Noise Reduction in Resource-Coupled Multi-Module Gene Circuits through Antithetic Feedback Control

Gene circuits within the same host cell often experience coupling, stemming from the competition for limited resources during transcriptional and translational processes. This resource competition introduces an additional layer of noise to gene expression. Here we present three multi-module antithetic control strategies: negatively competitive regulation (NCR) controller, alongside local and global controllers, aimed at reducing the gene expression noise within the context of resource competition. Through stochastic simulations and fluctuation-dissipation theorem (FDT) analysis, our findings highlight the superior performance of the NCR antithetic controller in reducing noise levels. Our research provides an effective control strategy for attenuating resource-driven noise and offers insight into the development of robust gene circuits.

Proteome characterization of liver-kidney comorbidity after microbial sepsis

Sepsis is a life-threatening condition that occurs when the body responds to an infection but subsequently triggers widespread inflammation and impaired blood flow. These pathologic responses can rapidly cause multiple organ dysfunction or failure either one by one or simultaneously. The fundamental common mechanisms involved in sepsis-induced multiple organ dysfunction remain unclear. Here, employing quantitative global and phosphoproteomics, we examine the liver's temporal proteome and phosphoproteome changes after moderate sepsis induced by cecum ligation and puncture. In total, 4593 global proteins and 1186 phosphoproteins according to 3275 phosphosites were identified. To characterize the liver-kidney comorbidity after sepsis, we developed a mathematical model and performed cross-analyses of liver and kidney proteome data obtained from the same set of mice. Beyond immune response, we showed the commonly disturbed pathways and key regulators of the liver-kidney comorbidity are linked to energy metabolism and consumption. Our data provide open resources to understand the communication between the liver and kidney as they work to fight infection and maintain homeostasis.

[Clinical and prognostic analysis of opsoclonus-myoclonus-ataxia syndrome in children]

Objective: To summarize the clinical and prognostic features of children with opsoclonus-myoclonus-ataxia syndrome (OMAS). Methods: A total of 46 patients who met the diagnostic criteria of OMAS in the Department of Neurology, Beijing Children's Hospital from June 2015 to June 2023 were retrospectively analyzed. Centralized online consultations or telephone visits were conducted between June and August 2023. The data of the children during hospitalization and follow-up were collected, including clinical manifestations, assistant examination, treatment and prognosis. According to the presence or absence of tumor, the patients were divided into two groups. The chi-square test or Mann-Whitney U test was used to compare the differences between the two groups. Univariate Logistic regression was used to analyze the factors related to OMAS recurrence and prognosis. Results: There were 46 patients, with 25 males and the onset age of 1.5 (1.2, 2.4) years. Twenty-six (57%) patients were diagnosed with neuroblastoma during the course of the disease, and no patients were categorized into the high-risk group. A total of 36 patients (78%) were followed up for≥6 months, and all of them were treated with first-line therapy with glucocorticoids, gammaglobulin and (or) adrenocorticotrophic hormone. Among the 36 patients, 9 patients (25%) were treated with second-line therapy for ≥3 months, including rituximab or cyclophosphamide, and 17 patients (47%) received chemotherapy related to neuroblastoma. At the follow-up time of 4.2 (2.2, 5.5) years, 10 patients (28%) had relapsed of OMAS. The Mitchell and Pike OMS rating scale score at the final follow-up was 0.5 (0, 2.0). Seven patients (19%) were mildly cognitively behind their peers and 6 patients (17%) were severely behind. Only 1 patient had tumor recurrence during follow-up. The history of vaccination or infection before onset was more common in the non-tumor group than in the tumor group (55%(11/20) vs. 23%(6/26), χ²=4.95, P=0.026). Myoclonus occurred more frequently in the non-tumor group (40%(8/20) vs. 4%(1/26), χ²=7.23, P=0.007) as the onset symptom. Univariate Logistic regression analysis showed that the tumor group had less recurrence (OR=0.19 (0.04-0.93), P=0.041). The use of second-line therapy or chemotherapy within 6 months of the disease course had a better prognosis (OR=11.64 (1.27-106.72), P=0.030). Conclusions: OMAS in children mostly starts in early childhood, and about half are combined with neuroblastoma. Neuroblastoma in combination with OMAS usually has a low risk classification and good prognosis. When comparing patients with OMAS with and without tumors, the latter have a more common infection or vaccination triggers, and myoclonus, as the onset symptom, is more common. Early addition of second-line therapy is associated with better prognosis in OMAS.

Anomalously bright single-molecule upconversion electroluminescence

Efficient upconversion electroluminescence is highly desirable for a broad range of optoelectronic applications, yet to date, it has been reported only for ensemble systems, while the upconversion electroluminescence efficiency remains very low for single-molecule emitters. Here we report on the observation of anomalously bright single-molecule upconversion electroluminescence, with emission efficiencies improved by more than one order of magnitude over previous studies, and even stronger than normal-bias electroluminescence. Intuitively, the improvement is achieved via engineering the energy-level alignments at the molecule-substrate interface so as to activate an efficient spin-triplet mediated upconversion electroluminescence mechanism that only involves pure carrier injection steps. We further validate the intuitive picture with the construction of delicate electroluminescence diagrams for the excitation of single-molecule electroluminescence, allowing to readily identify the prerequisite conditions for producing efficient upconversion electroluminescence. These findings provide deep insights into the microscopic mechanism of single-molecule upconversion electroluminescence and organic electroluminescence in general.

