Sequential window acquisition of all theoretical mass spectra (SWATH-MS) requires a spectral library to extract quantitative measurements from the mass spectrometry data acquired in data-independent acquisition mode (DIA). Large combined spectral libraries containing SWATH assays have been generated for humans and several other organisms, but so far no publicly available library exists for measuring the proteome of zebrafish, a rapidly emerging model system in biomedical research. Here, we present a large zebrafish SWATH spectral library to measure the abundance of 104,185 proteotypic peptides from 10,405 proteins. The library includes proteins expressed in 9 different zebrafish tissues (brain, eye, heart, intestine, liver, muscle, ovary, spleen, and testis) and provides an important new resource to quantify 40% of the protein-coding zebrafish genes. We employ this resource to quantify the proteome across brain, muscle, and liver and characterize divergent expression levels of paralogous proteins in different tissues. Data are available via ProteomeXchange (PXD010876, PXD010869) and SWATHAtlas (PASS01237).

Many bacteria take up carbohydrates by membrane-integral sugar specific phosphoenolpyruvate-dependent carbohydrate:phosphotransferase systems (PTS). Although the PTS is centrally involved in regulation of carbon metabolism in different bacteria, little is known about localization and putative oligomerization of the permease subunits (EII). Here, we analyzed localization of the fructose specific PtsF and the glucose specific PtsG transporters, as well as the general components EI and HPr from Corynebacterium glutamicum using widefield and single molecule localization microscopy. PtsF and PtsG form membrane embedded clusters that localize in a punctate pattern. Size, number and fluorescence of the membrane clusters change upon presence or absence of the transported substrate, and a direct influence of EI and HPr was not observed. In presence of the transport substrate, EII clusters significantly increased in size. Photo-activated localization microscopy data revealed that, in presence of different carbon sources, the number of EII proteins per cluster remains the same, however, the density of these clusters reduces. Our work reveals a simple mechanism for efficient membrane occupancy regulation. Clusters of PTS EII transporters are densely packed in absence of a suitable substrate. In presence of a transported substrate, the EII proteins in individual clusters occupy larger membrane areas.

Oxidative stress plays a vital role in the development of cerebral ischemic/reperfusion (I/R). Targeting oxidative stress is proposed to be an effective strategy to treat cerebral I/R injury. Gentiana macrophylla Pall is reported to have a potential protective effect against stroke. Swertiamarin (Swe), an active secoiridoid glycoside compound isolated from Gentiana macrophylla Pall, has been reported to possess antioxidative potential. This study is to explore whether Swe could prevent brain from I/R injury, and the related mechanisms of oxidative stress are also elucidated using mice middle cerebral artery occlusion (MCAO) model and primary hippocampal neurons oxygen-glucose deprivation/reperfusion (OGD/R) model. Swe (25, 100, or 400 mg/kg) was pretreated intraperitoneally for 7 days until establishment of the MCAO model, while hippocampal neurons were maintained in Swe (0.1, 1, or 10 μM) in the entire process of reoxygenation. The results indicated that Swe pretreatment markedly decreased infarct volume, apoptotic neurons, and oxidative damage and promoted neurologic recovery in vivo. It also decreased reactive oxygen species (ROS) and increased cell viability in vitro. Western blot analyses and immunofluorescence staining demonstrated that Swe pretreatment promoted Nrf2 nuclear translocation from Keap1-Nrf2 complex and enhanced the expressions of NAD(P)H: quinone oxidoreductase-1 (NQO1) and heme oxygenase-1 (HO-1) both in vivo and in vitro, while the expressions could be reversed by a Nrf2 inhibitor. The binding mode of Keap1 with Swe was also proposed by covalent molecular docking. Collectively, Swe could be considered as a promising protective agent against cerebral I/R injury through suppressing oxidative stress by activation of the Nrf2 protective pathway.

Toxoplasma gondii possesses a limited set of actin-regulatory proteins and relies on only three formins (FRMs) to nucleate and polymerize actin. We combined filamentous actin (F-actin) chromobodies with gene disruption to assign specific populations of actin filaments to individual formins. FRM2 localizes to the apical juxtanuclear region and participates in apicoplast inheritance. Restricted to the residual body, FRM3 maintains the intravacuolar cell-cell communication. Conoidal FRM1 initiates a flux of F-actin crucial for motility, invasion and egress. This flux depends on myosins A and H and is controlled by phosphorylation via PKG (protein kinase G) and CDPK1 (calcium-dependent protein kinase 1) and by methylation via AKMT (apical lysine methyltransferase). This flux is independent of microneme secretion and persists in the absence of the glideosome-associated connector (GAC). This study offers a coherent model of the key players controlling actin polymerization, stressing the importance of well-timed post-translational modifications to power parasite motility.

