Phase-separated biomolecular condensates for biocatalysis.

Nature often uses dynamically assembling multienzymatic complexes called metabolons to achieve spatiotemporal control of complex metabolic reactions. Researchers are aiming to mimic this strategy of organizing enzymes to enhance the performance of artificial biocatalytic systems. Biomolecular condensates formed through liquid-liquid phase separation (LLPS) can serve as a powerful tool to drive controlled assembly of enzymes. Diverse enzymatic pathways have been reconstituted within catalytic condensates in vitro as well as synthetic membraneless organelles in living cells. Furthermore, in vivo condensates have been engineered to regulate metabolic pathways by selectively sequestering enzymes. Thus, harnessing LLPS for controlled organization of enzymes provides an opportunity to dynamically regulate biocatalytic processes.

Safety, Effectiveness, and Treatment Persistence of Subcutaneous Vedolizumab in IBD: A Multicenter Study From the United Kingdom.

BACKGROUND AND AIMS: Despite intravenous (IV) vedolizumab being established for treatment of inflammatory bowel disease (IBD), the novel subcutaneous (SC) route of administration may provide numerous incentives to switch. However, large-scale real-world data regarding the long-term safety and effectiveness of this strategy are lacking. METHODS: IBD patients on IV vedolizumab across 11 UK sites agreed to transition to SC injections or otherwise continued IV treatment. Data regarding clinical disease activity (Simple Clinical Colitis Activity Index, partial Mayo score, and modified Harvey-Bradshaw Index), biochemical markers (C-reactive protein and calprotectin), quality of life (IBD control), adverse events, treatment persistence, and disease-related outcomes (namely corticosteroid use, IBD-related hospitalization, and IBD-related surgery) were retrospectively collected from prospectively maintained clinical records at baseline and weeks 8, 24, and 52. RESULTS: Data from 563 patients (187 [33.2%] Crohn's disease, 376 [66.8%] ulcerative colitis; 410 [72.8%] SC, 153 [27.2%] IV) demonstrated no differences in disease activity, remission rates, and quality of life between the SC and IV groups at all time points. Drug persistence at week 52 was similar (81.1% vs 81.2%; P = .98), as were rates of treatment alteration due to either active disease (12.2% vs 8.9%; P = .38) or adverse events (3.3% vs 6.3%; P = .41). At week 52, there were equivalent rates of adverse events (9.8% vs 7.8%; P = .572) and disease-related outcomes. IBD control scores were equivalent in both IV-IV and IV-SC groups. CONCLUSIONS: Switching to SC vedolizumab appears as effective, safe, and well tolerated as continued IV treatment and maintains comparable disease control and quality of life as IV treatment at 52 weeks.

Endoscopic retrograde cholangiopancreatography-related complications: risk stratification, prevention, and management.

Endoscopic retrograde cholangiopancreatography (ERCP) plays a crucial role in the management of pancreaticobiliary disorders. Although the ERCP technique has been refined over the past five decades, it remains one of the endoscopic procedures with the highest rate of complications. Risk factors for ERCP-related complications are broadly classified into patient-, procedure-, and operator-related risk factors. Although non-modifiable, patient-related risk factors allow for the closer monitoring and instatement of preventive measures. Post-ERCP pancreatitis is the most common complication of ERCP. Risk reduction strategies include intravenous hydration, rectal nonsteroidal anti-inflammatory drugs, and pancreatic stent placement in selected patients. Perforation is associated with significant morbidity and mortality, and prompt recognition and treatment of ERCP-related perforations are key to ensuring good clinical outcomes. Endoscopy plays an expanding role in the treatment of perforations. Specific management strategies depend on the location of the perforation and the patient's clinical status. The risk of post-ERCP bleeding can be attenuated by preprocedural optimization and adoption of intra-procedural techniques. Endoscopic measures are the mainstay of management for post-ERCP bleeding. Escalation to angioembolization or surgery may be required for refractory bleeding. Post-ERCP cholangitis can be reduced with antibiotic prophylaxis in high risk patients. Bile culture-directed therapy plays an important role in antimicrobial treatment.

Prognostic impact of presenting symptoms of patients with hepatocellular carcinoma.

