Faculty Bibliography

The de novo design of three protein chains that associate to form a heterotrimer (but not any of the possible two-chain heterodimers) and that can drive the assembly of higher-order branching structures is an important challenge for protein design. We designed helical heterotrimers with specificity conferred by buried hydrogen bond networks and large aromatic residues to enhance shape complementary packing. We obtained ten designs for which all three chains cooperatively assembled into heterotrimers with few or no other species present. Crystal structures of a helical bundle heterotrimer and extended versions, with helical repeat proteins fused to individual subunits, showed all three chains assembling in the designed orientation. We used these heterotrimers as building blocks to construct larger cyclic oligomers, which were structurally validated by electron microscopy. Our three-way junction designs provide new routes to complex protein nanostructures and enable the scaffolding of three distinct ligands for modulation of cell signaling.

BACKGROUND:The quality of evidence of the orthopedic literature has been often called into question. The fragility index (FI) has emerged as a means to evaluate the robustness of a significant result. Similarly, reverse fragility index (RFI) can be used for nonsignificant results to evaluate whether one can confidently conclude that there is no difference between groups. The analysis of FI and RFI in proximal humerus fracture (PHF) management is of particular interest, given ongoing controversy regarding optimal management and patient selection. The aim of this study was to report the FI, RFI and quality of the evidence in the proximal humerus fracture literature. METHODS:A systematic review was conducted based on the PRISMA (preferred reporting items for systematic reviews and meta-analyses) guidelines, which utilized EMBASE, MEDLINE and Cochrane Library databases. Inclusion criteria included randomized controlled clinical trials related to the management of proximal humerus fractures, published from 2000 to 2020 with dichotomous outcome measures and 1:1 allocation. The FI and RFI were calculated by successively changing one nonevent to an event for each outcome measure until the result was made nonsignificant or significant, respectively. The fragility quotient, (FQ), calculated by dividing the FI by the total sample size, was calculated as well. RESULTS:There were 25 studies that met our criteria with 48 outcome measures recorded. A total of 21 studies had at least one fragile result, with ten studies including a fragile result in the conclusion of the abstract. A total of 31 outcome measures had nonsignificant results and the median RFI was found to be 4, with 71% greater than number of patients lost to follow up. Seventeen outcomes had significant results, with a median FI of 1, with 65% greater than or equal to the number patients lost to follow up. A total of 18 of 25 studies (72%) included a power analysis. In particular, ten studies reported a statistical analysis of complication rates, 90% of which were fragile. The median FQ was found to be 0.037. CONCLUSIONS:The literature on PHF management is frequently fragile. Outcome measures are often fragile, particularly with regards to comparing complication rates and reoperation rates in treatment arms. Comparing to the studies in other subspecialties PHF RCTs are relatively more fragile and underpowered. Standardized reporting of FI, FQ and RFI can help the reader to reliably draw conclusions based on the fragility of outcome measures.

Evidence of comparing neural network differences between anxiety disorder subtypes is limited, while it is crucial to reveal the pathogenesis of anxiety disorders. The present study aimed to investigate specific and common resting-state functional connectivity (FC) networks in generalized anxiety disorder (GAD), panic disorder (PD), and healthy controls (HC). We employed the gRAICAR algorithm to decompose the resting-state fMRI into independent components and align the components across 61 subjects (22 GAD, 18 PD and 21 HC). The default mode network and precuneus network exhibited GAD-specific aberrance, the anterior default mode network showed atypicality specific to PD, and the right fronto-parietal network showed aberrance common to GAD and PD. Between GAD-specific networks, FC between bilateral dorsolateral prefrontal cortex (DLPFC) was positively correlated with interoceptive sensitivity. In the common network, altered FCs between DLPFC and angular gyrus, and between orbitofrontal cortex and precuneus, were positively correlated with anxiety severity and interoceptive sensitivity. The pathological mechanism of PD could closely relate to the dysfunction of prefrontal cortex, while GAD could involve more extensive brain areas, which may be related to fear generalization.

The incidence of esophageal adenocarcinoma (EA) has drastically increased in the United States since 1970s for unclear reasons. We hypothesized that the widespread usage of antibiotics has increased the procarcinogenic potential of the orodigestive microbiota along the sequence of gastroesophageal reflux (GR), Barrett's esophagus (BE) and EA phenotypes. This case control study included normal controls (NC) and three disease phenotypes GR, BE and EA. Microbiota in the mouth, esophagus, and stomach, and rectum were analyzed using 16S rRNA gene sequencing. Overall, we discovered 44 significant pairwise differences in abundance of microbial taxa between the four phenotypes, with 12 differences in the mouth, 21 in the esophagus, two in the stomach, and nine in the rectum. Along the GR→BE→EA sequence, oral and esophageal microbiota were more diversified, the dominant genus Streptococcus was progressively depleted while six other genera Atopobium, Actinomyces, Veillonella, Ralstonia, Burkholderia and Lautropia progressively enriched. In NC, Streptococcus appeared to control populations of other genera in the foregut via numerous negative and positive connections, while in disease states, the rich network was markedly simplified. Inferred gene functional content showed a progressive enrichment through the stages of EA development in genes encoding antibiotic resistance, ligands of Toll-like and NOD-like receptors, nitrate-nitrite-nitric oxide pathway and acetaldehyde metabolism. The orodigestive microbiota is in a progressive dysbiotic state along the GR-BE-EA sequence. The increasing dysbiosis and antibiotic and procarcinogenic genes in the disease states warrants further study to define their roles in EA pathogenesis.

