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We described Creptotrema cambeve n. sp. from the intestine of the Brazilian catfish Cambeva davisi (Haseman, 1911) (= Trichomycterus davisi ) based on integrative analyses using morphological and molecular approaches. Creptotrema cambeve n. sp. closely resembles morphologically Creptotrema paraense Vicente, Santos & Souza, 1978, which was described from a siluriform fish in Northern Brazil; however, the two species differ mainly in the oral and ventral sucker sizes and the distribution of the vitellaria. The phylogenetic analyses of the 28S rDNA placed the sequences of the new species in a monophyletic clade together with all other Creptotrema spp. and as sister taxon of Creptotrema cruste Alcantara, Ebert, Ferreira-Silva, Forti, Morais, Pérez-Ponce de León & Silva, 2024, a parasite from a Brazilian anuran. Genetic divergences between the new species and other Creptotrema spp. varied from 0.2% to 4.3%, further corroborating the distinction of the new taxon. Creptotrema cambeve n. sp. is the 18th nominal Creptotrema species known from South America and the 22nd erected in the genus. This is the first study reporting a trematode in Cambeva spp. hosts and the second parasitological survey carried out for Ca. davisi , a poorly known small endemic fish.

Introduction: Burns are defined as a traumatic injury, usually of thermal origin, that affects the epithelial and adjacent tissue and is classified according to the depth reached. Tissue repair involved in this type of injury is often a challenge both due to its severity and the multiplicity of complications. Regenerative medicine has focused on the use of low-level laser photobiomodulation therapy (LLLT) and adipose-derived stem cells (ADSC), especially in the early stages of the process, to promote better healing and shorten repair time. Therefore, aim of this study was to evaluate the action of LLLT (660 nm) and ADSC in the repair process of burned skin tissue and investigate the association of the techniques (LLLT and ADSC)., Materials and Methods: An in vivo study was carried out using 96 rats (Wister) with a scald burn model at a temperature of 95ºC, exposing the animal's back for 14 s. Animals were randomized into seven groups and three periods, five, 14 and 21 days. The groups included GC: Control group, ADSC-: Group treated with CD49d negative cells, ADSC+ : Group treated with positive CD49d cells, CULT: Group treated with conventional isolation cells, LLLT: Group treated only with LLLT Low Power Laser, ADSC-LLLT: Group treated with CD49d negative cells and LLLT. ADSC+LLLT: Group treated with positive CD49d cells and LLLT. The groups treated with LLLT (660 nm; 5 J/cm2) received irradiation three times a week, on alternate days for five, 14 and 21 days, according to the time of biopsy. ADSC-treated groups received one to three applications of the cells in a total volume of 1000 μL starting soon after the surgical debridement of the burn. Photographic monitoring was carried out at 5, 14 and 21 days after the beginning of the experiment to assess the degree of lesion contraction. Macroscopic, morphometric and histopathological analyzes were performed., Results: We showed significant re-epithelialization as well as an improvement in the healing process in the ADSC+, LLLT and ADSC+LLLT groups. We observed effects in the reduction of the inflammatory phase, increase in angiogenesis, decrease in oedema, greater collagen deposition, and better organization of the extracellular matrix compared to the other treatments. Moreover, the immunomagnetic separation of ADSC cells through the expression of the CD49d protein proved to be a useful means to obtain a more homogeneous population of cells with a role in tissue regeneration compared to the ADSC- and CULT groups., Conclusion: In conclusion, the association of ADSC+ with LLLT was effective in accelerating the burn repair process, stimulating cell proliferation and formation of more normal skin tissue., Competing Interests: Declaration of Competing Interest M.R. has received research grants through National Council for Scientific and Technological Development (CNPq) scholarship from Brazil., (Copyright © 2023 Elsevier Ltd and International Society of Burns Injuries. All rights reserved.)

Background and Objectives: A bacterial brain abscess is an emergency and should be drained of pus within 24 hours of diagnosis, as recently recommended. In this cross-sectional study, we investigated whether delaying pus drainage entails brain abscess expansion and what the underlying mechanism might be., Methods: Repeated brain MRI of 47 patients who did not undergo immediate pus drainage, pus osmolarity measurements, immunocytochemistry, proteomics, and 18F-fluorodeoxyglucose positron emission tomography., Results: Time from first to last MRI before neurosurgery was 1 to 14 days. Abscesses expanded in all but 2 patients: The median average increase was 23% per day (range 0%-176%). Abscesses expanded during antibiotic therapy and even if the pus did not contain viable bacteria. In a separate patient cohort, we found that brain abscess pus tended to be hyperosmolar (median value 360 mOsm; range 266-497; n = 14; normal cerebrospinal fluid osmolarity is ∼290 mOsm). Hyperosmolarity would draw water into the abscess cavity, causing abscess expansion in a ballooning manner through increased pressure in the abscess cavity. A mechanism likely underlying pus hyperosmolarity was the recruitment of neutrophils to the abscess cavity with ensuing neutrophil cell death and decomposition of neutrophil proteins and other macromolecules to osmolytes: Pus analysis showed the presence of neutrophil proteins (protein-arginine deiminases, citrullinated histone, myeloperoxidase, elastase, cathelicidin). Previous studies have shown very high levels of osmolytes (ammonia, amino acids) in brain abscess pus. 18F-fluorodeoxyglucose positron emission tomography showed focal neocortical hypometabolism 1 to 8 years after brain abscess, indicating long-lasting damage to brain tissue., Conclusion: Brain abscesses expand despite effective antibiotic treatment. Furthermore, brain abscesses cause lasting damage to surrounding brain tissue. These findings support drainage of brain abscesses within 24 hours of diagnosis., (Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the Congress of Neurological Surgeons.)

Structural modifications are an important tool for studying the properties of naturally occurring polyphenols. Regarding the preparation of acetyl esters, the presence of hydroxyl groups stabilized by intramolecular hydrogen bonds may pose an obstacle for the peracetylation of these compounds. In this paper, we present a facile protocol for the acetylation of selected polyphenols under mild reaction conditions by using acetic anhydride, catalytic amount 4-dimethylaminopyridine (DMAP) and dimethylformamide (DMF) as solvent. Reaction conditions were adjusted for optimal formation of peracetylated polyphenols while minimizing the formation of byproducts. Butyric anhydride was employed as an alternative acylating agent and showed similar results. Reaction yields varied from 78-97%, and products were obtained in high purity, as determined by LCMS(ESI+), 1 H NMR and 13 C NMR.

