Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrin-Mediated Signaling Induced by Simian Virus 40 Leads to Transient Uncoupling of Cortical Actin and the Plasma Membrane

: Simian Virus 40 (SV40) is a paradigm pathogen with multivalent binding sites for the sphin-golipid GM1, via which it induces its endocytosis for infection. Here we report that SV40 also utilizes cell surface integrins to activate signaling networks required for infection, even in the absence of the previously implicated glycosphingolipids. We identify ILK, PDK1, the RhoGAP GRAF1 and RhoA as core nodes of the signaling network activated upon SV40 engagement of integrins. We show that integrin-mediated signaling through host SV40 engagement induces the de-phosphorylation of Ezrin leading to uncoupling of the plasma membrane and cortical actin. Our results provide functional evidence for a mechanism by which SV40 activates signal transduction in human epithelial cells via integrins in the context of clathrin-independent endocytosis. Abstract The methionine salvage pathway is widely distributed among some eubacteria, yeast, plants and animals and recycles the sulfur-containing metabolite 5-methylthioadenosine (MTA) to methionine. In eukaryotic cells, the methionine salvage pathway takes place in the cytosol and usually involves six enzymatic activities: MTA phosphorylase (MTAP, EC 2.4.2.28), 5 9 - methylthioribose-1-phosphate isomerase (mtnA, EC 5.3.1.23), 5 9 -methylthioribulose-1-phosphate dehydratase (mtnB, EC: 4.2.1.109), 2,3-dioxomethiopentane-1-phosphate enolase/phosphatase (mtnC, EC 3.1.3.77), aci-reductone dioxygenase (mtnD, EC 1.13.11.54) and 4-methylthio-2-oxo-butanoate (MTOB) transaminase (EC 2.6.1.-). The aim of this study was to complete the available information on the methionine salvage pathway in human by identifying the enzyme responsible for the dehydratase step. Using a bioinformatics approach, we propose that a protein called APIP could perform this role. The involvement of this protein in the methionine salvage pathway was investigated directly in HeLa cells by transient and stable short hairpin RNA interference. We show that APIP depletion specifically impaired the capacity of cells to grow in media where methionine is replaced by MTA. Using a Shigella mutant auxotroph for methionine, we confirm that the knockdown of APIP specifically affects the recycling of methionine. We also show that mutation of three potential phosphorylation sites does not affect APIP activity whereas mutation of the potential zinc binding site completely abrogates it. Finally, we show that the N-terminal region of APIP that is missing in the short isoform is required for activity. Together, these results confirm the involvement of APIP in the methionine salvage pathway, which plays a key role in many biological functions like cancer, apoptosis, microbial proliferation and inflammation.
Metabolic inhibition with cyanide induces intracellular calcium release in pulmonary artery myocytes and Xenopus oocytes

We examined the effects of metabolic inhibition on intracellular Ca release in single pulmonary arterial smooth muscle cells (PASMCs). Severe metabolic inhibition with cyanide (CN, 10 mM) increased [Ca]i and activated Ca-activated Cl currents (ICl(Ca)) in PASMCs, responses that were greatly inhibited by BAPTA/AM or caffeine. Mild metabolic inhibition with CN (1 mM) increased spontaneous transient inward currents and Ca sparks in PASMCs. In Xenopus oocytes CN also induced Ca release and activated ICl(Ca), and these responses were inhibited by thapsigargin and cyclopiazonic acid to deplete SR Ca, whereas neither heparin nor anti-IP3R antibodies affected CN responses. In both PASMCs and oocytes, cyanide –evoked Ca release was inhibited by carbonyl cyanide m-chlorophenylhydrazone (CCCP) and oligomycin or CCCP and thapsigargin. Whereas hypoxic stimuli resulted in Ca release in pulmonary but not mesenteric artery myocytes, CN induced release in both cell types. We conclude that metabolic inhibition with CN increases [Ca]i in both pulmonary and systemic artery myocytes by stimulating Ca release from the SR and mitochondria.
Iterative evolution of supergene-based social polymorphism in ants

