Identification of new palmitoylated proteins in Toxoplasma gondii.

Protein palmitoylation has been shown to be an important post-translational modification in eukaryotic cells. This modification alters the localization and/or the function of the targeted protein. In recent years, protein palmitoylation has risen in importance in apicomplexan parasites as well. In Toxoplasma gondii, some proteins have been reported to be modified by palmitate. With the development of new techniques that allow the isolation of palmitoylated proteins, this significant post-translational modification has begun to be studied in more detail in T. gondii. Here we describe the palmitoylome of the tachyzoite stage of T. gondii using a combination of the acyl-biotin exchange chemistry method and mass spectrometry analysis. We identified 401 proteins found in multiple cellular compartments, with a wide range of functions that vary from metabolic processes, gliding and host-cell invasion to even regulation of transcription and translation. Besides, we found that more rhoptry proteins than the ones already described for Toxoplasma are palmitoylated, suggesting an important role for this modification in the invasion mechanism of the host-cell. This study documents that protein palmitoylation is a common modification in T. gondii that could have an impact on different cellular processes.

Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB.

Polycomb group (PcG) proteins are transcriptional repressors that control processes ranging from the maintenance of cell fate decisions and stem cell pluripotency in animals to the control of flowering time in plants. In Drosophila, genetic studies identified more than 15 different PcG proteins that are required to repress homeotic (HOX) and other developmental regulator genes in cells where they must stay inactive. Biochemical analyses established that these PcG proteins exist in distinct multiprotein complexes that bind to and modify chromatin of target genes. Among those, Polycomb repressive complex 1 (PRC1) and the related dRing-associated factors (dRAF) complex contain an E3 ligase activity for monoubiquitination of histone H2A (refs 1-4). Here we show that the uncharacterized Drosophila PcG gene calypso encodes the ubiquitin carboxy-terminal hydrolase BAP1. Biochemically purified Calypso exists in a complex with the PcG protein ASX, and this complex, named Polycomb repressive deubiquitinase (PR-DUB), is bound at PcG target genes in Drosophila. Reconstituted recombinant Drosophila and human PR-DUB complexes remove monoubiquitin from H2A but not from H2B in nucleosomes. Drosophila mutants lacking PR-DUB show a strong increase in the levels of monoubiquitinated H2A. A mutation that disrupts the catalytic activity of Calypso, or absence of the ASX subunit abolishes H2A deubiquitination in vitro and HOX gene repression in vivo. Polycomb gene silencing may thus entail a dynamic balance between H2A ubiquitination by PRC1 and dRAF, and H2A deubiquitination by PR-DUB.

Wavelets-based clustering of air quality monitoring sites.

This paper aims at providing a variance/covariance profile of a set of 36 monitoring stations measuring ozone (O3) and nitrogen dioxide (NO2) hourly concentrations, collected over the period 2005-2013, in Portugal mainland. The resulting individual profiles are embedded in a wavelet decomposition-based clustering algorithm in order to identify groups of stations exhibiting similar profiles. The results of the cluster analysis identify three groups of stations, namely urban, suburban/urban/rural, and a third group containing all but one rural stations. The results clearly indicate a geographical pattern among urban stations, distinguishing those located in Lisbon area from those located in Oporto/North. Furthermore, for urban stations, intra-diurnal and daily time scales exhibit the highest variance. This is due to the more relevant chemical activity occurring in high NO2 emissions areas which are responsible for high variability on daily profiles. These chemical processes also explain the reason for NO2 and O3 being highly negatively cross-correlated in suburban and urban sites as compared with rural stations. Finally, the clustering analysis also identifies sites which need revision concerning classification according to environment/influence type.

Overview of object oriented data analysis.

Object oriented data analysis is the statistical analysis of populations of complex objects. In the special case of functional data analysis, these data objects are curves, where a variety of Euclidean approaches, such as principal components analysis, have been very successful. Challenges in modern medical image analysis motivate the statistical analysis of populations of more complex data objects that are elements of mildly non-Euclidean spaces, such as lie groups and symmetric spaces, or of strongly non-Euclidean spaces, such as spaces of tree-structured data objects. These new contexts for object oriented data analysis create several potentially large new interfaces between mathematics and statistics. The notion of object oriented data analysis also impacts data analysis, through providing a framework for discussion of the many choices needed in many modern complex data analyses, especially in interdisciplinary contexts.