Enhancing circuit stability under growth feedback with supplementary repressive regulation

The field of synthetic biology and biosystems engineering increasingly acknowledges the need for a holistic design approach that incorporates circuit-host interactions into the design process. Engineered circuits are not isolated entities but inherently entwined with the dynamic host environment. One such circuit-host interaction, 'growth feedback', results when modifications in host growth patterns influence the operation of gene circuits. The growth-mediated effects can range from growth-dependent elevation in protein/mRNA dilution rate to changes in resource reallocation within the cell, which can lead to complete functional collapse in complex circuits. To achieve robust circuit performance, synthetic biologists employ a variety of control mechanisms to stabilize and insulate circuit behavior against growth changes. Here we propose a simple strategy by incorporating one repressive edge in a growth-sensitive bistable circuit. Through both simulation and in vitro experimentation, we demonstrate how this additional repressive node stabilizes protein levels and increases the robustness of a bistable circuit in response to growth feedback. We propose the incorporation of repressive links in gene circuits as a control strategy for desensitizing gene circuits against growth fluctuations.

Context-dependent redesign of robust synthetic gene circuits

Cells provide dynamic platforms for executing exogenous genetic programs in synthetic biology, resulting in highly context-dependent circuit performance. Recent years have seen an increasing interest in understanding the intricacies of circuit-host relationships, their influence on the synthetic bioengineering workflow, and in devising strategies to alleviate undesired effects. We provide an overview of how emerging circuit-host interactions, such as growth feedback and resource competition, impact both deterministic and stochastic circuit behaviors. We also emphasize control strategies for mitigating these unwanted effects. This review summarizes the latest advances and the current state of host-aware and resource-aware design of synthetic gene circuits.

Growth Feedback Confers Cooperativity in Resource-Competing Synthetic Gene Circuits

Modularity is a key concept in designing synthetic gene circuits, as it allows for constructing complex molecular systems using well-characterized building blocks. One of the major challenges in this field is that these modular components often do not function as expected when assembled into larger circuits. One of the major issues is caused by resource competition, where multiple genes in the circuit compete for the same limited cellular resources, such as transcription factors and ribosomes. In addition, the mutual inhibition between synthetic gene circuits and cell growth results in growth feedback that significantly impacts its host-circuit dynamics. However, the complexity of the gene circuit dynamics under intertwined resource competition and growth feedback is not fully understood. This study developed a theoretical framework to examine the dynamics of synthetic gene circuits by considering both growth feedback and resource competition. Our results suggest a cooperative behavior between resource-competing gene circuits under growth feedback. Cooperation or competition is non-monotonically determined by the metabolic burden threshold. These two diverse effects could lead to the activation or deactivation of one circuit by the other. Lastly, the cooperativity mediated by growth feedback can attenuate the winner-takes-all resource competition. These findings show that coupling growth feedback and resource competition plays a crucial role in the dynamics of the host-circuit system, and understanding its effects helps control unexpected gene expression behaviors.

Effects of growth feedback on gene circuits: A dynamical understanding

The successful integration of engineered gene circuits into host cells remains a significant challenge in synthetic biology due to circuit-host interactions, such as growth feedback, where the circuit influences cell growth and vice versa. Understanding the dynamics of circuit failures and identifying topologies resilient to growth feedback are crucial for both fundamental and applied research. Utilizing transcriptional regulation circuits with adaptation as a paradigm, we systematically study 435 distinct topological structures and uncover six categories of failures. Three dynamical mechanisms of circuit failures are identified: continuous deformation of the response curve, strengthened or induced oscillations, and sudden switching to coexisting attractors. Our extensive computations also uncover a scaling law between a circuit robustness measure and the strength of growth feedback. Despite the negative effects of growth feedback on the majority of circuit topologies, we identify a few circuits that maintain optimal performance as designed, a feature important for applications.

[Clinical characteristics and short-term prognosis of 22 cases with SARS-CoV-2 infection associated acute encephalopathy]