Science advances through rich, scholarly discussion. More than ever before, digital tools allow us to take that dialogue online. To chart a new future for open publishing, we must consider alternatives to the core features of the legacy print publishing system, such as an access paywall and editorial selection before publication. Although journals have their strengths, the traditional approach of selecting articles before publication ("curate first, publish second") forces a focus on "getting into the right journals," which can delay dissemination of scientific work, create opportunity costs for pushing science forward, and promote undesirable behaviors among scientists and the institutions that evaluate them. We believe that a "publish first, curate second" approach with the following features would be a strong alternative: authors decide when and what to publish; peer review reports are published, either anonymously or with attribution; and curation occurs after publication, incorporating community feedback and expert judgment to select articles for target audiences and to evaluate whether scientific work has stood the test of time. These proposed changes could optimize publishing practices for the digital age, emphasizing transparency, peer-mediated improvement, and post-publication appraisal of scientific articles.

Necrotic enteritis is an economically important poultry disease caused by the bacterium Clostridium perfringens. There are currently no necrotic enteritis vaccines commercially available for use in broiler birds, the most important target population. Salmonella-vectored vaccines represent a convenient and effective option for controlling this disease. We used a single attenuated Salmonella vaccine strain, engineered to lyse within the host, to deliver up to three C. perfringens antigens. Two of the antigens were toxoids, based on C. perfringens α-toxin and NetB toxin. The third antigen was fructose-1,6-bisphosphate aldolase (Fba), a metabolic enzyme with an unknown role in virulence. Oral immunization with a single Salmonella vaccine strain producing either Fba, α-toxoid and NetB toxoid, or all three antigens, was immunogenic, inducing serum, cellular and mucosal responses against Salmonella and the vectored C. perfringens antigens. All three vaccine strains were partially protective against virulent C. perfringens challenge. The strains delivering Fba only or all three antigens provided the best protection. We also demonstrate that both toxins and Fba are present on the C. perfringens cell surface. The presence of Fba on the cell surface suggests that Fba may function as an adhesin.

Risky sexual behaviors are associated with the transmission of sexually transmitted infections (STIs) and unwanted pregnancies, both major health concerns for youth worldwide. This review studies the effectiveness of narrated mass media programs in promoting safer sexual practices among youth in developed and developing countries.

The content and size of stone cell clusters affects the quality of pear fruit, and monolignol polymerization and deposition in the cell walls constitute a required step for stone cell formation. Laccase (LAC) is the key enzyme responsible for the polymerization of monolignols. However, there are no reports on the LAC family in pear (Pyrus bretschneideri), and the identity of the members responsible for lignin synthesis has not been clarified. Here, 41 LACs were identified in the whole genome of pear. All Pyrus bretschneideri LACs (PbLACs) were distributed on 13 chromosomes and divided into four phylogenetic groups (I-IV). In addition, 16 segmental duplication events were found, implying that segmental duplication was a primary reason for the expansion of the PbLAC family. LACs from the genomes of three Rosaceae species (Prunus mummer, Prunus persica, and Fragaria vesca) were also identified, and an interspecies collinearity analysis was performed. The phylogenetic analysis, sequence alignments and spatiotemporal expression pattern analysis suggested that PbLAC1, 5, 6, 29, 36 and 38 were likely associated with lignin synthesis and stone cell formation in fruit. The two target genes of Pyr-miR1890 (a microRNA identified from pear fruit that is associated with lignin and stone cell accumulation), PbLAC1 and PbLAC14, were selected for genetic transformation. Interfamily transfer of PbLAC1 into Arabidopsis resulted in a significant increase (approximately 17%) in the lignin content and thicker cell walls in interfascicular fibre and xylem cells, which demonstrated that PbLAC1 is involved in lignin biosynthesis and cell wall development. However, the lignin content and cell wall thickness were not changed significantly in the PbLAC14-overexpressing transgenic Arabidopsis plants. This study revealed the function of PbLAC1 in lignin synthesis and provides important insights into the characteristics and evolution of the PbLAC family.