The objective of this work was to isolate a polysaccharide similar to pectin from Crataeva tapia leaves, not yet reported in the literature, and to evaluate its antioxidant, cytotoxic and immunomodulatory profile. Pectin was extracted from the leaves in three stages, organic solvent followed by acidified water and ethanol precipitation. With the pectin obtained, the physicochemical characterization of the molecule was carried out using high-performance liquid chromatography, Fourier-transform infrared spectroscopy, nuclear magnetic resonance ( 13 C and 1 H) and different thermal and elemental analysis. Furthermore, the antioxidant activities were evaluated in vitro, and using human peripheral blood mononuclear cell culture, cytotoxicity and immunostimulatory actions were investigated. Physical and chemical analyses showed characteristic signs of pectin. Antioxidant activity tests showed that pectin had moderate to low antioxidant activity. Furthermore, pectin did not affect the viability of erythrocytes and PBMC and induced an immunostimulatory state when it promoted the production of cytokines IL-6, IL-10 and TNF-α and increased the activation of CD8 + T lymphocytes. This study showed that pectin from Crataeva tapia is not cytotoxic and promoted a pro-inflammatory profile in peripheral blood mononuclear cell with application as an immunostimulating and emulsifying compound., Competing Interests: Conflict of interestThe authors declare no conflict of interest., (© King Abdulaziz City for Science and Technology 2023, Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Ouabain is a cardiac glycoside that has a protective effect against neuroinflammation at low doses through Na + /K + -ATPase signaling and that can activate tumor necrosis factor (TNF) in the brain. TNF plays an essential role in neuroinflammation and regulates glutamate receptors by acting on two different receptors (tumor necrosis factor receptor 1 [TNFR1] and TNFR2) that have distinct functions and expression. The activation of constitutively and ubiquitously expressed TNFR1 leads to the expression of pro-inflammatory cytokines. Thus, this study aimed to elucidate the effects of ouabain in a TNFR1 knockout (KO) mouse model. Interestingly, the hippocampus of TNFR1 KO mice showed a basal increase in both TNFR2 membrane expression and brain-derived neurotrophic factor (BDNF) release, suggesting a compensatory mechanism. Moreover, ouabain activated TNF-α-converting enzyme/a disintegrin and metalloprotease 17 (TACE/ADAM17), decreased N-methyl-D-aspartate (NMDA) receptor subunit 2A (NR2A) expression, and induced anxiety-like behavior in both genotype animals, independent of the presence of TNFR1. However, ouabain induced an increase in interleukin (IL)-1β in the hippocampus, a decrease in IL-6 in serum, and an increase in NMDA receptor subunit 1 (NR1) only in wild-type (WT) mice, indicating that TNFR1 or TNFR2 expression may be important for some effects of ouabain. Collectively, our results indicate a connection between ouabain signaling and TNFR1, with the effect of ouabain partially dependent on TNFR1.

Research on the morphophysiological behavior of forest seeds during germination with respect to climate change is scarce. To date, there have been no studies on the biochemical or morphological aspects of Ormosia spp. In this study, we subjected Ormosia coarctata seeds to various temperature conditions to investigate temperature-dependent impacts on morphology, reactive oxygen species (ROS) generation, antioxidant systems, and storage systems. Analyses were performed on seeds exposed to 25, 35, and 40 °C for 48, 96, and 144 h. The morphology was evaluated by radiation using a Faxitron MX-20 device. ROS production (superoxide anion and hydrogen peroxide), malonaldehyde (MDA), carbonylated proteins, antioxidant enzyme activity (superoxide dismutase [SOD], ascorbate peroxidase [APX], catalase [CAT], and peroxidase [POX]), β-carotene, lycopene, glucose, and reserve enzyme activity (α- and β-amylase, lipase, and protease) were analyzed by spectrophotometry. Heat stress (40 °C) decreased germination by 76.2% and 78.1% (compared to 25 and 35 °C, respectively), caused damage to the external morphology of the seed, increased the content of ROS, MDA, and carbonylated proteins, and reduced APX, CAT, and POX activity. Furthermore, heat stress decreased glucose content and α-amylase activity. These results suggest that an increase of 5 °C in temperature negatively affects germination, promotes oxidative stress, and induces deterioration in O. coarctata seeds., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

As new pathogens emerge, new challenges must be faced. This is no different in infectious disease research, where identifying the best tools available in laboratories to conduct an investigation can, at least initially, be particularly complicated. However, in the context of an emerging virus, such as SARS-CoV-2, which was recently detected in China and has become a global threat to healthcare systems, developing models of infection and pathogenesis is urgently required. Cell-based approaches are crucial to understanding coronavirus infection biology, growth kinetics, and tropism. Usually, laboratory cell lines are the first line in experimental models to study viral pathogenicity and perform assays aimed at screening antiviral compounds which are efficient at blocking the replication of emerging viruses, saving time and resources, reducing the use of experimental animals. However, determining the ideal cell type can be challenging, especially when several researchers have to adapt their studies to specific requirements. This review strives to guide scientists who are venturing into studying SARS-CoV-2 and help them choose the right cellular models. It revisits basic concepts of virology and presents the currently available in vitro models, their advantages and disadvantages, and the known consequences of each choice., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Pires De Souza, Le Bideau, Boschi, Wurtz, Colson, Aherfi, Devaux and La Scola.)

Background: Uterine leiomyosarcoma (uLMS) are rare and malignant tumors that arise in the myometrium cells and whose diagnosis is based on histopathological features. Identifying diagnostic biomarkers for uLMS is a challenge due to molecular heterogeneity and the scarcity of samples. In vivo and in vitro models for uLMS are urgently needed. Knockout female mice for the catalytic subunit of the immunoproteasome PSMB9 (MIM:177045) develop spontaneous uLMS. This study aimed to analyze the role of PSMB9 in uLMS tumorigenesis and patient outcome., Methods: Molecular data from 3 non-related uLMS cohorts were integrated and analyzed by proteotranscriptomic using gene expression and protein abundance levels in 68 normal adjacent myometrium (MM), 66 uterine leiomyoma (LM), and 67 uLMS., Results: the immunoproteasome pathway is upregulated and the gene PMSB9 shows heterogeneous expression values in uLMS. Quartile group analysis showed no significant difference between groups high and low PSMB9 expression groups at 3-years overall survival (OS). Using CYBERSORTx analysis we observed 9 out of 17 samples in the high group clustering together due to high M2 macrophages and CD4 memory resting, and high CD8+/PSMB9 ratio was associated with better OS. The main pathway regulated in the high group is IFNγ and in the low is the ECM pathway dependent on the proto-oncogene SRC., Conclusion: these findings suggest 2 subtypes of uLMS (immune-related and ECM-related) with different candidate mechanisms of malignancy.

The SARS-CoV-2 pandemic started in the end of 2019 in Wuhan, China, which highlighted the scenario of frequent cross-species transmission events. From the outbreak possibly initiated by viral spill-over into humans from an animal reservoir, now we face the human host moving globally while interacting with domesticated and peridomestic animals. The emergence of a new virus into the ecosystem leads to selecting forces and species-specific adaptations. The adaptation of SARS-CoV-2 to other animals represents a risk to controlling the dissemination of this coronavirus and the emergence of new variants. Since 2020, several mink farms in Europe and the United States have had SARS-CoV-2 outbreaks with human-mink and mink-human transmission, where the mink-selected variants possibly hold evolutionary concerning advantages. Here we investigated the permissibility of mink lung-derived cells using two cell lines, Mv-1-Lu and ENL-R, against several lineages of SARS-CoV-2, including some classified as variants of concern. The viral release rate and the infectious titers indicate that these cells support infections by different SARS-CoV-2 lineages. The viral production occurs in the first few days after infection with the low viral release by these mink cells, which is often absent for the omicron variant for lung cells. The electron microscopy reveals that during the viral replication cycle, the endomembrane system of the mink-host cell undergoes typical changes while the viral particles are produced, especially in the first days of infection. Therefore, even if limited, mink lung cells may represent a selecting source for SARS-CoV-2 variants, impacting their transmissibility and pathogenicity and making it difficult to control this new coronavirus., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Le Bideau, Pires de Souza, Boschi, Baudoin, Penant, Jardot, Fenollar, Colson, Lenk and La Scola.)

Viruses generally are defined as lacking the fundamental properties of living organisms in that they do not harbor an energy metabolism system or protein synthesis machinery. However, the discovery of giant viruses of amoeba has fundamentally challenged this view because of their exceptional genome properties, particle sizes and encoding of the enzyme machinery for some steps of protein synthesis. Although giant viruses are not able to replicate autonomously and still require a host for their multiplication, numerous metabolic genes involved in energy production have been recently detected in giant virus genomes from many environments. These findings have further blurred the boundaries that separate viruses and living organisms. Herein, we summarize information concerning genes and proteins involved in cellular metabolic pathways and their orthologues that have, surprisingly, been discovered in giant viruses. The remarkable diversity of metabolic genes described in giant viruses include genes encoding enzymes involved in glycolysis, gluconeogenesis, tricarboxylic acid cycle, photosynthesis, and β-oxidation. These viral genes are thought to have been acquired from diverse biological sources through lateral gene transfer early in the evolution of Nucleo-Cytoplasmic Large DNA Viruses, or in some cases more recently. It was assumed that viruses are capable of hijacking host metabolic networks. But the giant virus auxiliary metabolic genes also may represent another form of host metabolism manipulation, by expanding the catalytic capabilities of the host cells especially in harsh environments, providing the infected host cells with a selective evolutionary advantage compared to non-infected cells and hence favoring the viral replication. However, the mechanism of these genes' functionality remains unclear to date., Competing Interests: DB, GP, DL, SK, JG, JS, PC, BL, SA No competing interests declared, (© 2022, Belhaouari et al.)

