Miracle-dz/UniFAR-FTUs huggingface dataset:
The pseudokinase domains of guanylyl cyclase–A and –B allosterically increase the affinity of their catalytic domains for substrate

Pseudokinase domains in natriuretic peptide receptors promote receptor activation through a conserved allosteric mechanism. Allosteric regulation through pseudokinase domains Pseudokinase domains are similar to kinase domains, but they lack catalytic activity. Although many domains originally classified as pseudokinases were subsequently shown to have limited or context-dependent kinase activity, some act as scaffolds or allosteric regulators. The natriuretic peptide receptors GC-A and GC-B contain both pseudokinase and guanylyl cyclase domains. By combining homology modeling with biochemical analysis of mutant proteins, Edmund et al. found that the pseudokinase domains of GC-A and GC-B were allosteric regulators of the guanylyl cyclase domains. ATP bound to and stabilized the pseudokinase domain similarly to its stabilization of the active conformation of the prototypical kinase PKA. This, in turn, stimulated the receptors’ guanylyl cyclase activities. Thus, the pseudokinase domains of GC-A and GC-B promote the catalytic activity of these receptors through an allosteric mechanism that is conserved with catalytically active kinases. Natriuretic peptides regulate multiple physiologic systems by activating transmembrane receptors containing intracellular guanylyl cyclase domains, such as GC-A and GC-B, also known as Npr1 and Npr2, respectively. Both enzymes contain an intracellular, phosphorylated pseudokinase domain (PKD) critical for activation of the C-terminal cGMP-synthesizing guanylyl cyclase domain. Because ATP allosterically activates GC-A and GC-B, we investigated how ATP binding to the PKD influenced guanylyl cyclase activity. Molecular modeling indicated that all the residues of the ATP-binding site of the prototypical kinase PKA, except the catalytic aspartate, are conserved in the PKDs of GC-A and GC-B. Kinase-inactivating alanine substitutions for the invariant lysine in subdomain II or the aspartate in the DYG-loop of GC-A and GC-B failed to decrease enzyme phosphate content, consistent with the PKDs lacking kinase activity. In contrast, both mutations reduced enzyme activation by blocking the ability of ATP to decrease the Michaelis constant without affecting peptide-dependent activation. The analogous lysine-to-alanine substitution in a glutamate-substituted phosphomimetic mutant form of GC-B also reduced enzyme activity, consistent with ATP stimulating guanylyl cyclase activity through an allosteric, phosphorylation-independent mechanism. Mutations designed to rigidify the conserved regulatory or catalytic spines within the PKDs increased guanylyl cyclase activity, increased sensitivity to natriuretic peptide, or reduced the Michaelis constant in the absence of ATP, consistent with ATP binding stabilizing the PKD in a conformation analogous to that of catalytically active kinases. We conclude that allosteric mechanisms evolutionarily conserved in the PKDs promote the catalytic activation of transmembrane guanylyl cyclases.
Racial/Ethnic Differences in Lung Cancer Incidence in the Multiethnic Cohort Study: An Update.

Background We previously found that African Americans and Native Hawaiians were at highest lung cancer risk compared with Japanese Americans and Latinos; whites were midway in risk. These differences were more evident at relatively low levels of smoking intensity, fewer than 20 cigarettes per day (CPD), than at higher intensity. Methods We apportioned lung cancer risk into three parts: age-specific background risk (among never smokers), an excess relative risk term for cumulative smoking, and modifiers of the smoking effect: race and years-quit smoking. We also explored the effect of replacing self-reports of CPD with a urinary biomarker-total nicotine equivalents-using data from a urinary biomarker substudy. Results Total lung cancers increased from 1979 to 4993 compared to earlier analysis. Estimated excess relative risks for lung cancer due to smoking for 50 years at 10 CPD (25 pack-years) ranged from 21.9 (95% CI = 18.0 to 25.8) for Native Hawaiians to 8.0 (95% CI = 6.6 to 9.4) for Latinos over the five groups. The risk from smoking was higher for squamous cell carcinomas and small cell cancers than for adenocarcinomas. Racial differences consistent with earlier patterns were seen for overall cancer and for cancer subtypes. Adjusting for predicted total nicotine equivalents, Japanese Americans no longer exhibit a lower risk, and African Americans are no longer at higher risk, compared to whites. Striking risk differences between Native Hawaiians and Latinos persist. Conclusions Racial differences in lung cancer risk persist in the Multiethnic Cohort study that are not easily explained by variations in self-reported or urinary biomarker-measured smoking intensities.
Airway Smooth Muscle–Specific Transcriptomic Signatures of Glucocorticoid Exposure

