bioRxiv ScienceSearch

Biology subjects

Fu, X.

Publications and source records attributed to Fu, X..

11 recordsLinked to original sources

Absence of GdX/UBL4A protects against inflammatory bowel diseases by regulating NF-κB signaling in DCs and macrophages

Nuclear factor-kappa B (NF-{kappa}B) activation is critical for innate immune responses. Here we report that the UBL4A (Ubiquitin-like protein 4A, also named GdX) enhances dendritic cells (DCs) and macrophages (M{varphi})-mediated innate immune defenses by positively regulating NF-{kappa}B signaling. GdX-deficient mice were resistant to LPS-induced endotoxin shock and DSS-induced colitis. DC- or M{varphi}-specific GdX-deficient mice displayed alleviated mucosal inflammation, and the production of pro-inflammatory cytokines by GdX-deficient DCs and M{varphi} was reduced. Mechanistically, we found that PTPN2 (TC45) and PP2A form a complex with RelA (p65) to mediate its dephosphorylation whereas GdX interrupts the TC45/PP2A/p65 complex formation and restrict p65 dephosphorylation by trapping TC45. Our study provides a mechanism by which NF-{kappa}B signaling is positively regulated by an adaptor protein GdX in DC or M{varphi} to maintain the innate immune response. Targeting GdX could be a strategy to reduce over-activated immune response in inflammatory diseases.

immunology

Structure of the ciliary axoneme at nanometer resolution reconstructed by TYGRESS

The resolution of subtomogram averages calculated from cryo-electron tomograms (cryo-ET) of crowded cellular environments is often limited due to signal loss in, and misalignment of the subtomograms. In contrast, single-particle cryo-electron microcopy (SP-cryo-EM) routinely reaches near-atomic resolution of isolated complexes. We developed a novel hybrid-method called \"TomographY-Guided 3D REconstruction of Subcellular Structures\" (TYGRESS) that combines cryo-ET with SP-cryo-EM to achieve close-to-nanometer resolution of complexes inside crowded environments. Using TYGRESS, we determined the native 3D structures of the intact ciliary axoneme with up to 12 [A] resolution. These results reveal many structures and details that were not visible by cryo-ET. TYGRESS is generally applicable to cellular complexes that are amenable to subtomogram averaging, bringing us a step closer to (pseudo-)atomic models of cells.\n\nOne Sentence SummaryA hybrid cryo-electron microscopy method reveals subcellular structures at unprecedented resolution.

cell biology

Mitogen-Activated Protein Kinase-Dependent Fiber-Type Regulation in Skeletal Muscle

Mitogen-activated protein kinases (MAPK) are conserved protein kinases that regulate a diverse array of cellular activities. Stress or mitogenic signals activate three primary branches of the greater MAPK cascade, each of which consists of a phosphorylation-dependent array of successively acting kinases. The extracellular signal-regulated kinase 1/2 (ERK1/2) branch is regulated by growth factory signaling at the cell membrane, leading to phosphorylation of the dual-specificity kinase MEK1, which is dedicated to ERK1/2 phosphorylation. Previous studies have established a link between MAPK activation and endurance exercise, but whether a single MAPK is responsible for establishing muscle metabolic fate is unclear. Using mouse genetics we observed that muscle-specific expression of a constitutively active MEK1 promotes greater ERK1/2 signaling that mediates fiber-type switching in mouse skeletal muscle to a slow, oxidative phenotype with type I myosin heavy chain expression. Induced expression of the activated MEK1 mutant using either a MyoD-Cre or myosin light chain-Cre strategy equally increased the number of type I fibers in skeletal muscle with significantly reduced size compared to controls. Moreover, activation of MEK1 in mature myofibers of an adult mouse using a transgene containing a tamoxifen inducible MerCreMer cDNA under the control of a skeletal -actin promoter produced a similar phenotype of switching towards a slow-oxidative program. Physiologic assessment of mice with greater skeletal muscle slow-oxidative fibers showed enhanced metabolic activity and oxygen consumption with greater fatigue resistance of individual muscles. In summary, these results show that sustained MEK1-ERK1/2 activity in skeletal muscle produces a fast-to-slow fiber-type switch, suggesting that modulation of this signaling pathway may represent a therapeutic approach to enhance the long-term metabolic effectiveness of muscle in vivo.