Background: The growth of malignant tumors is influenced by their microenvironment. Glioblastoma, an aggressive primary brain tumor, may have cysts containing fluid that represents the tumor microenvironment. The aim of this study was to investigate whether the cyst fluid of cystic glioblastomas contains growth-stimulating factors. Identification of such growth factors may pave the way for the development of targeted anti-glioblastoma therapies., Methods: We performed hormone analysis of cyst fluid from 25 cystic glioblastomas and proteomics analysis of cyst fluid from another 12 cystic glioblastomas., Results: Glioblastoma cyst fluid contained hormones within wide concentration ranges: Insulin-like growth factor 1 (0-13.7 nmol/L), insulin (1.4-133 pmol/L), erythropoietin (4.7-402 IU/L), growth hormone (0-0.93 µg/L), testosterone (0.2-10.1 nmol/L), estradiol (0-1.0 nmol/L), triiodothyronine (1.0-11.5). Tumor volume correlated with cyst fluid concentrations of growth hormone and testosterone. Survival correlated inversely with cyst fluid concentration of erythropoietin. Several hormones were present at concentrations that have been shown to stimulate glioblastoma growth in vitro. Concentrations of erythropoietin and estradiol (in men) were higher in cyst fluid than in serum, suggesting formation by tumor or brain tissue. Quantitatively, glioblastoma cyst fluid was dominated by serum proteins, illustrating blood-brain barrier leakage. Proteomics identified several proteins that stimulate tumor cell proliferation and invasiveness, others that inhibit apoptosis or mediate adaption to hypoxia and some that induce neovascularization or blood-brain barrier leakage., Conclusion: The microenvironment of glioblastomas is rich in growth-stimulating factors that may originate from the circulation, the tumor, or the brain. The wide variation in cyst fluid hormone concentrations may differentially influence tumor growth., (© 2022. The Author(s).)

Glucagon-like peptide-1 (GLP-1) is a human incretin hormone derived from the proglucagon molecule. GLP-1 receptor agonists are frequently used to treat type 2 diabetes mellitus and obesity. However, the hormone affects the liver, pancreas, brain, fat cells, heart, and gastrointestinal tract. The objective of this study was to perform a systematic review on the use of GLP-1 other than in treating diabetes. PubMed, Cochrane, and Embase were searched, and the PRISMA guidelines were followed. Nineteen clinical studies were selected. The results showed that GLP-1 agonists can benefit defined off-medication motor scores in Parkinson's Disease and improve emotional well-being. In Alzheimer's disease, GLP-1 analogs can improve the brain's glucose metabolism by improving glucose transport across the blood-brain barrier. In depression, the analogs can improve quality of life and depression scales. GLP-1 analogs can also have a role in treating chemical dependency, inhibiting dopaminergic release in the brain's reward centers, decreasing withdrawal effects and relapses. These medications can also improve lipotoxicity by reducing visceral adiposity and decreasing liver fat deposition, reducing insulin resistance and the development of non-alcoholic fatty liver diseases. The adverse effects are primarily gastrointestinal. Therefore, GLP-1 analogs can benefit other conditions besides traditional diabetes and obesity uses.

The recognition of ontogenetic edentulism in the Jurassic noasaurid Limusaurus inextricabilis shed new light on the dietary diversity within Ceratosauria, a stem lineage of non-avian theropod dinosaurs known for peculiar craniomandibular adaptations. Until now, edentulism in Ceratosauria was exclusive to adult individuals of Limusaurus. Here, an exceptionally complete skeleton of a new toothless ceratosaur, Berthasaura leopoldinae gen. et sp. nov., is described from the Cretaceous aeolian sandstones of the Bauru Basin, Southern Brazil. The specimen resembles adult individuals of Limusaurus by the absence of teeth but based on the unfused condition of several elements (e.g., skull, vertebral column) it clearly represents an ontogenetically immature individual, indicating that it might never have had teeth. The phylogenetic analysis performed here has nested Berthasaura leopoldinae as an early-divergent Noasauridae, not closely related to Limusaurus. It represents the most complete non-avian theropod from the Brazilian Cretaceous and preserves the most complete noasaurid axial series known so far. Moreover, the new taxon exhibits many novel osteological features, uncommon in non-avian theropods, and unprecedented even among South American ceratosaurs. These include not only toothless jaws but also a premaxilla with cutting occlusal edge, and a slightly downturned rostral tip. This indicate that B. leopoldinae unlikely had the same diet as other ceratosaurs, most being regarded as carnivorous. As the ontogenetically more mature specimens of Limusaurus, Berthasaura might have been herbivorous or at least omnivorous, corroborating with an early evolutionary divergence of noasaurids from the ceratosaurian bauplan by disparate feeding modes., (© 2021. The Author(s).)

Curcuma and its derivatives are associated with anti-inflammatory and antioxidant activities in the skin. They exhibit beneficial effects in wound healing and prevention of chronic ultraviolet B damage and may prevent facial redness such as rosacea and flushing. This review aims to provide an up-to-date and rigorous synthesis of studies that demonstrated the clinical efficacy of curcuminoids in the skin. We evaluated studies published in the MEDLINE-PubMed/PMC (National Library of Medicine) databases, and followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines for this review. This search included papers published in the past 10 years in controlled clinical trials, double-blind and randomized controlled studies, and case studies. The search resulted in 12 studies published in the past 10 years. Curcuma species (Curcuma longa and Curcuma aeruginosa) and curcumin were found to produce various dermatological effects, including influencing antioxidant and anti-inflammatory processes in the production of hyaluronan, increasing skin moisture, and reducing axillary hair growth. Curcuma was also found to reduce thickness, erythema, pruritus, burning and pain in psoriasis lesions and to improve radiodermatitis lesions. Our review results show that Curcuma species may play a role in skin health management and may exhibit various dermatological effects, thus it could be a new therapeutic arsenal for dermatology professionals. Nevertheless, more clinical trials should be conducted with humans to establish the optimum delivery method and dosages for different dermatological conditions., (© 2021 British Association of Dermatologists.)

Several comorbidities, including hypertension, have been associated with an increased risk of developing severe disease during SARS-CoV-2 infection. Angiotensin II receptor blockers (ARBs) are currently some of the most widely-used drugs to control blood pressure by acting on the angiotensin II type 1 receptor (AT1R). ARBs have been reported to trigger the modulation of the angiotensin I converting enzyme 2 (ACE2), the receptor used by the virus to penetrate susceptible cells, raising concern that such treatments may promote virus capture and increase their viral load in patients receiving ARBs therapy. In this in vitro study, we reviewed the effect of ARBs on ACE2 and AT1R expression and investigated whether treatment of permissive ACE2+/AT1R+ Vero E6 cells with ARBs alters SARS-CoV-2 replication in vitro in an angiotensin II-free system. After treating the cells with the ARBs, we observed an approximate 50% relative increase in SARS-CoV-2 production in infected Vero E6 cells that correlates with the ARBs-induced up-regulation of ACE2 expression. From this data, we believe that the use of ARBs in hypertensive patients infected by SARS-CoV-2 should be carefully evaluated., Competing Interests: CD declares owning shares in the Sanofi and Merck pharmaceutical companies. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Pires de Souza, Osman, Le Bideau, Baudoin, Jaafar, Devaux and La Scola.)