Lymphangiogenesis is a dynamic process that involves the directed migration of lymphatic endothelial cells (LECs) to form lymphatic vessels. The molecular mechanisms that underpin lymphatic vessel patterning are not fully elucidated and, to date, no global regulator of lymphatic vessel guidance is known. In this study, we identify the transmembrane cell signalling receptor Plexin D1 (Plxnd1) as a negative regulator of both lymphatic vessel guidance and lymphangiogenesis in zebrafish. plxnd1 is expressed in developing lymphatics and is required for the guidance of both the trunk and facial lymphatic networks. Loss of plxnd1 is associated with misguided intersegmental lymphatic vessel growth and aberrant facial lymphatic branches. Lymphatic guidance in the trunk is mediated, at least in part, by the Plxnd1 ligands, Semaphorin 3AA and Semaphorin 3C. Finally, we show that Plxnd1 normally antagonises Vegfr/Erk signalling to ensure the correct number of facial LECs and that loss of plxnd1 results in facial lymphatic hyperplasia. As a global negative regulator of lymphatic vessel development, the Sema/Plxnd1 signalling pathway is a potential therapeutic target for treating diseases associated with dysregulated lymphatic growth.

BACKGROUND:Potential complications of pelvic flow disruption during aortic aneurysm repair include buttock ischemia and mesenteric ischemia. Unilateral or bilateral hypogastric artery flow interruption, either from atherosclerosis or intentionally to facilitate aneurysm repair, is considered problematic in endovascular repair; however, it has not been well studied in open abdominal aortic aneurysm (AAA) repair (OAR). We sought to examine the effect of interruption of flow to one or both hypogastric arteries on outcomes after OAR. METHODS:The Society for Vascular Surgery Quality Initiative database was queried for all patients undergoing elective open AAA repair between 2003 and 2020. (redundant) Patients with appropriate data on their hypogastric arteries postoperatively were stratified into two groups-patent bilaterally (normal pelvic perfusion, NPP) and unilateral or bilateral occlusion or ligation (compromised pelvic perfusion, CPP). Primary endpoints were 30-day major morbidity (myocardial infarction, respiratory complications, renal injury, and lower extremity or intestinal ischemia) and mortality. RESULTS:During the study period, 9.492 patients underwent elective open AAA repair-860 (9.1%) with compromised pelvic perfusion and 8,632 (90.9%) with patent bilateral hypogastric arteries. The groups had similar cardiac risk factors, including a history of coronary artery disease, prior coronary intervention, and the use of P2Y12 inhibitors and statins. A majority of patients in the CPP cohort had concurrent iliac aneurysms (63.3% vs. 24.8%; P < 0.001). The perioperative mortality was significantly higher in patients with compromised pelvic perfusion (5.5% vs. 3.1%; P < 0.001). Bilateral flow interruption had a trend toward higher perioperative mortality compared to unilateral interruption (7.1% vs. 4.7%; P < 0.147). The CPP group also had increased rates of myocardial injury (6.7% vs. 4.7%; P = 0.012), renal complications (18.9% vs. 15.9%; P = 0.024), leg and bowel ischemia (3.5% vs. 2.1%; P = 0.008; and 5.7% vs. 3.4%; P < 0.001, respectively). On multivariable analysis, CPP was associated with increased perioperative mortality (OR 1.47, CI 1.14-1.88, P = 0.003). On Kaplan-Meier analysis, there was no difference in survival at 2 years postdischarge between the NPP and CPP cohorts (86.1% vs. 87.5%, log-rank P = 0.275). CONCLUSIONS:Compromised pelvic perfusion is associated with increased perioperative complications and higher mortality in patients undergoing OAR. The sequelae of losing pelvic perfusion, in addition to the presence of more complex atherosclerotic and aneurysmal disease resulting in more difficult dissection, likely contribute to these findings. Thus, patients considered for OAR who have occluded hypogastric arteries or aneurysmal involvement of the hypogastric artery preoperatively may be candidates for more conservative management beyond traditional size criteria.

