Functional resilience of mutually repressing motifs embedded in larger regulatory networks

Elucidating the design principles of regulatory networks driving cellular decision-making has important implications in understanding cell differentiation and guiding the design of synthetic circuits. Mutually repressing feedback loops between 'master regulators' of cell-fates can exhibit multistable dynamics, thus enabling multiple 'single-positive' phenotypes: (high A, low B) and (low A, high B) for a toggle switch, and (high A, low B, low C), (low A, high B, low C) and (low A, low B, high C) for a toggle triad. However, the dynamics of these two network motifs has been interrogated in isolation in silico, but in vitro and in vivo, they often operate while embedded in larger regulatory networks. Here, we embed these network motifs in complex larger networks of varying sizes and connectivity and identify conditions under which these motifs maintain their canonical dynamical behavior, thus identifying hallmarks of their functional resilience. We show that the in-degree of a motif - defined as the number of incoming edges onto a motif - determines its functional properties. For a smaller in-degree, the functional traits for both these motifs (bimodality, pairwise correlation coefficient(s), and the frequency of 'single-positive' phenotypes) are largely conserved, but increasing the in-degree can lead to a divergence from their stand-alone behaviors. These observations offer insights into design principles of biological networks containing these network motifs, as well as help devise optimal strategies for integration of these motifs into larger synthetic networks.

Primary Toxoplasma gondii infection-associated with hemophagocytic syndrome in a man with HIV infection: a case report

Background Reactivation of latent Toxoplasma gondii (T. gondii) infection is more common than primary infection in patients with human immunodeficiency virus (HIV). We report a rare case of primary T. gondii infection-associated hemophagocytic syndrome (HPS). Case presentation A man with HIV infection presented with fever, dyspnea and pancytopenia. He was diagnosed with primary T. gondii infection by the seroconversion from single-positive IgM antibody to double-positive IgM and IgG antibody. Metagenomic next-generation sequencing (mNGS) of a plasma sample yielded high reads of T. gondii DNA. He responded well to combined anti-Toxoplasma medicines and glucocorticoid treatment. Conclusions In patients with HPS and positive T. gondii IgM antibody, mNGS analysis of a peripheral blood sample is helpful in diagnosing disseminated T. gondii infection. The dynamic changes by serological detection for IgM and IgG of T. gondii further supported the inference that the patient has experienced a primary T. gondii infection.

A Murine Model of X-Linked Moesin-Associated Immunodeficiency (X-MAID) Reveals Defects in T Cell Homeostasis and Migration

X-linked moesin associated immunodeficiency (X-MAID) is a primary immunodeficiency disease in which patients suffer from profound lymphopenia leading to recurrent infections. The disease is caused by a single point mutation leading to a R171W amino acid change in the protein moesin (moesinR171W). Moesin is a member of the ERM family of proteins, which reversibly link the cortical actin cytoskeleton to the plasma membrane. Here, we describe a novel mouse model with global expression of moesinR171W that recapitulates multiple facets of patient disease, including severe lymphopenia. Further analysis reveals that these mice have diminished numbers of thymocytes and bone marrow precursors. X-MAID mice also exhibit systemic inflammation that is ameliorated by elimination of mature lymphocytes through breeding to a Rag1-deficient background. The few T cells in the periphery of X-MAID mice are highly activated and have mostly lost moesinR171W expression. In contrast, single-positive (SP) thymocytes do not appear activated and retain high expression levels of moesinR171W. Analysis of ex vivo CD4 SP thymocytes reveals defects in chemotactic responses and reduced migration on integrin ligands. While chemokine signaling appears intact, CD4 SP thymocytes from X-MAID mice are unable to polarize and rearrange cytoskeletal elements. This mouse model will be a valuable tool for teasing apart the complexity of the immunodeficiency caused by moesinR171W, and will provide new insights into how the actin cortex regulates lymphocyte function.