Species commonly exhibit alternative morphs, with individual fate being determined during development by either genetic factors, environmental cues or a combination thereof. Ants offer an interesting case study because many species are polymorphic in their social structure. Some colonies contain one queen while others contain many queens. This variation in queen number is generally associated with a suite of phenotypic and life-history traits, including mode of colony founding, queen lifespan, queen–worker dimorphism and colony size. The basis of this social polymorphism has been studied in five ant lineages, and remarkably social morph seems to be determined by a supergene in all cases. These ‘social supergenes’ tend to be large, having formed through serial inversions, and to comprise hundreds of linked genes. They have persisted over long evolutionary timescales, in multiple lineages following speciation events, and have spread between closely related species via introgression. Their evolutionary dynamics are unusually complex, combining recessive lethality, spatially variable selection, selfish genetic elements and non-random mating. Here, we synthesize the five cases of supergene-based social polymorphism in ants, highlighting interesting commonalities, idiosyncrasies and implications for the evolution of polymorphisms in general. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
Genomic architecture and functional unit of mimicry supergene in female limited Batesian mimic Papilio butterflies

It has long been suggested that dimorphic female-limited Batesian mimicry of two closely related Papilio butterflies, Papilio memnon and Papilio polytes, is controlled by supergenes. Whole-genome sequencing, genome-wide association studies and functional analyses have recently identified mimicry supergenes, including the doublesex (dsx) gene. Although supergenes of both the species are composed of highly divergent regions between mimetic and non-mimetic alleles and are located at the same chromosomal locus, they show critical differences in genomic architecture, particularly with or without an inversion: P. polytes has an inversion, but P. memnon does not. This review introduces and compares the detailed genomic structure of mimicry supergenes in two Papilio species, including gene composition, repetitive sequence composition, breakpoint/boundary site structure, chromosomal inversion and linkage disequilibrium. Expression patterns and functional analyses of the respective genes within or flanking the supergene suggest that dsx and other genes are involved in mimetic traits. In addition, structural comparison of the corresponding region for the mimicry supergene among further Papilio species suggests three scenarios for the evolution of the mimicry supergene between the two Papilio species. The structural features revealed in the Papilio mimicry supergene provide insight into the formation, maintenance and evolution of supergenes. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
Genomic architecture and functional effects of potential human inversion supergenes

Supergenes are involved in adaptation in multiple organisms, but they are little known in humans. Genomic inversions are the most common mechanism of supergene generation and maintenance. Here, we review the information about two large inversions that are the best examples of potential human supergenes. In addition, we do an integrative analysis of the newest data to understand better their functional effects and underlying genetic changes. We have found that the highly divergent haplotypes of the 17q21.31 inversion of approximately 1.5 Mb have multiple phenotypic associations, with consistent effects in brain-related traits, red and white blood cells, lung function, male and female characteristics and disease risk. By combining gene expression and nucleotide variation data, we also analysed the molecular differences between haplotypes, including gene duplications, amino acid substitutions and regulatory changes, and identify CRHR1, KANLS1 and MAPT as good candidates to be responsible for these phenotypes. The situation is more complex for the 8p23.1 inversion, where there is no clear genetic differentiation. However, the inversion is associated with several related phenotypes and gene expression differences that could be linked to haplotypes specific of one orientation. Our work, therefore, contributes to the characterization of both exceptional variants and illustrates the important role of inversions. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
Genomic architecture of supergenes: connecting form and function

Supergenes are tightly linked sets of loci that are inherited together and control complex phenotypes. While classical supergenes—governing traits such as wing patterns in Heliconius butterflies or heterostyly in Primula—have been studied since the Modern Synthesis, we still understand very little about how they evolve and persist in nature. The genetic architecture of supergenes is a critical factor affecting their evolutionary fate, as it can change key parameters such as recombination rate and effective population size, potentially redirecting molecular evolution of the supergene in addition to the surrounding genomic region. To understand supergene evolution, we must link genomic architecture with evolutionary patterns and processes. This is now becoming possible with recent advances in sequencing technology and powerful forward computer simulations. The present theme issue brings together theoretical and empirical papers, as well as opinion and synthesis papers, which showcase the architectural diversity of supergenes and connect this to critical processes in supergene evolution, such as polymorphism maintenance and mutation accumulation. Here, we summarize those insights to highlight new ideas and methods that illuminate the path forward for the study of supergenes in nature. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’.
A Selective Defect of IFN-γ- But Not of IFN-α-Induced JAK/STAT Pathway in a Subset of U937 Clones Prevents the Antiretroviral Effect of IFN-γ Against HIV-1