INTRODUCTIONS:Excessive mechanical stress is closely associated with cell death in various conditions. Exposure of chondrocytes to excessive mechanical loading leads to a catabolic response as well as exaggerated cell death. Ferroptosis is a recently identified form of cell death during cell aging and degeneration. However, it's potential association with mechanical stress remains to be illustrated. OBJECTIVES:To identify whether excessive mechanical stress can cause ferroptosis. To explore the role of mechanical overloading in chondrocyte ferroptosis. METHODS:) mice OA model and chondrocytes cultured with high strain mechanical stress. Furthermore, the role of Piezo1 ion channel in chondrocyte ferroptosis and OA development was explored by using its inhibitor (GsMTx4) and agonist (Yoda1). Additionally, chondrocyte was cultured in calcium-free medium with mechanical stress, and ferroptosis phenotype was tested. RESULTS:Human cartilage and mouse chondrocyte experiments revealed that mechanical overloading can induce GPX4-associated ferroptosis. Conditional knockout of GPX4 in cartilage aggravated experimental OA process, while additional treatment with ferroptosis suppressor protein (FSP-1) and coenzyme Q10 (CoQ10) abated OA development in GPX4-CKO mice. In mouse OA model and chondrocyte experiments, inhibition of Piezo1 channel activity increased GPX4 expression, attenuated ferroptosis phenotype and reduced the severity of osteoarthritis. Additionally, high strain mechanical stress induced ferroptosis damage in chondrocyte was largely abolished by blocking calcium influx through calcium-free medium. CONCLUSIONS:Our findings show that mechanical overloading induces ferroptosis through Piezo1 activation and subsequent calcium influx in chondrocytes, which might provide a potential target for OA treatment.

This report provides an overview of the discussions, presentations, and consensus thinking from the Workshop on Smart Data Collection for CryoEM held at the New York Structural Biology Center on April 6-7, 2022. The goal of the workshop was to address next generation data collection strategies that integrate machine learning and real-time processing into the workflow to reduce or eliminate the need for operator intervention.

PURPOSE/UNASSIGNED:Faculty modeling of desired behaviors has historically been a part of the apprenticeship model of clinical teaching, yet little is known about best practices for modeling. This study compared the educational impact of implicitly versus explicitly modeled communication skills among U.S. medical students. METHOD/UNASSIGNED:Fourth-year medical students from six U.S. academic medical centers were randomly assigned one simulated clinical encounter in which faculty provided either implicit or explicit modeling of important communication skills. Outcomes were assessed by electronic surveys immediately before and after the simulations. Students were blinded to the purpose of the study. RESULTS/UNASSIGNED: = 0.002). Participating faculty stated they would modify their teaching approach in response to their experiences in the study. CONCLUSIONS/UNASSIGNED:In a multi-center randomized trial, explicit faculty role-modeling led to greater uptake of communication knowledge, greater recognition of skills, and a greater sense that faculty expected these skills to be adopted by students. These results must be considered in the context, however, of a simulated environment and a short timeframe for assessing learning with students who volunteered for a simulated experience.

Cerebral malaria is a severe complication of Plasmodium falciparum infection characterized by the loss of blood-brain barrier (BBB) integrity, which is associated with brain swelling and mortality in patients. P. falciparum-infected red blood cells and inflammatory cytokines, like tumor necrosis factor alpha (TNF-α), have been implicated in the development of cerebral malaria, but it is still unclear how they contribute to the loss of BBB integrity. Here, a combination of transcriptomic analysis and cellular assays detecting changes in barrier integrity and endothelial activation were used to distinguish between the effects of P. falciparum and TNF-α on a human brain microvascular endothelial cell (HBMEC) line and in primary human brain microvascular endothelial cells. We observed that while TNF-α induced high levels of endothelial activation, it only caused a small increase in HBMEC permeability. Conversely, P. falciparum-infected red blood cells (iRBCs) led to a strong increase in HBMEC permeability that was not mediated by cell death. Distinct transcriptomic profiles of TNF-α and P. falciparum in HBMECs confirm the differential effects of these stimuli, with the parasite preferentially inducing an endoplasmic reticulum stress response. Our results establish that there are fundamental differences in the responses induced by TNF-α and P. falciparum on brain endothelial cells and suggest that parasite-induced signaling is a major component driving the disruption of the BBB during cerebral malaria, proposing a potential target for much needed therapeutics. IMPORTANCE Cerebral malaria is a severe complication of Plasmodium falciparum infection that causes the loss of blood-brain barrier integrity and frequently results in death. Here, we compared the effect of P. falciparum-infected red blood cells and inflammatory cytokines, like TNF-α, in the loss of BBB integrity. We observed that while TNF-α induced a small increase in barrier permeability, P. falciparum-infected red blood cells led to a severe loss of barrier integrity. Our results establish that there are fundamental differences in the responses induced by TNF-α and P. falciparum on brain endothelial cells and suggest that parasite-induced signaling is a major component driving the disruption of the BBB during cerebral malaria, proposing a potential target for much needed therapeutics.