The Diagnosis of Nontuberculous Mycobacterial Pulmonary Disease by Single Bacterial Isolation Plus Anti-GPL-Core IgA Antibody

To satisfy the microbiologic criteria of the current diagnostic guideline for nontuberculous mycobacterial pulmonary disease (PD), at least two positive sputum cultures of the same species of mycobacteria from sputum are required to avoid the casual isolation of mycobacteria. This study showed that the positivity of a serum anti-glycopeptidolipid (GPL)-core IgA antibody test has an excellent diagnostic ability among patients with radiologically suspected Mycobacterium avium complex (MAC)-PD or Mycobacterium abscessus (MAB)-PD who already had a single positive sputum culture test.

The presence of non-criteria manifestations negatively affects the prognosis of seronegative antiphospholipid syndrome patients: a multicenter study

Background Seronegative antiphospholipid syndrome (SN-APS) is often defined as the presence of APS criteria manifestations, negative antiphospholipid antibodies (aPL), and coexistence of APS non-criteria manifestations. Nevertheless, the impact of these non-criteria features is still unclear. On a different note, the relevance of one single aPL positive determination in patients with APS manifestations is another domain with limited evidence. We aim to compare the course of SN-APS and single-positive aPL (SP-aPL) patients with that of individuals with APS manifestations without non-criteria features/aPL positivity (controls). Methods Retrospective analysis of patients with thrombosis/obstetric morbidity assessed in two European hospitals between 2005 and 2020. Patients were divided into SN-APS, SP-aPL, and control groups. Clinical characteristics, comorbidities, and therapies were compared. Results A total of 82 patients were included in the SN-APS group, 88 in the SP-aPL group, and 185 in the control group. In Cox regression model, SN-APS displayed more thrombosis recurrence than controls (HR 3.8, 95% CI 2.2–6.5, p < 0.001) even when adjusting for the presence of hereditary thrombophilia, systemic lupus erythematosus, or contraceptive hormonal treatment. In SP-aPL, the difference in thrombosis recurrence did not reach statistical significance (p = 0.078). Indefinite anticoagulation (p < 0.001 and p = 0.008, respectively) and vitamin K antagonist (VKA) use (p < 0.001 in both cases) were more common in SN-APS/SP-aPL. Conclusion SN-APS displayed more thrombosis recurrence, indefinite anticoagulation, and VKA use than controls without non-criteria manifestations. The presence of such features in patients with thrombosis and negative aPL may negatively impact their clinical course.

Clinical Significance of Staphylococcus aureus in a Single Positive Blood Culture Bottle

Clinical significance of a single positive blood culture bottle (SPBCB) with Staphylococcus aureus is unclear. We aimed to assess the significance of a SPBCB by looking at the associated outcomes. We performed a retrospective, multicenter study of patients with a SPBCB with S. aureus using data collected from both electronic health records and the clinical microbiology laboratory. Overall, 534 patients with S. aureus bacteremia were identified and 118 (22.1%) had a SPBCB. Among cases with a SPBCB, 106 (89.8%) were classified as clinically significant while 12 (10.2%) were considered contaminated or of unclear significance. A majority (92.4%) of patients received antibiotic therapy but patients with clinically significant bacteremia were treated with longer courses (25.9 vs 5.7 days, P&lt;0.001). Significant differences in both frequency of echocardiography (65.1% vs 84.6%, P&lt;0.001), and infective endocarditis diagnosis (3.8% vs 14.2%, P=0.002) were seen in those with a single positive blood culture bottle compared to those with multiple positive bottles. A longer hospital length of stay, and higher 90-day, 6-month, and 1-year mortality rates were seen in patients with multiple positive blood culture bottles. A SPBCB with S. aureus was common among our patients. While this syndrome has a more favorable prognosis as compared to those with multiple positive blood cultures, clinicians should remain concerned as it portends a risk of infective endocarditis and mortality.

