KinasePhos is a novel web server for computationally identifying catalytic kinase-specific phosphorylation sites. The known phosphorylation sites from public domain data sources are categorized by ...their annotated protein kinases. Based on the profile hidden Markov model, computational models are learned from the kinase-specific groups of the phosphorylation sites. After evaluating the learned models, the model with highest accuracy was selected from each kinase-specific group, for use in a web-based prediction tool for identifying protein phosphorylation sites. Therefore, this work developed a kinase-specific phosphorylation site prediction tool with both high sensitivity and specificity. The prediction tool is freely available at http://KinasePhos.mbc.nctu.edu.tw/.
Disturbance of immunometabolic signaling is a key process involved in the progression of obesity. Microglia-the resident immune cells in the brain, initiate local immune responses. It is known that ...hypercaloric diets lead to microglial activation. Previously, we observed that hypothalamic microglial cells from mice fed high-fat diet (HFD) lose their day/night rhythm and are constantly activated. However, little is known about daily rhythmicity in microglial circadian, immune and metabolic functions, either in lean or obese conditions. Therefore, we hypothesized that HFD disturbs microglial immunometabolism in a day/night-dependent manner.
Obesity was induced in Wistar rats by feeding them HFD
for the duration of 8 weeks. Microglia were isolated from HFD- and chow-fed control animals at six time points during 24 h every 4 h starting 2 h after lights on, i.e., Zeitgeber Time 2 (ZT2). Gene expression was evaluated using quantitative RT-PCR. JTK_Cycle software was used to estimate daily rhythmicity. Statistical analysis was performed with two-way ANOVA test.
Consumption of the obesogenic diet resulted in a 40 g significantly higher body weight gain in week 8, compared to chow diet (
< 0.0001), associated with increased adiposity. We observed significant rhythmicity of circadian clock genes in microglia under chow conditions, which was partially lost in diet-induced obesity (DIO). Microglial immune gene expression also showed time-of-day differences, which were disrupted in HFD-fed animals. Microglia responded to the obesogenic conditions by a shift of substrate utilization with decreased glutamate and glucose metabolism in the active period of the animals, and an overall increase of lipid metabolism, as indicated by gene expression evaluation. Additionally, data on mitochondria bioenergetics and dynamics suggested an increased energy production in microglia during the inactive period on HFD. Finally, evaluation of monocyte functional gene expression showed small or absent effect of HFD on peripheral myeloid cells, suggesting a cell-specific microglial inflammatory response in DIO.
An obesogenic diet affects microglial immunometabolism in a time-of-day dependent manner. Given the central role of the brain in energy metabolism, a better knowledge of daily rhythms in microglial immunometabolism could lead to a better understanding of the pathogenesis of obesity.
Adoptive T cell immunotherapy is a promising treatment strategy for epithelial ovarian cancer (EOC). However, programmed death ligand-1 (PD-L1), highly expressed on EOC cells, interacts with ...programmed death-1 (PD-1), expressed on T cells, causing immunosuppression. This study aims to block PD-1/PD-L1 interactions by delivering PD-L1 siRNA, using various folic acid (FA)-functionalized polyethylenimine (PEI) polymers, to SKOV-3-Luc EOC cells, and investigate the sensitization of the EOC cells to T cell killing. To enhance siRNA uptake into EOC cells, which over express folate receptors, PEI is modified with FA or PEG-FA so that siRNA is complexed into nanoparticles with folate molecules on the surface. PEI modification with a single functional group lowers the polymer cytotoxicity compared to unmodified PEI. FA-conjugated polymers increase siRNA uptake into SKOV-3-luc cells and decrease unspecific uptake into monocytes. All polymers result in 40% to 50% PD-L1 protein knockdown. Importantly, SKOV-3-Luc cells treated with either PEI-FA or PEI- polyethylene glycol (PEG)-FA/PD-L1 siRNA complexes are up to twofold more sensitive to T cell killing compared to scrambled siRNA treated controls. These findings are the first to demonstrate that PD-L1 knockdown in EOC cells, via siRNA/FA-targeted delivery, are able to sensitize cancer cells to T cell killing.
Using polarized neutron reflectometry, we observe an induced magnetization of 75 ± 25 kA/m at 10 K in a La(0.7)Sr(0.3)MnO(3) (LSMO)/BiFeO(3) superlattice extending from the interface through several ...atomic layers of the BiFeO(3) (BFO). The induced magnetization in BFO is explained by density functional theory, where the size of band gap of BFO plays an important role. Considering a classical exchange field between the LSMO and BFO layers, we further show that magnetization is expected to extend throughout the BFO, which provides a theoretical explanation for the results of the neutron scattering experiment.
