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The object of the present study was the development of alternative methods for the direct determination of lead in undigested samples of human urine and serum by electrothermal atomic absorption spectrometry (ET AAS). Thus, some substances have been investigated to act as chemical modifiers. Volumes of 20 µL of diluted samples, 1 + 1, v/v for urine and 1 + 4, v/v for serum, with HNO3 1% v/v and 0.02% v/v of cetil trimethyl ammonium chloride (CTAC) were prepared directly in the autosampler cups and placed into the graphite furnace. For modifiers in solutions 10 µL were used. Pyrolysis and atomization temperature curves were used in all optimizations in the matrixes diluted as exposed. For urine with permanent iridium (500 µg), the best pyrolysis and atomization temperatures were 900 and 1600 ºC, respectively, with a characteristic mass of 12 pg (recommended of 10 pg), with symmetrical absorption pulses and corrected background. Spiked urine samples presented recoveries between 86 and 112% for Ir permanent. The analysis results of certified urine samples are in agreement with certified values (95% of confidence) for two levels of the metal. For serum, good results were obtained with the mixture of Zr+Rh or Ir+Rh as permanent modifiers, with characteristic masses of 9.8 and 8.1 pg, respectively. Recoveries from spiked serum samples varied between 98.6 and 100.1% (Ir+Rh) and between 93.9 and 105.2% (Zr+Rh). In both recovery studies, the relative standard deviation (n=3) was lower than 7%. Calibration for both samples were made with aqueous calibration curves and presented r² higher than 0.99. The limits of detection were 0.7 µg L-1 for serum samples, with Zr+Rh permanent, and 1.0 µg L-1 for urine with iridium permanent.

Abstract Background A few lineages of Group A streptococci (GAS) have been associated with a reemergence of severe invasive streptococcal disease in developed countries. However, the majority of the comparisons between invasive and non-invasive GAS isolates have been performed for collections of reduced genetic diversity or relied on limited typing information to distinguish clones. We characterized by several typing methods and compared a collection of 160 isolates recovered from normally sterile sites with 320 isolates associated with pharyngitis and recovered in the same time period in Portugal. Results Although most of the isolates belonged to clones that were equally prevalent in invasive infections and pharyngitis, we identified markers of invasiveness, namely the emm types 1 and 64, and the presence of the speA and speJ genes. In contrast, emm4, emm75, and the ssa and speL/M genes were significantly associated with pharyngitis. There was a strong agreement between the emm type, the superantigen (SAg) genes and the clusters defined by pulsed-field gel electrophoresis (PFGE) profiling. Therefore, combinations of particular emm types and SAg genes frequently co-occurred in the same PFGE cluster, but there was no synergistic or antagonistic interaction between them in determining invasiveness. Only macrolide-susceptible PFGE clones were significantly associated with invasive infections or pharyngitis, while the clones of resistant isolates sharing all other molecular properties analyzed were equally prevalent in the two groups of isolates. Conclusions This study confirmed the importance of the widely disseminated emm1-T1-ST28 clone in invasive infections but also identified other clones linked to either invasive infections (emm64-ST164) or pharyngitis (emm4-T4-ST39), which may be more limited in their temporal and geographical spread. Clonal properties like some emm types or SAg genes were associated with disease presentation, highlighting the importance of bacterial genetic factors to the outcome of GAS infections, although other, yet unidentified factors may also play an important role.

Abstract Background We examined the presence and function of tachykinins and the tachykinin-degrading enzymes neprilysin (NEP) and neprilysin-2 (NEP2) in human spermatozoa. Methods Freshly ejaculated semen was collected from forty-eight normozoospermic human donors. We analyzed the expression of substance P, neurokinin A, neurokinin B, hemokinin-1, NEP and NEP2 in sperm cells by reverse-transcriptase polymerase chain reaction (RT-PCR), western blot and immunocytochemistry assays and evaluated the effects of the neprilysin and neprilysin-2 inhibitor phosphoramidon on sperm motility in the absence and presence of tachykinin receptor-selective antagonists. Sperm motility was measured using WHO procedures or computer-assisted sperm analysis (CASA). Results The mRNAs of the genes that encode substance P/neurokinin A (TAC1), neurokinin B (TAC3), hemokinin-1 (TAC4), neprilysin (MME) and neprilysin-2 (MMEL1) were expressed in human sperm. Immunocytochemistry studies revealed that tachykinin and neprilysin proteins were present in spermatozoa and show specific and differential distributions. Phosphoramidon increased sperm progressive motility and its effects were reduced in the presence of the tachykinin receptor antagonists SR140333 (NK1 receptor-selective) and SR48968 (NK2 receptor-selective) but unmodified in the presence of SR142801 (NK3 receptor-selective). Conclusion These data show that tachykinins are present in human spermatozoa and participate in the regulation of sperm motility. Tachykinin activity is regulated, at least in part, by neprilysins.

Abstract Background Cell-surface glycoproteins play critical roles in cell-to-cell recognition, signal transduction and regulation, thus being crucial in cell proliferation and cancer etiogenesis and development. DPP IV and NEP are ubiquitous glycopeptidases closely linked to tumor pathogenesis and development, and they are used as markers in some cancers. In the present study, the activity and protein and mRNA expression of these glycoproteins were analysed in a subset of clear-cell (CCRCC) and chromophobe (ChRCC) renal cell carcinomas, and in renal oncocytomas (RO). Methods Peptidase activities were measured by conventional enzymatic assays with fluorogen-derived substrates. Gene expression was quantitatively determined by qRT-PCR and membrane-bound protein expression and distribution analysis was performed by specific immunostaining. Results The activity of both glycoproteins was sharply decreased in the three histological types of renal tumors. Protein and mRNA expression was strongly downregulated in tumors from distal nephron (ChRCC and RO). Moreover, soluble DPP IV activity positively correlated with the aggressiveness of CCRCCs (higher activities in high grade tumors). Conclusions These results support the pivotal role for DPP IV and NEP in the malignant transformation pathways and point to these peptidases as potential diagnostic markers.

Abstract Background The boundaries of bacterial species and the mechanisms underlying bacterial speciation are matters of intense debate. Theoretical studies have shown that recombination acts as a strong cohesive force preventing divergence in bacterial populations. Streptococcus pneumoniae populations have the telltale signs of high recombination with competence implicated as the major driving force behind gene exchange. Competence in S. pneumoniae is triggered by a quorum-sensing mechanism controlled by the competence-stimulating peptide pheromone. Results We studied the distribution of the two major pherotypes in the pneumococcal population and their association with serotype, antimicrobial resistance and genetic lineage. Using multilocus sequence data we evaluated pherotype influence on the dynamics of horizontal gene transfer. We show that pherotype is a clonal property of pneumococci. Standard population genetic analysis and multilocus infinite allele model simulations support the hypothesis that two genetically differentiated populations are defined by the major pherotypes. Conclusion Severe limitations to gene flow can therefore occur in bacterial species in the absence of geographical barriers and within highly recombinogenic populations. This departure from panmixia can have important consequences for our understanding of the response of pneumococci to human imposed selective pressures such as vaccination and antibiotic use.