IFN-γ induces transcription of several IFN-stimulated genes (ISGs). Recently, the IFN-γ-dependent Janus kinase (JAK)/STAT pathway has been shown to mediate the activation of some ISGs, by the sequential phosphorylation of two JAK kinases (JAK1 and JAK2) and of STAT1. Given that the JAK/STAT is the major, but not the only pathway linked to the IFN-γR, aim of our work was to investigate the signal-transduction pathway(s) by which IFN-γ exerts its effects on acute replication of HIV in monocytic cells. To this end, we utilized clones previously derived from the U937 promonocytic cell line, differing for their efficient (plus clones) or inefficient (minus clones) abilities of supporting HIV replication. Unlike IFN-α, IFN-γ did not inhibit HIV replication in plus clones, whereas virus production in minus cells was efficiently inhibited by both types of IFN. Plus clones generated a JAK/STAT signal-transduction pathway in response to IFN-α, but not IFN-γ. In contrast, minus clones responded to either cytokines. The functional defect of plus clones in response to IFN-γ was correlated to a selective defect of IFN-γR2, but not IFN-γR1, membrane expression. Surprisingly enough, IFN-γ stimulation of plus clones induced IFN-stimulated gene factor 3 (ISGF3γ). These results strongly support the hypothesis that the JAK/STAT pathway is responsible for the antiretroviral effect of IFN-γ, and further provide evidence for a potential second pathway triggered by IFN-γ in the absence of IFN-γR2 chain cell surface expression and involving ISGF3γ.
A preliminary study on the relationship between environmental endocrine disruptors and precocious puberty in girls

Abstract Objectives To explore the associations of environmental endocrine disruptors on precocious puberty in girls. Methods This was a case-control study in which 30 girls with precocious puberty and 46 age- and race-matched prepubertal females were enrolled. The concentrations of 10 environment endocrine disruptors (bisphenol A, bisphenol B, butylparaben, propylparaben, ethvlparaben, methylparaben, mono-butyl phthalate, mono-2-ethylhexyl phthalate, monoethyl phthalate, and monomethyl phthalate) in urine and 10 steroid hormones (dihydrotestosterone, corticosterone, hydrocortisone, 11-deoxycortisol, 17α-hydroxy progesterone, 4-androstene-3,17-dione, estrone, deoxycorticosterone, pregnenolone, and dehydroepiandrosterone) in serum were detected with the liquid chromatography-mass spectrometry (LC-MS). Results According to the Mann–Whitney U test, urinary levels of bisphenol A, monobutyl phthalate, and monomethyl phthalate were significantly higher in the precocious group than in the prepubertal group, and blood levels of hydrocortisone, 11-deoxycortisol, corticosterone, deoxycorticosterone, and pregnenolone were significantly lower in the precocious group than in the prepubertal group (p<0.05, VIP>1). Conclusions Our findings confirm the association between phthalate exposure and the incidence of precocious puberty in girls. Control and reduction of children exposure to phthalate esters should be considered as a health priority.
Prevalence of postpartum anaemia and iron deficiency by serum ferritin, soluble transferrin receptor and total body iron, and associations with ethnicity and clinical factors: a Norwegian population-based cohort study

Abstract Worldwide, there are limited data on the prevalence of postpartum anaemia and iron status. The aims of the present study were to assess the prevalence of anaemia and iron deficiency (ID) by three iron indicators 14 weeks postpartum, their relations to haemoglobin (Hb) and associations with ethnicity and clinical factors in a multi-ethnic population. We conducted a population-based cohort study of 573 women followed from early pregnancy. The prevalence of postpartum anaemia (Hb <12·0 g/dl) was 25 %. ID prevalence varied from 39 % by serum ferritin (SF <15 μg/l), to 19 % by soluble transferrin receptor (sTfR >4·4 mg/l) and 22 % by total body iron (TBI < 0 mg/kg). The mean Hb concentration was 12·8 g/dl in women with no ID, 12·6 g/dl in those with ID by SF only and 11·6 g/dl in those with ID by SF, sTfR and TBI. ID by sTfR and TBI defined by the current threshold values probably identified a more severe iron-deficient population compared with ID assessed by SF. Compared with Western Europeans, the prevalence of anaemia was at least the double in ethnic minorities (26–40 % v. 14 %; P < 0·01–0·05), and the prevalence of ID by sTfR and TBI, but not of ID by SF < 15 μg/l, was significantly higher in some minority groups. After adjustment for covariates, only South Asians had lower Hb and higher sTfR concentration. Insufficient iron intake, gestational anaemia or ID, and postpartum haemorrhage were associated with lower postpartum Hb concentration and poorer iron status.
Analysis of liquid column atomization by annular dual-nozzle gas jet flow