Phosphate (Pi) is an essential nutrient for plants but is normally fixed in soil, which limits plant growth and reproduction. In response to low availability of Pi, shoots and roots react differently ...but cooperatively to improve Pi acquisition from the rhizosphere and adjust Pi distribution and metabolism within plants. Shoot and root responses are coordinated by the trafficking of various kinds of systemic signals through the vasculature. Mutual communication between different tissues is necessary to integrate the environmental stimuli with the internal cues at the whole-plant level. Different approaches have been used to monitor or manipulate components in the vascular stream to reveal several candidates of systemic signals from roots or shoots, including photosynthates, phytohormones, microRNAs, and Pi. In addition, the downstream signalling pathways mediated by these signals have been discovered. The crosstalk among different signalling pathways has been revealed, showing the complexity of the Pi signalling network. In this review, we summarize the approaches used for studying systemic signalling and discuss recent progress and challenges in investigating the systemic signalling pathway that integrates Pi starvation responses to maintain Pi at physiological concentrations. Knowledge gained from this study may help improve the phosphorus use efficiency of crops.
Asymmetric implosion of inertial confinement fusion capsules is known, both experimentally and computationally, to reduce thermonuclear performance. This work shows that low-mode asymmetries degrade ...performance as a result of a decrease in the hydrodynamic disassembly time of the hot-spot core, which scales with the minimum dimension of the hot spot. The asymmetric shape of a hot spot results in decreased temperatures and areal densities and allows more alpha particles to escape, relative to an ideal spherical implosion, thus reducing alpha-energy deposition in the hot spot. Here, we extend previous ignition theory to include the hot-spot shape and quantify the effects of implosion asymmetry on both the ignition criterion and the capsule performance. The ignition criterion becomes more stringent with increasing deformation of the hot spot. The new theoretical results are validated by comparison with existing experimental data obtained at the National Ignition Facility. The shape effects on thermonuclear performance are relatively more noticeable for capsules having self-heating and high yields. The degradation of thermonuclear burn can be as high as 45% for shots with a yield lower than 2×10^{15} and less than 30% for shots with a higher yield.
Myocardial bridging is a congenital anomaly wherein a segment of a coronary artery passes under a ‘bridge’ of heart muscle rather than resting upon the heart’s surface. Although it is usually benign, ...myocardial bridging has been associated with adverse clinical events including ischaemia, arrhythmia and sudden death. Moreover, there is a tendency for atherosclerotic lesions to develop upstream of the bridge. These lesions may be the result of adverse fluid dynamic phenomena induced by the periodic compression of the artery by the overlying myocardial bridge. It is not possible to visualise these phenomena in vivo, and in this study we present an in vitro model capable of replicating the bridging conditions. This model is comprised of a pressure-measuring guide wire and catheter, a piston pump, a scaled artery model, and a ‘myocardial bridging mechanism’ which periodically compresses the artery model. A proportional-integral-derivative (PID) controller allowed the piston pump to recreate a patient-specific aortic pressure waveform upstream of the occluded artery model segment for each study. Stationary occlusions—achieved by placing 3D printed ‘stenosis inserts’ within the artery model—induced globally reduced pressures downstream of the stenosis when compared against the upstream pressure waveform. Conversely, the pressures downstream of the dynamic stenoses generated by the bridging mechanism closely matched the upstream pressures at all stages of the cardiac cycle except at the end of systole. This divergent pressure behaviour at the end of systole was similarly observed in vivo within a patient with a myocardial bridge. Flow visualisation using a laser sheet enabled dynamic flow structures to be observed, including recirculating flow regions, which may be precursors to arterial dysfunction.
Graphic abstract
Aim
To test the hypothesis that delayed menarche is associated with an increased microvascular complication risk among women with Type 1 diabetes.
Methods
We studied the female participants of an ...ongoing prospective study of childhood‐onset Type 1 diabetes diagnosed during the period 1950–1980. Of 325 women, we included data from 315 who had reached menarche by the study baseline (1986–1988) and who self‐reported their age at menarche. Both cross‐sectional and prospective analyses over the 25‐year follow‐up were used to assess the relationship of age at menarche with the prevalence, incidence and cumulative incidence of microvascular complications, comprising overt nephropathy, proliferative retinopathy and confirmed distal symmetric polyneuropathy.