Abstract Background In the mouse uterus, pregnancy is accompanied by changes in tachykinin and tachykinin receptor gene expression and in the uterotonic effects of endogenous tachykinins. In this study we have investigated whether changes in tachykinin expression and responses are a result of changes in ovarian steroid levels. Methods We quantified the mRNAs of tachykinins and tachykinin receptors in uteri from ovariectomized mice and studied their regulation in response to estrogen and progesterone using real-time quantitative RT-PCR. Early (3 h) and late (24 h) responses to estrogen were evaluated and the participation of the estrogen receptors (ER), ERalpha and ERbeta, was analyzed by treating mice with propylpyrazole triol, a selective ERalpha agonist, or diarylpropionitrile, a selective agonist of ERbeta. Results All genes encoding tachykinins (Tac1, Tac2 and Tac4) and tachykinin receptors (Tacr1, Tacr2 and Tacr3) were expressed in uteri from ovariectomized mice. Estrogen increased Tac1 and Tacr1 mRNA after 3 h and decreased Tac1 and Tac4 expression after 24 h. Tac2 and Tacr3 mRNA levels were decreased by estrogen at both 3 and 24 h. Most effects of estrogen were also observed in animals treated with propylpyrazole triol. Progesterone treatment increased the levels of Tac2. Conclusion These results show that the expression of tachykinins and their receptors in the mouse uterus is tightly and differentially regulated by ovarian steroids. Estrogen effects are mainly mediated by ERalpha supporting an essential role for this estrogen receptor in the regulation of the tachykinergic system in the mouse uterus.

Abstract Background We have investigated the expression of voltage-gated sodium channels in human spermatozoa and characterized their role in sperm motility. Methods Freshly ejaculated semen was collected from thirty normozoospermic human donors, with each donor supplying 2 different samples. Reverse transcription-polymerase chain reaction (RT-PCR) and immunofluorescence techniques were used to detect the mRNAs and proteins of interest. Sperm motility was measured by a computer-assisted sperm analysis system (CASA). Cytosolic free calcium was determined by fluorimetry in cells loaded with the fluorescent calcium indicator Fura-2. Results The mRNAs that encode the different Nav alpha subunits (Nav1.1-1.9) were all expressed in capacitated human spermatozoa. The mRNAs of the auxiliary subunits beta1, beta3 and beta4 were also present. Immunofluorescence studies showed that, with the exception of Nav1.1 and Nav1.3, the Nav channel proteins were present in sperm cells and show specific and different sites of localization. Veratridine, a voltage-gated sodium channel activator, caused time- and concentration-dependent increases in progressive sperm motility. In sperm suspensions loaded with Fura-2, veratridine did not modify intracellular free calcium levels. Conclusion This research shows the presence of voltage-gated sodium channels in human sperm and supports a role for these channels in the regulation of mature sperm function.

Abstract Background Microarray comparative genomic hybridization (aCGH) evaluates the distribution of genes of sequenced bacterial strains among unsequenced strains of the same or related species. As genomic sequences from multiple strains of the same species become available, multistrain microarrays are designed, containing spots for every unique gene in all sequenced strains. To perform two-color aCGH experiments with multistrain microarrays, the choice of control sample can be the genomic DNA of one strain or a mixture of all the strains used in the array design. This important problem has no universally accepted solution. Results We performed a comparative study of the two control sample options with a Streptococcus pneumoniae microarray designed with three fully sequenced strains. We separately hybridized two of these strains (R6 and G54) as test samples using the third strain alone (TIGR4) or a mixture of the three strains as control. We show that for both types of control it is advantageous to analyze spots in separate sets according to their expected control channel signal (5–15% AUC increase). Following this analysis, the use of a mix control leads to higher accuracies (5% increase). This enhanced performance is due to gains in sensitivity (21% increase, p = 0.001) that compensate minor losses in specificity (5% decrease, p = 0.014). Conclusion The use of a single strain control increases the error rate in genes that are part of the accessory genome, where more variation across unsequenced strains is expected, further justifying the use of the mix control.

Abstract Background Pili were recently recognized in Streptococcus pneumoniae and implicated in the virulence of this bacterium, which led to the proposal of using these antigens in a future pneumococcal vaccine. However, pili were found to be encoded by the rlrA islet that was not universally distributed in the species. We examined the distribution of the pilus islet, using the presence of the rlrA gene as a marker for the locus, among a collection of invasive isolates recovered in Portugal and analyzed its association with capsular serotypes, clusters defined by the pulsed-field gel electrophoretic profiles (PFGE) and multilocus sequence types. Results Only a minority of the isolates were positive for the presence of the rlrA gene (27%). There was a high correspondence between the serotype and the presence or absence of rlrA (Wallace coefficient, W = 0.778). In particular, there was an association between the presence of rlrA and the vaccine serotypes 4, 6B, 9V and 14 whereas the gene was significantly absent from other serotypes, namely 1, 7F, 8, 12B and 23F, a group that included a vaccine serotype (23F) and serotype 1 associated with enhanced invasiveness. Even within serotypes, there was variation in the presence of the pilus islet between PFGE clones and a higher Wallace coefficient (W = 0.939) indicates that carriage of the islet is a clonal property of pneumococci. Analysis of rlrA negative isolates revealed heterogeneity in the genomic region downstream of the rfl gene, the region where the islet is found in other isolates, compatible with recent loss of the islet in some lineages. Conclusion The pilus islet is present in a minority of pneumococcal isolates recovered from human invasive infections and is therefore not an essential virulence factor in these infections. Carriage of the pilus islet is a clonal property of pneumococci that may vary between isolates expressing the same serotype and loss and acquisition of the islet may be ongoing.

Abstract Background Biological information is commonly used to cluster or classify entities of interest such as genes, conditions, species or samples. However, different sources of data can be used to classify the same set of entities and methods allowing the comparison of the performance of two data sources or the determination of how well a given classification agrees with another are frequently needed, especially in the absence of a universally accepted "gold standard" classification. Results Here, we describe a novel measure – the Ranked Adjusted Rand (RAR) index. RAR differs from existing methods by evaluating the extent of agreement between any two groupings, taking into account the intercluster distances. This characteristic is relevant to evaluate cases of pairs of entities grouped in the same cluster by one method and separated by another. The latter method may assign them to close neighbour clusters or, on the contrary, to clusters that are far apart from each other. RAR is applicable even when intercluster distance information is absent for both or one of the groupings. In the first case, RAR is equal to its predecessor, Adjusted Rand (HA) index. Artificially designed clusterings were used to demonstrate situations in which only RAR was able to detect differences in the grouping patterns. A study with larger simulated clusterings ensured that in realistic conditions, RAR is effectively integrating distance and partition information. The new method was applied to biological examples to compare 1) two microbial typing methods, 2) two gene regulatory network distances and 3) microarray gene expression data with pathway information. In the first application, one of the methods does not provide intercluster distances while the other originated a hierarchical clustering. RAR proved to be more sensitive than HA in the choice of a threshold for defining clusters in the hierarchical method that maximizes agreement between the results of both methods. Conclusion RAR has its major advantage in combining cluster distance and partition information, while the previously available methods used only the latter. RAR should be used in the research problems were HA was previously used, because in the absence of inter cluster distance effects it is an equally effective measure, and in the presence of distance effects it is a more complete one.

