XIST directly regulates X-linked and autosomal genes in naive human pluripotent cells.

X chromosome inactivation (XCI) serves as a paradigm for RNA-mediated regulation of gene expression, wherein the long non-coding RNA XIST spreads across the X chromosome in cis to mediate gene silencing chromosome-wide. In female naive human pluripotent stem cells (hPSCs), XIST is in a dispersed configuration, and XCI does not occur, raising questions about XIST's function. We found that XIST spreads across the X chromosome and induces dampening of X-linked gene expression in naive hPSCs. Surprisingly, XIST also targets specific autosomal regions, where it induces repressive chromatin changes and gene expression dampening. Thereby, XIST equalizes X-linked gene dosage between male and female cells while inducing differences in autosomes. The dispersed Xist configuration and autosomal localization also occur transiently during XCI initiation in mouse PSCs. Together, our study identifies XIST as the regulator of X chromosome dampening, uncovers an evolutionarily conserved trans-acting role of XIST/Xist, and reveals a correlation between XIST/Xist dispersal and autosomal targeting.

FAM120A couples SREBP-dependent transcription and splicing of lipogenesis enzymes downstream of mTORC1.

The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth that stimulates macromolecule synthesis through transcription, RNA processing, and post-translational modification of metabolic enzymes. However, the mechanisms of how mTORC1 orchestrates multiple steps of gene expression programs remain unclear. Here, we identify family with sequence similarity 120A (FAM120A) as a transcription co-activator that couples transcription and splicing of de novo lipid synthesis enzymes downstream of mTORC1-serine/arginine-rich protein kinase 2 (SRPK2) signaling. The mTORC1-activated SRPK2 phosphorylates splicing factor serine/arginine-rich splicing factor 1 (SRSF1), enhancing its binding to FAM120A. FAM120A directly interacts with a lipogenic transcription factor SREBP1 at active promoters, thereby bridging the newly transcribed lipogenic genes from RNA polymerase II to the SRSF1 and U1-70K-containing RNA-splicing machinery. This mTORC1-regulated, multi-protein complex promotes efficient splicing and stability of lipogenic transcripts, resulting in fatty acid synthesis and cancer cell proliferation. These results elucidate FAM120A as a critical transcription co-factor that connects mTORC1-dependent gene regulation programs for anabolic cell growth.

Inferring Stochastic Rates from Heterogeneous Snapshots of Particle Positions.

Many imaging techniques for biological systems-like fixation of cells coupled with fluorescence microscopy-provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. These snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.

Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain.

The hybridization kinetic of an oligonucleotide to its template is a fundamental step in many biological processes such as replication arrest, CRISPR recognition, DNA sequencing, DNA origami, etc. Although single kinetic descriptions exist for special cases of this problem, there are no simple general prediction schemes. In this work, we have measured experimentally, with no fluorescent labelling, the displacement of an oligonucleotide from its substrate in two situations: one corresponding to oligonucleotide binding/unbinding on ssDNA and one in which the oligonucleotide is displaced by the refolding of a dsDNA fork. In this second situation, the fork is expelling the oligonucleotide thus significantly reducing its residence time. To account for our data in these two situations, we have constructed a mathematical model, based on the known nearest neighbour dinucleotide free energies, and provided a good estimate of the residence times of different oligonucleotides (DNA, RNA, LNA) of various lengths in different experimental conditions (force, temperature, buffer conditions, presence of mismatches, etc.). This study provides a foundation for the dynamics of oligonucleotide displacement, a process of importance in numerous biological and bioengineering contexts.

Single-molecule mechanical identification and sequencing.

High-throughput, low-cost DNA sequencing has emerged as one of the challenges of the postgenomic era. Here we present the proof of concept for a single-molecule platform that allows DNA identification and sequencing. In contrast to most present methods, our scheme is not based on the detection of the fluorescent nucleotides but on DNA hairpin length. By pulling on magnetic beads tethered by a DNA hairpin to the surface, the molecule can be unzipped. In this open state it can hybridize with complementary oligonucleotides, which transiently block the hairpin rezipping when the pulling force is reduced. By measuring from the surface to the bead of a blocked hairpin, one can determine the position of the hybrid along the molecule with nearly single-base precision. Our approach can be used to identify a DNA fragment of known sequence in a mix of various fragments and to sequence an unknown DNA fragment by hybridization or ligation.

Collaborative coupling between polymerase and helicase for leading-strand synthesis.