Abstract The atomization of a water column by a gas jet flow (Reynolds number $\sim O(10^{4}\unicode{x2013}10^{5})$) issued from a two-stage annular nozzle is investigated experimentally. Varying the nozzle geometry, the momentum flux ratio of the upper and lower jets, and the water flow rate, we measure the processes of atomization with high-speed imaging, analysed analytically into four regimes. In the bulk atomization regime, the atomization is driven by the lower jet, but it is forced to occur earlier by the stronger upper jet before the water column reaches the lower jet in the droplet atomization regime. Interestingly, the size of the atomized droplets remains unaffected by the momentum flux ratio of upper to lower jets. The atomization process is governed by the Rayleigh–Taylor instability, by which the estimated droplet size agrees well with the measurement. In the backflow regime, a strong reverse flow is induced to force a substantial portion of atomized droplets to be drawn backward to the nozzle; a floating liquid column regime is captured transitionally, i.e. the column stagnates near the lower nozzle when the water flow rate is very low. To understand the mechanisms of each regime, the single-phase jet flow is measured separately using particle image velocimetry, and implemented into the control volume analysis with which we predicted analytically and validated the conditions for the occurrence of each regime. It is found that the acceleration of gas flow (velocity gradient) experienced by the falling water is the key parameter to drive the atomization.
Developing soybean seed germination: low ABA and high EXP1 gene expression promote embryonic axis growth whereas the seed coat delays radicle protrusion

Abstract Seed germination implies an expansion process restarting the growth of the embryonic axis (Ax) and which is completed by radicle emergence through the seed covering layers. In developing soybean seeds, abscisic acid in Ax (ABAa) mainly inhibits Ax growth. Additionally, the expression of the EXP1 gene at the elongation zone (EZ) was found to be involved in the promotion of mature soybean Ax growth, which increased during water incubation and which was repressed by exogenous ABA. This work aimed to evaluate (1) the ABAa and EXP1 levels at the EZ and (2) the role of the seed coat (SC) in developing soybean seed germination. Whole seeds (Se), embryos (Em) and Ax at 25–45 d after anthesis (DAA) germinated in vitro, and germination performance increased with DAA. ABAa decreased in planta from 25 DAA until its critical non-inhibitory threshold (ABAc) at around physiological maturity (45 DAA). At earlier ages, the ABAc was reached during the in vitro incubation. Concomitantly, EXP1 transcripts accumulated with age into the pool of long-lived mRNAs and were up-regulated during incubation. Additionally, isolated Ax germinated faster, took up more water and increased its water potential more rapidly during incubation than Ax in Se. Also, a lower osmotic gradient was required to germinate at 45 DAA, when ABAa was no longer inhibitory. Simultaneously, the pressure to protrude SC through the micropylar area increased from 25 to 45 DAA. These results support the role of ABAa and EXP1 in controlling Ax growth and the SC in delaying radicle protrusion.
Turgor pressure change in stomatal guard cells arises from interactions between water influx and mechanical responses of their cell walls

Abstract Abstract The ability of plants to absorb CO2 for photosynthesis and transport water from root to shoot depends on the reversible swelling of guard cells that open stomatal pores in the epidermis. Despite decades of experimental and theoretical work, the biomechanical drivers of stomatal opening and closure are still not clearly defined. We combined mechanical principles with a growing body of knowledge concerning water flux across the plant cell membrane and the biomechanical properties of plant cell walls to quantitatively test the long-standing hypothesis that increasing turgor pressure resulting from water uptake drives guard cell expansion during stomatal opening. To test the alternative hypothesis that water influx is the main motive force underlying guard cell expansion, we developed a system dynamics model accounting for water influx. This approach connects stomatal kinetics to whole plant physiology by including values for water flux arising from water status in the plant .
Running title : Transcriptional targets of St BEL 5 1 2 3 4 5