Introduction: It is not known if the nature, number and duration of presenting symptoms at diagnosis of hepatocellular carcinoma impact on overall survival. This study examines whether the presenting symptoms of hepatocellular carcinoma have a significant impact on prognosis. Methods: The study cohort comprised 725 patients with symptomatic hepatocellular carcinoma seen in our department since October 1983. Another 545 patients were diagnosed on surveillance or from incidental findings. Presenting symptoms at diagnosis were documented. A survival census was performed on 31 October 2015 with the national registry of deaths. Presenting symptoms were examined for association with overall survival using multivariable Cox regression analysis. Survival analysis was done by Kaplan-Meier method with log-rank testing. Bivariate Pearson correlation was used to look for any association between duration of symptoms and overall survival. Results: Patients with symptomatic hepatocellular carcinoma had a significantly shorter survival than those diagnosed incidentally or on screening (94.0 vs. 786.0 days, P < 0.001). Survival was shorter in patients presenting with fluid retention (56.0 vs. 118.0 days, P < 0.001), jaundice (48.0 vs. 94.0 days, P = 0.017) and two or more symptoms (P = 0.010). Pain was associated with better survival (P < 0.001). On multivariable Cox regression analysis, only fluid retention (hazard ratio [HR] 1.56, 95% confidence interval [CI] 1.30-1.87) and jaundice (HR 1.36, 95% CI 1.07-1.74) were independently associated with shorter survival. There was no significant relationship between the duration of symptoms and overall survival. Conclusion: Patients with hepatocellular carcinoma who present with fluid retention or jaundice have significantly shorter overall survival. This is useful in assessing patients at the time of diagnosis.

Simultaneous enhancement of multiple functional properties using evolution-informed protein design.

Designing optimized proteins is important for a range of practical applications. Protein design is a rapidly developing field that would benefit from approaches that enable many changes in the amino acid primary sequence, rather than a small number of mutations, while maintaining structure and enhancing function. Homologous protein sequences contain extensive information about various protein properties and activities that have emerged over billions of years of evolution. Evolutionary models of sequence co-variation, derived from a set of homologous sequences, have proven effective in a range of applications including structure determination and mutation effect prediction. In this work we apply one of these models (EVcouplings) to computationally design highly divergent variants of the model protein TEM-1 ß-lactamase, and characterize these designs experimentally using multiple biochemical and biophysical assays. Nearly all designed variants were functional, including one with 84 mutations from the nearest natural homolog. Surprisingly, all functional designs had large increases in thermostability and most had a broadening of available substrates. These property enhancements occurred while maintaining a nearly identical structure to the wild type enzyme. Collectively, this work demonstrates that evolutionary models of sequence co-variation (1) are able to capture complex epistatic interactions that successfully guide large sequence departures from natural contexts, and (2) can be applied to generate functional diversity useful for many applications in protein design.

High spontaneous integration rates of end-modified linear DNAs upon mammalian cell transfection.

In gene therapy, potential integration of therapeutic transgene into host cell genomes is a serious risk that can lead to insertional mutagenesis and tumorigenesis. Viral vectors are often used as the gene delivery vehicle, but they are prone to undergoing integration events. More recently, non-viral delivery of linear DNAs having modified geometry such as closed-end linear duplex DNA (CELiD) have shown promise as an alternative, due to prolonged transgene expression and less cytotoxicity. However, whether modified-end linear DNAs can also provide a safe, non-integrating gene transfer remains unanswered. Herein, we compare the genomic integration frequency upon transfection of cells with expression vectors in the forms of circular plasmid, unmodified linear DNA, CELiDs with thioester loops, and Streptavidin-conjugated blocked-end linear DNA. All of the forms of linear DNA resulted in a high fraction of the cells being stably transfected-between 10 and 20% of the initially transfected cells. These results indicate that blocking the ends of linear DNA is insufficient to prevent integration.

Regular feedback to individual endoscopists is associated with improved adenoma detection rate and other key performance indicators for colonoscopy.