Although post-transplant cyclophosphamide (PTCY)-based prophylaxis has become a widely adopted strategy for preventing graft-versus-host disease (GVHD) in 9 out of 10 HLA-mismatched unrelated donors (MMUDs), allogeneic hematopoietic cell transplants (allo-HCTs), data on the safety and efficacy of PTCY in this setting remain limited. This single-center study investigates the outcomes of 94 adults with hematological malignancies undergoing MMUD allo-HCT with PTCY and tacrolimus (Tac) (PTCY-Tac) between 2014 and 2023. The median age was 53 years, and 60.6% were male. Peripheral blood stem cells were infused in all cases. By Day +100, the cumulative incidence of Grades II-IV and Grades III and IV acute GVHD were 33.0% and 9.7%, with 2-year incidence of moderate-to-severe chronic GVHD at 12.6%. By Day +30, 40.8% of patients experienced bacterial bloodstream infections, and 52.4% had cytomegalovirus (CMV) reactivation before letermovir prophylaxis. With letermovir's introduction, CMV reactivation rates dropped significantly, with only one case reported. At 3 years, overall survival was 60.8%, non-relapse mortality was 23%, and the cumulative incidence of relapse was 24.5%. HLA Class I or II mismatches did not affect key outcomes or GVHD rates. These findings demonstrate that PTCY-Tac offers effective GVHD prevention and favorable outcomes in MMUD allo-HCT, supporting its application for patients without fully matched donors., (© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Neospora caninum is a protozoan parasite that infects several species of animals (domestic and wild) and is one of the most common causes of abortion in cattle worldwide. To better understand the epidemiological chain of neosporosis, update the disease status and propose control measures to improve milk production in Rio Grande do Sul (RS), the present study aimed to evaluate the seroprevalence of N. caninum and its distribution in different municipalities of Rio Grande do Sul, Southern RS, Brazil, and determine the factors associated with exposure to N. caninum in small dairy cattle producers in this region. Cattle from 51 dairy farms located in nine municipalities in the southern region of RS were included in this study. Small dairy farmers were interviewed to collect information about the characteristics of their herds. The association between potential associated factors and seropositivity in cattle was assessed using a logistic regression model with a generalized estimating equation. Seroprevalence in individual animals and between herds was 33.9% (95% CI = 28.1-39.9) (121/309) and 80.4% (95% CI = 67.5-88.9) (41/51), respectively. The high seroprevalence found indicates that cattle are susceptible to exposure by N. caninum in a widespread manner in the Pelotas microregion. Furthermore, the sanitary management of cattle, the adaptation of tools that can improve the milk extraction technique and the technical monitoring of professionals who work on the properties can be effective alternatives for controlling N. caninum., Competing Interests: Conflict of interests: The authors declare that they have no conflict of interest.

Tendinopathy is an age-associated degenerative disease characterized by a loss in extracellular matrix (ECM). Since glucose and glutamine metabolism is critical to amino acid synthesis and known to be altered in aging, we sought to investigate if age-related changes in metabolism are linked to changes in ECM remodeling. We exposed young and aged tendon explants to various concentrations of glucose and glutamine to observe changes in metabolic processing (enzyme levels, gene expression, etc.) and matrix biosynthesis. Interestingly, we found that glutamine processing is affected by glucose levels, but this effect was lost with aging. ECM synthesis was altered in a protein-dependent manner by increased glucose and glutamine levels in young tendons. However, these changes were not conserved in aged tendons. Overall, our work suggests that glucose and glutamine metabolism is important for ECM homeostasis, and age-related changes in nutrient metabolism could be a key driver of tendon degeneration., Competing Interests: Declaration of Interests The authors declare no competing interests.

Pastry products constitute a significant segment of the food market. However, the high amount of fat used in their production poses a challenge when competing for the attention of modern consumers, who are more conscious of the health problems associated with the consumption of high-fat products. With this in mind, the main objective of this study is the reduction of the total fat and saturated fat contents of two bakery products, brioche-type bread and rice cake, by partial substitution of the main fat source with Chlorella vulgaris lipid extracts obtained through non-thermal high-pressure extraction (HPE). A reduction of 3% in the fat content of the brioche and a reduction of 11.4% in the total fat content of the rice cake were observed when the microalgae extracts were used to replace 10% of the margarine used in the brioche and 20% of the sunflower oil used in the rice cake. This substitution resulted in fat-reduced bakery products with similar physicochemical and nutritional properties to the full-fat controls. A triangle test demonstrated that no differences were perceived for the fat-reduced brioche, while in the rice cake, only slightly perceptible differences were detected. Moreover, brioche and rice cake containing the extract presented values of 1.22 ± 0.27 and 1.29 ± 0.39 mg GAE/g of total phenolic compounds, respectively. DPPH and FRAP activities were also quantified in 0.95 ± 0.38 and 1.83 ± 0.27 µmol AAE/g for brioche with extract and 1.10 ± 0.61 and 1.39 ± 0.39 µmol AAE/g for the rice cake with extract, respectively. The products were microbially stable for at least four days at room temperature. This study demonstrates the potential of using HPE microalgal lipid extracts as fat substitutes in bakery products.

Modern consumers demand the replacement of synthetic colorants with natural alternatives. Microalgae can serve as an alternative source for these colorants since they hold significant amounts of pigments. This study aimed to evaluate the potential of using microalgae biomass and extracts as natural colorants for pastry and confectionary products. The application of different biomass and levels of Chlorella vulgaris (White, Honey, and a mixture of both) was evaluated in brioche-type breads as egg substitute to confer the typical yellow coloration to the product. A mixture of 1% Chlorella vulgaris (White: Honey [1:1]) showed potential as egg substitute, having minimal impact on the physical-chemical, microbiological, nutritional, and sensory characteristics of the products. Hydroalcoholic Tetraselmis chuii extracts were applied in fondant at a concentration of 0.05%, providing a green coloration with minimal impact on the quality of the product. This study supported the potential of using microalgae, biomass, and extracts, as alternative natural colorants in pastry and confectionary products., Competing Interests: The authors declare that they do not have any conflict of interest., (© 2024 The Author(s). Food Science & Nutrition published by Wiley Periodicals LLC.)

The present work intends to discuss parameter estimation and statistical analysis in adsorption. The Langmuir and Tóth isotherm models are compared for a set of carbon dioxide adsorption data on 13X zeolite from literature at different temperatures: 303, 323, 373, and 423 K. Statistical analyses were performed under frequentist and Bayesian perspectives. Under the frequentist statistical view, parameters were estimated using Maximum Likelihood estimation (MLE). Statistical analyses of parameters were performed by confidence regions in terms of elliptical approximation and likelihood region, while the evaluation of models was performed by chi-square statistics. The results showed that, for these nonlinear models, the elliptical region offers a poor approximation of the parameter estimates' confidence region, especially for the most correlated parameter pairs. Additionally, the four-parameter Tóth's equation yields less correlated parameters than the three-parameter Langmuir model. From a Bayesian perspective, the Markov chain Monte Carlo (MCMC) technique facilitated the reconstruction of the probability density functions of parameters as well as enabled the propagation of parametric uncertainties in the model responses. Finally, the accurate assessment of experimental uncertainty significantly influences the evaluation of models and their respective parameters., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Staphylococcus aureus is an opportunistic pathogen that has emerged as a major public health threat due to the increased incidence of its drug resistance. S. aureus presents a remarkable capacity to adapt to different niches due to the plasticity of its energy metabolism. In this work, we investigated the energy metabolism of S. aureus , focusing on the alternative NADH:quinone oxidoreductases, NDH-2s. S. aureus presents two genes encoding NDH-2s (NDH-2A and NDH-2B) and lacks genes coding for Complex I, the canonical respiratory NADH:quinone oxidoreductase. This observation makes the action of NDH-2s crucial for the regeneration of NAD + and, consequently, for the progression of metabolism. Our study involved the comprehensive biochemical characterization of NDH-2B and the exploration of the cellular roles of NDH-2A and NDH-2B, utilizing knockout mutants (Δ ndh-2a and Δ ndh-2b ). We show that NDH-2B uses NADPH instead of NADH, does not establish a charge-transfer complex in the presence of NADPH, and its reduction by this substrate is the catalytic rate-limiting step. In the case of NDH-2B, the reduction of the flavin is inherently slow, and we suggest the establishment of a charge transfer complex between NADP + and FADH 2 , as previously observed for NDH-2A, to slow down quinone reduction and, consequently, prevent the overproduction of reactive oxygen species, which is potentially unnecessary. Furthermore, we observed that the lack of NDH-2A or NDH-2B impacts cell growth, volume, and division differently. The absence of these enzymes results in distinct metabolic phenotypes, emphasizing the unique cellular roles of each NDH-2 in energy metabolism.IMPORTANCE Staphylococcus aureus is an opportunistic pathogen, posing a global challenge in clinical medicine due to the increased incidence of its drug resistance. For this reason, it is essential to explore and understand the mechanisms behind its resistance, as well as the fundamental biological features such as energy metabolism and the respective players that allow S. aureus to live and survive. Despite its prominence as a pathogen, the energy metabolism of S. aureus remains underexplored, with its respiratory enzymes often escaping thorough investigation. S. aureus bioenergetic plasticity is illustrated by its ability to use different respiratory enzymes, two of which are investigated in the present study. Understanding the metabolic adaptation strategies of S. aureus to bioenergetic challenges may pave the way for the design of therapeutic approaches that interfere with the ability of the pathogen to successfully adapt when it invades different niches within its host., Competing Interests: The authors declare no conflict of interest.