Objective: To investigate the clinical features and short-term prognosis of patients with SARS-CoV-2 infection associated acute encephalopathy (AE). Methods: Retrospective cohort study. The clinical data, radiological features and short-term follow-up of 22 cases diagnosed with SARS-CoV-2 infection associated AE in the Department of Neurology, Beijing Children's Hospital from December 2022 to January 2023 were retrospectively analyzed. The patients were divided into cytokine storm group, excitotoxic brain damage group and unclassified encephalopathy group according to the the clinicopathological features and the imaging features. The clinical characteristics of each group were analyzed descriptively. Patients were divided into good prognosis group (≤2 scores) and poor prognosis group (>2 scores) based on the modified Rankin scale (mRS) score of the last follow-up. Fisher exact test or Mann-Whitney U test was used to compare the two groups. Results: A total of 22 cases (12 females, 10 males) were included. The age of onset was 3.3 (1.7, 8.6) years. There were 11 cases (50%) with abnormal medical history, and 4 cases with abnormal family history. All the enrolled patients had fever as the initial clinical symptom, and 21 cases (95%) developed neurological symptoms within 24 hours after fever. The onset of neurological symptoms included convulsions (17 cases) and disturbance of consciousness (5 cases). There were 22 cases of encephalopathy, 20 cases of convulsions, 14 cases of speech disorders, 8 cases of involuntary movements and 3 cases of ataxia during the course of the disease. Clinical classification included 3 cases in the cytokine storm group, all with acute necrotizing encephalopathy (ANE); 9 cases in the excitotoxicity group, 8 cases with acute encephalopathy with biphasic seizures and late reduced diffusion (AESD) and 1 case with hemiconvulsion-hemiplegia syndrome; and 10 cases of unclassified encephalopathy. Laboratory studies revealed elevated glutathione transaminase in 9 cases, elevated glutamic alanine transaminase in 4 cases, elevated blood glucose in 3 cases, and elevated D-dimer in 3 cases. Serum ferritin was elevated in 3 of 5 cases, serum and cerebrospinal fluid (CSF) neurofilament light chain protein was elevated in 5 of 9 cases, serum cytokines were elevated in 7 of 18 cases, and CSF cytokines were elevated in 7 of 8 cases. Cranial imaging abnormalities were noted in 18 cases, including bilateral symmetric lesions in 3 ANE cases and "bright tree appearance" in 8 AESD cases. All 22 cases received symptomatic treatment and immunotherapy (intravenous immunoglobulin or glucocorticosteroids), and 1 ANE patient received tocilizumab. The follow-up time was 50 (43, 53) d, and 10 patients had a good prognosis and 12 patients had a poor prognosis. No statistically significant differences were found between the two groups in terms of epidemiology, clinical manifestations, biochemical indices, and duration of illness to initiate immunotherapy (all P>0.05). Conclusions: SARS-CoV-2 infection is also a major cause of AE. AESD and ANE are the common AE syndromes. Therefore, it is crucial to identify AE patients with fever, convulsions, and impaired consciousness, and apply aggressive therapy as early as possible.

Back focal plane imaging for light emission from a tunneling junction in a low-temperature ultrahigh-vacuum scanning tunneling microscope

We report the design and realization of the back focal plane (BFP) imaging for the light emission from a tunnel junction in a low-temperature ultrahigh-vacuum (UHV) scanning tunneling microscope (STM). To achieve the BFP imaging in a UHV environment, a compact "all-in-one" sample holder is designed and fabricated, which allows us to integrate the sample substrate with the photon collection units that include a hemisphere solid immersion lens and an aspherical collecting lens. Such a specially designed holder enables the characterization of light emission both within and beyond the critical angle and also facilitates the optical alignment inside a UHV chamber. To test the performance of the BFP imaging system, we first measure the photoluminescence from dye-doped polystyrene beads on a thin Ag film. A double-ring pattern is observed in the BFP image, arising from two kinds of emission channels: strong surface plasmon coupled emissions around the surface plasmon resonance angle and weak transmitted fluorescence maximized at the critical angle, respectively. Such an observation also helps to determine the emission angle for each image pixel in the BFP image and, more importantly, proves the feasibility of our BFP imaging system. Furthermore, as a proof-of-principle experiment, electrically driven plasmon emissions are used to demonstrate the capability of the constructed BFP imaging system for STM induced electroluminescence measurements. A single-ring pattern is obtained in the BFP image, which reveals the generation and detection of the leakage radiation from the surface plasmon propagating on the Ag surface. Further analyses of the BFP image provide valuable information on the emission angle of the leakage radiation, the orientation of the radiating dipole, and the plasmon wavevector. The UHV-BFP imaging technique demonstrated here opens new routes for future studies on the angular distributed emission and dipole orientation of individual quantum emitters in UHV.

Cephalic inferior vena cava non-clamping technique versus standard procedure for robot-assisted laparoscopic level II-III thrombectomy: a prospective cohort study

BACKGROUND

Renal tumour can invade the venous system and ~4-10% patients with renal tumour had venous thrombus. Although the feasibility of robot-assisted laparoscopic inferior vena cava thrombectomy (RAL-IVCT) in patients with inferior vena cava (IVC) thrombus has been validated, the wide application is still a challenge due to the complexity of IVC control. The objective was to describe our novel cephalic IVC non-clamping technique and to compare the outcomes versus standard RAL-IVCT.

MATERIALS AND METHODS

A prospective single-centre cohort containing 30 patients with level II-III IVC thrombus was established since August 2020. Fifteen patients underwent cephalic IVC non-clamping approach and 15 patients received standard RAL-IVCT. The authors decided the surgical technique according to the echocardiographic assessment of the right heart and IVC.

