bluuebunny/crossref_metadata_2025 huggingface dataset:
Predictability of Endoscopic Success for Foregut and Bariatric Leak in an Experienced Quaternary Center
Authors: Leeds Steven G , Chin Kevin , Rasmussen Madeline L , Bittle Anella K , Ogola Gerald O , Ward Marc A
Published: June 2022

BACKGROUND:

Leaks of the esophagus and stomach are difficult to manage and associated with significant morbidity and mortality. Endoscopic therapy can manage these leaks without surgical intervention. Our goal is to create a scoring tool to aid in predicting the success of endoscopic therapy in these patients.

STUDY DESIGN:

An IRB-approved prospectively maintained database was retrospectively reviewed for all patients treated for gastrointestinal leaks from July 2013 to January 2021, including patients treated for esophageal and stomach leaks. Endpoints include success of leak closure for patients treated solely by endoscopic therapy (ET) compared with surgical therapy as failed endoscopic therapy (FET). A multivariable logistic regression model was fitted to identify independent risk factors for predicting success of endoscopic therapy, and a scoring calculator was developed.

RESULTS:

There were 80 patients (60 females) with a mean age of 50 years. The ET group included 59 patients (74%), whereas the FET group included 21 patients (26%). Patient demographics, comorbidities, surgical history, and timing of leak diagnosis were used. Multivariable analysis resulted in 4 variables associated with higher probability of successful endoscopic leak management without need for additional surgery. These included increased age, lower BMI, lack of previous bariatric surgery, and quicker identification of the leak. Consequently, a scoring nomogram was developed with values from 0 to 22.

CONCLUSION:

Our data show the development of a scoring calculator capable of quantifying the likelihood of success treating foregut and bariatric leaks with endoscopic therapies. This can be used clinically to guide treatment decisions.
Operative Time and 30-Day Outcomes in Bariatric Surgery: Comparison between Robotic and Laparoscopic Approach: 4-Year MBSAQIP Database Analysis
Authors: Ho Katherine , Hsu Chiu-Hsieh , Maegawa Felipe , Ashouri Yazan , Ho Helen , Ajmal Saad , Ghaderi Iman
Published: June 2022

BACKGROUND:

The main criticism of robotic surgery is longer operative time (OT). The aim of this study was to examine the variables that determine OT, the association between OT and 30-day outcomes, and the effect of the robotic approach in bariatric surgery.

STUDY DESIGN:

MBSAQIP data for 2016 to 2019 were queried. Logistic regression was performed to examine the association between OT and outcomes for each surgical approach while adjusting for patients’ characteristics. The results of each fitted logistic regression model were reported as odds ratio and the associated 95% CI.

RESULTS:

A total of 666,182 patients underwent robotic sleeve gastrectomy (R-SG), laparoscopic sleeve gastrectomy, robotic Roux-en-Y gastric bypass (R-RYGB), laparoscopic Roux-en-Y gastric bypass, robotic duodenal switch (R-DS), and laparoscopic duodenal switch). More patients underwent laparoscopic surgery (89.7%) than robotic surgery (10.3%). OT for robotic cases was longer than for laparoscopic cases (p < 0.0001). Longer OT was associated with increased odds of adverse 30-day outcomes irrespective of the surgical approach. The association between OT and adverse outcomes was stronger in the laparoscopic cohort. There was no significant difference in postoperative outcomes when comparing the laparoscopic and robotic approaches after adjusting for OT, except a lower reoperation rate for R-SG (p = 0.03) and readmission rates in R-RYGB and R-DS (p < 0.01). The variability of OT was higher in the laparoscopic group and was more affected by the first assistant.

CONCLUSIONS:

The outcomes in robotic bariatric surgery were comparable with the laparoscopic approach despite longer OT. Use of robotic surgery decreased the variability in OT.
Asystole During Electroconvulsive Therapy
Authors: Hartnett Sophie , Rex Steffen , Sienaert Pascal
Published: June 2022

Asystole presenting at the start of electrical stimulus application during electroconvulsive therapy (ECT) is a relatively common occurrence. It is most likely caused by vagal nerve stimulation, affecting autonomic cardiac tone. This article reviews the effect of the electrode placement (EP) on the incidence and severity of bradycardia and asystole. A systematic literature review was conducted using the Embase and PubMed databases, up to September 2021, searching for studies evaluating the effect of EP on bradycardia and/or asystole during ECT. Nine case reports describing asystole in patients receiving ECT almost exclusively reported the association with bitemporal (BT) EP. One small descriptive study found no significant effect of EP on cardiac pauses. The results from 4 cohort studies, however, suggest that a right unilateral placement bears a higher risk for developing bradycardia and asystole than BT and bifrontal ECT. The available evidence suggests that right unilateral ECT holds a greater risk for the development of bradycardia and asystole than BT and bifrontal EP.
Mirror-Image Comparison of Maintenance Electroconvulsive Treatment Effectiveness in Affective and Psychotic Disorders
Authors: Bağcaz Arda , Başar Koray
Published: June 2022

Objectives

The study aimed to investigate the effectiveness of maintenance electroconvulsive therapy (mECT) with respect to the hospitalization duration, number of hospitalizations, and major and minor treatment changes with a mirror-image study design.