STAT3 is a pleiotropic transcription factor overactivated in 70% of solid tumours. We have recently reported that inactivating mutations on residues susceptible to post-translational modifications (PTMs) in only one of the monomers (i.e. asymmetric) caused changes in the cellular distribution of STAT3 homodimers. Here, we used more controlled experimental conditions, i.e. without the interference of endogenous STAT3 (STAT3-/- HeLa cells) and in the presence of a defined cytokine stimulus (Leukemia Inhibitory Factor, LIF), to provide further evidence that asymmetric PTMs affect the nuclear translocation of STAT3 homodimers. Time-lapse microscopy for 20 min after LIF stimulation showed that S727 dephosphorylation (S727A) and K685 inactivation (K685R) slightly enhanced the nuclear translocation of STAT3 homodimers, while K49 inactivation (K49R) delayed STAT3 nuclear translocation. Our findings suggest that asymmetrically modified STAT3 homodimers could be a new level of STAT3 regulation and, therefore, a potential target for cancer therapy., (© 2023. The Author(s).)

The local disruptions caused by the genes of one disease can influence the pathways associated with the other diseases resulting in comorbidity. For gene therapies, it is necessary to prioritize the key genes that regulate common biological mechanisms to tackle the issues caused by overlapping diseases. This work proposes a clustering-based computational approach for prioritising the comorbid genes within the overlapping disease modules by analyzing Protein-Protein Interaction networks. For this, a sub-network with gene interactions of the disease pair was extracted from the interactome. The edge weights are assigned by combining the pairwise gene expression correlation and betweenness centrality scores. Further, a weighted graph clustering algorithm is applied and dominant nodes of high-density clusters are ranked based on clustering coefficients and neighborhood connectivity. Case studies based on neurodegenerative diseases such as Amyotrophic Lateral Sclerosis- Spinal Muscular Atrophy (ALS-SMA) pair and cancers such as Ovarian Carcinoma-Invasive Ductal Breast Carcinoma (OC-IDBC) pair were conducted to examine the efficacy of the proposed method. To identify the mechanistic role of top-ranked genes, we used Functional and Pathway enrichment analysis, connectivity analysis with leave-one-out (LOO) method, analysis of associated disease-related protein complexes, and prioritization tools such as TOPPGENE and Heml2.0. From pathway analysis, it was observed that the top 10 genes obtained using the proposed method were associated with 10 pathways in ALS-SMA comorbidity and 15 in the case of OC-IDBC, while that in similar methods like SAPDSB and S2B were 4, 6 respectively for ALS-SMA and 9, 10 respectively for OC-IDBC. In both case studies, 70 % of the disease-specific benchmark protein complexes were linked to top-ranked genes of the proposed method while that of SAPDSB and S2B were 55 % and 60 % respectively. Additionally, it was found that the removal of the top 10 genes disconnect the network into 14 distinct components in the case of ALS-SMA and 9 in the case of OC-IDBC. The experimental results shows that the proposed method can be effectively used for identifying key genes in comorbidity and can offer insights about the intricate molecular relationship driving comorbid diseases., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

In this study, different extraction methods and conditions were used for the extraction of antioxidants from brown macroalgae Fucus spiralis . The extraction methodologies used were ultrasound-assisted extraction (ultrasonic bath and ultrasonic probe), extraction with a vortex, extraction with an Ultra-Turrax ® homogenizer, and high-pressure-assisted extraction. The extracts were analyzed for their total phenolic content (TPC) and their antioxidant activity, and evaluated through the 2,2-difenil-1-picrilhidrazil (DPPH) free radical scavenging method and ferric reducing antioxidant power (FRAP) assay. Ultrasonic probe-assisted extraction yielded the highest values of TPC (94.78-474.16 mg gallic acid equivalents/g extract). Regarding the antioxidant activity, vortex-assisted extraction gave the best DPPH results (IC 50 1.89-16 µg/mL), while the highest FRAP results were obtained using the Ultra-Turrax ® homogenizer (502.16-1188.81 μmol ascorbic acid equivalents/g extract). For each extraction method, response surface methodology was used to analyze the influence of the experimental conditions "extraction time" (t), "biomass/solvent ratio" (R), "solvent" (S, water % in water/ethanol mixture), and "pressure" (P) on TPC, DPPH, and FRAP of the F. spiralis extracts. In general, higher TPC content and higher antioxidant capacity (lower IC 50 and higher FRAP) were obtained with higher R, t, and P, and lower S (higher ethanol %). The model regarding the combined effects of independent variables t, R, and S on the FRAP response values for vortex-assisted extractions best fitted the experimental data ( R 2 0.957), with optimal extraction conditions of t = 300 s, R = 50 g, and S = 25%.

Organotropism has been known since 1889, yet this vital component of metastasis has predominantly stayed elusive. This mini-review gives an overview of the current understanding of the underlying mechanisms of organotropism and metastases development by focusing on the formation of the pre-metastatic niche, immune defenses against metastases, and genomic alterations associated with organotropism. The particular case of brain metastases is also addressed, as well as the impact of organotropism in cancer therapy. The limited comprehension of the factors behind organotropism underscores the necessity for efficient strategies and treatments to manage metastases., 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 © 2024 Carrolo, Miranda, Vilhais, Quintela, Sousa, Costa and Pinto.)

The interest in seaweeds as an abundant feedstock to obtain valuable and multitarget bioactive ingredients is continuously growing. In this work, we explore the potential of Gracilaria gracilis, an edible red seaweed cultivated worldwide for its commercial interest as a source of agar and other ingredients for cosmetic, pharmacological, food, and feed applications. G. gracilis growth conditions were optimized through vegetative propagation and sporulation while manipulating the physicochemical conditions to achieve a large biomass stock. Green extraction methodologies with ethanol and water were performed over the seaweed biomass. The bioactive potential of extracts was assessed through a set of in vitro assays concerning their cytotoxicity, antioxidant, and antimicrobial properties. Additionally, dried seaweed biomass was incorporated into pasta formulations to increase food's nutritional value. Pigments extracted from G. gracilis have also been incorporated into yogurt as a natural colorant, and their stability was evaluated. Both products were submitted to the appreciation of a semi-trained sensorial panel aiming to achieve the best final formulation before reaching the market. Results support the versatility of G. gracilis whether it is applied as a whole biomass, extracts and/or pigments. Through implementing several optimized protocols, this work allows the development of products with the potential to profit the food, cosmetic, and aquaculture markets, promoting environmental sustainability and a blue circular economy. Moreover, and in line with a biorefinery approach, the residual seaweed biomass will be used as biostimulant for plant growth or converted to carbon materials to be used in water purification of the in-house aquaculture systems of MARE-Polytechnic of Leiria, Portugal.