The demographic shift toward an older population will increase the number of prostate cancer cases. A challenge in the treatment of prostate cancer is to avoid undertreatment of patients at high risk of progression following curative treatment. These men can benefit from early salvage treatment. An explorative cohort consisting of tissue from 16 patients who underwent radical prostatectomy, and were either alive or had died from prostate cancer within 10 years postsurgery, was analyzed by mass spectrometry analysis. Following proteomic and bioinformatic analyses, major vault protein (MVP) was identified as a putative prognostic biomarker. A publicly available tissue proteomics dataset and a retrospective cohort of 368 prostate cancer patients were used for validation. The prognostic value of the MVP was verified by scoring immunohistochemical staining of a tissue microarray. High level of MVP was associated with more than 4-fold higher risk for death from prostate cancer (hazard ratio = 4.41, 95% confidence interval: 1.45-13.38; P = 0.009) in a Cox proportional hazard models, adjusted for Cancer of the Prostate Risk Assessments Post-surgical (CAPRA-S) score and perineural invasion. Decision curve analyses suggested an improved standardized net benefit, ranging from 0.06 to 0.18, of adding MVP onto CAPRA-S score. This observation was confirmed by receiver operator characteristics curve analyses for the CAPRA-S score versus CAPRA-S and MVP score (area under the curve: 0.58 versus 0.73). From these analyses, one can infer that MVP levels in combination with CAPRA-S score might add onto established risk parameters to identify patients with lethal prostate cancer., (© The Author(s) 2021. Published by Oxford University Press.)

The ongoing outbreak of novel coronavirus pneumonia (COVID-19) caused by SARS-CoV-2 infection has spread rapidly worldwide. The major transmission routes of SARS-CoV-2 are recognised as inhalation of aerosol/droplets and person-to-person contact. However, some studies have demonstrated that live SARS-CoV-2 can be isolated from the faeces and urine of infected patients, which can then enter the wastewater system. The currently available evidence indicates that the viral RNA present in wastewater may become a potential source of epidemiological data. However, to investigate whether wastewater may present a risk to humans such as sewage workers, we investigated whether intact particles of SARS-CoV-2 were observable and whether it was possible to isolate the virus in wastewater. Using a correlative strategy of light microscopy and electron microscopy (CLEM), we demonstrated the presence of intact and degraded SARS-like particles in RT-qPCR SARS-CoV-2-positive sewage sample collected in the city of Marseille. However, the viral infectivity assessment of SARS-CoV-2 in the wastewater was inconclusive, due to the presence of other viruses known to be highly resistant in the environment such as enteroviruses, rhinoviruses, and adenoviruses. Although the survival and the infectious risk of SARS-CoV-2 in wastewater cannot be excluded from our study, additional work may be required to investigate the stability, viability, fate, and decay mechanisms of SARS-CoV-2 thoroughly in wastewater.

Giant viruses have brought new perspectives on the virosphere. They have been increasingly described in humans, including in several metagenomic studies. Here, we searched into the metagenome of the 5300-year-old Ötzi mummy for the presence of giant virus-related sequences using MG-Digger pipeline. We found 19 reads (0.00006% of the total read number) that best matched (mean ± standard deviation (range) for e-values of 5.0E-6 ± 1.4E-6 (6.0E-5-4.0E-10) and for amino acid identity of 69.9 ± 8.7% (46.4-84.9%) and most significantly with sequences from various giant viruses, including mostly mimiviruses. This expands current knowledge on the ubiquity and relationship with humans of giant viruses.

The morphoanatomical characteristics of leaves were associated with altitude, hillside, and the cup quality of coffee produced in the Matas de Minas region. Although the small magnitude, there are correlations between cup quality with altitude and morpho-anatomical traits. Despite facing the differences of management inherent to 363 sampling sites, Northwestern hillside had significant lower cup quality, whereas only stomata density (SD) and thickness of the leaf epidermis in the adaxial face (AdET) showed significant differences between hillsides. Altitude, leaf mass per area (LMA) and SD, and to a lesser extent the thickness of the leaf epidermis in the abaxial face (AbET), were correlated (Spearman's correlation) with cup quality. Interestingly, AbET correlations were negative. Mantel's test significant correlations were found between coffee cup quality vs. altitude, LMA and petiole phloem area (PPhA). The spatial autocorrelation was significant only with LMA. Also, SD, to a lesser extent, was associated with cup quality. Despite the complexity of the association among the environment, plant growth and development, this is the first report to associate morpho-anatomical features of the leaf with the coffee cup traits. Even with the expectation of genotype/species vs environment interactions, and the influence of other parameters associated with post-harvest, roasting and brewing, the evaluation of LMA, SD, AdET, AbET and the thickness of the palisade parenchyma (PPT) allow a novel approach to access coffee cup quality., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

We report two cases of Langerhans cell histiocytosis (LCH) in the oral cavity of children. An 11-month-old girl was referred for evaluation of a nodular and sessile lesion in the alveolar ridge covering the primary left mandibular central incisor. The second patient was a seven-year-old boy with an ulcerated lesion in the gingiva covered by necrotic areas, extending to the sulcus of the vestibule. The patients underwent incisional biopsies and histopathological exams showed a proliferation of Langerhans and eosinophil cells, suggesting a diagnosis of LCH, which was confirmed by positive immunohistochemical expression of S100 and CD1.

Background: Several metal-based molecules that display cytotoxicity against multiple cell lines have been pursued in an attempt to fight against cancer and to overcome the typical side effects of drugs like cisplatin. In this scenario, ruthenium complexes have been extensively studied due to their activity in both in vitro and in vivo biological systems, including various cancer cell strains., Objective: We aimed to develop a method to synthesize novel [Ru(NO)(bpy) 2 L 2 ] 2+ complexes containing amino acid ligands by using an alternative Click Chemistry approach, namely the copper azide-alkyne cycloaddition reaction (CuAAC reaction), to construct nitrosyl/nitrite complexes bearing a modified lysine residue., Methods: We synthesized a new ligand by Click Chemistry approach and new compounds bearing the unprecedented ligand. Cytotoxicity was assessed by the classical MTT colorimetric assay. MCF-7 and MDAMB- 231 cells were used as breast cancer cell models. MCF-10 was used as a model of healthy cells., Results: Amino acid ligands related to N 3 -Lys(Fmoc) and the new pyLys were successfully synthesized by the diazotransfer reaction and the CuAAC reaction, respectively. The latter reaction involves coupling between N 3 -Lys(Fmoc) and 3ethynylpyridine. Both N 3 -Lys(Fmoc) and the new pyLys were introduced into the ruthenium bipyridine complex I, or cis-[Ru II (NO)(NO 2 )(bpy) 2 ] 2+ , to generate the common nitro-based complex III, which was further converted to the final complex IV. Results of the MTT assay proved the cytotoxic effect of cis- [Ru II (NO)(pyLysO-)(bpy) 2 ](PF 6 ) 2 against the mammalian breast cancer cells MCF-7 and MDA-MB231., Conclusion: The viability assays revealed that complex IV, bearing a NO group and a modified lysine residue, was able to release NO and cross tumor cell membranes. In this work, Complex IV was observed to be the most active ruthenium bipyridine complex against the mammalian breast cancer cells MCF-7 and MDA-MB231: it was approximately twice as active as cisplatin, whilst complexes I-III proved to be less cytotoxic than complex IV. Additional tests using healthy MCF 10A cells showed that complexes II-IV were three- to sixfold less toxic than cisplatin, which suggested that complex IV was selective against cancer cells., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.net.)