Glucocorticoids, commonly used asthma controller medications, decrease symptoms in most patients, but some remain symptomatic despite high-dose treatment. The physiological basis underlying the glucocorticoid response, especially in asthma patients with severe, refractory disease, is not fully understood. We sought to identify differences between the transcriptomic response of airway smooth muscle (ASM) cells derived from donors with fatal asthma and donors without asthma to glucocorticoid exposure and to compare ASM-specific changes with those observed in other cell types. In cells derived from nine donors with fatal asthma and eight donors without asthma, RNA sequencing was used to measure ASM transcriptome changes after exposure to budesonide (100 nM 24 h) or control vehicle (DMSO). Differential expression results were obtained for this dataset, as well as 13 publicly available glucocorticoid-response transcriptomic datasets corresponding to seven cell types. Specific genes were differentially expressed in response to glucocorticoid exposure (7,835 and 6,957 in ASM cells derived from donors with fatal asthma and donors without asthma, respectively; adjusted P value < 0.05). Transcriptomic changes in response to glucocorticoid exposure were similar in ASM derived from donors with fatal asthma and donors without asthma, with enriched ontological pathways that included cytokine- and chemokine-related categories. A comparison of glucocorticoid-induced changes in the nonasthma ASM transcriptome with those observed in six other cell types showed that ASM has a distinct glucocorticoid-response signature that is also present in ASM cells from donors with fatal asthma.
Day-to-day friends' victimization, aggression perpetration, and morning cortisol activity in late adolescents.

This study investigates bidirectional associations between adolescents' daily experiences of victimization and aggression perpetration within friendships. We investigated (a) across-day associations between victimization and aggression perpetration; (b) morning cortisol activity as a moderator of cross-day victimization and aggression links; and (c) potential sex differences in these patterns. For 4 consecutive days, 99 adolescents (Mage = 18.06, SD = 1.09, 46 females) reported whether they were victimized by or aggressive toward their friends. On three of these days, adolescents provided three morning saliva samples. Multilevel path analyses showed that across days, victimization and aggression were bidirectionally linked, but only for male adolescents. Additionally, for male adolescents, morning cortisol output (but not morning cortisol increase) moderated the association between victimization and next-day aggression; victimization predicted greater next-day aggression for boys with low, but not high, morning cortisol output. Findings implicate a physiological factor that may modify daily links between victimization and aggression in male adolescent friendships.
Antimicrobial Microwebs of DNA–Histone Inspired from Neutrophil Extracellular Traps

Neutrophil extracellular traps (NETs) are decondensed chromatin networks released by neutrophils that can trap and kill pathogens but can also paradoxically promote biofilms. The mechanism of NET functions remains ambiguous, at least in part, due to their complex and variable compositions. To unravel the antimicrobial performance of NETs, a minimalistic NET‐like synthetic structure, termed “microwebs,” is produced by the sonochemical complexation of DNA and histone. The prepared microwebs have structural similarity to NETs at the nanometer to micrometer dimensions but with well‐defined molecular compositions. Microwebs prepared with different DNA to histone ratios show that microwebs trap pathogenic Escherichia coli in a manner similar to NETs when the zeta potential of the microwebs is positive. The DNA nanofiber networks and the bactericidal histone constituting the microwebs inhibit the growth of E. coli. Moreover, microwebs work synergistically with colistin sulfate, a common and a last‐resort antibiotic, by targeting the cell envelope of pathogenic bacteria. The synthesis of microwebs enables mechanistic studies not possible with NETs, and it opens new possibilities for constructing biomimetic bacterial microenvironments to better understand and predict physiological pathogen responses.
Identification of new regulators through transcriptome analysis that regulate anthocyanin biosynthesis in apple leaves at low temperatures

Anthocyanin pigments play many roles in plants, including providing protection against biotic and abiotic stresses. To identify new regulatory genes in apple (Malus domestica) that may be involved in regulating low temperature induced anthocyanin biosynthesis, we performed RNA-seq analysis of leaves from the ‘Gala’ apple cultivar following exposure to a low temperature (16 °C). A visible red color appeared on the upper leaves and the anthocyanin content increased significantly after the low temperature treatment. Genes from the flavonoid biosynthesis pathway were significantly enriched among the differentially expressed genes, and the expression of several transcription factors was shown by WGCNA (weighted gene co-expression network analysis) to correlate with anthocyanin accumulation, including members of the MYB, MADS, WRKY, WD40, Zinc Finger and HB-ZIP families. Three MYB transcription factors (MdMYB12, MdMYB22 and MdMYB114), which had several CBF/DREB response elements in their promoters, were significantly induced by low temperature exposure and their expression also correlated highly with anthocyanin accumulation. We hypothesize that they may act as regulators of anthocyanin biosynthesis and be regulated by CBF/DREB transcription factors in apple leaves under low temperature conditions. The analyses presented here provide insights into the molecular mechanisms underlying anthocyanin accumulation during low temperature exposure.
Highly variable vancomycin‐resistant enterococci in the north‐eastern part of the Czech Republic