Objective: Monitoring of key performance indicators (KPIs) is a vital element of endoscopy quality improvement. Adenoma detection rate (ADR) is considered the best marker for colonoscopic quality as it inversely correlates with subsequent colonic cancer incidence and mortality, while polyp detection rate (PDR) is an easier-to-calculate surrogate for ADR. This study assessed whether regular feedback to individual endoscopists about their KPIs improved departmental performance. Methods: Individual KPIs were calculated for a period of 8 years (January 2012-December 2019) and fed back to all endoscopists at 6 monthly intervals, alongside anonymised indicators for other endoscopists, aggregate departmental performance data and benchmarks. An automated natural language processing software (EndoMineR) was used to identify adenomas in pathology reports and calculate ADR. Linear regressions were calculated for departmental ADR, PDR and other KPIs at 6 monthly intervals. Results: 39 359 colonoscopies (average 2460 in every 6-month period, range 1799-3059) were performed by an average of 42 (range 34-50) endoscopists. A continuous improvement in collective performance including ADR (12.7%-21.0%, R2 0.92, p<0.001) and PDR (19.0%-29.6%, R2 0.77, p<0.001) was observed throughout the study. Other KPIs showed similar improvement. The detection of non-neoplastic polyps did not increase. When analysed separately, ADR and PDR appeared to improve for gastroenterologists and nurse endoscopists but not for surgeons. Conclusion: Regular feedback with individual and departmental KPIs was associated with improved ADR and overall performance throughout the 8-year study period. Concomitant monitoring of ADR and PDR may prevent 'gaming' behaviour and ensure that genuine improvement is achieved.

Comparative effectiveness of a second-line biologic in patients with ulcerative colitis: vedolizumab followed by an anti-TNF versus anti-TNF followed by vedolizumab.

Background: Sequential drug treatment with biological agents in ulcerative colitis (UC) is becoming increasingly complex. There are few studies comparing head-to-head outcomes in second-line treatments. The study assesses whether using anti-tumour necrosis factor (anti-TNF)-α therapy following the α4ß7 integrin blocker vedolizumab (VDZ) or VDZ after an anti-TNF has more favourable clinical outcomes in UC in a real-world outpatient setting. Methods: Patients with UC who were exposed to first-line anti-TNF (adalimumab or infliximab) or VDZ who subsequently switched to the alternate class between May 2013 and August 2020 were identified by reviewing patient databases at 10 hospitals. Data were collected retrospectively using patient records. Baseline demographics, disease activity indices, biochemical markers, endoscopic Mayo score, colectomy rates, treatment persistence and urgent hospital utilisation composite endpoint (UHUC) rates were examined over a 52-week period. Results: Second-line week 52 treatment persistence was higher in the VDZ group (71/81, 89%) versus the anti-TNF group (15/34, 44%; p=0.0001), as were week 52 colectomy-free survival (VDZ: 77/80, 96%, vs anti-TNF: 26/32, 81%; p=0.009), week 52 UHUC survival (VDZ: 68/84, 81%, vs anti-TNF: 20/34, 59%; p=0.002) and week 52 corticosteroid-free clinical remission (CFCR) rates (VDZ: 22/34, 65%, vs anti-TNF: 4/20, 20%; p=0.001). Conclusion: Compared with second-line anti TNF usage, the VDZ second-line cohort had significantly higher 52-week treatment persistence, UHUC survival, higher colectomy-free survival rates and higher week 52 CFCR. These data suggest that VDZ is an effective biologic in UC as a second-line therapy after anti-TNF exposure. It highlights the effect of biological order on clinically important outcomes.

Ultrastrong nanotwinned titanium alloys through additive manufacturing.

Titanium alloys, widely used in the aerospace, automotive and energy sectors, require complex casting and thermomechanical processing to achieve the high strengths required for load-bearing applications. Here we reveal that additive manufacturing can exploit thermal cycling and rapid solidification to create ultrastrong and thermally stable titanium alloys, which may be directly implemented in service. As demonstrated in a commercial titanium alloy, after simple post-heat treatment, adequate elongation and tensile strengths over 1,600 MPa are achieved. The excellent properties are attributed to the unusual formation of dense, stable and internally twinned nanoprecipitates, which are rarely observed in traditionally processed titanium alloys. These nanotwinned precipitates are shown to originate from a high density of dislocations with a dominant screw character and formed from the additive manufacturing process. The work here paves the way to fabricate structural materials with unique microstructures and excellent properties for broad applications.

Transnasal endoscopy: moving from endoscopy to the clinical outpatient-blue sky thinking in oesophageal testing.