developmental biology

Astrocytes amplify neuronal dendritic volume transmission

In addition to their support role in neurotransmitter and ion buffering, astrocytes directly regulate neurotransmission at synapses via local bidirectional signaling with neurons. Here, we reveal a new form of neuronal-astrocytic signaling that transmits retrograde dendritic signals to upstream neurons to activate recurrent synaptic circuits. Norepinephrine activates 1-adrenoreceptors in hypothalamic corticotropin releasing factor (CRF) neurons to stimulate dendritic release, which triggers an astrocytic calcium response and release of ATP; ATP stimulates action potentials in upstream glutamate and GABA neurons to activate recurrent excitatory and inhibitory synaptic circuits to the CRF neurons. Thus, norepinephrine activates a novel retrograde signaling mechanism in CRF neurons that engages astrocytes in order to extend dendritic volume transmission to reach distal presynaptic glutamate and GABA neurons, thereby amplifying volume transmission mediated by dendritic release.

neuroscience

Hair regeneration by small molecules that activate autophagy

Hair plays important roles, ranging from the conservation of body heat to the preservation of psychological well-being. Hair loss or alopecia affects millions worldwide and can occur because of aging, hormonal dysfunction, autoimmunity, or as a side effect of cancer treatment (Gilhar et al., 2012; Petukhova et al., 2010). Methods that can be used to regrow hair are highly sought after, but lacking. Here we report that hair regeneration can be stimulated by small molecules that activate autophagy, including the longevity metabolites -ketoglutarate and -ketobutyrate, and the prescription drugs rapamycin and metformin which impinge on TOR and AMPK signaling.

developmental biology

Spatial Self-Organization Resolves Conflicts Between Individuality and Collective Migration

Collective behavior can spontaneously emerge when individuals follow common rules of interaction. However, the behavior of each individual will differ due to existing genetic and non-genetic variation within the population. It remains unclear how this individuality is managed to achieve collective behavior. We quantified individuality in bands of clonal Escherichia coli cells that migrate collectively along a channel by following a self-generated gradient of attractant. We discovered that despite substantial differences in individual chemotactic abilities, the cells are able to migrate as a coherent group by spontaneously sorting themselves within the moving band. This sorting mechanism ensures that differences between individual chemotactic abilities are compensated by differences in the local steepness of the traveling gradient each individual must navigate, and determines the minimum performance required to travel with the band. By resolving conflicts between individuality and collective migration, this mechanism enables populations to maintain advantageous diversity while on the move.

biophysics

Dissociable effects of prediction and integration during language comprehension: Evidence from a large-scale study using brain potentials

Composing sentence meaning is easier for predictable words than for unpredictable words. Are predictable words genuinely predicted, or simply more plausible and therefore easier to integrate with sentence context? We addressed this persistent and fundamental question using data from a recent, large-scale (N = 334) replication study, by investigating the effects of word predictability and sentence plausibility on the N400, the brains electrophysiological index of semantic processing. A spatiotemporally fine-grained mixed effects multiple regression analysis revealed overlapping effects of predictability and plausibility on the N400, albeit with distinct spatiotemporal profiles. Our results challenge the view that the predictability-dependent N400 reflects the effects of either prediction or integration, and suggest that semantic facilitation of predictable words arises from a cascade of processes that activate and integrate word meaning with context into a sentence-level meaning.

neuroscience

An internal sensor detects dietary amino acids and promotes food consumption in Drosophila

