A Patient-Centered Textbook Outcome Measure Effectively Discriminates Contemporary Elective Open Abdominal Aortic Aneurysm Repair Quality.

INTRODUCTION: There is persistent controversy surrounding the merit of surgical volume benchmarks being used solely as a sufficient proxy for assessing the quality of open abdominal aortic aneurysm (AAA) repair. Importantly, operative volume quotas may fail to reflect a more nuanced and comprehensive depiction of surgical outcomes most relevant to patients. Accordingly, we herein propose a patient-centered "textbook outcome" (TO) for AAA repair that is analogous to other large magnitude extirpative operations performed in other surgical specialties, and test its feasibility to discriminate hospital performance using Society for Vascular Surgery (SVS) volume guidelines. METHODS: All elective open infrarenal AAA repairs (OAR) in the SVS-Vascular Quality Initiative were examined (2009-2022). The primary end-point was a TO, defined as a composite of no in-hospital complication or re-intervention/re-operation, length of stay ≤ 10-days, home discharge and 1-year survival. The discriminatory ability of the TO measure was assessed by comparing centers that did or did not meet the SVS annual OAR volume threshold recommendation (high-volume ≥ 10 OARs/year; low-volume <10 OARs/year). Logistic regression and multivariable models adjusted for patient and procedure-related differences. RESULTS: A total of 9,657 OARs across 198 centers were analyzed (mean age-69.5±8.4, female-26%, non-white-12%). A TO was identified in 44% (N = 4,293) of the overall cohort. The incidence of individual TO components included: no in-hospital complication (61%), no in-hospital re-intervention/re-operation (92%), LOS ≤ 10-days (78%), home discharge (76%), and 1-year survival (91%). Median annual center volume was 6 [IQR 3, 10] and a majority of centers did not meet the SVS volume suggested threshold (<10 OARs/year: N = 148 [74%]). However, most patients (N = 6,265 of 9,657 [65%]) underwent OAR in high-volume hospitals. When comparing high and low-volume centers, a TO was more likely to occur in high-volume institutions: ≥10 OARs/year, 46% vs. <10 OARs/year, 42%; P=.0006. The association of a protective effect for higher center volume remained after risk adjustment: OR 1.1, 95%CI 1.05-1.26; P=.003. CONCLUSIONS: Textbook outcomes for elective OAR reflect a more nuanced and comprehensive patient centered proxy to measure care delivery consistent with other surgical specialties. Surprisingly, a TO was achieved in < 50% of elective AAA cases nationally. Though the likelihood of a TO appears to correlate with SVS center volume recommendations, it more importantly reflects elements which may be prioritized by patients and thus offers insights into further improving real-world AAA care.

Preoperative risk factors for 1-year mortality in patients undergoing fenestrated endovascular aortic aneurysm repair in the US Aortic Research Consortium.