Vancomycin‐resistant enterococci (VRE) are nosocomial pathogens of increasing medical importance. This study involved 121 VRE selectively obtained from a representative set of 1464 samples collected from various sources in the north‐eastern part of the Czech Republic. In total, 119 VRE belonged to Enterococcus faecium and two to Enterococcus faecalis. All isolates of E. faecium were resistant to at least three antibiotic classes. The resistance genes vanA, erm(B), tet(M), tet(L), aac(3)‐IIIa and aac(6′)‐aph(2′′) were detected. We assigned the E. faecium to sequence types ST5, ST18, ST38, ST64, ST92, ST273, ST549 and ST640. In E. faecium isolates, we identified the presence of replicases rep20pLG1, rep2pRE25, rep17pRUM, rep21pVEF1/2 and rep14pRI1, as well as relaxases relpEF1, relpLG1, relpCIZ2, relpRE25 and relpRUM. The presence of the toxin–antitoxin system axe–txe was detected mainly among isolates of hospital origin. The A and D types of transposon Tn1546 were those occurring most frequently.
Motivating landowners to recruit neighbors for private land conservation

Encouraging motivated landowners to not only engage in conservation action on their own property but also to recruit others may enhance effectiveness of conservation on private lands. Landowners may only engage in such recruitment if they believe their neighbors care about the conservation issue, will positively respond to their conservation efforts, and are likely to take action for the conservation cause. We designed a series of microinterventions that can be added to community meetings to change these beliefs to encourage landowner engagement in recruitment of others. The microinterventions included neighbor discussion, public commitment making, collective goal setting, and increased observability of contributions to the conservation cause. In a field experiment, we tested whether adding microinterventions to traditional knowledge‐transfer outreach meetings changed those beliefs so as to encourage landowners in Hawaii to recruit their neighbors for private lands conservation. We delivered a traditional outreach meeting about managing the invasive little fire ant (Wasmannia auropunctata) to 5 communities and a traditional outreach approach with added microinterventions to 5 other communities. Analysis of pre‐ and post‐surveys of residents showed that compared with the traditional conservation outreach approach, the microinterventions altered a subset of beliefs that landowners had about others. These microinterventions motivated reputationally minded landowners to recruit and coordinate with other residents to control the invasive fire ant across property boundaries. Our results suggest integration of these microinterventions into existing outreach approaches will encourage some landowners to facilitate collective conservation action across property boundaries.
Antimicrobial Activity of Six Essential Oils Against a Group of Human Pathogens: A Comparative Study

Essential oils are concentrated natural extracts derived from plants, which were proved to be good sources of bioactive compounds with antioxidative and antimicrobial properties. This study followed the effect of some commonly used essential oils in micellar and aqueous extract on some of the most common pathogenic bacteria. Frankincense, myrtle, thyme, lemon, oregano and lavender essential oils were tested against Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa. Both micellar and aqueous extracts were used for determination of their minimal inhibitory (MIC) and bactericidal concentrations (MBC). The most active oils were oregano, thyme, lemon and lavender, while the least active were frankincense and myrtle. Oregano oil presented up to 64 times lower MICs/MBCs than ethylic alcohol, if considered as standard, on all bacteria. Most susceptible bacteria were the Gram-positive cocci, including methicillin resistant S. aureus, while the most resistant was P. aeruginosa. With some exceptions, the best activity was achieved by micelles suspension of essential oils, with MICs and MBCs ranging from 0.1% to > 50% v/v. Only oregano and lavender aqueous extracts presented bactericidal activity and only on K. pneumoniae (MIC = 6.3%). Thyme, lemon and oregano oils present significantly lower overall average MICs for their micellar form than for their aqueous extracts. The present results may suggest some formulas of colloid or micelle suspensions of whole essential oils such as oregano, thyme or lemon oil, that may help in antimicrobial fight. Aqueous extracts of oregano or thyme oil with good antibacterial activity could also be used in selected cases.
Physical Activity and Sedentary Time: Association with Metabolic Health and Liver Fat