Background: COVID-19 has severely affected UK endoscopy services with an estimate 86% loss of activity during the first wave. Subsequent delays in diagnostic and surveillance procedures highlight the need for novel solutions to tackle the resultant backlog. Transnasal endoscopy (TNE) provides an attractive option compared with conventional upper gastrointestinal endoscopy given its limited use of space, no sedation and reduced nursing resources. Our experience: We describe piloting and then establishing an outpatient model TNE service in the pandemic era and the implications on resource allocation, training and workforce. We also discuss our experiences and outline ways in which services can evolve to undertake more complex endoscopic diagnostic and therapeutic work. Over 90% of patients describe no discomfort and those who have previously experienced conventional transoral endoscopy preferred the transnasal approach. We describe a low complication rate (0.8%) comprising two episodes of mild epistaxis. The average procedure duration was reasonable (9.9±5.0 min) with full adherence to Joint Advisory Group quality standards. All biopsies assessed were deemed sufficient for diagnosis including those for surveillance procedures. Discussion: TNE can offer a safe, tolerable, high-quality service outside of a conventional endoscopy setting. Expanding procedural capacity without impacting on the current endoscopy footprint has great potential in recovering endoscopy services following the COVID-19 pandemic. Looking forward, TNE has potential to be used both within the endoscopy suite as part of therapeutic procedures, or outside of the endoscopy unit in outpatient clinics, community hospitals, or mobile units and to achieve this in a more sustainable and environmentally friendly way.

Natural and Designed Proteins Inspired by Extremotolerant Organisms Can Form Condensates and Attenuate Apoptosis in Human Cells.

Many organisms can survive extreme conditions and successfully recover to normal life. This extremotolerant behavior has been attributed in part to repetitive, amphipathic, and intrinsically disordered proteins that are upregulated in the protected state. Here, we assemble a library of approximately 300 naturally occurring and designed extremotolerance-associated proteins to assess their ability to protect human cells from chemically induced apoptosis. We show that several proteins from tardigrades, nematodes, and the Chinese giant salamander are apoptosis-protective. Notably, we identify a region of the human ApoE protein with similarity to extremotolerance-associated proteins that also protects against apoptosis. This region mirrors the phase separation behavior seen with such proteins, like the tardigrade protein CAHS2. Moreover, we identify a synthetic protein, DHR81, that shares this combination of elevated phase separation propensity and apoptosis protection. Finally, we demonstrate that driving protective proteins into the condensate state increases apoptosis protection, and highlights the ability of DHR81 condensates to sequester caspase-7. Taken together, this work draws a link between extremotolerance-associated proteins, condensate formation, and designing human cellular protection.

Filamentous chaperone protein-based hydrogel stabilizes enzymes against thermal inactivation.

We report a filamentous chaperone-based protein hydrogel capable of stabilizing enzymes against thermal inactivation. The hydrogel backbone consists of a thermostable chaperone protein, the gamma-prefoldin (γPFD) from Methanocaldococcus jannaschii, which self-assembles into a fibrous structure. Specific coiled-coil interactions engineered into the wildtype γPFD trigger the formation of a cross-linked network of protein filaments. The structure of the filamentous chaperone is preserved through the designed coiled-coil interactions. The resulting hydrogel enables entrapped enzymes to retain greater activity after exposure to high temperatures, presumably by virtue of the inherent chaperone activity of the γPFD.

COVID 19: Designing and conducting an online mini-multiple interview (MMI) in a dynamic landscape.

Introduction: The COVID-19 pandemic presented numerous, significant challenges for medical schools, including how to select the best candidates from a pool of applicants when social distancing and other measures prevented "business as usual" admissions processes. However, selection into medical school is the gateway to medicine in many countries, and it is critical to use processes which are evidence-based, valid and reliable even under challenging circumstances. Our challenge was to plan and conduct a multiple-mini interview (MMI) in a dynamic and stringent safe distancing context.Methods: This paper reports a case study of how to plan, re-plan and conduct MMIs in an environment where substantially tighter safe distancing measures were introduced just before the MMI was due to be delivered.Results: We report on how to design and implement a fully remote, online MMI which ensured the safety of candidates and assessors.Discussion: We discuss the challenges of this approach and also reflect on broader issues associated with selection into medical school during a pandemic. The aim of the paper is to provide broadly generalizable guidance to other medical schools faced with the challenge of selecting future students under difficult conditions.