BACKGROUND: Early survival (1-year) after elective repair of complex abdominal aortic aneurysms (AAA) or thoracoabdominal aortic aneurysms (TAAA) can be used as an indicator of successful repair and provides a reasonable countermeasure to the annual rupture risk based on diameter. We aimed to identify preoperative factors associated with 1-year mortality after fenestrated or branched endovascular aortic repair (F/BEVAR) and develop a predictive model for 1-year mortality based on patient-specific risk profiles. METHODS: The US-Aortic Research Consortium database was queried for all patients undergoing elective F/BEVAR for complex AAA (cAAA) or TAAA from 2005 to 2022. The primary outcome was 1-year survival based on preoperative risk profile. Multivariable Cox regression was used to determine preoperative variables associated with 1-year mortality overall and by extent of aortic pathology. Logistic regression was performed to build a predictive model for 1-year mortality based on number of risk factors present. RESULTS: A total of 2099 patients met the inclusion criteria for this study (cAAA: n = 709 [34.3%]; type 1-3 TAAA: n = 777 [37.6%]; type 4-5 TAAA: n = 580 [28.1%]). Multivariable Cox regression identified the following significant risk factors associated with 1-year mortality: current smoker, chronic obstructive pulmonary disease, congestive heart failure (CHF), aortic diameter >7 cm, age >75 years, extent 1-3, creatinine >1.7 mg/dL, and hematocrit <36%. When stratified by extent of aortic involvement, multivariable Cox regression revealed risk factors for 1-year mortality in cAAA (CHF maximum aortic diameter >7 cm, hematocrit <36 mg/dL, and current smoking status), type 1-3 TAAA (chronic obstructive pulmonary disease, CHF, and age >75 years), and type 4-5 TAAA (age >75 years, creatinine >1.7 mg/dL, and hematocrit <36 mg/dL). Logistic regression was then used to develop a predictive model for 1-year mortality based on patient risk profile. Appraisal of the model revealed an area under the curve of 0.64 (P < .001), and an observed to expected ratio of 0.85. CONCLUSIONS: This study describes multiple risk factors associated with an increase in 1-year mortality after F/BEVAR. Given that elective repair of cAAA or TAAA is offered to some patients in whom future rupture risk outweighs operative risk, these findings suggest that highly comorbid patients with smaller aneurysms may not benefit from repair. Descriptive and predictive models for 1-year mortality based on patient risk profiles can serve as an adjunct in clinical decision-making when considering elective F/BEVAR.

Distinct regions within SAP25 recruit O-linked glycosylation, DNA demethylation, and ubiquitin ligase and hydrolase activities to the Sin3/HDAC complex.

Epigenetic control of gene expression is crucial for maintaining gene regulation. Sin3 is an evolutionarily conserved repressor protein complex mainly associated with histone deacetylase (HDAC) activity. A large number of proteins are part of Sin3/HDAC complexes, and the function of most of these members remains poorly understood. SAP25, a previously identified Sin3A associated protein of 25 kDa, has been proposed to participate in regulating gene expression programs involved in the immune response but the exact mechanism of this regulation is unclear. SAP25 is not expressed in HEK293 cells, which hence serve as a natural knockout system to decipher the molecular functions uniquely carried out by this Sin3/HDAC subunit. Using molecular, proteomic, protein engineering, and interaction network approaches, we show that SAP25 interacts with distinct enzymatic and regulatory protein complexes in addition to Sin3/HDAC. While the O-GlcNAc transferase (OGT) and the TET1 /TET2/TET3 methylcytosine dioxygenases have been previously linked to Sin3/HDAC, in HEK293 cells, these interactions were only observed in the affinity purification in which an exogenously expressed SAP25 was the bait. Additional proteins uniquely recovered from the Halo-SAP25 pull-downs included the SCF E3 ubiquitin ligase complex SKP1/FBXO3/CUL1 and the ubiquitin carboxyl-terminal hydrolase 11 (USP11), which have not been previously associated with Sin3/HDAC. Finally, we use mutational analysis to demonstrate that distinct regions of SAP25 participate in its interaction with USP11, OGT/TETs, and SCF(FBXO3).) These results suggest that SAP25 may function as an adaptor protein to coordinate the assembly of different enzymatic complexes to control Sin3/HDAC-mediated gene expression.

Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes.

Ribonucleoprotein complexes are composed of RNA, RNA-dependent proteins (RDPs) and RNA-binding proteins (RBPs), and play fundamental roles in RNA regulation. However, in the human malaria parasite, Plasmodium falciparum, identification and characterization of these proteins are particularly limited. In this study, we use an unbiased proteome-wide approach, called R-DeeP, a method based on sucrose density gradient ultracentrifugation, to identify RDPs. Quantitative analysis by mass spectrometry identifies 898 RDPs, including 545 proteins not yet associated with RNA. Results are further validated using a combination of computational and molecular approaches. Overall, this method provides the first snapshot of the Plasmodium protein-protein interaction network in the presence and absence of RNA. R-DeeP also helps to reconstruct Plasmodium multiprotein complexes based on co-segregation and deciphers their RNA-dependence. One RDP candidate, PF3D7_0823200, is functionally characterized and validated as a true RBP. Using enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq), we demonstrate that this protein interacts with various Plasmodium non-coding transcripts, including the var genes and ap2 transcription factors.