Background: Spinal Muscular Atrophy (SMA) and Amyotrophic Lateral Sclerosis (ALS) share phenotypic and molecular commonalities, including the fact that they can be caused by mutations in ubiquitous proteins involved in RNA metabolism, namely SMN, TDP-43 and FUS. Although this suggests the existence of common disease mechanisms, there is currently no model to explain the resulting motor neuron dysfunction. In this work we generated a parallel set of Drosophila models for adult-onset RNAi and tagged neuronal expression of the fly orthologues of the three human proteins, named Smn, TBPH and Caz, respectively. We profiled nuclear and cytoplasmic bound mRNAs using a RIP-seq approach and characterized the transcriptome of the RNAi models by RNA-seq. To unravel the mechanisms underlying the common functional impact of these proteins on neuronal cells, we devised a computational approach based on the construction of a tissue-specific library of protein functional modules, selected by an overall impact score measuring the estimated extent of perturbation caused by each gene knockdown., Results: Transcriptome analysis revealed that the three proteins do not bind to the same RNA molecules and that only a limited set of functionally unrelated transcripts is commonly affected by their knock-down. However, through our integrative approach we were able to identify a concerted effect on protein functional modules, albeit acting through distinct targets. Most strikingly, functional annotation revealed that these modules are involved in critical cellular pathways for motor neurons, including neuromuscular junction function. Furthermore, selected modules were found to be significantly enriched in orthologues of human neuronal disease genes., Conclusions: The results presented here show that SMA and ALS disease-associated genes linked to RNA metabolism functionally converge on neuronal protein complexes, providing a new hypothesis to explain the common motor neuron phenotype. The functional modules identified represent promising biomarkers and therapeutic targets, namely given their alteration in asymptomatic settings., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Microbes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large populations that collectively secrete massive amounts of secondary metabolites and alter their environment. Yet, the conditions favoring secondary metabolism despite the potential costs for primary metabolism remain unclear. Here we investigated the biosurfactants that the bacterium Pseudomonas aeruginosa makes and secretes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that the ability to make surfactants from glycerol varies inconsistently across the phylogenetic tree; instead, lineages that lost this ability are also worse at reducing the oxidative stress of primary metabolism on glycerol. Experiments with different carbon sources support a link with oxidative stress that explains the inconsistent distribution across the P. aeruginosa phylogeny and suggests a general principle: P. aeruginosa lineages produce surfactants if they can reduce the oxidative stress produced by primary metabolism and have excess resources, beyond their primary needs, to afford secondary metabolism. These results add a new layer to the regulation of a secondary metabolite unessential for primary metabolism but important to change physical properties of the environments surrounding bacterial populations., Competing Interests: GS, CL, CL, YC, ZW, KR, FP, JY, JX No competing interests declared, (© 2022, Santamaria, Liao et al.)

The most consumed fish species in Portugal do not correspond to the most caught fish species on the Portuguese coast. From the point of view of ocean sustainability and economics, it is important to study unexploited or underexploited fish species that have the potential to be introduced into the food market. This potential can be reflected by their nutritional value, where mineral elements are often overlooked despite their importance in human health. Therefore, it is important to study the elemental concentration of those fish species, which should also include seasonal variations of essential mineral elements such as Ca, P, Mg, Na, K, Fe, Cu, Mn, Zn, and I, and non-essential elements such as As, Ni, Cd, and Pb. This work is part of a project that studied five fish species with the potential to be brought to the market: three species with low commercial value (Trachurus picturatus, Spondyliosoma cantharus and Trigla lyra) and two species with no commercial value (Serranus cabrilla and Capros aper), caught over a year in the coast of Portugal. Mineral elements were quantified by ICP-OES (ICP-MS for I). The results showed that the studied fish species present significant elemental concentrations, similar to those found in the most caught fish species in Portugal. Trachurus picturatus was found to be a source of Fe, and all species are sources of I. Overall, Spondyliosoma cantharus proved to be the most element-rich species. Sensorially, Cu was related to "metallic odour" and Fe to "metallic flavour", and I was related to "seaweed odour" and "seawater flavour". Additionally, toxic elements such as Cd, Pb, Ni and As were not detected. The corresponding Hazard Quotients (HQ) show the safety of the consumption of these fish species concerning the content of potentially toxic elements., (Copyright © 2022 Elsevier Ltd. All rights reserved.)

Protein-protein interactions (PPI) play an essential role in the biological processes that occur in the cell. Therefore, the dissection of PPI networks becomes decisive to model functional coordination and predict pathological de-regulation. Cellular networks are dynamic and proteins display varying roles depending on the tissue-interactomic context. Thus, the use of centrality measures in individual proteins fall short to dissect the functional properties of the cell. For this reason, there is a need for more comprehensive, relational, and context-specific ways to analyze the multiple actions of proteins in different cells and identify specific functional assemblies within global biomolecular networks. Under this framework, we define Biological Interacting units (BioInt-U) as groups of proteins that interact physically and are enriched in a common Gene Ontology. A search strategy was applied on 33 tissue-specific (TS) PPI networks to generate BioInt libraries associated with each particular human tissue. The cross-tissue comparison showed that housekeeping assemblies incorporate different proteins and exhibit distinct network properties depending on the tissue. Furthermore, disease genes (DGs) of tissue-associated pathologies preferentially accumulate in units in the expected tissues, which in turn were more central in the TS networks. Overall, the study reveals a tissue-specific functional diversification based on the identification of specific protein units and suggests vulnerabilities specific of each tissue network, which can be applied to refine protein-disease association methods., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s).)

Background: This study aimed to evaluate the accuracy and oncological results of sentinel lymph node biopsy in patients with early lip and oral cavity squamous cell carcinoma (SCC) in a real-world scenario., Methods: Retrospective study including seven Brazilian centers., Results: Four-hundred and seven cN0 patients were accrued for 20 years. The rate of occult metastasis was 23.1% and 22 patients (5.4%) had regional failure. We found, for 5 years of follow-up, 85.3% of regional recurrence-free survival; 77.1% of disease-free survival; 73.7% of overall survival; and 86.7% of disease-specific survival. The rate of false-negative cases was 5.4%., Conclusion: In a real-world scenario, sentinel lymph node biopsy for patients with SCC of the lip and oral cavity proved feasible in different settings and to be oncologically safe, with similar rates of occult lymph node metastasis and false-negative cases, when compared to elective neck dissection, and with similar long-term survival to that reported historically., (© 2022 Wiley Periodicals LLC.)

Target species diversification is essential for fisheries sustainability and fish market revitalization. Fish discards are a widely recognized problem resulting from fisheries worldwide, and are of major concern for all sector players, from administrations, to fishermen, and scientists. However, non-target species are seldom studied, and information on nutritional profiles and seasonal changes in nutritional properties is generally lacking. This study assessed the seasonal nutritional composition of two unexploited ( Serranus cabrilla , Capros aper ) and three low commercial value fish species ( Trachurus picturatus , Spondyliosoma cantharus , and Trigla lyra ), captured on the Portuguese coast over 1 year. Significant seasonal variations were observed in the nutritional composition of all the species studied. Moisture and ash contents varied from 70% to 81% and from 5% to 13%, respectively. The maximum fat contents were 5% for C. aper and 4% for T. picturatus , allowing to classify all studied fishes as lean. The highest protein contents were recorded for C. aper (25%) and S. cantharus (20%). The unexploited and low commercial value fish species studied were shown to be good fat and protein sources, comparable to commonly consumed species, such as cod and salmon, having a great potential to become commonly consumed fish in Portugal., (© 2022 The Authors. Food Science & Nutrition published by Wiley Periodicals LLC.)