RESULTS

The non-clamping group had less operative time (median 148 versus 185 min, P =0.04), and lower Clavien-grade II complication rate (26.7% versus 80.0%, P =0.003). The median intraoperative blood loss were 400 ml [interquartile range (IQR) 275-615 mL] and 800 ml (IQR 350-1300 ml), respectively ( P =0.05). The most common complication in standard RAL-IVCT group was liver dysfunction. No gas embolism, hypercapnia or tumour thrombus dislodgment occurred in non-clamping group. After a median follow-up of 17.0 months (IQR 13.5-18.5 months) and 15.5 months (IQR 13.0-17.0 months), two patients (16.7%) in the non-clamping group and 3 patients (20.0%) in the standard RAL-IVCT group died (hazard ratio 0.59, 95% CI 0.10-3.54, P =0.55).

CONCLUSIONS

The cephalic IVC non-clamping technique can be performed safely with acceptable surgical outcomes and short-term oncologic outcomes in patients with level II-III IVC thrombus. Compared with standard procedure, it had less operative time and lower complication rate.

The role of prophylactic antibiotics in elective inguinal tension-free hernia repair: A systematic review and meta-analysis

Whether to use antibiotics to prevent surgical site infection in elective inguinal tension-free hernia repair has been controversial. To systematically evaluate the effect of prophylactic antibiotic application in elective inguinal tension-free hernia repair, we identified all published randomised controlled trials of the effect of prophylactic antibiotic application on elective inguinal tension-free hernia repair were collected by computer retrieval from the China National Knowledge Infrastructure; VIP Database; Wanfang Database; China Biomedical Literature Database; and PubMed, EMBASE and Cochrane Library databases. Meta-analysis was performed by RevMan 5.3 software. The meta-analysis showed that the total incidence of surgical site infections [P = 0.003] and the incidence of superficial surgical site infections [P = 0.004] in the antibiotic group (AG) were lower than those in the non-antibiotic group (NAG). There was no significant difference in the total incidence of postoperative infections [P = 0.06], deep surgical site infections [P = 0.26] and seroma [P = 0.52] between the AG and the NAG. Based on current evidence, the application of prophylactic antibiotics in elective inguinal tension-free hernia repair can prevent the total incidence of surgical site infections and that of superficial surgical site infections but cannot prevent the total incidence of postoperative infection events, incidence of deep surgical site infections and incidence of seroma.

[Molecular genetic characteristics of a family which coinheritance of rare-88 C>G (HBB:c.-138 C>G) β-thalassemia mutation with α-thalassemia and review of the literature]

The molecular genetic characteristics of a family with rare -88 C>G (HBB: c.-138 C>G) β-thalassemia gene mutation were studied using cohort study. The cohort study was conducted from June to August 2022 by Prenatal Diagnosis Center of Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center. The phenotype and genotype were analyzed by hematological cytoanalyzer, automatic electrophoretic analysis system, and next-generation sequencing (NGS). And then, Sanger sequencing was used to verify the rare gene results. The results showed that the proband, her father, her uncle and her younger male cousin had discrete microcytosis (MCV 70.1 fl, 71.9 fl, 73.1 fl and 76.6 fl, respectively) and hypochromia (MCH 21.5 pg,22.0 pg,22.6 pg and 23.5 pg, respectively), elevated hemoglobin A2 level (5.3%, 5.4%, 5.4% and 5.5%, respectively), slightly elevated or normal fetal hemoglobin (Hb F), but no anemia. The proband was identified to have co-inherited ɑ-thalassemia (Hb Westmead gene heterozygous mutation, ɑ^wsɑ/ɑɑ) and β-thalassemia with a rare -88 C>G (HBB: c.-138 C>G) heterozygous mutation (β^{-88 C>G}/β^N). Her mother had the same α-thalassemia as the proband. Her father, her uncle and her younger male cousin had the same rare -88 C>G heterozygous mutations as the proband. While her grandmother and younger brother were not carrier of thalassemia. In conclusion, 4 cases of rare -88 C>G(HBB:c.-138 C>G) heterozygous mutation had been detected in a Chinese family. Carriers of this beta-thalassemia are clinically asymptomatic. This study enriches the knowledge of the thalassemia mutation spectrum in Chinese people and provides valuable information for genetic counseling, prenatal diagnosis, and prevention of thalassemia, providing a scientific basis for improving the quality of birth population and preventing birth defects.

Leveraging an established neighbourhood-level, open access wastewater monitoring network to address public health priorities: a population-based study

BACKGROUND

Before the COVID-19 pandemic, the US opioid epidemic triggered a collaborative municipal and academic effort in Tempe, Arizona, which resulted in the world's first open access dashboard featuring neighbourhood-level trends informed by wastewater-based epidemiology (WBE). This study aimed to showcase how wastewater monitoring, once established and accepted by a community, could readily be adapted to respond to newly emerging public health priorities.