Adequate protein intake is crucial for animals. Despite the recent progress in understanding protein hunger and satiety in the fruit fly Drosophila melanogaster, how fruit flies assess prospective dietary protein sources and ensure protein consumption remains elusive. We show here that three specific amino acids, L-glutamate (L-Glu), L-alanine (L-Ala), and L-aspartate (L-Asp), rapidly promote food consumption in fruit flies when present in food. The effect of dietary amino acids to promote food consumption is independent of mating experience and internal nutritional status. Genetic analysis identifies six brain neurons expressing diuretic hormone 44 (DH44) as a sensor of dietary amino acids. DH44+ neurons can be directly activated by these three amino acids, and are both necessary and sufficient for dietary amino acids to promote food consumption. By conducting single cell RNAseq analysis, we also identify an amino acid transporter, CG13248, which is highly expressed in DH44+ neurons and is required for dietary amino acids to promote food consumption. Therefore, these data suggest that dietary amino acids may enter DH44+ neurons via CG13248 and modulate their activity and hence food consumption. Taken together, these data identify an internal amino acid sensor in the fly brain that evaluate food sources post-ingestively and facilitates adequate protein intake.

neuroscience

Sugar metabolism changes in response to the ultraviolet B irradiation of peach (Prunus persica L.)

The protected cultivation of peach (Prunuspersica L.) trees is more economical and efficient than traditional cultivation, resulting in increased farmers incomes, but the peach sugar contents are lower than in open planting. In the greenhouse, a high-sugar variety of peach Lumi 1 was irradiated with 1.44 KJ{middle dot}m-2.d-1 intensity ultraviolet B radiation. The soluble sugar contents in fruit, peel and leaf were quantified using liquid chromatography. Overall, sucrose and sorbitol increased before the second fruit-expansion period. To further understand the mechanisms regulating sucrose and sorbitol accumulation in peach fruit, expression profiles of genes involved in sugar metabolism and transport were measured. The activity and translocation protein contents of these enzymes were measured by enzyme-linked immunosorbent assay. The increased sucrose synthase activity and sucrose transporter level in the pericarp promoted the synthesis of sucrose and intake of sucrose into fruit. Sorbitol transport into fruit was promoted by the increased sorbitol transporter protein levels in leaves. In summary, greenhouse the sucrose and sorbitol contents were increased when supplemented with 1.44 kJ{middle dot}m-2{middle dot}d-1 ultraviolet B radiation before the second fruit-expansion period of peach.

plant biology

Limits on prediction in language comprehension: A multi-lab failure to replicate evidence for probabilistic pre-activation of phonology