Introduction: Sentinel lymph node biopsy is a proven method for staging the neck in patients with early oral cavity squamous cell carcinoma because it results in less comorbidity than the traditional method of selective neck dissection, with the same oncological results. However, the real effect of that method on the quality of life of such patients remains unknown., Objective: The present study aimed to evaluate the quality of life of patients with oral cavity squamous cell carcinoma T1/T2N0 submitted to sentinel lymph node biopsy compared to those that received selective neck dissection., Methods: Cross-sectional study including 24 patients, after a 36 month follow-up, 15 of them submitted to the sentinel lymph node biopsy and 9 to selective neck dissection. All patients answered the University of Washington quality of life questionnaire., Results: The evaluation of the questionnaires showed a late worsening of the domains appearance (p=0.035) and chewing (p=0.041), as well as a decrease of about 10% of general quality of life (p=0.025) in patients undergoing selective neck dissection ​​in comparison to those undergoing sentinel lymph node biopsy., Conclusion: Patients with early-stage oral cavity squamous cell carcinoma undergoing sentinel lymph node biopsy presented better late results of general quality of life, mainly regarding appearance and chewing, when compared to patients submitted to selective neck dissection., (Copyright © 2020 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.)

Mycobacterium tuberculosis , the causative agent of tuberculosis, is composed of several lineages characterized by a genome identity higher than 99%. Although the majority of the lineages are associated with humans, at least four lineages are adapted to other mammals, including different M. tuberculosis ecotypes. Host specificity is associated with higher virulence in its preferred host in ecotypes such as M. bovis . Deciphering what determines the preference of the host can reveal host-specific virulence patterns. However, it is not clear which genomic determinants might be influencing host specificity. In this study, we apply a combination of unsupervised and supervised classification methods on genomic data of ~27,000 M. tuberculosis clinical isolates to decipher host-specific genomic determinants. Host-specific genomic signatures are scarce beyond known lineage-specific mutations. Therefore, we integrated lineage-specific mutations into the iEK1011 2.0 genome-scale metabolic model to obtain lineage-specific versions of it. Flux distributions sampled from the solution spaces of these models can be accurately separated according to host association. This separation correlated with differences in cell wall processes, lipid, amino acid and carbon metabolic subsystems. These differences were observable when more than 95% of the samples had a specific growth rate significantly lower than the maximum achievable by the models. This suggests that these differences might manifest at low growth rate settings, such as the restrictive conditions M. tuberculosis suffers during macrophage infection.

Objective: The aim of this study was to compare the role of a chest physiotherapy (CP) intervention to no intervention on the respiratory status of children under two years of age, with mild-to-moderate bronchiolitis., Methods: Out of 80 eligible children observed in the Emergency Room, 45 children completed the study with 28 randomized to the intervention group and 17 to the control group. The intervention protocol, applied in an ambulatory setting, consisted of combined techniques of passive prolonged slow expiration, rhinopharyngeal clearance and provoked cough. The control group was assessed with no chest physiotherapy intervention. The efficacy of chest physiotherapy was assessed using the Kristjansson Respiratory Score at the admission and discharge of the visit to the Emergency Room and during clinical visits at day 7 and day 15., Results: There was a significant improvement in the Kristjansson Respiratory Score in the intervention group compared to the control group at day 15 [1.2 (1.5) versus 0.3 (0.5); p -value = 0 . 005 , in the control and intervention groups, respectively], with a mean difference (95% CI) of - 0 . 9 ( - 1 . 6 to - 0 . 3 )., Conclusion: Chest physiotherapy had a positive impact on the respiratory status of children with mild-to-moderate bronchiolitis., Clinical Trial Registration: https://clinicaltrials.gov/ct2/show/NCT04260919., Competing Interests: The authors declare no potential conflicts of interest with respect to the research, authorship and/or publication of this paper., (© 2021, Hong Kong Physiotherapy Association.)

We live in a world of limited biological resources and ecosystems, which are essential to feed people. Consequently, diversifying target species and considering full exploitation are essential for fishery sustainability. The present study focuses on the valorization of three low commercial value fish species (blue jack mackerel, Trachurus picturatus ; black seabream, Spondyliosoma cantharus ; and piper gurnard, Trigla lyra ) and of two unexploited species (comber, Serranus cabrilla and boarfish, Capros aper ) through the development of marine-based food products with added value. A preliminary inquiry with 155 consumers from Região de Lisboa e Vale do Tejo (Center of Portugal) was conducted to assess fish consumption, the applicability of fish product innovation, and the importance of valorizing discarded fish. Five products (black seabream ceviche , smoked blue jack mackerel pâté, dehydrated piper gurnard, fried boarfish, and comber pastries) were developed and investigated for their sensory characteristics and consumer liking by hedonic tests to 90 consumers. The most important descriptors were identified for each product (texture, flavor, color, and appearance). Comber pastries had the highest purchase intention (88%), followed by black seabream ceviche (85%) and blue jack mackerel pâté (76%). Sensory evaluations showed a clear tendency of consumers to accept reformulated products, with the introduction of the low-value and unexploited species under study.

Overfishing is increasing over time, and according to FAO (Food and Agriculture Organization), about one third of the world's fish stocks are now overfished. Thus, diversifying the target species is essential for fisheries sustainability contributing to improve resource-efficient processes. Non-target species can be valuable resources for the development of new food products. However, those species are scarcely studied, and it is of high importance to trace their seasonal sensory profile as a first step towards their valorisation. Therefore, in this study, seasonal influence on sensory properties of five low commercial value or unexploited fish species, namely Trachurus picturatus (blue jack mackerel), Spondyliosoma cantharus (black seabream), Trigla lyra (piper gurnard), Serranus cabrilla (comber) and Capros aper (boarfish), was assessed in order to identify the most favourable season for catching each species. Fish samples were assessed by a panel of 16 semi-trained assessors for sensory attributes previously identified. The evaluation takes place every 2 months. Statistical differences were reported between attributes and seasons for all species, except for T. lyra , which did not present any difference in its sensory attributes throughout the year.

Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause the recessive genetic disease cystic fibrosis, where the chloride transport across the apical membrane of epithelial cells mediated by the CFTR protein is impaired. CFTR protein trafficking to the plasma membrane (PM) is the result of a complex interplay between the secretory and membrane recycling pathways that control the number of channels present at the membrane. In addition, the ion transport activity of CFTR at the PM is modulated through post-translational protein modifications. Previously we described that spleen tyrosine kinase (SYK) phosphorylates a specific tyrosine residue in the nucleotide-binding domain 1 domain and this modification can regulate the PM abundance of CFTR. Here we identified the underlying biochemical mechanism using peptide pull-down assays followed by mass spectrometry. We identified in bronchial epithelial cells that the adaptor protein SHC1 recognizes tyrosine-phosphorylated CFTR through its phosphotyrosine-binding domain and that the formation of a complex between SHC1 and CFTR is induced at the PM in the presence of activated SYK. The depletion of endogenous SHC1 expression was sufficient to promote an increase in CFTR at the PM of these cells. The results identify a SYK/SHC1 pathway that regulates the PM levels of CFTR channels, contributing to a better understanding of how CFTR-mediated chloride secretion is regulated.

Objective: Several respiratory scores have been created to evaluate bronchiolitis' severity level, but it is still not clear which is the best score. The aim of this study is to compare the Wang Respiratory Score (WRS) and the Kristjansson Respiratory Score (KRS) in the setting of an emergency room., Methods: We performed a prospective observational study with 60 infants with bronchiolitis admitted to a paediatric emergency department. For both scores, we assessed inter-rater reliability between two different health professionals (physician and physiotherapist), internal consistency, and correlation with SpO 2 testing the intraclass-correlation coefficient (ICC), weighted kappa, Cronbach α coefficient and Spearman tests, respectively., Results: The inter-rater reliability was higher in KRS (ICC 0.79) and the Cronbach α and weighted kappa had similar values in KRS versus WRS. The correlation between the KRS/WRS and SpO 2 was poor/moderate upon admission and discharge for the first observer and the second observer., Conclusions: While the internal consistency was similar in both scores, inter-rater reliability of KRS was higher than WRS, which allows us to conclude that it would have more consistent results when used to assess bronchiolitis' level of severity by health personnel in a busy hospital emergency room., Competing Interests: The authors declare no potential conflicts of interest with respect to the research, authorship, and/or publication of this paper., (© 2020, Hong Kong Physiotherapy Association.)