Screening Patterns in Abusive Abdominal Trauma

Background: Diagnosis of abusive abdominal trauma (AAT) is often clinically occult. Abdominal CT is the preferred method to diagnose abdominal injuries. However, due to risk of ionizing radiation, and cost, it is performed only in selected children. Recently, elevated liver enzymes were used to screen for occult AAT, but its accuracy is unknown due to inconsistent methodology and results. Objective: To determine the accuracy of elevated liver enzymes (transaminases) in the diagnosis of AAT and if pancreatic enzymes and clinical findings help in patients’ selection for abdominal CT. Methods: A retrospective (2011-2020) study on children younger than 3 years suspected of child abuse. The study group included children that had abdominal CT for suspected AAT, while the control group included similar number of children randomized from 5208 children evaluated for child abuse without an abdominal CT. Patients who had an incomplete medical record, were evaluated for cardiac arrest, or had a CT without contrast were excluded. Results: AAT is rare 0.6% (30/5434) in children suspected of child abuse. Transaminases were obtained in 99.1% of the AAT patients and 55.3% of the control cases. 93.1% (27/29) patients with abdominal injuries had elevated transaminases. The specificity and sensitivity for the transaminases in detecting positive abdominal CT was 93.3% and 90.0%, respectively. Only one additional case was identified with elevated pancreatic enzymes and negative transaminases. There was no clinical or imaging findings that could differentiate between patients with negative and positive abdominal CT scans. Based only on elevated transaminases, 11 CT scans need to be performed for a single positive study. Conclusion/Potential Impact: Transaminases have high sensitivity in predicting AAT. Universal use of transaminases in all children suspected of child abuse may result in 11 CT scans for one positive study. Therefore, more clinical judgement is necessary in selecting patients for CT.

Transformation of magnetic data to the pole and vertical dip and a related apparent susceptibility transform: exact and approximate approaches

The dipolar character of magnetic data means that there is a high and a low associated with each source. The relative positions and sizes of these highs and lows, varies depending on the magnetic latitude or the inclination of the Earth’s magnetic field. One method for dealing with this complexity is to transform the data to what would collected if the inclination were vertical (as at the magnetic pole); a process that is unstable at low magnetic latitudes. Unfortunately, remanent magnetization adversely impacts the success of this transformation. A second approach is to calculate the analytic-signal amplitude (ASA) of the data, which creates a single positive feature for each source or edge, with the shape being only weakly dependent on the inclination and the presence of remanent magnetization. The ASA anomalies can appear to be relatively broad, so features sometimes merge together on map views of the ASA. A subsequent transformation of the ASA using an appropriate transforming tilt angle can generate a magnetic field of a body that is at the pole and has a vertical dip. The transformation is exact for contacts when calculated from the first-order ASA, but the sign of the transformed data can be incorrect depending on whether you are over one edge or the other edge of a discrete source body. Another, approximate transformation of the zeroth-order ASA does not have this issue and gives good results on synthetic data provided that any noise is handled appropriately. The resulting maps outline the magnetic source bodies and have amplitudes proportional to an apparent magnetic susceptibility. On field data from Black Hill, South Australia, the approximate transformation generates an image that is simple to interpret and enhances some features less obvious on other enhancements of the data.

Chromatin organizer SATB1 controls the cell identity of CD4+ CD8+ double-positive thymocytes by compacting super-enhancers

CD4+ and CD8+ double-positive (DP) thymocytes are at a crucial stage during the T cell development in the thymus. DP cells rearrange the T cell receptor gene Tcra to generate T cell receptors with TCRβ. Then DP cells differentiate into CD4 or CD8 single-positive (SP) thymocytes, Regulatory T cells, or invariant nature kill T cells (iNKT) according to the TCR signal. Chromatin organizer SATB1 is highly expressed in DP cells and plays an essential role in regulating Tcra rearrangement and differentiation of DP cells. Here we explored the mechanism of SATB1 orchestrating gene expression in DP cells. Single-cell RNA sequencing assay of SATB1-deficient thymocytes showed that the cell identity of DP thymocytes was changed, and the genes specifically highly expressed in DP cells were down-regulated. The super-enhancers regulate the expressions of the DP-specific genes, and the SATB1 deficiency reduced the super-enhancer activity. Hi-C data showed that interactions in super-enhancers and between super-enhancers and promoters decreased in SATB1 deficient thymocytes. We further explored the regulation mechanism of two SATB1-regulating genes, Ets2 and Bcl6, in DP cells and found that the knockout of the super-enhancers of these two genes impaired the development of DP cells. Our research reveals that SATB1 globally regulates super-enhancers of DP cells and promotes the establishment of DP cell identity, which helps understand the role of SATB1 in thymocyte development.