CRISPR/Cas-directed programmable assembly of multi-enzyme complexes.

We describe a versatile CRISPR/Cas-based strategy to construct multi-enzyme complexes scaffolded on a DNA template in programmable patterns. Catalytically inactive dCas9 nuclease was used in combination with SpyCatcher-SpyTag chemistry to assemble enzymes in a highly modular fashion. Five enzymes comprising the violacein biosynthesis pathway were precisely organized in nanometer proximity; a notable increase in violacein production demonstrated the benefits of scaffolding.

Enhancing geriatric oncology training through a combination of novice mentoring and peer and near-peer mentoring: A thematic analysis ofmentoring in medicine between 2000 and 2017.

OBJECTIVES: Training in Geriatric Oncology is in crisis, facing increasing demands in the face of a growing population of older adults, a lack of trainers, and the need to adapt training to different settings and trainee needs. A combination of novice mentoring and near-peer and peer mentoring (C-NP mentoring) has been proposed to provide trainees with personalized training and additional support. This study proposes to evaluate the possibility of establishing a C-NP mentoring program in geriatric oncology, through extrapolation of data from well-established practices in Internal Medicine programs. MATERIALS AND METHODS: A systematic scoping review was carried out to provide scope of prevailing data and highlight the key processes behind effective C-NP mentoring programs. Six reviewers carried out independent literature searches on C-NP mentoring in medicine using Embase, ERIC, PubMed, and Scopus databases for articles published between 1st January 2000 and 31st December 2017. The Best Evidence Medical Education (BEME) collaboration guide and the STORIES (STructured apprOach to the Reporting In healthcare education of Evidence Synthesis) statement were used to develop a narrative from the thematic analysis of selected articles. Braun & Clarke (2006)'s approach to thematic analyses [1] and Sambunjak et al. (2010)'s approach of "negotiated consensual validation" were then used to identify the final list of themes. RESULTS: 3913 citations were identified, 133 full-text articles were reviewed, and fifteen full-text articles were included. Thematic analysis was employed to circumnavigate mentoring's context-specific nature and identified ten semantic themes including the need, outcomes, obstacles, and improvements for C-NP mentoring, mentee and mentor participation and training, and matching and mentoring processes. CONCLUSION: Data from this review allows the forwarding of the C-NP Mentoring Framework that will potentially enhance Geriatric Oncology training. The framework ensures a balance of consistency in recruitment, training, matching, pre-mentoring meetings, assessments processes, and flexibility to inculcate personalized aspects to the training and support. The C-NP Mentoring Framework will also enable effective oversight of the program and timely support of mentees in need.

Production of Multicomponent Protein Templates for the Positioning and Stabilization of Enzymes.

Harnessing the ability of proteins to self-assemble into complex structures has enabled the creation of templates for applications in nanotechnology. Protein templates can be used to position functional molecules in regular patterns with nanometer precision over large surface areas. A difficult but successful approach to building customizable protein templates involves designing novel protein-protein interfaces to join protein building blocks into ordered arrangements. This approach was illustrated recently by engineering the protein interfaces of a molecular chaperone to produce filamentous templates composed of repeating subunits. In this chapter, we describe how these multicomponent protein templates can be produced recombinantly, assembled into filaments, and used as material templates. The templates enable the positioning and alignment of functional molecules at varying distances along the length of the filament, which can be demonstrated using a Förster resonance energy transfer (FRET) assay. In addition, we describe a method to quantify the chaperone ability of these filaments to stabilize and protect other proteins from thermal-induced aggregation-a useful property for bionanotechnology applications that involve molecular scaffolds for positioning and stabilizing enzymes.

Comparison of Corneal Epithelial and Stromal Thickness between Keratoconic and Normal Eyes in an Asian Population.