In the last few decades, the idea that people routinely and implicitly predict upcoming words during language comprehension has turned from a controversial hypothesis to a widely-accepted assumption. Current theories of language comprehension1-3 posit prediction, or context-based pre-activation, as an essential mechanism occurring at all levels of linguistic representation (semantic, morpho-syntactic and phonological/orthographic) and facilitating the integration of words into the unfolding discourse representation. The strongest evidence to date for phonological pre-activation comes from DeLong, Urbach and Kutas4, who monitored participants electrophysiological brain responses as they read sentences, presented one word at a time, with expected/unexpected indefinite article + noun combinations like, \"The day was breezy so the boy went outside to fly a kite/an airplane\". The sentences varied expectations ( cloze probability) for a consonant- or vowel-initial noun, as determined in a sentence-completion task using other participants. Expectedly, the amplitude of the N400 event-related potential (ERP) decreased (became less negative) with increasing cloze reflecting ease of processing5-6. Whereas the decreased N400 at the noun could be due to its pre-activation or because high-cloze nouns are easier to integrate, crucially, N400s at the immediately-preceding article a or an showed the same relationship with cloze, i.e., encountering an indefinite article that mismatched a highly-expected word (e.g., an when expecting kite) also elicited a larger N400. This led to the claim that participants pre-activated highly-expected nouns, including their initial phonemes, based on the preceding context, with larger N400s on mismatching articles reflecting disconfirmation of this prediction.\n\nThe Delong et al. study warranted stronger conclusions than related results available at the time. Unlike previous work, it did not rely on the precursory visual-depiction of upcoming nouns, clearly de-confounded prediction and integration effects, and tested for graded phonological pre-activation of specific word form. Correspondingly, the study has been enthusiastically received as strong evidence for probabilistic phonological pre-activation, receiving over 650 citations to date and featuring in authoritative reviews2-3. However, there is good cause to question the soundness of the original finding (and the appropriateness of the analysis used). Attempts to replicate the critical article-effect have failed7. Moreover, an earlier, alternative analysis of the same data by the authors8 failed to reach statistical significance, but was omitted from the published report.\n\nTo obtain more definitive evidence, we conducted a direct replication study spanning 9 laboratories (Ntotal = 334). We pre-registered one replication analysis that was faithful to the original, and one single-trial analysis that modeled subject- and item-level variance using linear mixed-effects models. Applying the replication analysis to our article data (Figure 1a), the original finding did not replicate: no laboratory observed a significant negative relationship between cloze and N400 at central-parietal electrodes. In contrast, the negative relationship was successfully replicated for the nouns: 6 laboratories observed such an effect and 2 laboratories observed relatively strong but non-significant effects in the expected direction (range r = .30 to .50). In the single-trial analysis (Fig. 1b-c), there was no statistically significant effect of cloze on article-N400s, also with stricter control for pre-article voltage levels (Supplementary Fig. 1). Crucially, there was a strong and significant cloze effect on noun-N400s (in all laboratories), which was significantly different from that on article-N400s. We observed no significant differences between laboratories for article or noun effects. Exploratory Bayesian analyses with priors based on DeLong et al. further support our conclusions (Fig. 1d, Supplementary Fig. 2). Finally, a control experiment confirmed our participants sensitivity to the a/an rule during online language comprehension (Supplementary Fig. 3).\n\nO_FIG O_LINKSMALLFIG WIDTH=173 HEIGHT=200 SRC=\"FIGDIR/small/111807_fig1.gif\" ALT=\"Figure 1\">\nView larger version (72K):\norg.highwire.dtl.DTLVardef@1231330org.highwire.dtl.DTLVardef@1c0eb43org.highwire.dtl.DTLVardef@95a28forg.highwire.dtl.DTLVardef@1e38ee6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1C_FLOATNO A multi-lab failure to replicate evidence for probabilistic pre-activation of phonology. (a) Pre-registered replication analysis: Pearsons r correlations between ERP amplitude and article/noun cloze probability per EEG channel (* P < 0.05) and per laboratory. (b, c) Pre-registered single-trial analysis: (b) Grand-average ERPs elicited by relatively expected and unexpected words (cloze higher/lower than 50%) at electrode Cz, with standard deviation are shown in dotted lines, and (c) the relationship between cloze and N400 amplitude as illustrated by the mean ERP values per cloze value (number of observations reflected in circle size), along with the regression line and 95% confidence interval. A change in article cloze from 0 to 100 is associated with a change in amplitude of 0.296 {micro}V (95% confidence interval: -.08 to .67), {chi}2(1) = 2.31, p = .13. A change in noun-cloze from 0 to 100 is associated with a change in amplitude of 2.22 {micro}V (95% confidence interval: 1.75 to 2.69), {chi}2(1) = 56.5, p < .001. The effect of cloze on noun-N400s was statistically different from its effect on article-N400s, {chi}2(1) = 31.38, p < .001. (d) Bayes factor analysis associated with the replication analysis, quantifying the obtained evidence for the null hypothesis (H0) that N400 is not impacted by cloze, or for the alternative hypothesis (H1) that N400 is impacted by cloze with the size and direction of effect reported by DeLong et al. Scalp maps show the common logarithm of the replication Bayes factor for each electrode, capped at log(100) for presentation purposes. Electrodes that yielded at least moderate evidence for or against the null hypothesis (Bayes factor of [&ge;] 3) are marked by an asterisk. At posterior electrodes where DeLong et al. found their effects, our article data yielded strong to extremely strong evidence for the null hypothesis, whereas our noun data yielded extremely strong evidence for the alternative hypothesis (upper graphs). These results were also found when applying a 500 ms pre-word baseline correction (lower graphs).\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC=\"FIGDIR/small/111807_figS1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@bad459org.highwire.dtl.DTLVardef@1cb4d98org.highwire.dtl.DTLVardef@534676org.highwire.dtl.DTLVardef@1371c54_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 1.C_FLOATNO Exploratory single-trial analyses: The relationship between cloze and ERP amplitude as illustrated by the mean ERP values per cloze value (number of observations reflected in circle size), along with the regression line and 95% confidence interval, from four exploratory analyses. We performed tests which used longer baseline time windows (200 ms, upper left panel; 500 ms, upper right panel) to better control for pre-article voltage levels, or which used the pre-registered baseline and applied a 0.1 Hz high-pass filter (lower left panel) to better control for slow signal drift (while presumably not affecting N400 activity). All three tests reduced the initially observed effect of article-cloze (200 ms baseline, = .25, CI [-.12, .62], {chi}2(1) = 1.35, p = .19; 500 ms baseline, = .14, CI [-.25, .53], {chi}2(1) = 0.46, p = .50; 0.1 Hz filter: = 0.09, CI [-.22, .41], {chi}2(1) = 0.33, p = .56). An analysis in the 500 to 100 ms time window before article-onset (lower right panel) revealed a non-significant effect of cloze that resembled the pattern observed after article-onset, = .16, CI [-.07, .39], {chi}2(1) = 1.82, p = .18. Combined, these results suggest that the results obtained with the pre-registered analysis at least partly reflected the effects of slow signal drift that existed before the articles were presented.