Treatment Location Variation for Chronic Limb-Threatening Ischemia in Patients With Kidney Failure.

INTRODUCTION: End-stage kidney disease (ESKD) is an established risk factor for chronic limb-threatening ischemia (CLTI). Procedural location for ESKD patients has not been well described. This study aims to examine variation in index procedural location in ESKD versus non-ESKD patients undergoing peripheral vascular intervention for CLTI and identify preoperative risk factors for tibial interventions. METHODS: Chronic limb-threatening ischemia (CLTI) patients were identified in the Vascular Quality Initiative (VQI) peripheral vascular intervention dataset. Patient demographics and comorbidities were compared between patients with and without ESKD and those undergoing index tibial versus nontibial interventions. A multivariable logistic regression evaluating risk factors for tibial intervention was conducted. RESULTS: A total of 23,480 procedures were performed on CLTI patients with 13.6% (n = 3154) with ESKD. End-stage kidney disease (ESKD) patients were younger (66.56 ± 11.68 versus 71.66 ± 12.09 y old, P = 0.019), more often Black (40.6 versus 18.6%, P < 0.001), male (61.2 versus 56.5%, P < 0.001), and diabetic (81.8 versus 60.0%, P < 0.001) than non-ESKD patients. Patients undergoing index tibial interventions had higher rates of ESKD (19.4 versus 10.6%, P < 0.001) and diabetes (73.4 versus 57.5%, P < 0.001) and lower rates of smoking (49.9 versus 73.0%, P < 0.001) than patients with nontibial interventions. ESKD (odds ratio (OR) 1.67, 95% confidence interval (CI) 1.52-1.86, P < 0.001), Black race (OR 1.19, 95% CI 1.09-1.30, P < 0.001), and diabetes (OR 1.82, 95% CI 1.71-2.00, P < 0.001) were risk factors for tibial intervention. CONCLUSIONS: Patients with ESKD and CLTI have higher rates of diabetes and tibial disease and lower rates of smoking than non-ESKD patients. Tibial disease was associated with ESKD, diabetes, and Black race.

Distinct states of nucleolar stress induced by anticancer drugs.

Ribosome biogenesis is a vital and highly energy-consuming cellular function occurring primarily in the nucleolus. Cancer cells have an elevated demand for ribosomes to sustain continuous proliferation. This study evaluated the impact of existing anticancer drugs on the nucleolus by screening a library of anticancer compounds for drugs that induce nucleolar stress. For a readout, a novel parameter termed 'nucleolar normality score' was developed that measures the ratio of the fibrillar center and granular component proteins in the nucleolus and nucleoplasm. Multiple classes of drugs were found to induce nucleolar stress, including DNA intercalators, inhibitors of mTOR/PI3K, heat shock proteins, proteasome, and cyclin-dependent kinases (CDKs). Each class of drugs induced morphologically and molecularly distinct states of nucleolar stress accompanied by changes in nucleolar biophysical properties. In-depth characterization focused on the nucleolar stress induced by inhibition of transcriptional CDKs, particularly CDK9, the main CDK that regulates RNA Pol II. Multiple CDK substrates were identified in the nucleolus, including RNA Pol I- recruiting protein Treacle, which was phosphorylated by CDK9 in vitro. These results revealed a concerted regulation of RNA Pol I and Pol II by transcriptional CDKs. Our findings exposed many classes of chemotherapy compounds that are capable of inducing nucleolar stress, and we recommend considering this in anticancer drug development.