METHODS

In this population-based study in Greater Tempe, Arizona, an existing opioid monitoring WBE network was modified to track SARS-CoV-2 transmission through the analysis of 11 contiguous wastewater catchments. Flow-weighted and time-weighted 24 h composite samples of untreated wastewater were collected at each sampling location within the wastewater collection system for 3 days each week (Tuesday, Thursday, and Saturday) from April 1, 2020, to March 31, 2021 (Area 7 and Tempe St Luke's Hospital were added in July, 2020). Reverse transcription quantitative PCR targeting the E gene of SARS-CoV-2 isolated from the wastewater samples was used to determine the number of genome copies in each catchment. Newly detected clinical cases of COVID-19 by zip code within the City of Tempe, Arizona were reported daily by the Arizona Department of Health Services from May 23, 2020. Maricopa County-level new positive cases, COVID-19-related hospitalisations, deaths, and long-term care facility deaths per day are publicly available and were collected from the Maricopa County Epidemic Curve Dashboard. Viral loads of SARS-CoV-2 (genome copies per day) measured in wastewater from each catchment were aggregated at the zip code level and city level and compared with the clinically reported data using root mean square error to investigate early warning capability of WBE.

FINDINGS

Between April 1, 2020, and March 31, 2021, 1556 wastewater samples were analysed. Most locations showed two waves in viral levels peaking in June, 2020, and December, 2020-January, 2021. An additional wave of viral load was seen in catchments close to Arizona State University (Areas 6 and 7) at the beginning of the fall (autumn) semester in late August, 2020. Additionally, an early infection hotspot was detected in the Town of Guadalupe, Arizona, starting the week of May 4, 2020, that was successfully mitigated through targeted interventions. A shift in early warning potential of WBE was seen, from a leading (mean of 8·5 days [SD 2·1], June, 2020) to a lagging (-2·0 days [1·4], January, 2021) indicator compared with newly reported clinical cases.

INTERPRETATION

Lessons learned from leveraging an existing neighbourhood-level WBE reporting dashboard include: (1) community buy-in is key, (2) public data sharing is effective, and (3) sub-ZIP-code (postal code) data can help to pinpoint populations at risk, track intervention success in real time, and reveal the effect of local clinical testing capacity on WBE's early warning capability. This successful demonstration of transitioning WBE efforts from opioids to COVID-19 encourages an expansion of WBE to tackle newly emerging and re-emerging threats (eg, mpox and polio).

FUNDING

National Institutes of Health's RADx-rad initiative, National Science Foundation, Virginia G Piper Charitable Trust, J M Kaplan Fund, and The Flinn Foundation.

Negatively Competitive Incoherent Feedforward Loops Mitigate Winner-Take-All Resource Competition

The effects of host resource limitations on the function of synthetic gene circuits have gained significant attention over the past years. Hosts, having evolved resource capacities optimal for their own genome, have been repeatedly demonstrated to suffer from the added burden of synthetic genetic programs, which may in return pose deleterious effects on the circuit's function. Three resource controller archetypes have been proposed previously to mitigate resource distribution problems in dynamic circuits: the local controller, the global controller, and a "negatively competitive" regulatory (NCR) controller that utilizes synthetic competition to combat resource competition. The dynamics of negative feedback forms of these controllers have been previously investigated, and here we extend the analysis of these resource allocation strategies to the incoherent feedforward loop (iFFL) topology. We demonstrate that the three iFFL controllers can attenuate Winner-Take-All resource competition between two bistable switches. We uncover that the parameters associated with the synthetic competition in the NCR iFFL controller are paramount to its increased efficacy over the local controller type, while the global controllers demonstrate to be relatively ineffectual. Interestingly, unlike the negative feedback counterpart topologies, iFFL controllers exhibit a unique coupling of switch activation thresholds which we term the "coactivation threshold shift" effect. Finally, we demonstrate that a nearly fully orthogonal set of bistable switches could be achieved by pairing an NCR controller with an appropriate level of controller resource consumption.

Emergence of qualitative states in synthetic circuits driven by ultrasensitive growth feedback

The mutual interactions between the synthetic gene circuits and the host growth could cause unexpected outcomes in the dynamical behaviors of the circuits. However, how the steady states and the stabilities of the gene circuits are affected by host cell growth is not fully understood. Here, we developed a mathematical model for nonlinear growth feedback based on published experimental data. The model analysis predicts that growth feedback could significantly change the qualitative states of the system. Bistability could emerge in a circuit without positive feedback, and high-order multistability (three or more steady states) arises in the self-activation and toggle switch circuits. Our results provide insight into the potential effects of ultrasensitive growth feedback on the emergence of qualitative states in synthetic circuits and the corresponding underlying mechanism.

The mutual inhibitory effect between synthetic gene circuits and cell growth produces growth feedback in the host-circuit system. Previous studies have demonstrated that the growth feedback could significantly impact the dynamics of the host-circuit system. However, the complexity of the growth feedback impact is not fully understood. Here, our data analysis displays ultrasensitive growth feedback between the cells and synthetic gene circuits under different growth conditions. To study the effect of ultrasensitive growth feedback on the host-circuit system, we develop a mathematical modeling framework. Our results reveal the emergence of qualitative states on the host-circuit system induced by ultrasensitive growth feedback. We found an emergence of bistability in a simple synthetic gene circuit with a constitutive promoter. Also, tristability could be seen in self-activation and toggle switch circuits. Our research uncovered the effect of ultrasensitive growth feedback in synthetic gene circuits and host interactions. Understanding the effects of ultrasensitive growth feedback could help scientists and engineers identify unexpected outcomes in gene circuits and formulate control strategies.