Rapid and processive leading-strand DNA synthesis in the bacteriophage T4 system requires functional coupling between the helicase and the holoenzyme, consisting of the polymerase and trimeric clamp loaded by the clamp loader. We investigated the mechanism of this coupling on a DNA hairpin substrate manipulated by a magnetic trap. In stark contrast to the isolated enzymes, the coupled system synthesized DNA at the maximum rate without exhibiting fork regression or pauses. DNA synthesis and unwinding activities were coupled at low forces, but became uncoupled displaying separate activities at high forces or low dNTP concentration. We propose a collaborative model in which the helicase releases the fork regression pressure on the holoenzyme allowing it to adopt a processive polymerization conformation and the holoenzyme destabilizes the first few base pairs of the fork thereby increasing the efficiency of helicase unwinding. The model implies that both enzymes are localized at the fork, but does not require a specific interaction between them. The model quantitatively reproduces homologous and heterologous coupling results under various experimental conditions.

Mechanism of strand displacement synthesis by DNA replicative polymerases.

Replicative holoenzymes exhibit rapid and processive primer extension DNA synthesis, but inefficient strand displacement DNA synthesis. We investigated the bacteriophage T4 and T7 holoenzymes primer extension activity and strand displacement activity on a DNA hairpin substrate manipulated by a magnetic trap. Holoenzyme primer extension activity is moderately hindered by the applied force. In contrast, the strand displacement activity is strongly stimulated by the applied force; DNA polymerization is favoured at high force, while a processive exonuclease activity is triggered at low force. We propose that the DNA fork upstream of the holoenzyme generates a regression pressure which inhibits the polymerization-driven forward motion of the holoenzyme. The inhibition is generated by the distortion of the template strand within the polymerization active site thereby shifting the equilibrium to a DNA-protein exonuclease conformation. We conclude that stalling of the holoenzyme induced by the fork regression pressure is the basis for the inefficient strand displacement synthesis characteristic of replicative polymerases. The resulting processive exonuclease activity may be relevant in replisome disassembly to reset a stalled replication fork to a symmetrical situation. Our findings offer interesting applications for single-molecule DNA sequencing.

Protocol for building a user-friendly temperature control system to support microscopes, microfluidic chambers, and custom incubators.

Biological experiments require precise temperature control, necessitating an integrated adjustable temperature system for instruments such as microscopes, microfluidic chambers, or custom incubators. We present a protocol for building a user-friendly temperature control system suitable for both in vitro and in vivo assays. We describe steps for preparing materials, assembling the printed circuit board and enclosure, and fine-tuning the heating algorithm for accuracy. This system can maintain a stable temperature of up to 60°C with stabilities under 0.06°C.

Emergence of Neisseria gonorrhoeae Clone with Reduced Susceptibility to Sitafloxacin in China: An In Vitro and Genomic Study.

Drug-resistant Neisseria gonorrhoeae poses an urgent threat to public health. Recently, sitafloxacin, a new-generation fluoroquinolone, has shown high in vitro activity against drug-resistant N. gonorrhoeae. However, data on its effectiveness in clinical isolates remains limited. In this study, we collected 507 N. gonorrhoeae isolates from 21 hospitals in Shanghai, China, during 2020 and 2021. Antimicrobial susceptibility testing revealed that sitafloxacin minimum inhibitory concentrations (MICs) exhibited a bimodal distribution, ranging from <0.004 to 2 mg/L. The MIC50 and MIC90 for sitafloxacin were 0.125 mg/L and 0.5 mg/L, respectively, which are 32 and 16 times lower than those for ciprofloxacin (4 mg/L and 8 mg/L, respectively). Sitafloxacin demonstrated high in vitro activity against isolates resistant to either ceftriaxone, azithromycin, or both. Notably, among the isolates with reduced sitafloxacin susceptibility (MIC ≥ MIC90), 83.7% (36/43) were identified as sequence type (ST) 8123. Further phylogenetic analysis showed that ST8123 has evolved into two subclades, designated as subclade-I and subclade-II. A majority of the isolates (80%, 36/45) within subclade-I exhibited reduced susceptibility to sitafloxacin. In contrast, all isolates from subclade-II were found to be susceptible to sitafloxacin. Subsequent genomic investigations revealed that the GyrA-S91F, D95Y, and ParC-S87N mutations, which were exclusively found in ST8123 subclade-I, might be linked to reduced sitafloxacin susceptibility. Our study reveals that sitafloxacin is a promising antibiotic for combating drug-resistant N. gonorrhoeae. However, caution is advised in the clinical application of sitafloxacin for treating N. gonorrhoeae infections due to the emergence of a clone exhibiting reduced susceptibility.

Transcutaneous auricular vagus nerve stimulation enhanced emotional inhibitory control via increasing intrinsic prefrontal couplings.