Ribosomes are cell structures within a compartment called the nucleolus that are required to make proteins, which are essential for cell function. Due to their uncontrolled growth and division, cancer cells require many proteins and therefore have a particularly high demand for ribosomes. Due to this, some anti-cancer drugs deliberately target the activities of the nucleolus. However, it was not clear if anti-cancer drugs with other targets also disrupt the nucleolus, which may result in side effects. Previously, it had been difficult to study how nucleoli work, partly because in human cells they vary naturally in shape, size, and number. Potapova et al. used fluorescent microscopy to develop a new way of assessing nucleoli based on the location and ratio of certain proteins. These measurements were used to calculate a "nucleolar normality score". Potapova et al. then tested over a thousand anti-cancer drugs in healthy and cancerous human cells. Around 10% of the tested drugs changed the nucleolar normality score when compared to placebo treatment, indicating that they caused nucleolar stress. For most of these drugs, the nucleolus was not the intended target, suggesting that disrupting it was an unintended side effect. Drugs inhibiting proteins called cyclin-dependent kinases caused the most drastic changes in the size and shape of nucleoli, disrupting them completely. These kinases are known to be involved in activating enzymes required for general transcription. Potapova et al. showed that they also are involved in production of ribosomal RNA, revealing an additional role in coordinating ribosome assembly. Taken together, the findings suggest that evaluating the effect of new anti-cancer drugs on the nucleolus could help to develop future treatments with less toxic side effects. The experiments also reveal new avenues for researching how cyclin-dependent kinases control the production of RNA more generally.

Interventions in Carotid Artery Surgery: An Overview of Current Management and Future Implications.

Atherosclerotic carotid artery disease has been well studied over the last half-century by multiple randomized controlled trials attempting to elucidate the appropriate modality of therapy for this disease process. Surgical techniques have evolved from carotid artery endarterectomy and transfemoral carotid artery stenting to the development of hybrid techniques in transcarotid artery revascularization. In this article, the authors provide a review of the available literature regarding operative and medical management of carotid artery disease.

Accidental central venous catheter cannulation into aberrant arterial anatomy requiring endovascular intervention.

Central venous catheter placement continues to be an extremely common procedure throughout hospital systems. Although ultrasound guidance can mitigate some placement risks, misplacement of lines into neighboring structures, such as arteries, remains an unfortunate complication. In this report, we will discuss an 83-year-old female with aberrant left subclavian artery and right sided arch, which provided for successful stent graft coverage of arterial injury secondary to accidental subclavian artery cannulation with a central venous catheter with preservation of the right common carotid artery and avoidance of a potentially morbid sternotomy.

Differences in Long-Term Outcomes in End-Stage Kidney Disease Patients with Chronic Limb-Threatening Ischemia.

BACKGROUND: End-stage kidney disease (ESKD) is a risk factor for peripheral arterial disease and major adverse limb events following infra-inguinal bypass. Despite comprising an important patient population, ESKD patients are rarely analyzed as a subgroup and are underrepresented in vascular surgery guidelines. This study aims to compare the long-term outcomes of patients with and without ESKD undergoing endovascular peripheral vascular intervention (PVI) for chronic limb-threatening ischemia (CLTI). METHODS: CLTI patients with and without ESKD from 2007-2020 were identified in the Vascular Quality Initiative PVI dataset. Patients with prior bilateral interventions were excluded. Patients undergoing femoral-popliteal and tibial interventions were included. Mortality, reintervention, amputation, and occlusion rates at 21 months following intervention were examined. Statistical analyses were completed with the t-test, chi-square, and Kaplan-Meier curves. RESULTS: The ESKD cohort was younger (66.4 ± 11.8 vs. 71.6 ± 12.1 years, P < 0.001) with higher rates of diabetes (82.2 vs. 60.9%, P < 0.001) the non-ESKD cohort. Long-term follow-up was available for 58.4% (N = 2,128 procedures) of ESKD patients and 60.8% (N = 13,075 procedures) of non-ESKD patients. At 21 months, ESKD patients had a higher mortality (41.7 vs. 17.4%, P < 0.001) and a higher amputation rate (22.3 vs. 7.1%, P < 0.001); however, they had a lower reintervention rate (13.2 vs. 24.6%, P < 0.001). CONCLUSIONS: CLTI patients with ESKD have worse long-term outcomes at 2 years following PVI than non-ESKD patients. Mortality and amputation are higher with ESKD, while the reintervention rate is lower. Development of guidelines within the ESKD population has the potential to improve limb salvage.