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC=\"FIGDIR/small/111807_figS2.gif\" ALT=\"Figure 2\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@124ffa2org.highwire.dtl.DTLVardef@af29aorg.highwire.dtl.DTLVardef@bd69d1org.highwire.dtl.DTLVardef@16e3b98_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 2.C_FLOATNO Results from exploratory Bayesian mixed-effects model analyses, represented by posterior distributions for the effect of cloze on ERP amplitudes in the N400 window. The x-axis shows cloze effect sizes (i.e., changes in microvolts associated with an increase from 0% cloze probability to 100% cloze probability). The black line indicates the posterior distribution of effects; higher values of the posterior density at a given effect size indicate higher probability that this is the true effect size in the population. The peak of the posterior distribution roughly corresponds to the point estimate of the effect size (the regression coefficient) fitted from the Bayesian mixed effect model, i.e., the most likely value of the true effect size. The middle 95% of the posterior distribution, shaded in pink, corresponds to a two-tailed 95% credible interval for the effect sizei.e., an interval that we can be 95% confident contains the true effect. The green dotted line indicates the prior distribution (i.e., our expectation about where the true effect would lie before the data were collected), which is centered on 1.25V, the effect observed by Delong and colleagues (2005). The black connected dots illustrate the ratio between the posterior and prior distribution (i.e., the Bayes Factor) at the effect size of 0V; for example, a Bayes Factor of 4 suggests we can be 4 times more certain that the true effect is zero after having conducted this experiment than before, or, in other words, that the data increased our confidence in the null effect of zero fourfold. We performed these analyses for each of the linear mixed-effects model analysis we performed. We note that in all the article-analyses, the posterior probability of the estimated effect being greater than zero is around 80 or 90%, but this is also the case for the pre-stimulus variable, suggesting that the observed patterns arise before the articles are seen. In none of our article-analyses did zero lie outside the obtained credible interval, whereas for the nouns, zero lay outside the credible interval. These results are consistent with a failure to replicate the DeLong et al. article-effect and successful replication of the noun-effect.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=133 HEIGHT=200 SRC=\"FIGDIR/small/111807_figS3.gif\" ALT=\"Figure 3\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@ab14forg.highwire.dtl.DTLVardef@1fed126org.highwire.dtl.DTLVardef@55369corg.highwire.dtl.DTLVardef@747668_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOSupplementary Figure 3.C_FLOATNO P600 effects at electrode Pz per lab associated with flouting of the English a/an rule in the control experiment. Plotted ERPs show the grand-average difference waveform and standard deviation for ERPs elicited by ungrammatical expressions (an kite) minus those elicited by grammatical expressions (a kite). This control experiment followed in the same experimental session as the main experiment and was carried to rule out that an observed lack of a statistically significant, article-elicited prediction effect in the main experiment reflected a general insensitivity of our participants to the a/an rule. In each laboratory, nouns following incorrect articles elicited a late positive-going waveform compared to nouns following correct articles, starting at about 500 ms after word onset and strongest at parietal electrodes. This standard P600 effect was confirmed in a single-trial analysis, {chi}2(1) = 83.09, p < .001, and did not significantly differ between labs, {chi}2(8) = 8.98, p = .35.\n\nC_FIG\n\nDespite a sample size 10 times larger than the original and improved statistical analysis, we observed no statistically significant effect of cloze on article-N400s, while replicating the strong and statistically significant effect of cloze on noun-N400s4,6. The effect of cloze on article-N400s, if existent, must be very small to evade detection given our expansive approach. Whether such an effect would constitute convincing evidence for routine phonological pre-activation as assumed in theories of language comprehension3 can be questioned, but, more generally, such an effect cannot be meaningfully studied in typical small-scale studies. Consequently, current theoretical positions may be based on potentially unreliable findings and require revision. In particular, the strong prediction view that claims that pre-activation routinely occurs across all - including phonological - levels3, can no longer be viewed as having strong empirical support.\n\nOur results do not constitute evidence against prediction in general. We note a lack of convincing evidence specifically for phonological pre-activation, which would have to be measured before a noun appears and unobscured by processes instigated by the noun itself.\n\nHowever, our results neither support nor necessarily exclude phonological pre-activation. Unlike gender-marked articles9 (e.g., in Dutch or Spanish) that agree with nouns irrespective of intervening words, English a/an articles index the subsequent word, which is not always a noun. Maybe our participants did not use mismatching articles to disconfirm predicted nouns, possibly because it was not a viable strategy (American and British English corpus data show a mere 33% chance that a noun follows such articles). Perhaps a revision of the predicted meaning is required to trigger differential ERPs.\n\nDeLong et al. recently described filler-sentences in their experiment10, cf. 7, which were omitted from their original report, and were neither provided nor mentioned to us upon our request for their stimuli. DeLong used the existence of these filler-sentences to dismiss an alternative explanation of their results, namely that an unusual experimental context wherein every sentence contains an article-noun combination leads participants to strategically predict upcoming nouns. Importantly, we failed to replicate their article-effects despite an experimental context that could inadvertently encourage strategic prediction. Therefore, the difference between their experiment and ours cannot explain the different results, and may even strengthen our conclusions.\n\nIn sum, our findings do not support a strong prediction view involving routine and probabilistic pre-activation of phonological word form based on preceding context.\n\nMoreover, our results further highlight the importance of direct replication, large sample size studies, transparent reporting and of pre-registration to advance reproducibility and replicability in the neurosciences.