Pictures of farm animals and their husbandry systems are frequently presented in the media and are mostly connected to discussions surrounding farm animal welfare. How such pictures are perceived by the broader public is not fully understood thus far. It is presumable that the animals' expressions and body languages as well as their depicted environment or husbandry systems affect public perception. Therefore, the aim of this study is to test how the evaluation of a picture showing a farmed pig is influenced by portrayed attributes, as well as participants' perceptions of pigs' abilities in general, and if connection to agriculture has an influence. In an online survey, 1,019 German residents were shown four modified pictures of a pig in a pen. The pictures varied with regards to facial expression and body language of the pig ('happy' versus 'unhappy' pig) and the barn setting (straw versus slatted floor pen). Respondents were asked to evaluate both the pen and the welfare of the pig. Two Linear Mixed Models were calculated to analyze effects on pig and pen evaluation. For the pictures, the pen had the largest influence on both pig and pen evaluation, followed by the pig's appearance and participants' beliefs in pigs' mental and emotional abilities, as well as their connection to agriculture. The welfare of both the 'happy' and the 'unhappy' pig was assessed to be higher in the straw setting compared to the slatted floor setting in our study, and even the 'unhappy pig' on straw was perceived more positively than the 'happy pig' on slatted floor. The straw pen was evaluated as being better than the slatted floor pen on the pictures we presented but the pens also differed in level of dirt on the walls (more dirt in the slatted floor pen), which might have influenced the results. Nevertheless, the results suggest that enduring aspects of pictures such as the husbandry system influence perceptions more than a momentary body expression of the pig, at least in the settings tested herein.

Glomerular filtration rate estimating equations using serum creatinine are not validated in most African settings. We compared serum creatinine and estimated glomerular filtration rate (eGFR) in HIV positive and negative adults and assessed the performance of eGFR equations ((Cockcroft and Gault (CG), Modification of Diet in Renal Disease (MDRD), and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI)) compared to 24-hour creatinine clearance in HIV positive adults.

Nine wild Iberian provenances of Castanea sativa Mill. grouped in two gene pools, North Iberian Peninsula and Mediterranean, were evaluated for several adaptive traits in two provenance-progeny trials with the aim of evaluating the role of natural selection in shaping adaptive variation and increasing our understanding of the genetic structure of this species, as well as reporting complete information on the genetic variation among and within the studied populations. An annual growth rhythm experiment was evaluated during the first 3 years after establishment for phenology, growth, stem form and survival, and a periodic drought-stress experiment was evaluated for dry weight, growth, survival and other related drought traits in both well-watered and drought-stress treatments. The high genetic variability reported in both trials is largely due to the genetic variation among populations. The significant differences reported between quantitative genetic and neutral marker differentiation indicated the local adaptation of these populations through directional selection, mainly for phenology, growth and biomass allocation. A clinal variation among populations was determined through correlations of phenology with latitude and xerothermic index of the provenances, showing that central and southern Mediterranean populations had earlier phenology than northern populations and that drought played a relevant role in this differentiation. The significant correlation between phenological traits and the ancestry values in the Mediterranean gene pool supported the different pattern of behavior between both gene pools and also indicated the existence of two ecotypes: xeric and mesophytic ecotypes, corresponding to Mediterranean and North Iberian gene pools, respectively. The results obtained in the drought-stress experiment confirmed that, in general terms, xeric populations showed a greater adaptability to drought, with more developed root systems and higher survival than northern populations. Moreover, the genetic variability observed within populations indicated the potential response capacity of Iberian C. sativa populations to undergo fast adaptive evolution.

To explore the experiences of patients at risk for cardiovascular disease in primary care with the Activate intervention in relation to their success in increasing their physical activity.

Worldwide, there is growing evidence that quality of international normalized ratio (INR) control in atrial fibrillation patients treated with Vitamin K Antagonists (VKA) is suboptimal. However, sex disparities in population-based real-world settings have been scarcely studied, as well as patterns of switching to second-line Non-VKA oral anticoagulants (NOAC). We aimed to assess the quality of INR control in atrial fibrillation patients treated with VKA in the region of Valencia, Spain, for the whole population and differencing by sex, and to identify factors associated with poor control. We also quantified switching to Non-VKA oral anticoagulants (NOAC) and we identified factors associated to switching.

Most indicators proposed for assessing quality of care in obstetrics are process indicators and do not directly measure health effects, and cannot always be identified from routinely available databases. Our objective was to propose a set of indicators to assess the quality of hospital obstetric care from maternal morbidity outcomes identifiable in permanent hospital discharge databases.

The etiologic relationship between wasting and stunting is poorly understood, largely because of a lack of high-quality longitudinal data from children at risk of undernutrition.