Investigating glycemic control in patients undergoing lower extremity bypass within an enhanced recovery pathway at a single institution.

BACKGROUND: Enhanced recovery pathways (ERPs) aim to lower perioperative stress to facilitate recovery. Limited fasting combined with carbohydrate loading is a common ERP element. The effect of limited fasting has not been elucidated in patients with diabetes. Given the known deleterious effects of poor glycemic control in the perioperative period, such as increased rates of surgical site infection, the associations of preoperative limited fasting with perioperative glycemic control and early outcomes after lower extremity bypass (LEB) were investigated. METHODS: A single institutional retrospective review of patients who underwent infrainguinal LEB from 2016 to 2022 was performed. The ERP was initiated in May 2018. Patients were stratified by diabetes diagnosis and preoperative hemoglobin A1C (HbA1C) levels. Perioperative glycemic control was compared between the limited fasting and traditional fasting patients (nil per os at midnight). Limited fasting was defined as a clear liquid diet until 2 hours before surgery with recommended carbohydrate loading consisting of 400 cc of a clear sports drink (approximately 30 g of carbohydrates). All limited fasting patients were within the ERP. Early perioperative hyperglycemia (EPH) was defined as blood glucose of >180 mg/dL within the first 24 hours of surgery. Perioperative outcomes such as surgical site infection, readmission, reinterventions, and complications were also compared. RESULTS: A total of 393 patients were included (limited fasting patients N = 135; traditional fasting patients N = 258). A trend toward EPH was seen in all limited fasting groups. Evaluating limited fasting within diabetic patients revealed that 74.5% of limited fasting-diabetic patients had EPH compared with 49.6% of traditional fasting-diabetic patients (P = .001). When stratified by the HbA1C level, a significantly higher rate of EPH was seen in the HbA1c >8.0% groups, with 90.5% in the limited fasting patients compared with 67.9% in traditional fasting patients (P = .05). Limited fasting-diabetic patients experience a longer postoperative length of stay at 5.0 days (interquartile range: 3, 9) vs 4.0 days (2, 6) in nondiabetic patients (P = .016). CONCLUSIONS: ERP limited fasting was associated with early perioperative hyperglycemia after LEB, particularly in patients with HbA1C >8.0%. Due to the high prevalence of diabetic patients undergoing LEB under ERP, the role of limited fasting and common glycemic elements of ERP may need to be re-evaluated in this subpopulation.

Circadian rhythm disruption linked to skeletal muscle dysfunction in the Mexican Cavefish.

It has become clear that circadian clocks in peripheral tissues play important functions. Disruption of the circadian clock in skeletal muscle, for example, results in insulin resistance, sarcomere disorganization, and muscle weakness1. Interestingly, cavefish, which exhibit a disrupted central clock, exhibit similar muscle phenotypes2,3,4, raising the question of whether they are caused by alterations to central or peripheral clocks. Here, we demonstrate a loss in clock function in the skeletal muscle of the Mexican Cavefish Astyanax mexicanus that is associated with reduced rhythmicity of a large number of genes and disrupted nocturnal protein catabolism. Some of the identified genes are associated with metabolic dysfunction in humans.

Circadian rhythm disruption is associated with skeletal muscle dysfunction within the blind Mexican Cavefish.