Background: Inhibitory control represents a core executive function that critically facilitates adaptive behavior and survival in an ever-changing environment. Non-invasive transcutaneous auricular vagus nerve stimulation (taVNS) has been hypothesized to improve behavioral inhibition performance, however the neurocomputational mechanism of taVNS-induced neuroenhancement remains elusive. Method: In the current study, we investigated the efficacy of taVNS in a sham-controlled between-subject functional near infrared spectroscopy (fNIRS) experiment with an emotional face Go/No-Go paradigm in ninety healthy young adults. Results: After a data quality check, eighty-two subjects were included in the final data analysis. Behaviorally, the taVNS improved No-Go response accuracy, together with computational modeling using Hierarchical Bayesian estimation of the Drift Diffusion Model (HDDM) indicating that it specifically reduced the information accumulation rate for Go responses, and this was negatively associated with increased accuracy of No-Go responses. On the neural level, taVNS enhanced engagement of the bilateral inferior frontal gyrus (IFG) during inhibition of angry expression faces and modulated functional couplings (FCs) within the prefrontal inhibitory control network. Mediation models revealed that taVNS-induced facilitation of inhibitory control was critically mediated by a decreased information accumulation for Go responses and concomitantly enhanced neurofunctional coupling between the inferior and orbital frontal cortex. Discussion: Our findings demonstrate a potential for taVNS to improve emotional inhibitory control via reducing pre-potent responses and enhancing FCs within prefrontal inhibitory control networks, suggesting a promising therapeutic role in treating specific disorders characterized by inhibitory control deficits.

Inferring stochastic rates from heterogeneous snapshots of particle positions.

Many imaging techniques for biological systems - like fixation of cells coupled with fluorescence microscopy - provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics they intend to capture. These snapshot observations contain no information about individual trajectories, but still encode information about movement and demographic dynamics, especially when combined with a well-motivated biophysical model. The relationship between spatially evolving populations and single-moment representations of their collective locations is well-established with partial differential equations (PDEs) and their inverse problems. However, experimental data is commonly a set of locations whose number is insufficient to approximate a continuous-in-space PDE solution. Here, motivated by popular subcellular imaging data of gene expression, we embrace the stochastic nature of the data and investigate the mathematical foundations of parametrically inferring demographic rates from snapshots of particles undergoing birth, diffusion, and death in a nuclear or cellular domain. Toward inference, we rigorously derive a connection between individual particle paths and their presentation as a Poisson spatial process. Using this framework, we investigate the properties of the resulting inverse problem and study factors that affect quality of inference. One pervasive feature of this experimental regime is the presence of cell-to-cell heterogeneity. Rather than being a hindrance, we show that cell-to-cell geometric heterogeneity can increase the quality of inference on dynamics for certain parameter regimes. Altogether, the results serve as a basis for more detailed investigations of subcellular spatial patterns of RNA molecules and other stochastically evolving populations that can only be observed for single instants in their time evolution.

Cost-efficient boundary-free surface patterning achieves high effective-throughput of time-lapse microscopy experiments.

Time-lapse microscopy plays critical roles in the studies of cellular dynamics. However, setting up a time-lapse movie experiments is not only laborious but also with low output, mainly due to the cell-losing problem (i.e., cells moving out of limited field of view), especially in a long-time recording. To overcome this issue, we have designed a cost-efficient way that enables cell patterning on the imaging surfaces without any physical boundaries. Using mouse embryonic stem cells as an example system, we have demonstrated that our boundary-free patterned surface solves the cell-losing problem without disturbing their cellular phenotype. Statistically, the presented system increases the effective-throughput of time-lapse microscopy experiments by an order of magnitude.

The protective role of parental involvement at home in negative psychological outcomes among Chinese adolescents during the COVID-19 epidemic.

BACKGROUND: The COVID-19 outbreak has generated many negative psychological outcomes, such as depression, in adolescents. Exploration of protective factors for adolescent mental health is urgently needed, and no research has examined the role of parental involvement. METHODS: From March to April 2020, valid data were collected from 1663 Chinese adolescents through online demographic and other questionnaires. Parental involvement at home was assessed by an adapted questionnaire on parental support in learning at home, stress since the COVID-19 outbreak was measured by the Perceived Stress Scale, and three negative psychological outcomes (i.e., depression, anxiety, and posttraumatic stress symptoms (PTSS)) were measured by the Center for Epidemiologic Studies Depression Scale, Zung Self-rating Anxiety Scale, and PTSD Check List-Civilian Version, respectively. RESULTS: In total, 35.4%, 21% and 25% of adolescents had depression symptoms, anxiety symptoms, and PTSS, respectively. Three moderated mediation models consistently showed the following: a. Parental involvement indirectly reduced the three psychological problems by alleviating perceived stress, and the indirect effects were not moderated by sex. b. There were negative direct effects of parental involvement on the three psychological problems, and the links were not moderated by sex. c. Sex moderated the associations between perceived stress and the three psychological problems. LIMITATIONS: The cross-sectional design and the sampling of all participants from one junior high school impeded causal inferences and the generalization of our findings, respectively. CONCLUSIONS: We found similar indirect and direct protective roles of parental involvement in boys' and girls' mental health, and girls were more vulnerable to stress.