Fish is a very perishable food and therefore several storage strategies need to be employed to increase its shelf-life, guaranteeing its safety and quality from catch to consumption. Despite the advances in modern fish storage technologies, chilling and freezing are still the most common preservation methods used onboard. The present review aims to summarize strategies to increase the shelf-life of fresh (chilled) and frozen fish, as whole, gutted, or fillet, involving the assessment of different traditional cooling and freezing conditions of different fish species caught in different locations. Although there are other factors that influence the fish shelf-life, such as the fish species and the stress suffered during catch, storage time and temperature and the amount of ice are some of the most important. In addition, the way that fish is stored (whole, fillet, or gutted) also contributes to the final quality of the product. In most studies, whole chilled and frozen fish present longer shelf-life than those preserved as gutted and filleted. However, it should be noted that other factors related to the organism, capture method, and transport to the preparation/processing industry should be considered for shelf-life extension.

Cystic fibrosis is a condition caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR). It is also thought to increase the activity of epithelial sodium channels (ENaC). The altered function of these ion channels is one of the causes of the thick dehydrated mucus that characterizes the disease and is partially responsible for recurrent pulmonary infections and inflammation events that ultimately destroy the lungs of affected subjects. Phosphoinositides are signaling lipids that regulate numerous cellular processes and membrane proteins, including ENaC. Inhibition of diacylglycerol kinase (DGK), an enzyme of the phosphoinositide pathway, reduces ENaC function. We propose a computational analysis that is based on the combination of two existing mathematical models: one representing the dynamics of phosphoinositides and the other explaining how phosphatidylinositol 4,5-bisphosphate (PI(4,5)P 2 ) influences ENaC activity and, consequently, airway surface liquid. This integrated model permits, for the first time, a detailed assessment of the intricate interactions between DGK and ENaC and is consistent with available literature data. In particular, the computational approach allows comparisons of two competing hypotheses regarding the regulation of ENaC. The results strongly suggest that the regulation of ENaC is primarily exerted through the control of PI(4,5)P 2 production by type-I phosphatidylinositol-4-phosphate 5-kinase (PIP5KI), which in turn is controlled by phosphatidic acid (PA), the product of the DGK reaction.

Cystic Fibrosis (CF), the most common lethal autosomic recessive disorder among Caucasians, is caused by mutations in the gene encoding the Cystic Fibrosis Transmembrane conductance Regulator (CFTR) protein, a cAMP-regulated chloride channel expressed at the apical surface of epithelial cells. Cyclic AMP regulates both CFTR channel gating through a protein kinase A (PKA)-dependent process and plasma membane (PM) stability through activation of the exchange protein directly activated by cAMP1 (EPAC1). This cAMP effector, when activated promotes the NHERF1:CFTR interaction leading to an increase in CFTR at the PM by decreasing its endocytosis. Here, we used protein interaction profiling and bioinformatic analysis to identify proteins that interact with CFTR under EPAC1 activation as possible regulators of this CFTR PM anchoring. We identified an enrichment in cytoskeleton related proteins among which we characterized CAPZA2 and INF2 as regulators of CFTR trafficking to the PM. We found that CAPZA2 promotes wt-CFTR trafficking under EPAC1 activation at the PM whereas reduction of INF2 levels leads to a similar trafficking promotion effect. These results suggest that CAPZA2 is a positive regulator and INF2 a negative one for the increase of CFTR at the PM after an increase of cAMP and concomitant EPAC1 activation. Identifying the specific interactions involving CFTR and elicited by EPAC1 activation provides novel insights into late CFTR trafficking, insertion and/or stabilization at the PM and highlighs new potential therapeutic targets to tackle CF disease., (© 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)

Cystic fibrosis (CF) is a genetic disease caused by mutations in the gene encoding CF transmembrane conductance regulator (CFTR), a chloride channel normally expressed at the surface of epithelial cells. The most frequent mutation, resulting in Phe-508 deletion, causes CFTR misfolding and its premature degradation. Low temperature or pharmacological correctors can partly rescue the Phe508del-CFTR processing defect and enhance trafficking of this channel variant to the plasma membrane (PM). Nevertheless, the rescued channels have an increased endocytosis rate, being quickly removed from the PM by the peripheral protein quality-control pathway. We previously reported that rescued Phe508del-CFTR (rPhe508del) can be retained at the cell surface by stimulating signaling pathways that coax the adaptor molecule ezrin (EZR) to tether rPhe508del-Na + /H + -exchange regulatory factor-1 complexes to the actin cytoskeleton, thereby averting the rapid internalization of this channel variant. However, the molecular basis for why rPhe508del fails to recruit active EZR to the PM remains elusive. Here, using a proteomics approach, we characterized and compared the core components of wt-CFTR- or rPhe508del-containing macromolecular complexes at the surface of human bronchial epithelial cells. We identified calpain 1 (CAPN1) as an exclusive rPhe508del interactor that prevents active EZR recruitment, impairs rPhe508del anchoring to actin, and reduces its stability in the PM. We show that either CAPN1 down-regulation or its chemical inhibition dramatically improves the functional rescue of Phe508del-CFTR in airway cells. These observations suggest that CAPN1 constitutes an appealing target for pharmacological intervention, as part of CF combination therapies restoring Phe508del-CFTR function., (© 2019 Matos et al.)

The lung epithelium is lined with a layer of airway surface liquid (ASL) that is crucial for healthy lung function. ASL thickness is controlled by two ion channels: epithelium sodium channel (ENaC) and cystic fibrosis (CF) transmembrane conductance regulator (CFTR). Here, we present a minimal mathematical model of ENaC, CFTR and ASL regulation that sheds light on the control of ENaC by the short palate lung and nasal epithelial clone 1 (SPLUNC1) protein and by phosphatidylinositol 4,5-biphosphate (PI(4,5)P 2 ). The model, despite its simplicity, yields a good fit to experimental observations and is an effective tool for exploring the interplay between ENaC, CFTR and ASL. Steady-state data and dynamic information constrain the model's parameters without ambiguities. Testing the hypothesis that PI(4,5)P 2 protects ENaC from ubiquitination suggests that this protection does not improve the model results and that the control of the ENaC opening probability by PI(4,5)P 2 is sufficient to explain all available data. The model analysis further demonstrates that ASL at the steady state is sensitive to small changes in PI(4,5)P 2 abundance, particularly in CF conditions, which suggests that manipulation of phosphoinositide metabolism may promote therapeutic benefits for CF patients.