Wavelike electronic energy transfer in donor-acceptor molecular systems through quantum coherence

Quantum-coherent intermolecular energy transfer is believed to play a key role in light harvesting in photosynthesis and photovoltaics. So far, a direct, real-space demonstration of quantum coherence in donor-acceptor systems has been lacking because of the fragile quantum coherence in lossy molecular systems. Here, we precisely control the separations in well-defined donor-acceptor model systems and unveil a transition from incoherent to coherent electronic energy transfer. We monitor the fluorescence from the heterodimers with subnanometre resolution through scanning tunnelling microscopy induced luminescence. With decreasing intermolecular distance, the dipole coupling strength increases and two new emission peaks emerge: a low-intensity peak blueshifted from the donor emission, and an intense peak redshifted from the acceptor emission. Spatially resolved spectroscopic images of the redshifted emission exhibit a σ antibonding-like pattern and thus indicate a delocalized nature of the excitonic state over the whole heterodimer due to the in-phase superposition of molecular excited states. These observations suggest that the exciton can travel coherently through the whole heterodimer as a quantum-mechanical wavepacket. In our model system, the wavelike quantum-coherent transfer channel is three times more efficient than the incoherent channel.

A Nomogram Predicting the Progression-Free Survival of Nonmetastatic Renal Cell Carcinoma Patients With Venous Thrombus After Surgery

Objectives

To demonstrate the progression-free survival (PFS) of nonmetastatic renal cell carcinoma (RCC) patients with venous thrombus after radical nephrectomy and venous thrombectomy (RN-VT) and to develop and validate a nomogram to predict the PFS of patients after RN-VT.

Materials and Methods

We reported our prospective follow-up data of RCC patients with venous thrombus from January 2014 to September 2020 (n = 199). We used the Kaplan–Meier method to assess the PFS. The Cox proportional hazards regression model was used to determine the predictors. Nomograms predicting the PFS was established, and external validation was performed. Calibration curves and decision curves were generated to assess the predictive efficacy and clinical benefit.

Results

After a median follow-up of 32 months, 79 patients (39.7%) had disease progression and the median PFS was 41.0 months (95% CI 34.8–53.2 months). The 1-year, 3-year, and 5-year PFS rates were 78.4%, 45.4%, and 30.0%, respectively. Multivariate analysis showed that Fuhrman grade [grade 4: hazard ratio (HR) 1.92, 95% CI 1.10–3.34, P = 0.02], pathological type (papillary RCC: HR 3.02, 95% CI 1.79–5.10, P < 0.001), perinephric fat invasion (HR 1.54, 95% CI 1.12–2.10, P = 0.007), sarcomatoid differentiation (HR 2.97, 95% CI 1.24–7.13, P = 0.02) were associated with a worse PFS, and adjuvant therapy (HR 0.32, 95% CI 0.18–0.59, P < 0.001) could lead to a better PFS. A nomogram based on the predictors was externally validated to have good discrimination and calibration, and it could improve PFS prediction to obtain a clinical benefit.

Conclusions

We constructed and validated a nomogram to predict the 1-year, 3-year, and 5-year PFS of M0 RCC patients with venous thrombus after surgery. The model can help identify patients who can benefit the most from surgery and develop the criteria for clinical trial enrollment.

[Clinical characteristics and gene analysis of GRIN2B gene related neurological developmental disorders in children]

Objective: To analyse the clinical and gene characteristics of GRIN2B gene related neurological developmental disorders in children. Methods: The data of 11 children with GRIN2B gene related neurological developmental disorders from November 2016 to February 2021 were collected from Department of Neurology, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health and analyzed retrospectively. The clinical features, electroencephalogram (EEG), brain imaging and gene testing results were summarized. Results: Among 11 children 6 were boys and 5 were girls. Two of them were diagnosed with developmental and epileptic encephalopathy. The ages of seizures onset were 3 months and 9 months, respectively. Seizure types included epileptic spasm, tonic seizures, tonic spasm and focal seizures, and 1 patient also had startle attacks. EEG showed interictal multifocal epileptiform discharges. Both of them were added with more than 2 anti-seizure drugs, which were partially effective but could not control. They had moderate to severe mental and motor retardation. The phenotype of 9 cases was developmental delay or intellectual disability without epilepsy, age of visit 1 year to 6 year and 4 months of whom 5 cases had severe developmental delay, 2 cases had moderate and 2 cases had mild delay. Multi-focal epileptiform discharges were observed in 3 cases, no abnormality was found in 3 cases, and the remaining 3 cases did not undergo EEG examination. Ten cases underwent brain magnetic resonance imaging (MRI), 6 cases had nonspecific abnormalities and 4 cases were normal. Nine GRIN2B gene heterozygous variants were detected by next-generation sequencing in these 11 patients, 8 cases had missense variants and 1 case had nonsense variant, all of which were de novo and 3 of which were novel. Missense variants were found in 10 patients, among them 6 cases had severe developmental delay, 3 cases had moderate and 1 case had mild developmental delay, but the patient with nonsense variant showed mild developmental delay without epilepsy. Conclusions: The phenotypes of GRIN2B gene related neurological developmental disorders in children are diverse, ranging from mild intellectual impairment without epilepsy to severe epileptic encephalopathy. Patients with epileptic phenotype usually have an onset age of infancy, and spasm and focal seizures are the most common seizure types. And the epiletice episodes are refractory. Most of the patients with missense variants had severe developmental delay.