PURPOSE: To assess corneal epithelial and stromal thickness in keratoconic and normal eyes by spectral domain optical coherence tomography (SDOCT) in an Asian population. METHODS: Forty-three keratoconic and 24 normal eyes were studied and examined using SDOCT. Keratoconic eyes with corneal scarring were excluded. Epithelial and stromal thickness was assessed at 25 points, 0.5 mm apart, across the central 6 mm of the pupil centre in the horizontal and vertical meridians. The correlation between epithelial and stromal thickness in both keratoconic and normal eyes (at the corneal centre) was also assessed. RESULTS: The corneal epithelium at the pupil centre was significantly thinner in keratoconic eyes (p < 0.05) than in controls. Epithelial thickness varied widely in keratoconic eyes compared to controls (p < 0.05). The epithelium and stroma were significantly thinner inferiorly and temporally in keratoconic eyes (p < 0.05). There was a significant correlation between epithelial and stromal thickness (at the pupil centre) in the keratoconus group (rs = 0.348, p < 0.001) but not the normal group (rs = 0.036, p = 0.376). CONCLUSIONS: Corneal epithelial thickness was markedly thinner and varied in keratoconic eyes compared to controls. Epithelial thinning occurred secondary to the abnormal elevation of the stroma. These findings are useful in detecting early keratoconus and in the evaluation of refractive surgery candidates.

Rifaximin reduces the incidence of spontaneous bacterial peritonitis, variceal bleeding and all-cause admissions in patients on the liver transplant waiting list.

BACKGROUND: Rifaximin reduces the risk of overt hepatic encephalopathy (HE) and is associated with significant reductions in hospitalisations and 30-day readmissions. AIM: To examine the outcomes of patients listed for liver transplantation with a diagnosis of HE on rifaximin compared to those naïve to the drug. METHODS: Patient records of those listed for liver transplantation over a 2-year period were retrospectively reviewed. Patients were included if they had at least two episodes of overt HE resulting in hospitalisation or were encephalopathic at the time of assessment. RESULTS: Of the 622 patients listed for transplantation, 101 had HE. Sixty-six patients were treated with rifaximin and 35 were naïve at listing. The use of concurrent lactulose was not significantly different between groups. Median MELD score was similar (15 [14-16)] rifaximin-treated and 16 [14-18] rifaximin-naïve). Patients on the waiting list treated with rifaximin had reduced all-cause admissions, episodes of spontaneous bacterial peritonitis and variceal bleeding. Mean length of stay was 9 days (95% CI 6-12) in the rifaximin-treated group vs 14 (95% CI 7-21) in the rifaximin-naïve group. Multivariate regression analysis demonstrated that rifaximin was independently associated with an increase in average days to readmission (adjusted effect estimate 71, 95% CI 3-140 days) and reduced likelihood of requirement for prioritisation on the waiting list (odds ratio 0.29; 95% CI 0.89-0.93). CONCLUSION: Rifaximin prescribed for HE in patients listed for liver transplantation improved outcomes with significant reduction in admissions related to spontaneous bacterial peritonitis, ascites and variceal bleeding.

Enhanced Enzyme Activity through Scaffolding on Customizable Self-Assembling Protein Filaments.

Precisely organized enzyme complexes are often found in nature to support complex metabolic reactions in a highly efficient and specific manner. Scaffolding enzymes on artificial materials has thus gained attention as a promising biomimetic strategy to design biocatalytic systems with enhanced productivity. Herein, a versatile scaffolding platform that can immobilize enzymes on customizable nanofibers is reported. An ultrastable self-assembling filamentous protein, the gamma-prefoldin (γ-PFD), is genetically engineered to display an array of peptide tags, which can specifically and stably bind enzymes containing the counterpart domain through simple in vitro mixing. Successful immobilization of proteins along the filamentous template in tunable density is first verified using fluorescent proteins. Then, two different model enzymes, glucose oxidase and horseradish peroxidase, are used to demonstrate that scaffold attachment could enhance the intrinsic catalytic activity of the immobilized enzymes. Considering the previously reported ability of γ-PFD to bind and stabilize a broad range of proteins, the filament's interaction with the bound enzymes may have created a favorable microenvironment for catalysis. It is envisioned that the strategy described here may provide a generally applicable methodology for the scaffolded assembly of multienzymatic complexes for use in biocatalysis.

Engineering bioorthogonal protein-polymer hybrid hydrogel as a functional protein immobilization platform.

We demonstrate the synthesis of protein-polymer hybrid hydrogel that can be used as a platform for immobilizing functional proteins. Orthogonal chemistry was employed for cross-linking the hybrid network and conjugating proteins to the gel backbone, allowing for the convenient, one-pot formation of a functionalized hydrogel. The resulting hydrogel had tunable mechanical properties, was stable in solution, and biocompatible.