Xenarthrans-anteaters, sloths, and armadillos-have essential functions for ecosystem maintenance, such as insect control and nutrient cycling, playing key roles as ecosystem engineers. Because of habitat loss and fragmentation, hunting pressure, and conflicts with domestic dogs, these species have been threatened locally, regionally, or even across their full distribution ranges. The Neotropics harbor 21 species of armadillos, 10 anteaters, and 6 sloths. Our data set includes the families Chlamyphoridae (13), Dasypodidae (7), Myrmecophagidae (3), Bradypodidae (4), and Megalonychidae (2). We have no occurrence data on Dasypus pilosus (Dasypodidae). Regarding Cyclopedidae, until recently, only one species was recognized, but new genetic studies have revealed that the group is represented by seven species. In this data paper, we compiled a total of 42,528 records of 31 species, represented by occurrence and quantitative data, totaling 24,847 unique georeferenced records. The geographic range is from the southern United States, Mexico, and Caribbean countries at the northern portion of the Neotropics, to the austral distribution in Argentina, Paraguay, Chile, and Uruguay. Regarding anteaters, Myrmecophaga tridactyla has the most records (n = 5,941), and Cyclopes sp. have the fewest (n = 240). The armadillo species with the most data is Dasypus novemcinctus (n = 11,588), and the fewest data are recorded for Calyptophractus retusus (n = 33). With regard to sloth species, Bradypus variegatus has the most records (n = 962), and Bradypus pygmaeus has the fewest (n = 12). Our main objective with Neotropical Xenarthrans is to make occurrence and quantitative data available to facilitate more ecological research, particularly if we integrate the xenarthran data with other data sets of Neotropical Series that will become available very soon (i.e., Neotropical Carnivores, Neotropical Invasive Mammals, and Neotropical Hunters and Dogs). Therefore, studies on trophic cascades, hunting pressure, habitat loss, fragmentation effects, species invasion, and climate change effects will be possible with the Neotropical Xenarthrans data set. Please cite this data paper when using its data in publications. We also request that researchers and teachers inform us of how they are using these data., (© 2019 The Authors. Ecology © 2019 The Ecological Society of America.)

In cystic fibrosis, the most common disease-causing mutation is F508del, which causes not only intracellular retention and degradation of CFTR, but also defective channel gating and decreased membrane stability of the small amount that reaches the plasma membrane (PM). Thus, pharmacological correction of mutant CFTR requires targeting of multiple cellular defects in order to achieve clinical benefit. Although small-molecule compounds have been identified and commercialized that can correct its folding or gating, an efficient retention of F508del CFTR at the PM has not yet been explored pharmacologically despite being recognized as a crucial factor for improving functional rescue of chloride transport. In ongoing efforts to determine the CFTR interactome at the PM, we used three complementary approaches: targeting proteins binding to tyrosine-phosphorylated CFTR, protein complexes involved in cAMP-mediated CFTR stabilization at the PM, and proteins selectively interacting at the PM with rescued F508del-CFTR but not wt-CFTR. Using co-immunoprecipitation or peptide-pull down strategies, we identified around 400 candidate proteins through sequencing of complex protein mixtures using the nano-LC Triple TOF MS technique. Key candidate proteins were validated for their robust interaction with CFTR-containing protein complexes and for their ability to modulate the amount of CFTR expressed at the cell surface of bronchial epithelial cells. Here, we describe how we explored the abovementioned experimental datasets to build a protein interaction network with the aim of identifying novel pharmacological targets to rescue CFTR function in cystic fibrosis (CF) patients. We identified and validated novel candidate proteins that were essential components of the network but not detected in previous proteomic analyses.

Discovering disease-associated genes (DG) is strategic for understanding pathological mechanisms. DGs form modules in protein interaction networks and diseases with common phenotypes share more DGs or have more closely interacting DGs. This prompted the development of Specific Betweenness (S2B) to find genes associated with two related diseases. S2B prioritizes genes frequently and specifically present in shortest paths linking two disease modules. Top S2B scores identified genes in the overlap of artificial network modules more than 80% of the times, even with incomplete or noisy knowledge. Applied to Amyotrophic Lateral Sclerosis and Spinal Muscular Atrophy, S2B candidates were enriched in biological processes previously associated with motor neuron degeneration. Some S2B candidates closely interacted in network cliques, suggesting common molecular mechanisms for the two diseases. S2B is a valuable tool for DG prediction, bringing new insights into pathological mechanisms. More generally, S2B can be applied to infer the overlap between other types of network modules, such as functional modules or context-specific subnetworks. An R package implementing S2B is publicly available at https://github.com/frpinto/S2B .

Objectives/hypothesis: Locoregional recurrences of oral cavity squamous cell carcinoma (SCC) may be diagnosed during follow-up of surgically treated patients. Nevertheless, few studies have investigated factors that impact salvage surgery failure and the mortality rates of these patients. The objectives were to identify predictive factors of salvage surgery failure and mortality in patients who undergo surgical treatment for recurrent oral cavity SCC and to compare the overall survival rates of these patients with those of patients who undergo only one surgical treatment., Study Design: Retrospective cohort study., Methods: Forty-six patients submitted to salvage surgery for local or locoregional recurrence., Results: The presence of lymph node metastasis and positive surgical margins at the salvage surgery time were the only independent factors associated with both recurrence rates (hazard ratio [HR]: 5.04 and 2.82, respectively) and mortality (HR: 3.51 and 3.24, respectively). When the overall survival rates of the 199 patients who only underwent one surgical treatment were compared to those of the 46 patients subjected to salvage surgery, a similarity was evident when patients who underwent salvage surgery did not have a new disease recurrence (70.7% vs. 54.7%, respectively; P = .158). Likewise, patients with new recurrences after salvage surgery and patients who received palliative treatment for relapsed disease had similar overall survival rates (0.6% vs. 0.0%, respectively; P = .475)., Conclusions: The presence of lymph node metastasis at the time of recurrence and positive surgical margins after the salvage surgery were associated with a worse overall survival rate in patients with oral cavity SCC relapse., Level of Evidence: 2b. Laryngoscope, 128:1113-1119, 2018., (© 2017 The American Laryngological, Rhinological and Otological Society, Inc.)

Phosphoinositides are signalling lipids that constitute a complex network regulating many cellular processes. We propose a computational model that accounts for all species of phosphoinositides in the plasma membrane of mammalian cells. The model replicates the steady-state of the pathway and most known dynamic phenomena. Sensitivity analysis demonstrates model robustness to alterations in the parameters. Model analysis suggest that the greatest contributor to phosphatidylinositol 4,5-biphosphate (PI(4,5)P 2 ) production is a flux representing the direct transformation of PI into PI(4,5)P 2 , also responsible for the maintenance of this pool when phosphatidylinositol 4-phosphate (PI(4)P) is decreased. PI(5)P is also shown to be a significant source for PI(4,5)P 2 production. The model was validated with siRNA screens that knocked down the expression of enzymes in the pathway. The screen monitored the activity of the epithelium sodium channel (ENaC), which is activated by PI(4,5)P 2 . While the model may deepen our understanding of other physiological processes involving phosphoinositides, we highlight therapeutic effects of ENaC modulation in Cystic Fibrosis (CF). The model suggests control strategies where the activities of the enzyme phosphoinositide 4-phosphate 5-kinase I (PIP5KI) or the PI4K + PIP5KI + DVL protein complex are decreased and cause an efficacious reduction in PI(4,5)P 2 levels while avoiding undesirable alterations in other phosphoinositide pools.

Background: The purpose of the present study was to investigate the role of tumor volume in the prognosis of patients with oral cavity squamous cell carcinoma (SCC)., Methods: One hundred twenty-three patients with T4a oral cavity SCCs underwent surgical treatment. The volumes of the primary cancer were calculated by the multiplication of 3 macroscopic dimensions of the surgical specimen and related to recurrence and death., Results: There were 54 recurrences (43.9%) and 75 deaths (60.9%). The mean tumor volume among the patients living without disease during the follow-up period was 28.2 cc, compared to 88.2 cc for patients living with disease, and to 78.9 cc for patients who died of the disease (p < .001). Multivariate analyses showed that volume and perineural invasion were independent factors for recurrence, whereas volume and lymph node metastasis were independent factors for death., Conclusion: Among patients who already have advanced cancers, tumor volume can significantly impact their prognoses. © 2017 Wiley Periodicals, Inc. Head Neck 39: 960-964, 2017., (© 2017 Wiley Periodicals, Inc.)