[Clinical characteristics and gene analysis of SYNGAP1-related epilepsy in children]

Objective: To summarize the clinical characteristics of SYNGAP1-related epilepsy in children. Methods: Data of 13 patients with SYNGAP1 gene variants diagnosed with epilepsy at Department of Neurology, Beijing Children's Hospital were collected retrospectively from March 2017 to October 2020 and the patients were followed up. The clinical features, electroencephalogram(EEG), brain imaging, gene results and treatment were summarized. Results: Twelve patients were followed up successfully among the 13 patients with SYNGAP1 variants. The last follow-up age was 5 years and 7 months (3 years and 1 month to 9 years).The onset age of seizures was 2 years (4 months to 3 years). Seizure types included eyelid myoclonia with or without absence (9 cases), myoclonic seizure (5 cases), atypical absence (4 cases), suspicious atonic seizures(4 cases),unclassified fall attack (6 cases), and the frequency of seizures varied from several times to more than 100 times per day. Four cases had the mimic phenotype of myoclonic astatic epilepsy. The seizures of 10 cases could be triggered by eating (5 cases), emotion (5 cases), fever (3 cases), voice (2 cases), fatigue (2 cases), etc. Electroencephalography (10 cases) showed interictal generalized or focal epileptiform discharges (9 cases), and atypical aphasia (4 cases), myoclonic seizure (2 cases) and eyelid myoclonic seizure (1 case) were monitored. Of the 12 cases, 9 were added with valproate, all of which were effective (the frequency of seizures reduced>50%). Five cases received combined levetiracetam, in 3 the treatments were effective. To last follow-up, 3 cases were seizure free from 6 months to 1 year and 1 month, but the remaining 7 cases still had seizures, one or several times per day. All 13 cases had developmental retardation (speech ability impaired mostly), 2 cases were severe, 10 cases were moderate, 1 case was mild. The SYNGAP1 gene variants of 13 patients were all de novo, including 12 variants. Among them, 4 were frameshift variants, 4 were nonsense variants, 2 were missense variants and 2 were splice site variants. Conclusions: Patients with SYNGAP1-related epilepsy have an early onset age and many seizure types. The main seizure type is eyelid myoclonia with or without absence, and other seizure types include myoclonic seizure, atypical absence, unclassified fall attack, etc. Valproate is effective in most patients, but seizures in some patients might be intractable. Most patients have developmental delay (mainly moderate and severe), speech ability impaired mostly.

Control of tissue homeostasis, tumorigenesis, and degeneration by coupled bidirectional bistable switches

The Hippo-YAP/TAZ signaling pathway plays a critical role in tissue homeostasis, tumorigenesis, and degeneration disorders. The regulation of YAP/TAZ levels is controlled by a complex regulatory network, where several feedback loops have been identified. However, it remains elusive how these feedback loops contain the YAP/TAZ levels and maintain the system in a healthy physiological state or trap the system in pathological conditions. Here, a mathematical model was developed to represent the YAP/TAZ regulatory network. Through theoretical analyses, three distinct states that designate the one physiological and two pathological outcomes were found. The transition from the physiological state to the two pathological states is mechanistically controlled by coupled bidirectional bistable switches, which are robust to parametric variation and stochastic fluctuations at the molecular level. This work provides a mechanistic understanding of the regulation and dysregulation of YAP/TAZ levels in tissue state transitions.

Tissue development and homeostasis require well-controlled cell proliferation. Lack of this control could lead to degenerative or tumorigenic diseases. Signaling pathways have been explored in promoting or inhibiting these diseases. The Hippo signaling pathway is one of these, which has been found to control tissue homeostasis and organ size through cell proliferation and apoptosis, as evidenced by extensive experimental data. However, the question remains of how tissue can transition from a homeostatic state to either a degenerative or tumorigenic state. By theoretically analyzing a mathematical model of its regulatory network, we present a mechanism that underlies Hippo signaling to control tissue transition from a homeostatic state to a disease state. This provides us with a mechanistic understanding of how the parts of the regulatory network are coordinated for the transitions between the homeostasis state and the disease states. In addition, we looked at the role of system noise and found that it could promote the transition to one of the disease states. Our model allows for experimental hypotheses to be generated and could lead to the development of therapeutic strategies by targeting the Hippo signaling pathway.