Mechanisms of adaptation and evolution in Toxoplasma gondii.

Toxoplasma has high host flexibility, infecting all nucleated cells of mammals and birds. This implies that during its infective process the parasite must constantly adapt to different environmental situations, which in turn leads to modifications in its metabolism, regulation of gene transcription, translation of mRNAs and stage specific factors. There are conserved pathways that support these adaptations, which we aim to elucidate in this review. We begin by exploring the widespread epigenetic mechanisms and transcription regulators, continue with the supportive role of Heat Shock Proteins (Hsp), the translation regulation, stress granules, and finish with the emergence of contingency genes in highly variable genomic domains, such as subtelomeres. Within epigenetics, the discovery of a new histone variant of the H2B family (H2B.Z), contributing to T. gondii virulence and differentiation, but also gene expression regulation and its association with the metabolic state of the parasite, is highlighted. Associated with the regulation of gene expression are transcription factors (TFs). An overview of the main findings on TF and development is presented. We also emphasize the role of Hsp90 and Tgj1 in T. gondii metabolic fitness and the regulation of protein translation. Translation regulation is also highlighted as a mechanism for adaptation to conditions encountered by the parasite as well as stress granules containing mRNA and proteins generated in the extracellular tachyzoite. Another important aspect in evolution and adaptability are the subtelomeres because of their high variability and gene duplication rate. Toxoplasma possess multigene families of membrane proteins and contingency genes that are associated with different metabolic stresses. Among them parasite differentiation and environmental stresses stand out, including those that lead tachyzoite to bradyzoite conversion. Finally, we are interested in positioning protozoa as valuable evolution models, focusing on research related to the Extended Evolutionary Synthesis, based on models recently generated, such as extracellular adaptation and ex vivo cyst recrudescence.

Evaluation of the criteria for renewal of LHRH agonists in patients with prostate cancer: results of the ANAREN Study.

Introduction: Injectable extended-release formulations of luteinizing hormone-releasing hormone agonists (LHRHa) have simplified the treatment of prostate cancer with a satisfactory level of androgen castration. This study aims to determine the percentage of patients whose initial LHRHa prescription was renewed during follow-up, how many changed formulation and how their quality of life evolved. Methods: This is an observational, prospective, multicentre study of men with prostate cancer who were to receive treatment with LHRHa (triptorelin every 3 or 6 months, leuprorelin every 3 or 6 months, or goserelin every 3 months) for 24 months. The treatment used was recorded and quality of life was assessed (QLQ-PR25 questionnaire) at four follow-up visits. Results: A total of 497 men (median age 75 years) were evaluated. The median exposure to LHRHa was 24 months. The initial prescription was renewed in 95.7% at follow-up 1 and 75% at follow-up 4. The main reason for changing from a 6-month to a 3-month formulation was a preference for sequential treatment (according to the investigator) and to see the physician more frequently (according to the patient). The main reason for switching from the 3-month to 6-month formulation was simplification of treatment (according to the investigator) and for convenience (according to the patient). Findings in the QLQ-PR25 questionnaire revealed no changes in urinary or bowel symptoms, though an improvement in sexual activity was reported. Practically all investigators and patients were satisfied/very satisfied with the treatment. Conclusion: Changes in formulation were scarce and generally justified by convenience factors or personal preferences. Patients maintained a good health status, with a high rate of retention of LHRHa treatment. Clinical Trial Registration: Study number: A-ES-52014-224.A plain language summary is provided as supplementary material (available at: https://www.drugsincontext.com/wp-content/uploads/2024/05/dic.2024-2-2-Suppl.pdf).

The IRE1α-XBP1 arm of the unfolded protein response is a host factor activated in SARS-CoV-2 infection.