Introduction/Purpose To investigate whether (a) lower levels of daily physical activity (PA) and greater sedentary time accounted for contrasting metabolic phenotypes (higher liver fat/presence of metabolic syndrome [METS+] vs lower liver fat/absence of metabolic syndrome [METS−]) in individuals of similar body mass index and (b) the association of sedentary time on metabolic health and liver fat. Methods Ninety-eight habitually active participants (53 female, 45 male; age, 39 ± 13 yr; body mass index 26.9 ± 5.1 kg·m−2), underwent assessments of PA (SenseWear armband; wear time ~98%), cardiorespiratory fitness (V˙O2 peak), body composition (magnetic resonance imaging and magnetic resonance spectroscopy) and multiorgan insulin sensitivity (oral glucose tolerance test). We undertook a) cross-sectional analysis comparing four groups: nonobese or obese, with and without metabolic syndrome (METS+ vs METS−) and b) univariate and multivariate regression for sedentary time and other levels of PA in relation to liver fat. Results Light, moderate, and vigorous PA did not account for differences in metabolic health between individuals, whether nonobese or obese, although METS+ individuals were more sedentary, with a higher number, and prolonged bouts (~1–2 h). Overall, sedentary time, average daily METS and V˙O2 peak were each independently associated with liver fat percentage. Each additional hour of daily sedentary time was associated with a 1.15% (95% confidence interval, 1.14%–1.50%) higher liver fat content. Conclusions Greater sedentary time, independent of other levels of PA, is associated with being metabolically unhealthy; even in habitually active people, lesser sedentary time, and higher cardiorespiratory fitness and average daily METS is associated with lower liver fat.
BMP signaling is required for amphioxus tail regeneration

ABSTRACT Amphioxus, a cephalochordate, is an ideal animal in which to address questions about the evolution of regenerative ability and the mechanisms behind the invertebrate to vertebrate transition in chordates. However, the cellular and molecular basis of tail regeneration in amphioxus remains largely ill-defined. We confirmed that the tail regeneration of amphioxus Branchiostoma japonicum is a vertebrate-like epimorphosis process. We performed transcriptome analysis of tail regenerates, which provided many clues for exploring the mechanism of tail regeneration. Importantly, we showed that BMP2/4 and its related signaling pathway components are essential for the process of tail regeneration, revealing an evolutionarily conserved genetic regulatory system involved in regeneration in many metazoans. We serendipitously discovered that bmp2/4 expression is immediately inducible by general wounds and that expression of bmp2/4 can be regarded as a biomarker of wounds in amphioxus. Collectively, our results provide a framework for understanding the evolution and diversity of cellular and molecular events of tail regeneration in vertebrates. Summary: Cellular, transcriptome and gene functional analyses revealed that tail regeneration of amphioxus is a vertebrate-like epimorphic process, in which the BMP signaling pathway plays key roles.
Flirting with resistance: children’s expressions of autonomy during middle childhood

ABSTRACT Purpose: Developmental research suggests that children’s early non-compliance can be understood as “resistance”, an agentic response to parental control where children express their autonomy within a close relationship context. Research with toddlers and adolescents suggests that children’s resistance strategies can be differentiated using the dimensions of assertiveness, social skill, and overt versus covert expression. This study explores children’s strategies for expressing resistance during the neglected period of middle childhood. Method: Forty children, 9–13 years of age, participated for 1 week in a study focused on children’s experiences of socialization and parent–child relationships. Procedures included a 5-day event diary, and a 1-hour semi-structured interview about the rules and expectations in their home and their strategies of resistance. Results: Thematic analysis identified a rich repertoire of strategies for resisting unwelcome parental demands. These included overt resistance, such as negotiation, argument, and expressions of non-acceptance and covert resistance such as covert transgressions and cognitive non-acceptance of parental demands when compelled to comply. Conclusion: The findings were interpreted as reflecting children’s development of assertiveness and social skill as they expressed their autonomy in the interpersonal context of the interdependent but asymmetrical relationship with their parents.
Designing Online Interventions in Consideration of Young People’s Concepts of Well-Being: Exploratory Qualitative Study

Background A key challenge in developing online well-being interventions for young people is to ensure that they are based on theory and reflect adolescent concepts of well-being. Objective This exploratory qualitative study aimed to understand young people’s concepts of well-being in Australia. Methods Data were collected via workshops at five sites across rural and metropolitan sites with 37 young people from 15 to 21 years of age, inclusive. Inductive, data-driven coding was then used to analyze transcripts and artifacts (ie, written or image data). Results Young adults’ conceptions of well-being were diverse, personally contextualized, and shaped by ongoing individual experiences related to physical and mental health, along with ecological accounts acknowledging the role of family, community, and social factors. Key emerging themes were (1) positive emotions and enjoyable activities, (2) physical wellness, (3) relationships and social connectedness, (4) autonomy and control, (5) goals and purpose, (6) being engaged and challenged, and (7) self-esteem and confidence. Participants had no difficulty describing actions that led to positive well-being; however, they only considered their own well-being at times of stress. Conclusions In this study, young people appeared to think mostly about their well-being at times of stress. The challenge for online interventions is to encourage young people to monitor well-being prior to it becoming compromised. A more proactive focus that links the overall concept of well-being to everyday, concrete actions and activities young people engage in, and that encourages the creation of routine good habits, may lead to better outcomes from online well-being interventions.