Activation of beta-1 adrenoreceptor (β1-AR) in the kidney releases renin that plays a major role in the maintenance of blood pressure. Genetic variation in β1-AR could therefore alter the physiological and clinical effects of this hormone. We tested this hypothesis in patients from a primary care cohort being screened for primary hyperaldosteronism (n = 467).

Mesenchymal stromal cells (MSCs) gradually become attractive candidates for cardiac inflammation modulation, yet understanding of the mechanism remains elusive. Strikingly, recent studies indicated that exosomes secreted by MSCs might be a novel mechanism for the beneficial effect of MSCs transplantation after myocardial infarction. We therefore explored the role of MSC-derived exosomes (MSC-Exo) in the immunomodulation of macrophages after myocardial ischaemia/reperfusion (I/R) and its implications in cardiac injury repair.

Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 targeting ancient chloroplast editing sites in flowering plants. Here, we report on alternative evolutionary pathways for DOT4 addressing rpoC1eU488SL, a chloroplast editing site in the RNA polymerase β' subunit mRNA. Upon loss of rpoC1eU488SL by C-to-T conversion, DOT4 got lost multiple times independently in angiosperm evolution with intermediate states of DOT4 orthologs in various stages of degeneration. Surprisingly, we now also observe degeneration and loss of DOT4 despite retention of a C in the editing position (in Carica, Coffea, Vicia, and Spirodela). We find that the cytidine remains unedited, proving that DOT4 was not replaced by another editing factor. Yet another pathway of DOT4 evolution is observed among the Poaceae. Although the rpoC1eU488SL edit has been lost through C-to-T conversion, DOT4 orthologs not only remain conserved but also have their array of PPRs extended by six additional repeats. Here, the loss of the ancient target has likely allowed DOT4 to adapt for a new function. We suggest rps3 antisense transcripts as previously demonstrated in barley (Hordeum vulgare) arising from promotor sequences newly emerging in the rpl16 intron of Poaceae as a new candidate target for the extended PPR stretch of DOT4. Altogether, DOT4 and its target show more flexible pathways for evolution than the previously explored editing factors CLB19, CRR28, and RARE1. Certain plant clades (e.g., Amaranthus, Vaccinium, Carica, the Poaceae, Fabales, and Caryophyllales) show pronounced dynamics in the evolution of editing sites and corresponding factors.

Genes acquired by horizontal gene transfer (HGT) may provide the recipient organism with potentially new functions, but proper expression level and integration of the transferred genes in the novel environment are not granted. Notably, transferred genes can differ from the receiving genome in codon usage preferences, leading to impaired translation and reduced functionality. Here, we characterize the genomic and proteomic changes undergone during experimental evolution of Escherichia coli after HGT of three synonymous versions, presenting very different codon usage preference, of an antibiotic resistance gene. The experimental evolution was conducted with and without the corresponding antibiotic and the mutational patterns and proteomic profiles after 1,000 generations largely depend on the experimental growth conditions (e.g., mutations in antibiotic off-target genes), and on the synonymous gene version transferred (e.g., mutations in genes responsive to translational stress). The transfer of an exogenous gene extensively modifies the whole proteome, and these proteomic changes are different for the different version of the transferred gene. Additionally, we identified conspicuous changes in global regulators and in intermediate metabolism, confirmed the evolutionary ratchet generated by mutations in DNA repair genes and highlighted the plasticity of bacterial genomes accumulating large and occasionally transient duplications. Our results support a central role of HGT in fuelling evolution as a powerful mechanism promoting rapid, often dramatic genotypic and phenotypic changes. The profound reshaping of the pre-existing geno/phenotype allows the recipient bacteria to explore new ways of functioning, far beyond the mere acquisition of a novel function.

The yeast Starmerella bombicola NBRC10243 is an excellent producer of sophorolipids, which are among the most useful biosurfactants. The primary alcoholic metabolic pathway of S. bombicola has been elucidated using alcohol oxidase FAO1, but the secondary alcohol metabolic pathway remains unknown. Although the FAO1 mutant was unable to grow with secondary alcohols and seemed to be involved in the secondary alcohol metabolism pathway of S. bombicola, it had very low activity toward secondary alcohols. By analyzing the products of secondary alcohol metabolism, alkyl polyglucosides hydroxylated at the ω position in the alkyl chain of the secondary alcohol were observed in the FAO1 mutant, but not in the wild-type yeast. In the double mutant of FAO1 and UGTA1, accumulation of 1,13-tetradecandiol and 2,13-tetradecandiol was observed. The above results indicated that hydroxylation occurred first at the ω and ω-1 positions in the secondary alcohol metabolism of S. bombicola, followed by primary alcohol oxidation.