Mosquitoes (Diptera: Culicidae) are one of the most important disease vector species in the world. Many species have a high degree of anthropophilia and are often found in human habitations. In the present study, we have inventoried the nocturnal mosquito assemblage in intra-, peri-, and extradomicile environments in four municipalities in Pará, Brazil. At each municipality, a residence was selected and the mosquitoes were sampled using the protected human attraction capture and Shannon trap methods in April (rainy season) and August 2018 (dry season). We have collected a total of 696 mosquito specimens belonging to 8 genera and 17 species. The most abundant species were Mansonia (Mansonoides) titillans (Walker) (366/696, 52.6%), Anopheles (Nyssorhynchus) albitarsis Lynch-Arribálzaga (97/696, 13.9%), and Culex (Culex) quinquefasciatus Say (93/696, 13.4%). Mosquito richness, abundance, and composition did not differ between intra-, peri-, and extradomicile environments suggesting limited habitat segregation among the different species. However, mosquito species richness and mosquito species abundance were significantly higher during the rainy season than during the dry season, suggesting increased mosquito activity during the rainy season. We detected several important vector species of human diseases including Aedes (Stegomyia) aegypti (Linnaeus), Anopheles (Nyssorhynchus) darlingi Root, Haemagogus (Conopostegus) leucocelaenus (Dyar and Shannon), Coquillettidia (Coquillettidia) venezuelensis (Theobald), and Culex (Culex) quinquefasciatus which are the main transmitters of dengue, malaria, yellow fever, mayaro, and oropouche fever, respectively. As inventories of disease-carrying mosquitoes in the region are very scarce, mainly in residential environments, our results suggest high potential for mosquito-borne disease transmission in Pará State., (© The Author(s) 2020. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

The PII family comprises a group of widely distributed signal transduction proteins ubiquitous in prokaryotes and in the chloroplasts of plants. PII proteins sense the levels of key metabolites ATP, ADP, and 2-oxoglutarate, which affect the PII protein structure and thereby the ability of PII to interact with a range of target proteins. Here, we performed multiple ligand fishing assays with the PII protein orthologue GlnZ from the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense to identify 37 proteins that are likely to be part of the PII protein-protein interaction network. Among the PII targets identified were enzymes related to nitrogen and fatty acid metabolism, signaling, coenzyme synthesis, RNA catabolism, and transcription. Direct binary PII-target complex was confirmed for 15 protein complexes using pulldown assays with recombinant proteins. Untargeted metabolome analysis showed that PII is required for proper homeostasis of important metabolites. Two enzymes involved in c-di-GMP metabolism were among the identified PII targets. A PII-deficient strain showed reduced c-di-GMP levels and altered aerotaxis and flocculation behavior. These data support that PII acts as a major metabolic hub controlling important enzymes and the homeostasis of key metabolites such as c-di-GMP in response to the prevailing nutritional status. IMPORTANCE The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting nitrogen-fixing bacterium Azospirillum brasilense The interactome data along with metabolome analysis suggest that PII functions as a master metabolic regulator hub. We provide evidence that PII proteins act to regulate c-di-GMP levels in vivo and cell motility and adherence behaviors., (Copyright © 2020 Gerhardt et al.)

Although the knowledge of bone histology of non-avian theropods has advanced considerably in recent decades, data about the bone tissue patterns, growth dynamics and ontogeny of some taxa such as abelisauroids are still limited. Here we describe the bone microstructure and growth dynamics of the Brazilian noasaurine Vespersaurus paranaensis using five femora and six tibiae and quantify the annual growth marks through retrocalculation of missing ones to estimate ontogenetic ages. The femoral series comprises four femoral histological classes (FHC I-IV), varying from two annuli or LAGs to seven LAGs. Femora show that sexual maturity was achieved around the seventh to tenth year of life, whereas the tibiae suggest it was earlier (around three to five years old). Tibiae represent three histological classes (THC I-III) displaying from three to nine LAGs. Two tibiae (THC III) exhibit an external fundamental system indicating that these specimens reached full skeletal size. The heterogeneous maturity observed in Vespersaurus hind limb bones could result from differential allometry scaling between femora and tibiae length with the body length. The predominant parallel-fibered bone matrix suggests that Vespersaurus grew more slowly than most theropods, including other abelisauroids, in a pattern shared with the noasaurines Masiakasaurus knopfleri from Madagascar and CPPLIP 1490 from Brazil. This deviation from the typical theropod growth pattern may be mainly correlated with small body size, but also may related to resource limitation imposed by the arid climate prevailing in southwestern Gondwana during Cretaceous. Moreover, given the ecological and phylogenetic similarities among these taxa, such features would probably be apomorphic within Noasauridae., Competing Interests: The authors declare that they have no competing interests., (© 2020 Souza et al.)

In reverse vaccinology approaches, complete proteomes of bacteria are submitted to multiple computational prediction steps in order to filter proteins that are possible vaccine candidates. Most available tools perform such analysis only in a single strain, or a very limited number of strains. But the vast amount of genomic data had shown that most bacteria contain pangenomes, i.e., their genomic information contains core, conserved genes, and random accessory genes specific to each strain. Therefore, in reverse vaccinology methods it is of the utmost importance to define core proteins and core epitopes. EpitoCore is a decision-tree pipeline developed to fulfill that need. It provides surfaceome prediction of proteins from related strains, defines core proteins within those, calculate their immunogenicity, predicts epitopes for a given set of MHC alleles defined by the user, and then reports if epitopes are located extracellularly and if they are conserved among the core homologs. Pipeline performance is illustrated by mining peptide vaccine candidates in Mycobacterium avium hominissuis strains. From a total proteome of ~4,800 proteins per strain, EpitoCore predicted 103 highly immunogenic core homologs located at cell surface, many of those related to virulence and drug resistance. Conserved epitopes identified among these homologs allows the users to define sets of peptides with potential to immunize the largest coverage of tested HLA alleles using peptide-based vaccines. Therefore, EpitoCore is able to provide automated identification of conserved epitopes in bacterial pangenomic datasets., (Copyright © 2020 Fiuza, Lima and de Souza.)

NAD + is a central metabolite participating in core metabolic redox reactions. The prokaryotic NAD synthetase enzyme NadE catalyzes the last step of NAD + biosynthesis, converting nicotinic acid adenine dinucleotide (NaAD) to NAD + Some members of the NadE family use l-glutamine as a nitrogen donor and are named NadE Gln Previous gene neighborhood analysis has indicated that the bacterial nadE gene is frequently clustered with the gene encoding the regulatory signal transduction protein PII, suggesting a functional relationship between these proteins in response to the nutritional status and the carbon/nitrogen ratio of the bacterial cell. Here, using affinity chromatography, bioinformatics analyses, NAD synthetase activity, and biolayer interferometry assays, we show that PII and NadE Gln physically interact in vitro , that this complex relieves NadE Gln negative feedback inhibition by NAD + This mechanism is conserved in distantly related bacteria. Of note, the PII protein allosteric effector and cellular nitrogen level indicator 2-oxoglutarate (2-OG) inhibited the formation of the PII-NadE Gln complex within a physiological range. These results indicate an interplay between the levels of ATP, ADP, 2-OG, PII-sensed glutamine, and NAD + , representing a metabolic hub that may balance the levels of core nitrogen and carbon metabolites. Our findings support the notion that PII proteins act as a dissociable regulatory subunit of NadE Gln , thereby enabling the control of NAD + biosynthesis according to the nutritional status of the bacterial cell., (© 2020 Santos et al.)