SARS-CoV-2 infection can cause severe pneumonia, wherein exacerbated inflammation plays a major role. This is reminiscent of the process commonly termed cytokine storm, a condition dependent on a disproportionated production of cytokines. This state involves the activation of the innate immune response by viral patterns and coincides with the biosynthesis of the biomass required for viral replication, which may overwhelm the capacity of the endoplasmic reticulum and drive the unfolded protein response (UPR). The UPR is a signal transduction pathway composed of three branches that is initiated by a set of sensors: inositol-requiring protein 1 (IRE1), protein kinase RNA-like ER kinase (PERK), and activating transcription factor 6 (ATF6). These sensors control adaptive processes, including the transcriptional regulation of proinflammatory cytokines. Based on this background, the role of the UPR in SARS-CoV-2 replication and the ensuing inflammatory response was investigated using in vivo and in vitro models of infection. Mice and Syrian hamsters infected with SARS-CoV-2 showed a sole activation of the Ire1α-Xbp1 arm of the UPR associated with a robust production of proinflammatory cytokines. Human lung epithelial cells showed the dependence of viral replication on the expression of UPR-target proteins branching on the IRE1α-XBP1 arm and to a lower extent on the PERK route. Likewise, activation of the IRE1α-XBP1 branch by Spike (S) proteins from different variants of concern was a uniform finding. These results show that the IRE1α-XBP1 system enhances viral replication and cytokine expression and may represent a potential therapeutic target in SARS-CoV-2 severe pneumonia.

Loss of the VHR dual-specific phosphatase causes cell-cycle arrest and senescence.

Protein tyrosine phosphatases regulate important processes in eukaryotic cells and have critical functions in many human diseases including diabetes to cancer. Here, we report that the human Vaccinia H1-related (VHR) dual-specific protein tyrosine phosphatase regulates cell-cycle progression and is itself modulated during the cell cycle. Using RNA interference (RNAi), we demonstrate that cells lacking VHR arrest at the G1-S and G2-M transitions of the cell cycle and show the initial signs of senescence, such as flattening, spreading, appearance of autophagosomes, beta-galactosidase staining and decreased telomerase activity. In agreement with this notion, cells lacking VHR were found to upregulate p21(Cip-Waf1), whereas they downregulated the expression of genes for cell-cycle regulators, DNA replication, transcription and mRNA processing. Loss of VHR also caused a several-fold increase in serum-induced activation of its substrates, the mitogen-activated protein (MAP) kinases Jnk and Erk. VHR-induced cell-cycle arrest was dependent on this hyperactivation of Jnk and Erk, and was reversed by Jnk and Erk inhibition or knock-down. We conclude that VHR is required for cell-cycle progression as it modulates MAP kinase activation in a cell-cycle phase-dependent manner.

A functional variant of lymphoid tyrosine phosphatase is associated with type I diabetes.

We report that a single-nucleotide polymorphism (SNP) in the gene (PTPN22) encoding the lymphoid protein tyrosine phosphatase (LYP), a suppressor of T-cell activation, is associated with type 1 diabetes mellitus (T1D). The variants encoded by the two alleles, 1858C and 1858T, differ in a crucial amino acid residue involved in association of LYP with the negative regulatory kinase Csk. Unlike the variant encoded by the more common allele 1858C, the variant associated with T1D does not bind Csk.

Proteomics Applications in Toxoplasma gondii: Unveiling the Host-Parasite Interactions and Therapeutic Target Discovery.

Toxoplasma gondii, a protozoan parasite with the ability to infect various warm-blooded vertebrates, including humans, is the causative agent of toxoplasmosis. This infection poses significant risks, leading to severe complications in immunocompromised individuals and potentially affecting the fetus through congenital transmission. A comprehensive understanding of the intricate molecular interactions between T. gondii and its host is pivotal for the development of effective therapeutic strategies. This review emphasizes the crucial role of proteomics in T. gondii research, with a specific focus on host-parasite interactions, post-translational modifications (PTMs), PTM crosstalk, and ongoing efforts in drug discovery. Additionally, we provide an overview of recent advancements in proteomics techniques, encompassing interactome sample preparation methods such as BioID (BirA*-mediated proximity-dependent biotin identification), APEX (ascorbate peroxidase-mediated proximity labeling), and Y2H (yeast two hybrid), as well as various proteomics approaches, including single-cell analysis, DIA (data-independent acquisition), targeted, top-down, and plasma proteomics. Furthermore, we discuss bioinformatics and the integration of proteomics with other omics technologies, highlighting its potential in unraveling the intricate mechanisms of T. gondii pathogenesis and identifying novel therapeutic targets.