neuroscience

PGC-1α coordinates with Bcl-2 to control cell cycle in U251 cells through reducing ROS

B-cell lymphoma 2 (Bcl-2) has a dual function, acting both as an oncogene and an anti-tumor gene. It is well known that Bcl-2 exerts its tumor promoting function through the mitochondrial pathway. However, the mechanism by which Bcl-2 suppresses tumor formation is not well understood. We have previously shown that Bcl-2 inhibits cell cycle progression from the G0/G1 to the S phase after serum starvation, and that quiescent Bcl-2 expressing cells maintained a significant lower level of mitochondrial reactive oxygen species (ROS) than the control cells. Based on the fact that ROS mediate cell cycle progression, and are controlled by peroxisome proliferator-activated receptor-{gamma} co-activator 1 (PGC-1), a key molecule induced by prolonged starvation and involved in mitochondrial metabolism, we hypothesized that PGC-1 might be related with the cell cycle function of Bcl-2. Here, we showed that PGC-1 was upregulated upon Bcl-2 overexpression and downregulated following Bcl-2 knockdown during serum starvation. Knockdown of PGC-1 activated Bcl-2 expression. Taken together, our results suggest that after serum depletion, PGC-la might coordinate with Bcl-2 to reduce ROS, which in turn delay cell cycle progression.\n\nSummary statementPGC-1 coordinate with Bcl-2 delay cell cycle progression to reduce ROS after serum depletion in human glioma U251 cells.

biochemistry