Serum integrative omics reveals the landscape of human diabetic kidney disease

Objective

Diabetic kidney disease (DKD) is the most common microvascular complication of type 2 diabetes mellitus (2-DM). Currently, urine and kidney biopsy specimens are the major clinical resources for DKD diagnosis. Our study proposes to evaluate the diagnostic value of blood in monitoring the onset of DKD and distinguishing its status in the clinic.

Methods

This study recruited 1,513 participants including healthy adults and patients diagnosed with 2-DM, early-stage DKD (DKD-E), and advanced-stage DKD (DKD-A) from 4 independent medical centers. One discovery and four testing cohorts were established. Sera were collected and subjected to training proteomics and large-scale metabolomics.

Results

Deep profiling of serum proteomes and metabolomes revealed several insights. First, the training proteomics revealed that the combination of α₂-macroglobulin, cathepsin D, and CD324 could serve as a surrogate protein biomarker for monitoring DKD progression. Second, metabolomics demonstrated that galactose metabolism and glycerolipid metabolism are the major disturbed metabolic pathways in DKD, and serum metabolite glycerol-3-galactoside could be used as an independent marker to predict DKD. Third, integrating proteomics and metabolomics increased the diagnostic and predictive stability and accuracy for distinguishing DKD status.

Conclusions

Serum integrative omics provide stable and accurate biomarkers for early warning and diagnosis of DKD. Our study provides a rich and open-access data resource for optimizing DKD management.

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Serum proteomics and metabolomics are novel, noninvasive approaches to detect DKD.

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Integrated serum omics enhances the diagnostic stability and accuracy of DKD diagnoses.

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Galactose/glycerolipid metabolism is the major disturbed metabolic pathway in DKD.

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Serum metabolite glycerol-3-galactoside is an independent predictive marker of DKD.

The hepatocyte growth factor/c-met pathway is a key determinant of the fibrotic kidney local microenvironment

The kidney local microenvironment (KLM) plays a critical role in the pathogenesis of kidney fibrosis. However, the composition and regulation of a fibrotic KLM remain unclear. Through a multidisciplinary approach, we investigated the roles of the hepatocyte growth factor/c-met signaling pathway in regulating KLM formation in various chronic kidney disease (CKD) models. We performed a retrospective analysis of single-cell RNA sequencing data and determined that tubular epithelial cells and macrophages are two major cell populations in a fibrotic kidney. We then created a mathematical model that predicted loss of c-met in tubular cells would cause greater responses to injury than loss of c-met in macrophages. By generating c-met conditional knockout mice, we validated that loss of c-met influences epithelial plasticity, myofibroblast activation, and extracellular matrix synthesis/degradation, which ultimately determined the characteristics of the fibrotic KLM. Our findings open the possibility of designing effective therapeutic strategies to retard CKD.

[Clinical and imaging features of Chlamydia psittaci pneumonia: an analysis of 48 cases in China]

Objective: To explore the clinical characteristics, imaging findings, laboratory tests and treatment strategies for Chlamydia psittaci pneumonia. Methods: From January 1, 2019 to January 20, 2021, 48 cases of Psittacosis from 11 hospitals in China were diagnosed via metagenomic next-generation sequencing(mNGS). The data of all patients on occupational history, clinical manifestations, laboratory tests, chest computed tomography(CT)findings, treatment outcomes and prognosis were retrospectively analyzed. Results: Among the 48 patients, there were 29 males and 19 females, with a mean age of (57.1±10.3) years. Thirty patients had a confirmed history of exposure to poultry. The onset to admission interval was (6.5±3.2) days, and hospital stay was (12.4±4.8) days. Clinical manifestations included fever (100%, 48/48), relative bradycardia (71%, 34/48), cough (54.2%, 26/48), sputum (27.1%, 13/48), fatigue (16.7%, 8/48), headache and delirium (20.8%, 9/48), and gastrointestinal symptoms (16.7%, 8/48). Laboratory data showed that white blood cells were (8.0±3.8)×10⁹/L, and the proportion of neutrophils increased in 44 patients. The level of C-reactive protein was (155.3±74.1)mg/L, and that of procalcitonin (PCT)in 59.5% of patients was more than 0.5 μg/L. Percentages of patients with increased lactate dehydrogenase and creatine kinase were 82.9% and 45.2%, respectively. Chest CT scans showed unilateral lung involvement in 34 cases(70.8%) and single lobe involvement in 27 cases(56.3%).The most common imaging change was consolidation, with 38 cases (79.2%) showing lobar consolidation. In terms of treatment, 25 patients were treated with fluoroquinolones alone, 6 patients with doxycycline alone, and 13 patients with combined treatment. The combined-treatment group and the doxycycline alone group were similar in the course of defervescence. The combined treatment group and the doxycycline alone group were both superior to the fluoroquinolones alone group. However, 11 patients were admitted to ICU, all of them received artificial ventilation, and 5 cases developed shock, and one died. Conclusions: Chlamydia psittaci pneumonia is an animal-derived infectious disease with unique features in clinical symptoms, laboratory tests and chest imaging. Appropriate treatment is able to significantly shorten the course of disease and improve the prognosis.