Dynamics and functional roles of splicing factor autoregulation.

Non-core spliceosome components are essential, conserved regulators of alternative splicing. They provide concentration-dependent control of diverse pre-mRNAs. Many splicing factors direct unproductive splicing of their own pre-mRNAs through negative autoregulation. However, the impact of such feedback loops on splicing dynamics at the single-cell level remains unclear. Here, we developed a system to quantitatively analyze negative autoregulatory splicing dynamics by splicing factor SRSF1 in response to perturbations in single HEK293 cells. We show that negative autoregulatory splicing provides critical functions for gene regulation, establishing a ceiling of SRSF1 protein concentration, reducing cell-cell heterogeneity in SRSF1 levels, and buffering variation in transcription. Most important, it adapts SRSF1 splicing activity to variations in demand from other pre-mRNA substrates. A minimal mathematical model of autoregulatory splicing explains these experimentally observed features and provides values for effective biochemical parameters. These results reveal the unique functional roles that splicing negative autoregulation plays in homeostatically regulating transcriptional programs.

Psychological suzhi moderates state anxiety and heart rate responses to acute stress in male adolescents.

Psychological suzhi has increasingly been recognized to buffer chronic stress and improve mental health. However, few studies have examined the role of psychological suzhi in the response to acute stress. The current study aimed to investigate whether psychological suzhi can buffer state anxiety and heart rate responses to acute stress in adolescents. Healthy male adolescents (N = 63) were classified into high (N = 30) or low (N = 33) psychological suzhi groups based on the Chinese norm of adolescent psychological suzhi scale-simplified version. They completed both the modified Trier Social Stress Test for Groups and a specific control condition, with heart rate and state anxiety assessed. Data were analysed with mixed-design repeated measures analysis of variance. The results showed that the modified Trier Social Stress Test for Groups condition effectively induced an increase in state anxiety and heart rate. Furthermore, individuals with higher levels of psychological suzhi showed lower state anxiety and heart rate stress responses. The present study indicated that psychological suzhi is an important internal resource against acute stress, which may inform interventions for male adolescents exposed to acute stress.

Transcutaneous auricular vagus nerve stimulation increases eye-gaze on salient facial features and oxytocin release.

Non-invasive, transcutaneous electrical stimulation of the auricular branch of the vagus nerve (taVNS) via the ear is used therapeutically in epilepsy, pain, and depression, and may also have beneficial effects on social cognition. However, the underlying mechanisms of taVNS are unclear and evidence regarding its role in social cognition improvement is limited. To investigate the impact of taVNS on social cognition we have studied its effects on gaze toward emotional faces in combination with eye-tracking and on the release of the neuropeptide oxytocin which plays a key role in influencing social cognition and motivation. A total of 54 subjects were enrolled (49 were included in the final analysis) in a sham-controlled, participant-blind, crossover experiment, consisting of two treatment sessions 1 week apart. In one session participants received 30-min taVNS (tragus), and in the other, they received 30-min sham (earlobe) stimulation with the treatment order counterbalanced. The proportion of time spent viewing the faces and facial features (eyes, nose, and mouth) was measured together with resting pupil size. Additionally, saliva samples were taken for the measurement of oxytocin concentrations by enzyme-linked immunoassay. Saliva oxytocin concentrations increased significantly after taVNS compared to sham stimulation, while resting pupil size did not. In addition, taVNS increased time spent viewing the nose region irrespective of face emotion, and this was positively correlated with increased saliva oxytocin concentrations. Our findings suggest that taVNS biases visual attention toward socially salient facial features across different emotions and this is associated with its effects on increasing endogenous oxytocin release.

Daily Stress and Behavioral Problems in Chinese Children: The Moderating Roles of Family Functioning and the Classroom Environment.