Azospirillum brasilense is a diazotrophic microorganism capable of associating with roots of important grasses and cereals, promoting plant growth and increasing crop yields. Nitrogen levels and the Ntr regulatory system control the nitrogen metabolism in A. brasilense . This system comprises the nitrogen regulatory proteins GlnD, which is capable of adding uridylyl groups to the PII proteins, GlnB (PII-1) and GlnZ (PII-2), under limiting nitrogen levels. Under such conditions, the histidine kinase NtrB (nitrogen regulatory protein B) cannot interact with GlnB and phosphorylate NtrC (nitrogen regulatory protein C). The phosphorylated form of NtrC acts as a transcriptional activator of genes involved in the metabolism of alternative nitrogen sources. Considering the key role of NtrC in nitrogen metabolism in A. brasilense , in this work we evaluated the proteomic and metabolomic profiles of the wild-type FP2 strain and its mutant ntrC grown under high and low nitrogen. Analysis of the integrated data identifies novel NtrC targets, including proteins involved in the response against oxidative stress (i.e., glutathione S -transferase and hydroperoxide resistance protein), underlining the importance of NtrC to bacterial survival under oxidative stress conditions.

A series of 3-substituted-7-aminoalcoxy-coumarin was designed and evaluated as cholinesterase inhibitors and antioxidants. All compounds were effective in inhibiting AChE with potencies in the nanomolar range. The 3-(4-(dimethylamino)phenyl)-7-aminoethoxy-coumarin (6a) was considered a hit, showing good AChE inhibition potency (IC 50  = 20 nM) and selectivity (IC 50 BuChE/AChE = 354), quite similar to the reference drug donepezil (IC 50 = 6 nM; IC 50 BuChE/AChE = 365), also presenting antioxidant properties, low citotoxicity and good-predicted ADMET properties. The mode of action (mixed-type) and SAR analysis for this series of compounds were described by means of kinetic and molecular modeling evaluations.

In multiple sclerosis (MS), B cells are trafficking across the blood-brain barrier, but it is not known how this relates to the synthesis of oligoclonal IgG. We used quantitative mass spectrometry of oligoclonal bands and high-throughput sequencing of immunoglobulin heavy-chain variable transcripts to study the longitudinal B cell response in the cerebrospinal fluid (CSF) and blood of two MS patients. Twenty of 22 (91%) and 25 of 28 (89%) of oligoclonal band peptides persisted in samples collected 18 months apart, in spite of a dynamic exchange across the blood-CSF barrier of B lineage cells connecting to oligoclonal IgG., (Copyright © 2019 Elsevier B.V. All rights reserved.)

In proteomics, peptide information within mass spectrometry (MS) data from a specific organism sample is routinely matched against a protein sequence database that best represent such organism. However, if the species/strain in the sample is unknown or genetically poorly characterized, it becomes challenging to determine a database which can represent such sample. Building customized protein sequence databases merging multiple strains for a given species has become a strategy to overcome such restrictions. However, as more genetic information is publicly available and interesting genetic features such as the existence of pan- and core genes within a species are revealed, we questioned how efficient such merging strategies are to report relevant information. To test this assumption, we constructed databases containing conserved and unique sequences for 10 different species. Features that are relevant for probabilistic-based protein identification by proteomics were then monitored. As expected, increase in database complexity correlates with pangenomic complexity. However, Mycobacterium tuberculosis and Bordetella pertussis generated very complex databases even having low pangenomic complexity. We further tested database performance by using MS data from eight clinical strains from M. tuberculosis , and from two published datasets from Staphylococcus aureus . We show that by using an approach where database size is controlled by removing repeated identical tryptic sequences across strains/species, computational time can be reduced drastically as database complexity increases.

Costameres are signaling hubs at the sarcolemma and important contact points between the extracellular matrix and cell interior, sensing and transducing biomechanical signals into a cellular response. The transmembrane proteoglycan syndecan-4 localizes to these attachment points and has been shown to be important in the initial stages of cardiac remodeling, but its mechanistic function in the heart remains insufficiently understood. Here, we sought to map the cardiac interactome of syndecan-4 to better understand its function and downstream signaling mechanisms. By combining two different affinity purification methods with MS analysis, we found that the cardiac syndecan-4 interactome consists of 21 novel and 29 previously described interaction partners. Nine of the novel partners were further validated to bind syndecan-4 in HEK293 cells ( i.e. CAVIN1/PTRF, CCT5, CDK9, EIF2S1, EIF4B, MPP7, PARVB, PFKM, and RASIP). We also found that 19 of the 50 interactome partners bind differently to syndecan-4 in the left ventricle lysate from aortic-banded heart failure (ABHF) rats compared with SHAM-operated animals. One of these partners was the well-known mechanotransducer muscle LIM protein (MLP), which showed direct and increased binding to syndecan-4 in ABHF. Nuclear translocation is important in MLP-mediated signaling, and we found less MLP in the nuclear-enriched fractions from syndecan-4 -/- mouse left ventricles but increased nuclear MLP when syndecan-4 was overexpressed in a cardiomyocyte cell line. In the presence of a cell-permeable syndecan-4-MLP disruptor peptide, the nuclear MLP level was reduced. These findings suggest that syndecan-4 mediates nuclear translocation of MLP in the heart., (© 2019 Mathiesen et al.)

Zika virus (ZIKV) is an arbovirus belonging to the Flaviviridae family and the genus Flavivirus. Infection with ZIKV causes a mild, self-limiting febrile illness called Zika fever. However, ZIKV infection has been recently associated with microcephaly and Guillain-Barré syndrome. Vaccines for the disease are a high priority of World Health Organization. Several studies are currently being conducted to develop a vaccine against ZIKV, but until now there is no licensed ZIKV vaccine. This study used a novel immunoinformatics approach to identify potential T-cell immunogenic epitopes present in the structural and nonstructural proteins of ZIKV. Fourteen T-cell candidate epitopes were identified on ZIKV structural and nonstructural proteins: pr 36-50 ; C 61-75 ; C 103-117 ; E 374-382 ; E 477-491 ; NS2a 90-104 ; NS2a 174-188 ; NS2a 179-193 ; NS2a 190-204 ; NS2a 195-209 ; NS2a 200-214 ; NS3 175-189 ; and NS4a 82-96 ; NS4a 99-113 . Among these epitopes, only E 374-382 is a human leukocyte antigen (HLA) type I restricted epitope. All identified epitopes showed a low similarity with other important flaviviruses but had a high conservation rate among the ZIKV strains and a high population coverage rate. Therefore, these predicted T-cell epitopes are potential candidates targets for development of vaccines to prevent ZIKV infection.

Background: Zinc (Zn) deficiency is a major human health concern worldwide, and biofortification (genetic and agronomic) is a complementary solution for increasing micronutrient contents, including Zn. Cassava (Manihot esculenta Crantz) has been used for Zn biofortification because it is an important staple crop in most countries affected by malnutrition and Zn deficiency. Thus studies on biofortification of this crop can improve its nutritional quality. Zn content in cassava clones enriched with β-carotene or lycopene and cultivated under different areas and soil managements was investigated to evaluate the influence of genotypic variation and agronomic management on Zn status in the plant., Results: A clone-specific response to total Zn content in the soil was found, with clones 26, 215, and 240 (β-carotene enriched) and clones 341 and 395 (lycopene enriched) being the most responsive. For both experiments, there was a positive interaction between total soil Zn and Zn content in the roots., Conclusions: Our results suggest that, by combining plant breeding and agronomic strategies, it is possible to enrich cassava roots with both zinc and β-carotene or lycopene. © 2018 Society of Chemical Industry., (© 2018 Society of Chemical Industry.)

Western blotting (WB) is widely used to test antibody specificity, but the assay has low throughput and precision. Here we used preparative gel electrophoresis to develop a capture format for WB. Fractions with soluble, size-separated proteins facilitated parallel readout with antibody arrays, shotgun mass spectrometry (MS) and immunoprecipitation followed by MS (IP-MS). This pipeline provided the means for large-scale implementation of antibody validation concepts proposed by an international working group on antibody validation (IWGAV).