Circadian control of physiology and metabolism is pervasive throughout nature, with circadian disruption contributing to premature aging, neurodegenerative disease, and type 2 diabetes (Musiek et al. 2016; Panda, 2016). It has become increasingly clear that peripheral tissues, such as skeletal muscle, possess cell-autonomous clocks crucial for metabolic homeostasis (Gabriel et al. 2021). In fact, disruption of the skeletal muscle circadian rhythm results in insulin resistance, sarcomere disorganization, and muscle weakness in both vertebrates and non-vertebrates - indicating that maintenance of a functional muscle circadian rhythm provides an adaptive advantage. We and others have found that cavefish possess a disrupted central circadian rhythm and, interestingly, a skeletal muscle phenotype strikingly similar to circadian knock-out mutants; namely, muscle loss, muscle weakness, and insulin resistance (Olsen et al. 2022; Riddle et al. 2018; Mack et al. 2021). However, whether the cavefish muscle phenotype results from muscle-specific circadian disruption remains untested. To this point, we investigated genome-wide, circadian-regulated gene expression within the skeletal muscle of the Astyanax mexicanus - comprised of the river-dwelling surface fish and troglobitic cavefish - providing novel insights into the evolutionary consequence of circadian disruption on skeletal muscle physiology.

Serial Capture Affinity Purification and Integrated Structural Modeling of the H3K4me3 Binding and DNA Damage Related WDR76:SPIN1 Complex.

WDR76 is a multifunctional protein involved in many cellular functions. With a diverse and complicated protein interaction network, dissecting the structure and function of specific WDR76 complexes is needed. We previously demonstrated the ability of the Serial Capture Affinity Purification (SCAP) method to isolate specific complexes by introducing two proteins of interest as baits at the same time. Here, we applied SCAP to dissect a subpopulation of WDR76 in complex with SPIN1, a histone marker reader that specifically recognizes trimethylated histone H3 lysine4 (H3K4me3). In contrast to the SCAP analysis of the SPIN1:SPINDOC complex, H3K4me3 was copurified with the WDR76:SPIN1 complex. In combination with crosslinking mass spectrometry, we built an integrated structural model of the complex which revealed that SPIN1 recognized the H3K4me3 epigenetic mark while interacting with WDR76. Lastly, interaction network analysis of copurifying proteins revealed the potential role of the WDR76:SPIN1 complex in the DNA damage response. Teaser: In contrast to the SPINDOC/SPIN1 complex, analyses reveal that the WDR76/SPIN1 complex interacts with core histones and is involved in DNA damage.

Aortic visceral segment instability is evident following thoracic endovascular aortic repair for acute and subacute type B aortic dissection.

BACKGROUND: Anatomic remodeling within the thoracic aorta following thoracic endovascular aortic repair (TEVAR) for type B aortic dissection (TBAD) has been well documented. However, less is known about the response of the untreated visceral aorta. In the present study, we investigated the visceral aortic behavior after TEVAR for acute or subacute TBAD to identify any associations with the clinical outcomes. METHODS: A multicenter retrospective review was performed of all imaging studies for all patients who had undergone TEVAR for acute (0-14 days) and subacute (14-90 days) nontraumatic TBAD from 2006 to 2020. The cohort was inclusive of those with uncomplicated, high-risk, and complicated (defined in accordance with the Society for Vascular Surgery reporting guidelines) dissections. Centerline aortic measurements of the true and false lumen and total aortic diameter (TAD) were taken at standardized locations relative to the aortic anatomy within each aortic zone (the zones were defined by the Society for Vascular Surgery reporting guidelines). Diameter changes over time were evaluated using repeated measures mixed effects linear growth modeling. Visceral segment instability (VSI) was defined as any growth in the TAD of ≥5 mm within aortic zones 5 through 9. RESULTS: A total of 82 patients were identified. The median length of imaging follow-up was 2.1 years (interquartile range, 0.75-4.5 years), with 15% of the cohort having follow-up >5 years. VSI was present in 55% of the cohort, with an average maximal increase in the TAD of 10.4 ± 6.3 mm during a median follow-up of 2.1 years (interquartile range, 0.75-4.5 years). Approximately one third of the cohort had experienced rapid VSI (growth ≥5 mm in the first year), and 4.8% of the cohort had developed a large paravisceral aortic aneurysm (TAD ≥5 cm) secondary to VSI. Linear growth modeling identified significant predictable growth in the TAD across all visceral zones. Zone 7 had the highest rate of TAD dilation, with a fixed effect estimated rate of 1.3 mm/y (95% confidence interval [CI], 0.23-2.1; P = .022). The preoperative factor most strongly associated with VSI was a cumulative number of zones dissected of six or more (odds ratio, 6.4; 95% CI, 1.07-8.6; P = .041). The odds for aortic reintervention were significantly increased for cases in which VSI led to the development of a paravisceral aortic aneurysm of ≥5 cm (odds ratio, 3.7; 95% CI, 1.1-13; P = .038). CONCLUSIONS: VSI was identified in most patients who had undergone TEVAR for management of acute and subacute TBAD. The preoperative anatomic features such as the dissection extent, rather than the procedural details of graft coverage, might play a more significant role in VSI occurrence. Significant TAD growth had occurred in all visceral segments. These results highlight the importance of lifelong surveillance following TEVAR and identified a subset of patients who might have an increased risk of reintervention.