Grounded in the stress-coping model, our study examined family functioning and the classroom environment as protective factors in the relationship between daily stress and behavioral problems in Chinese children. The participants were 1,450 children (51.7% male, M age = 10.91 years, SD = 0.96) in the fourth, fifth, and sixth grades at five schools. The children completed the questionnaires measuring daily stress, family functioning, and the classroom environment. Additionally, their parents rated their behavioral problems. The latent moderated structural (LMS) equation approach was used to test moderator effects. After controlling for sex and grade, our results indicate that daily stress positively predicted the children's behavioral problems. Both family functioning and the classroom environment moderated the relationship between daily stress and behavioral problems. Further assessment of latent interaction effects indicate that buffering effects on behavioral problems were most prominent in conditions involving low stress. In sum, families and schools should not ignore children's minor stressors, as interventions involving family functioning and favorable classroom environments may help to reduce behavioral problems in children who report low levels of daily stress.

Protease Biosensor by Conversion of a Homogeneous Assay into a Surface-Tethered Electrochemical Analysis Based on Streptavidin-Biotin Interactions.

This work proposed a new sensing strategy for protease detection by converting a homogeneous assay into a surface-tethered electrochemical analysis. Streptavidin (SA), a tetramer protein, was used as the sensing unit based on the SA-biotin coupling chemistry. Caspase-3 was used as the model analyte, and a biotinylated peptide with a sequence of biotin-GDEVDGK-biotin was designed as the substrate. Specifically, the peptide substrate could induce an assembly of SA to form (SA-biotin-GDEVDGK-biotin)n aggregates through SA-biotin interactions, which was confirmed by atomic force microscopy (AFM). The peptide substrate-induced assembly of SA was facilely initiated on an electrode-liquid surface by modification of the electrode with SA. The in situ formation of (SA-biotin-GDEVDGK-biotin)n aggregates created an insulating layer, thus limiting the electron transfer of ferricyanide. Once the peptide substrate was cleaved into two shorter fragments (biotin-GDEVD and GK-biotin) by caspase-3, the resulting products would compete with biotin-GDEVDGK-biotin to bind SA proteins immobilized on the electrode surface and distributed in a solution, thus preventing the in situ formation of (SA-biotin-GDEVDGK-biotin)n assemblies. With the simple principle of the substrate-induced assembly of SA, a dual-signal amplification was achieved with improved sensitivity. Taking advantage of high sensitivity, simple principle, and easy operation, this method can be augmented to design various surface-tethered biosensors for practical applications.

Secure Attachment Priming Amplifies Approach Motivation for Infant Faces Among Childless Adults.

Existing studies have indicated that priming secure attachment alters adults' neural responses to infant faces. However, no study has examined whether this effect exists for motivational behavioral responses, and none of the previous studies included adult faces as a baseline to determine whether the security prime enhances responses to human faces in general or infant faces alone. To address this limitation, the current study recruited 160 unmarried and childless adults in the first phase, and all of them completed a battery of questionnaires, including the Interest in Infants, the Experiences in Close Relationships (ECR), and State Adult Attachment Measure (SAAM). A week later, after priming, 152 (76 security-primed vs. 76 neutrally primed) participants completed the SAAM and a behavioral program assessing their motivational responses to both adult and infant faces (i.e., liking, representational, and evoked responses). A manipulation check showed that the security prime was effective. Then, generalized linear mixed-effects models (GLMMs) showed that security priming enhances adults' liking, representational, and evoked responses (three components of the motivational system) only to infant faces and not to adult faces. Moreover, hierarchical regression analysis indicated that, even after security priming, there was a substantial linear relationship between positive motivation toward infant faces and the state of adult secure attachment. In summary, this study demonstrated for the first time that promoting the state of adult secure attachment can effectively enhance the effect size of the baby face schema. The current results were interpreted according to Bowlby's view of the attachment behavioral system.

The role of sex and femininity in preferences for unfamiliar infants among Chinese adults.

Guided by parental investment theory and social role theory, this study aimed to understand current contradictory results regarding sex differences in response to infant faces by considering the effect of gender role orientation. We recruited 300 adults in China and asked them to complete an Interest in Infants questionnaire and a Bem Sex Role Inventory and then administered a behavioral assessment that used unfamiliar infant faces with varying expressions (laughing, neutral, and crying) as stimuli to gauge three components of motivation towards infants (i.e., liking, representational responding, and evoked responding). The results demonstrated that sex differences emerged only in self-reported interest in infants, but no difference was found between the sexes in terms of their hedonic reactions to infant faces. Furthermore, femininity was found to correlate with preferences for infants in both verbal and visual tests, but significant interactive effects of feminine traits and sex were found only in the behavioral test. The findings indicated that men's responses to infants were influenced more by their feminine traits than were women's responses, potentially explaining the greater extent to which paternal (vs. maternal) investment is facultative.