In Stylosanthes humilis, salt stress tolerance is associated with ethylene production by the seeds, however, how salt stress controls seed germination and ethylene production is poorly understood. Here, we studied the hormonal and metabolic changes triggered by salt stress on germination of S. humilis seeds. Salt stress led to decreased seed germination and ethylene production, concomitantly with higher abscisic acid (ABA) production by seeds. Treatment with NaCl and ABA promoted distinct changes in energy metabolism, allowing seeds to adapt to salt stress conditions. Treatment with the ABA biosynthesis inhibitor fluridone or ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) reversed the effects of salt stress on seed germination and ethylene production. Moreover, ethylene concentration was decreased by increasing the pH of the salt solution. High pH, however, did not influence concentration of ABA in seeds under salt stress. We conclude that biosynthesis of ABA and ethylene in response to salt stress constitutes a point of convergence that provides flexibility to regulate energy metabolism and embryo growth potential of S. humilis seeds within a given pH condition., (Copyright © 2018 Elsevier Masson SAS. All rights reserved.)

OBJECTIVE What determines the extent of tissue destruction during brain abscess formation is not known. Pyogenic brain infections cause destruction of brain tissue that greatly exceeds the area occupied by microbes, as seen in experimental studies, pointing to cytotoxic factors other than microbes in pus. This study examined whether brain abscess pus contains cytotoxic proteins that might explain the extent of tissue destruction. METHODS Pus proteins from 20 human brain abscesses and, for comparison, 7 subdural empyemas were analyzed by proteomics mass spectrometry. Tissue destruction was determined from brain abscess volumes as measured by MRI. RESULTS Brain abscess volume correlated with extracellular pus levels of antibacterial proteins from neutrophils and macrophages: myeloperoxidase (r = 0.64), azurocidin (r = 0.61), lactotransferrin (r = 0.57), and cathelicidin (r = 0.52) (p values 0.002-0.018), suggesting an association between leukocytic activity and tissue damage. In contrast, perfringolysin O, a cytotoxic protein from Streptococcus intermedius that was detected in 16 patients, did not correlate with abscess volume (r = 0.12, p = 0.66). The median number of proteins identified in each pus sample was 870 (range 643-1094). Antibiotic or steroid treatment prior to pus evacuation did not reduce the number or levels of pus proteins. Some of the identified proteins have well-known neurotoxic effects, e.g., eosinophil cationic protein and nonsecretory ribonuclease (also known as eosinophil-derived neurotoxin). The cellular response to brain infection was highly complex, as reflected by the presence of proteins that were specific for neutrophils, eosinophils, macrophages, platelets, fibroblasts, or mast cells in addition to plasma and erythrocytic proteins. Other proteins (neurofilaments, myelin basic protein, and glial fibrillary acidic protein) were specific for brain cells and reflected damage to neurons, oligodendrocytes, and astrocytes, respectively. Pus from subdural empyemas had significantly higher levels of plasma proteins and lower levels of leukocytic proteins than pus from intracerebral abscesses, suggesting greater turnover of the extracellular fluid of empyemas and washout of pus constituents. CONCLUSIONS Brain abscess pus contains leukocytic proteins that are neurotoxic and likely participate actively in the excessive tissue destruction inherent in brain abscess formation. These findings underscore the importance of rapid evacuation of brain abscess pus.

Global characterization of tissue proteomes from small amounts of biopsy material has become feasible because of advances in mass spectrometry and bioinformatics tools. In celiac disease (CD), dietary gluten induces an immune response that is accompanied by pronounced remodeling of the small intestine. Removal of gluten from the diet abrogates the immune response, and the tissue architecture normalizes. In this study, differences in global protein expression of small intestinal biopsy specimens from CD patients were quantified by analyzing formalin-fixed, paraffin-embedded material using liquid chromatography-mass spectrometry and label-free protein quantitation. Protein expression was compared in biopsy specimens collected from the same patients before and after 1-year treatment with gluten-free diet (n = 10) or before and after 3-day gluten provocation (n = 4). Differential expression of proteins in particular from mature enterocytes, neutrophils, and plasma cells could distinguish untreated from treated CD mucosa, and Ig variable region IGHV5-51 expression was found to serve as a CD-specific marker of ongoing immune activation. In patients who had undergone gluten challenge, coordinated up-regulation of wound response proteins, including the CD autoantigen transglutaminase 2, was observed. Our study provides a global and unbiased assessment of antigen-driven changes in protein expression in the celiac intestinal mucosa., (Copyright © 2018 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)

Recently, FGFR1 was found to be overexpressed in osteosarcoma and represents an important target for precision medicine. However, because targeted cancer therapy based on FGFR inhibitors has so far been less efficient than expected, a detailed understanding of the target is important. We have here applied proximity-dependent biotin labeling combined with label-free quantitative mass spectrometry to identify determinants of FGFR1 activity in an osteosarcoma cell line. Many known FGFR interactors were identified ( e.g. FRS2, PLCG1, RSK2, SRC), but the data also suggested novel determinants. A strong hit in our screen was the tyrosine phosphatase PTPRG. We show that PTPRG and FGFR1 interact and colocalize at the plasma membrane where PTPRG directly dephosphorylates activated FGFR1. We further show that osteosarcoma cell lines depleted for PTPRG display increased FGFR activity and are hypersensitive to stimulation by FGF1. In addition, PTPRG depletion elevated cell growth and negatively affected the efficacy of FGFR kinase inhibitors. Thus, PTPRG may have future clinical relevance by being a predictor of outcome after FGFR inhibitor treatment., (© 2018 by The American Society for Biochemistry and Molecular Biology, Inc.)

Changes in the concentration of sugars and sucrose metabolism enzymes can characterize the developmental stages of a seed. In recalcitrant species such as Hevea brasiliensis L., little is known about these changes. We aimed to evaluate the three main stages of development of rubber tree seeds - histodifferentiation, cell elongation and accumulation of reserves. The activities of acid and neutral invertases (E.C. 3.2.1.26) and sucrose synthase (EC 2.4.1.13), and the concentrations of reducing sugars (RS), total soluble sugars (TSS) and sucrose (Suc) were determined concomitantly with the histochemical and anatomical evaluation of seed structure. Histodifferentiation in rubber tree seeds occurs up to 75 days after anthesis (DAA). The concentration of RS is high and of Suc is low during seed histodifferentiation, which occurs along with a visible increase in the number of cell divisions. After that period, there is an increase in the concentration of Suc (mg g -1 ) and in the number and size of starch granules, and a decrease in the concentration of RS (mg g -1 ). At that point, cell elongation occurs. At 135 DAA, there is an inversion in the concentration of these two sugars and an increase in reserve accumulation. Thus, in seeds of the evaluated clone, the period up to 75 DAA is characterized as the histodifferentiation stage, while from that time up to 120 DAA the cell elongation stage takes place. The final stage of seed maturation and reserve accumulation begins at 135 DAA, and the seed, including the embryo, is completely formed at 175 DAA., (© 2017 Scandinavian Plant Physiology Society.)