Intravascular Ultrasound for the Evaluation and Management of Retroperitoneal, Genitourinary Malignancies.

PURPOSE OF REVIEW: Herein we provide a review of intravascular ultrasound (IVUS) and its ability to assist in the evaluation and surgical management of advanced retroperitoneal, genitourinary tumors. RECENT FINDINGS: Advanced retroperitoneal tumors such as advanced renal cell carcinoma, bulky retroperitoneal lymphadenopathy associated with advanced testicular carcinoma, large adrenal tumors, and retroperitoneal sarcomas can invade, compress, or distort vascular anatomy making surgical resection challenging and high risk. Intravascular ultrasonography is commonly used by vascular and cardiothoracic surgery to provide a real time assessment of vascular invasion, compression, and aberrant anatomy to assist with pre-operative and/or intraoperative decision-making. However, the application of this technology to assist with cancer surgery has been limited. The use of intravascular ultrasound prior to radical, extirpative, retroperitoneal surgery involving large vessels can aid in the planning and execution of such challenging operations.

Perturbation of BRMS1 interactome reveals pathways that impact metastasis.

Breast Cancer Metastasis Suppressor 1 (BRMS1) expression is associated with longer patient survival in multiple cancer types. Understanding BRMS1 functionality will provide insights into both mechanism of action and will enhance potential therapeutic development. In this study, we confirmed that the C-terminus of BRMS1 is critical for metastasis suppression and hypothesized that critical protein interactions in this region would explain its function. Phosphorylation status at S237 regulates BRMS1 protein interactions related to a variety of biological processes, phenotypes [cell cycle (e.g., CDKN2A), DNA repair (e.g., BRCA1)], and metastasis [(e.g., TCF2 and POLE2)]. Presence of S237 also directly decreased MDA-MB-231 breast carcinoma migration in vitro and metastases in vivo. The results add significantly to our understanding of how BRMS1 interactions with Sin3/HDAC complexes regulate metastasis and expand insights into BRMS1's molecular role, as they demonstrate BRMS1 C-terminus involvement in distinct protein-protein interactions.

Dynamic changes in anaerobic digester metabolic pathways and microbial populations during acclimatisation to increasing ammonium concentrations.

Transitions in microbial community structure in response to increasing ammonia concentrations were determined by monitoring mesophilic anaerobic digesters seeded with a predominantly acetoclastic methanogenic community from a sewage sludge digester. Ammonia concentration was raised by switching the feed to source segregated domestic food waste and applying two organic loading rates (OLR) and hydraulic retention times (HRT) in paired digesters. One of each pair was dosed with trace elements (TE) known to be essential to the transition, with the other unsupplemented digester acting as a control. Samples taken during the trial were used to determine the metabolic pathway to methanogenesis using 14C labelled acetate. Partitioning of 14C between the product gases was interpreted via an equation to indicate the proportion produced by acetoclastic and hydrogenotrophic routes. Archaeal and selected bacterial groups were identified by 16S rRNA sequencing, to determine relative abundance and diversity. Acclimatisation for digesters with TE was relatively smooth, but OLR and HRT influenced both metabolic route and community structure. The 14C ratio could be used quantitatively and, when interpreted alongside archaeal community structure, showed that at longer HRT and lower loading Methanobacteriaceae were dominant and hydrogenotrophic activity accounted for 77% of methane production. At the higher OLR and shorter HRT, Methanosarcinaceae were dominant with the 14C ratio indicating simultaneous production of methane by acetoclastic and hydrogenotrophic pathways: the first reported observation of this in digestion under mesophilic conditions. Digesters without TE supplementation showed similar initial changes but, as expected failed to complete the transition to stable operation.

Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling.

The SNF2 family ATPase Amplified in Liver Cancer 1 (ALC1) is the only chromatin remodeling enzyme with a poly(ADP-ribose) (PAR) binding macrodomain. ALC1 functions together with poly(ADP-ribose) polymerase PARP1 to remodel nucleosomes. Activation of ALC1 cryptic ATPase activity and the subsequent nucleosome remodeling requires binding of its macrodomain to PAR chains synthesized by PARP1 and NAD+ A key question is whether PARP1 has a role(s) in ALC1-dependent nucleosome remodeling beyond simply synthesizing the PAR chains needed to activate the ALC1 ATPase. Here, we identify PARP1 separation-of-function mutants that activate ALC1 ATPase but do not support nucleosome remodeling by ALC1. Investigation of these mutants has revealed multiple functions for PARP1 in ALC1-dependent nucleosome remodeling and provides insights into its multifaceted role in chromatin remodeling.

Driving integrative structural modeling with serial capture affinity purification.

Streamlined characterization of protein complexes remains a challenge for the study of protein interaction networks. Here we describe serial capture affinity purification (SCAP), in which two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multistep affinity enrichment of specific protein complexes. The multifunctional capabilities of this protein-tagging system also permit in vivo validation of interactions using acceptor photobleaching Förster resonance energy transfer and fluorescence cross-correlation spectroscopy quantitative imaging. By coupling SCAP to cross-linking mass spectrometry, an integrative structural model of the complex of interest can be generated. We demonstrate this approach using the Spindlin1 and SPINDOC protein complex, culminating in a structural model with two SPINDOC molecules docked on one SPIN1 molecule. In this model, SPINDOC interacts with the SPIN1 interface previously shown to bind a lysine and arginine methylated sequence of histone H3. Our approach combines serial affinity purification, live cell imaging, and cross-linking mass spectrometry to build integrative structural models of protein complexes.

A Rapid, Sensitive, Low-Cost Assay for Detecting Hydrogenotrophic Methanogens in Anaerobic Digesters Using Loop-Mediated Isothermal Amplification.

Understanding how the presence, absence, and abundance of different microbial genera supply specific metabolic functions for anaerobic digestion (AD) and how these impact on gas production is critical for a long-term understanding and optimization of the AD process. The strictly anaerobic methanogenic archaea are essential for methane production within AD microbial communities. Methanogens are a phylogenetically diverse group that can be classified into three metabolically distinct lineages based on the substrates they use to produce methane. While process optimization based on physicochemical parameters is well established in AD, measurements that could allow manipulation of the underlying microbial community are seldom used as they tend to be non-specific, expensive, or time-consuming, or a combination of all three. Loop-mediated isothermal amplification (LAMP) assays combine a simple, rapid, low-cost detection technique with high sensitivity and specificity. Here, we describe the optimization of LAMP assays for the detection of four different genera of hydrogenotrophic methanogens: Methanoculleus, Methanothermobacter, Methanococcus, and Methanobrevibacter spp. By targeting archaeal elongation factor 2 (aEF2), these LAMP assays provide a rapid, low-cost, presence/absence indication of hydrogenotrophic methanogens that could be used as a real-time measure of process conditions. The assays were shown to be sensitive to 1 pg of DNA from most tested methanogen species, providing a route to a quantitative measure through simple serial dilution of samples. The LAMP assays described here offer a simple, fast, and affordable method for the specific detection of four different genera of hydrogenotrophic methanogens. Our results indicate that this approach could be developed into a quantitative measure that could provide rapid, low-cost insight into the functioning and optimization of AD and related systems.