Results
In cross‐sectional analyses at baseline, the odds of overt nephropathy increased 1.24 times (P=0.02) with each annual increase in age at menarche, and 3.2 times (P=0.009) in those with delayed menarche compared with women with normal menarche onset, after adjustment. Similarly, the cumulative incidence of overt nephropathy increased 1.16 times (P=0.01) with each older year of menarche and women with delayed menarche were at twofold increased risk of overt nephropathy (hazard ratio 2.30, P=0.001) compared with women with normal menarche onset. However, age at menarche was not significantly associated with either proliferative retinopathy or confirmed distal symmetric polyneuropathy after adjusting for covariates.
Conclusions
Age at menarche was significantly associated with the prevalence and cumulative incidence of overt nephropathy, but not with proliferative retinopathy or confirmed distal symmetric polyneuropathy in Type 1 diabetes. Women with delayed menarche may therefore be targeted for early screening and timely interventions to prevent the development of nephropathy.
What's new?
Delayed menarche is a common finding in women with Type 1 diabetes, but its association with microvascular complications has not been extensively studied.
In this prospective cohort of women with childhood‐onset Type 1 diabetes, age at menarche was significantly associated with both the prevalence and cumulative incidence of macroalbuminuria.
Age at menarche was, however, not associated with proliferative retinopathy or confirmed distal symmetric polyneuropathy.
Piwi proteins function in an RNAi‐like pathway that silences transposons. Piwi‐associated RNAs, also known as piRNAs, act as a guide to identify Piwi targets. The tudor domain‐containing protein ...Tdrd1 has been linked to this pathway but its function has thus far remained unclear. We show that zebrafish Tdrd1 is required for efficient Piwi‐pathway activity and proper nuage formation. Furthermore, we find that Tdrd1 binds both zebrafish Piwi proteins, Ziwi and Zili, and reveals sequence specificity in the interaction between Tdrd1 tudor domains and symmetrically dimethylated arginines (sDMAs) in Zili. Finally, we show that Tdrd1 complexes contain piRNAs and RNA molecules that are longer than piRNAs. We name these longer transcripts Tdrd1‐associated transcripts (TATs). TATs likely represent cleaved Piwi pathway targets and may serve as piRNA biogenesis intermediates. Altogether, our data suggest that Tdrd1 acts as a molecular scaffold for Piwi proteins, bound through specific tudor domain–sDMA interactions, piRNAs and piRNA targets.
In zebrafish the tudor domain protein, Tdrd1, functions as a scaffold binding PIWI proteins and indirectly Tdrd1‐associated transcripts (TATs), which likely represent cleaved Piwi pathway targets and piRNA biogenesis intermediates.
Inflammatory mediators that originate in vascular and extravascular tissues promote coronary lesion formation. Adipose tissue may function as an endocrine organ that contributes to an inflammatory ...burden in patients at risk of cardiovascular complications. In this study, we sought to compare expression of inflammatory mediators in epicardial and subcutaneous adipose stores in patients with critical CAD.
Paired samples of epicardial and subcutaneous adipose tissues were harvested at the outset of elective CABG surgery (n=42; age 65+/-10 years). Local expression of chemokine (monocyte chemotactic protein MCP-1) and inflammatory cytokines (interleukin IL-1beta, IL-6, and tumor necrosis factor TNF-alpha) was analyzed by TaqMan real-time reverse transcription-polymerase chain reaction (mRNA) and by ELISA (protein release over 3 hours). Significantly higher levels of IL-1beta, IL-6, MCP-1, and TNF-alpha mRNA and protein were observed in epicardial adipose stores. Proinflammatory properties of epicardial adipose tissue were noted irrespective of clinical variables (diabetes, body mass index, and chronic use of statins or ACE inhibitors/angiotensin II receptor blockers) or plasma concentrations of circulating biomarkers. In a subset of samples (n=11), global gene expression was explored by DNA microarray hybridization and confirmed the presence of a broad inflammatory reaction in epicardial adipose tissue in patients with coronary artery disease. The above findings were paralleled by the presence of inflammatory cell infiltrates in epicardial adipose stores.
Epicardial adipose tissue is a source of several inflammatory mediators in high-risk cardiac patients. Plasma inflammatory biomarkers may not adequately reflect local tissue inflammation. Current therapies do not appear to eliminate local inflammatory signals in epicardial adipose tissue.
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