1. Running title: Transcriptional targets of StBEL5 1 2 3 4 5 Pooja Sharma, Tian Lin, and David J. Hannapel* 6 7 8 9 Plant Biology Major, 253 Horticulture Hall 10 Iowa State University, Ames, IA 50011-1100 11 Fax: 515-294-0730 12 Voice: 515-294-9130 13 Email: djh@iastate.edu 14 15 16 17 18 * corresponding author 19 email: djh@iastate.edu 20 21 22 23 24 25 26 27 Plant Physiology Preview. Published on November 9, 2015, as DOI:10.1104/pp.15. 01314
NSS_A_301668 283..290

1Department of Physical Medicine and Rehabilitation, Chang Gung Memorial Hospital, Keelung, Taiwan; 2School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; 3Department of Physical Medicine and Rehabilitation, Chang Gung Memorial Hospital, Linkou, Taiwan; 4Graduate Institute of Early Intervention, College of Medicine, Chang Gung University, Taoyuan, Taiwan Background and Purpose: Obstructive sleep apnea (OSA) increases risk of stroke recurrence and mortality in ischemic stroke patients. However, equivocal treatment effects warrant further categorization of post-stroke OSA for risk stratification and individualized treatment planning. Methods: The study recruited 232 ischemic stroke patients with moderate-to-severe OSA admitted for inpatient rehabilitation consecutively. Latent class analysis was performed based on sex, age, smoking, daytime sleepiness, depression, obesity, sedative use, atrial fibrillation, diabetes, dyslipidemia, hypertension, recurrent stroke and dysphagia. The augmentation index, a marker of arterial stiffness, was measured by applanation tonometry. Results: A three-cluster model provided the best fit. Cluster 1 (n=84, 36.2%) was older in age, predominantly female, with the highest hypopnea index and prevalence of atrial fibrillation. Moreover, patients in Cluster 1 had significantly higher augmentation index than those in Cluster 2. Cluster 2 patients (N=80, 34.5%) were of older age, predominantly male, with the highest prevalence of depression, the lowest prevalence of hypertension and had the most normal body mass index (BMI). Additionally, Cluster 2 had less nocturnal hypoxia as compared to Cluster 3. Cluster 3 (n=68, 29.3%) was the youngest in age, predominantly male, with the highest BMI, cumulative risk score, and prevalence of dyslipidemia of the three clusters. Conclusion: Post-stroke OSA can be categorized into three clinical phenotypes. Patients in Clusters 1 and 3 both had elevated cardiovascular risk and treatment can be based on their distinct characteristics. Patients in Cluster 2 had relatively lower risk of cardiovascular events and the benefits of OSA treatment requires further study.
Austin of Nutrition and Food Effect of Pretreatments on Physical and Thermal Properties of Bael ( Aegle marmelos Correa) Fruit Pulp During Storage

The study was performed to evaluate the effect of pretreatment on various physical and thermal properties of Bael pulp. The fruit pulp of Bael fruit was extracted and TSS of the extracted pulp was raised to 25°Brix by adding 65°Brix sugar syrup. The pH of pulp was set at 3.0 and 3.5, which was heated at 80- 85°C for 15, 20 and 25 minutes and kept at refrigerated conditions for 80 days. The product was analyzed for TSS, pH, titratable acidity, colour values, thermal properties and yeast and mold counts during storage. The TSS, pH, titratable acidity, colour-L*, a*, b*, thermal conductivity and specific heat ranged between 18-25°Brix, 2.6-3.5, 0.15-0.35%, 20.32-56.87, 2.95-20.28, 23.58-64.01, 0.37- 0.76 w/m°C, 1.73-2.50 J/g°C respectively. The microbial load in terms of yeast and mold counts was also under the prescribed limits for 60 days under the refrigerated conditions. Minimum colour change and maximum sensory score was observed at 3 pH and 15 min heating under refrigerated storage. The zero or first order models were well fitted for the responses of the bael pulp (3 pH, 15 min) stored under refrigerated conditions.