Modeling ncRNA-Mediated Circuits in Cell Fate Decision: From Systems Biology to Synthetic Biology.

Noncoding RNAs (ncRNAs) play critical roles in essential cell fate decisions. However, the exact molecular mechanisms underlying ncRNA-mediated bistable switches remain elusive and controversial. In recent years, systematic mathematical and quantitative experimental analyses have made significant contributions to elucidating the molecular mechanisms of controlling ncRNA-mediated cell fate decision processes.

Mitigating Winner-Take-All Resource Competition through Antithetic Control Mechanism.

Competition among genes for limited transcriptional and translational resources impairs the functionality and modularity of synthetic gene circuits. Traditional control mechanisms, such as feedforward and negative feedback loops, have been proposed to alleviate these challenges, but they often focus on individual modules or inadvertently increase the burden on the system. In this study, we introduce three novel multimodule control strategies─local regulation, global regulation, and negatively competitive regulation (NCR)─that employ an antithetic regulatory mechanism to mitigate resource competition.

Phase Separation to Resolve Growth-Related Circuit Failures.

Fluctuations in host cell growth poses a significant challenge to synthetic gene circuits, often disrupting circuit function. Existing solutions typically rely on circuit redesign with alternative topologies or additional control elements, yet a broadly applicable approach remains elusive. Here, we introduce a new strategy based on liquid-liquid phase separation (LLPS) to stabilize circuit performance.

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.

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.

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.

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.

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.

[Treatment outcome of laparoscopic partial nephrectomy in patients with renal tumors of moderate to high complexity].

Objective: To investigate the treatment outcome of laparoscopic partial nephrectomy in the patients with renal tumors of moderate to high complexity (R.E.N.

[Risk factors for massive hemorrhage after radical nephrectomy and removal of venous tumor thrombus].

Objective: To investigate and analyze the risk factors of massive hemorrhage in patients with renal cell carcinoma and venous tumor thrombus undergoing radical nephrectomy and removal of venous tumor thrombus.

Methods: From January 2014 to June 2020, 241 patients with renal cancer and tumor thrombus in a single center of urology at Peking University Third Hospital were retrospectively analyzed. All patients underwent radical nephrectomy and removal of venous tumor thrombus.

[Clinicopathologic features and prognosis of young renal tumors with tumor thrombus].

Objective: To retrospectively analyze clinical data of patients under 40 years old who underwent surgical treatment for renal tumors with tumor thrombus from January 2016 to December 2022 at Peking University Third Hospital, and to evaluate the surgical effect and investigate the relationship between clinicopathological characteristics and prognosis.

Methods: The clinical data of 17 young patients with renal tumor thrombus were retrospectively analyzed, and the clinicopathological features and prognosis were summarized. The patients were grouped according to the presence or absence of symptoms, 2017 American Joint Committee on Cancer (AJCC) clinical stage, and postoperative combined adjuvant therapy.

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.

Effects of growth feedback on adaptive 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 more than four hundred topological structures and uncover various categories of failures.

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.

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.

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 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.

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.

Double-edged role of resource competition in gene expression noise and control.

Despite extensive investigation demonstrating that resource competition can significantly alter the deterministic behaviors of synthetic gene circuits, it remains unclear how resource competition contributes to the gene expression noise and how this noise can be controlled. Utilizing a two-gene circuit as a prototypical system, we uncover a surprising double-edged role of resource competition in gene expression noise: competition decreases noise through introducing a resource constraint but generates its own type of noise which we name as "resource competitive noise." Utilization of orthogonal resources enables retainment of the noise reduction conferred by resource constraint while removing the added resource competitive noise.

Spermatic cord anastomosing hemangioma mimicking a malignant inguinal tumor: A case report and literature review.

Background: Anastomosing hemangioma (AH) is a rare vascular tumor and occurs in various organs. It is difficult to distinguish AH from malignant tumors even through multimodal imaging examination. AH located in the inguinal region is even rare.

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.

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.

Oncologic Outcomes of Renal Cell Carcinoma Patients Undergoing Radical Nephrectomy and Venous Thrombectomy: Prospective Follow-Up from a Single Center.

Purpose: To evaluate the long-term oncologic outcomes of renal cell carcinoma (RCC) patients with venous thrombus after radical nephrectomy and venous thrombectomy (RN-VT) and to determine the prognostic factors.

Methods And Materials: We reported our follow-up data of RCC patients with venous thrombus from January 2014 to September 2020. We used the Kaplan-Meier method to assess the overall survival (OS), cancer-specific survival (CSS), and recurrence-free survival (RFS).