The carbohydrate-uptake phosphorelay PTS system plays a key role in metabolic regulation in Bacteria controlling the utilization of secondary carbon sources. Some bacteria, such as Escherichia coli, encode a paralogous system named PTS Ntr (nitrogen related PTS). PTS Ntr is composed of EI Ntr (ptsP), NPr (ptsO), and EIIA Ntr (ptsN). These proteins act as a phosphorelay system from phosphoenolpyruvate to EI Ntr , NPr and them to EIIA Ntr . PTS Ntr is not involved in carbohydrate uptake and it may be dedicated to performing regulatory functions. The phosphorylation state of EI Ntr is regulated by allosteric binding of glutamine and 2-oxoglutarate, metabolites whose intracellular levels reflect the nitrogen status. Although PTS Ntr is designated as having nitrogen-sensory properties, no major effect of this system on nitrogen regulation has been described in E. coli. Here we show that an E. coli ptsN deletion mutant has impaired growth in minimal medium. Proteome analysis of the ∆ptsN strain under different nitrogen regimes revealed no involvement in regulation of the canonical nitrogen regulatory (Ntr) system. The proteomic data support the conclusion that ptsN is required to balance the activities of the sigma factors RpoS and RpoD in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed., Significance: The nitrogen related PTS Ntr phosphorelay system has been hypothesized to participate in the control of nitrogen metabolism. Here we used a proteomics approach to show that an Escherichia coli ptsN null strain, which misses the final module of PTS Ntr phosphorelay, has no significant effects on nitrogen metabolism under different nitrogen regimes. We noted that ptsN is required for fitness under minimal medium and for the proper balance between RpoS and sigma 70 activities in such way that, in the absence of ptsN, RpoS-dependent genes are preferentially expressed., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Cancer/testis (CT) genes are excellent candidates for cancer immunotherapies because of their restrict expression in normal tissues and the capacity to elicit an immune response when expressed in tumor cells. In this study, we provide a genome-wide screen for CT genes with the identification of 745 putative CT genes. Comparison with a set of known CT genes shows that 201 new CT genes were identified. Integration of gene expression and clinical data led us to identify dozens of CT genes associated with either good or poor prognosis. For the CT genes related to good prognosis, we show that there is a direct relationship between CT gene expression and a signal for CD8+ cells infiltration for some tumor types, especially melanoma., Competing Interests: CONFLICTS OF INTEREST The authors declare that they have no conflicts of interest.

Mucosal antigens induce generation of lamina propria plasma cells (PCs) that secrete dimeric immunoglobulin A (IgA) destined for transport across the epithelium. In addition, blood contains monomeric IgA. To study the relationship between mucosal and systemic antibody responses, we took advantage of celiac disease patient samples for isolation of gut PCs as well as serum IgA and IgG reactive with a gluten-derived peptide or the autoantigen transglutaminase 2. Proteomic analysis of serum IgA revealed antigen-specific V-gene preferences, which matched those found in gut PCs. Further, gut PC CDR-H3 sequences were abundant in serum IgA but also detectable in serum IgG. Our data indicate that the same B cell clones that give rise to gut PCs also contribute to the serum antibody pool. However, serum IgA antibodies had a molecular composition distinct from that of IgA antibodies secreted in the gut, suggesting that individual B cell clones give rise to different PC populations., (Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.)

The sodium (Na + )-calcium (Ca 2+ ) exchanger 1 (NCX1) is an antiporter membrane protein encoded by the SLC8A1 gene. In the heart, it maintains cytosolic Ca 2+ homeostasis, serving as the primary mechanism for Ca 2+ extrusion during relaxation. Dysregulation of NCX1 is observed in end-stage human heart failure. In this study, we used affinity purification coupled with MS in rat left ventricle lysates to identify novel NCX1 interacting proteins in the heart. Two screens were conducted using: (1) anti-NCX1 against endogenous NCX1 and (2) anti-His (where His is histidine) with His-trigger factor-NCX1 cyt recombinant protein as bait. The respective methods identified 112 and 350 protein partners, of which several were known NCX1 partners from the literature, and 29 occurred in both screens. Ten novel protein partners (DYRK1A, PPP2R2A, SNTB1, DMD, RABGGTA, DNAJB4, BAG3, PDE3A, POPDC2, STK39) were validated for binding to NCX1, and two partners (DYRK1A, SNTB1) increased NCX1 activity when expressed in HEK293 cells. A cardiac NCX1 protein-protein interaction map was constructed. The map was highly connected, containing distinct clusters of proteins with different biological functions, where "cell communication" and "signal transduction" formed the largest clusters. The NCX1 interactome was also significantly enriched with proteins/genes involved in "cardiovascular disease" which can be explored as novel drug targets in future research., (© 2017 The Authors. Proteomics Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In this manuscript we describe Proteogenomics Viewer, a web-based tool that collects MS peptide identification, indexes to genomic sequence and structure, assigns exon usage, reports the identified protein isoforms with genomic alignments and, most importantly, allows the inspection of MS2 information for proper peptide identification. It also provides all performed indexing to facilitate global analysis of the data. The relevance of such tool is that there has been an increase in the number of proteogenomic efforts to improve the annotation of both genomics and proteomics data, culminating with the release of the two human proteome drafts. It is now clear that mass spectrometry-based peptide identification of uncharacterized sequences, such as those resulting from unpredicted exon joints or non-coding regions, is still prone to a higher than expected false discovery rate. Therefore, proper visualization of the raw data and the corresponding genome alignments are fundamental for further data validation and interpretation. Also see the video abstract here: http://youtu.be/5NzyRvuk4Ac., (© 2017 WILEY Periodicals, Inc.)

Melanoma is responsible for most deaths among skin cancers and conventional and palliative care chemotherapy are limited due to the development of chemoresistance. We used proteomic analysis to identify cellular responses that lead to chemoresistance of human melanoma cell lines to cisplatin. A systems approach to the proteomic data indicated the participation of specific cellular processes such as oxidative phosphorylation, mitochondrial organization and homeostasis, as well as the unfolded protein response (UPR) to be required for the survival of cells treated with cisplatin. Prohibitin (PHB) was among the proteins consistently accumulated, interacting with the functional clusters associated with resistance to cisplatin. We showed PHB accumulated at different levels in melanoma cell lines under stressing stimuli, such as (i) treatment with temozolomide (TMZ), dacarbazine (DTIC) and cisplatin; (ii) serum deprivation; (iii) tunicamycin, an UPR inducer. Prohibitin accumulated in the mitochondria of melanoma cells after cisplatin and tunicamycin treatment and its de novo accumulation led to chemoresistance melanoma cell lines. In contrast, PHB knock-down sensitized melanoma cells to cisplatin and tunicamycin treatment. We conclude that PHB participates in the survival of cells exposed to different stress stimuli, and can therefore serve as a target for the sensitization of melanoma cells to chemotherapy.

Objective: To evaluate the results of home nursing interventions according to the satisfaction of the elderly users., Methods: Ex-post facto evaluative, qualitative and descriptive research, conducted from November 2015 to January 2016 with 12 dependent elderly individuals accompanied by an extension project in the city of Maringá, PR, Brazil. Data were collected after home interventions based on the Single-User Treatment Project, by means of semi-structured interviews subjected to content analysis and the theoretical framework of Donabedian., Results: The following thematic categories emerged: "home nursing intervention: synonymous with joy, distraction and bonding" and" home nursing intervention: health and lifestyle transformations"., Conclusion: The home nursing interventions had positive results that signal the quality of the provided care.

Nitrogen is needed for the biosynthesis of biomolecules including proteins and nucleic acids. In the absence of fixed nitrogen prokaryotes such as E. coli immediately ceases growth. Ammonium is the preferred nitrogen source for E. coli supporting the fastest growth rates. Under conditions of ammonium limitation, E. coli can use alternative nitrogen sources to supply ammonium ions and this reprogramming is led by the induction of the NtrC regulon. Here we used label free proteomics to determine the dynamics of E. coli proteins expression in response to ammonium starvation in both the short (30min) and the longer (60min) starvation. Protein abundances and post-translational modifications confirmed that activation of the NtrC regulon acts as the first line of defense against nitrogen starvation. The ribosome inactivating protein Rmf was induced shortly after ammonium exhaustion and this was preceded by induction of other ribosome inactivating proteins such as Hpf and RaiA supporting the hypothesis that ribosome shut-down is a key process during nitrogen limitation stress. The proteomic data revealed that growth arrest due to nitrogen starvation correlates with the accumulation of proteins involved in DNA condensation, RNA and protein catabolism and ribosome hibernation. Collectively, these proteome adaptations will result in metabolic inactive cells which are likely to exhibit multidrug tolerance., (Copyright © 2016 Elsevier B.V. All rights reserved.)