Methods

Medical charts of patients who received at least a 3-month-long course of mECT were reviewed. The records of 36 patients (17 with psychotic disorders, 19 with affective disorders) were retrospectively examined for 2 periods with the same duration; during the mECT (post-mECT) and before the mECT (pre-mECT). The hospitalization duration, the number of hospitalizations, and major and minor treatment changes, which were assumed to provide information on the effectiveness of the interventions, were recorded and compared between these periods. Statistical analysis was performed using generalized estimating equation models conducted with age, diagnostic category, and observation time as covariates. In addition, the relapse and recurrence rates and time to relapse/recurrence were analyzed.

Results

Comparison of pre-mECT and post-mECT periods revealed that mECT, applied in an individualized schedule combined with pharmacotherapy, was associated with a lower frequency (P < 0.001; rate ratio [RR], 0.161; 95% confidence interval [CI], 0.087–0.297), shorter duration of hospitalization (P < 0.001; RR, 0.123; 95% CI, 0.056–0.271), and lower number of major treatment changes (P = 0.007; RR, 0.522; 95% CI, 0.324–0.840), irrespective of diagnoses. The relapse/recurrence rates were similar in the 2 diagnostic categories (P = 1.000; 26.3% vs 29.4%).

Conclusions

Maintenance ECT should be increasingly considered an important treatment modality in patients with affective and psychotic disorders after an effective course of ECT.
No evidence of metabolic costs following adaptive immune activation or reactivation in house sparrows
Authors: Buttemer William A. , O'Dwyer Terence W. , Astheimer Lee B. , Klasing Kirk C. , Hoye Bethany J.
Published: June 2022

The energy cost of adaptive immune activation in endotherms is typically quantified from changes in resting metabolic rate following exposure to a novel antigen. An implicit assumption of this technique is that all variation in energy costs following antigenic challenge is due solely to adaptive immunity, while ignoring potential changes in the energy demands of ongoing bodily functions. We critically assess this assumption by measuring both basal metabolic rate (BMR) and exercise-induced maximal metabolic rate (MMR) in house sparrows before and after the primary and two subsequent vaccinations with either saline (sham) or two novel antigens (keyhole limpet haemocyanin and sheep red blood cells; KLH and SRBC, respectively). We also examined the effect of inducing male breeding levels of testosterone (T) on immune responses and their metabolic costs in both males and females. Although there was a moderate decrease in KLH antibody formation in T-treated birds, there was no effect of T on BMR, MMR or immunity to SRBC. There was no effect of vaccination on BMR but, surprisingly, all vaccinated birds maintained MMR better than sham-treated birds as the experiment progressed. Our findings caution against emphasizing energy costs or nutrient diversion as being responsible for reported fitness reductions following activation of adaptive immunity.
The bug in a teacup—monitoring arthropod–plant associations with environmental DNA from dried plant material
Authors: Krehenwinkel Henrik , Weber Sven , Künzel Sven , Kennedy Susan R.
Published: June 2022

Environmental DNA analysis (eDNA) has revolutionized the field of biomonitoring in the past years. Various sources have been shown to contain eDNA of diverse organisms, for example, water, soil, gut content and plant surfaces. Here we show that dried plant material is a highly promising source for arthropod community eDNA. We designed a metabarcoding assay to enrich diverse arthropod communities while preventing amplification of plant DNA. Using this assay, we analysed various commercially produced teas and herbs. These samples recovered ecologically and taxonomically diverse arthropod communities, a total of over a thousand species in more than 20 orders, many of them specific to their host plant and its geographical origin. Atypically for eDNA, arthropod DNA in dried plants shows very high temporal stability, opening up plant archives as a source for historical arthropod eDNA. Considering these results, dried plant material appears excellently suited as a novel tool to monitor arthropods and arthropod–plant interactions, detect agricultural pests and identify the geographical origin of imported plant material. The simplicity of our approach and the ability to detect highly diverse arthropod communities from all over the world in tea bags also highlights its utility for outreach purposes and to raise awareness about biodiversity.
Wave spectroscopy in a driven granular material
Authors: Berhanu Michael , Merminod Simon , Castillo Gustavo , Falcon Eric
Published: June 2022

Driven granular media constitute model systems in out-of-equilibrium statistical physics. By assimilating the motions of granular particles to those of atoms, by analogy, one can obtain macroscopic equivalent of phase transitions. Here, we study fluid-like and crystal-like two-dimensional states in a driven granular material. In our experimental device, a tunable magnetic field induces and controls remote interactions between the granular particles. We use high-speed video recordings to analyse the velocity fluctuations of individual particles in stationary regime. Using statistical averaging, we find that the particles self-organize into collective excitations characterized by dispersion relations in the frequency-wavenumber space. These findings thus reveal that mechanical waves analogous to condensed matter phonons propagate in driven granular media. When the magnetic coupling is weak, the waves are longitudinal, as expected for a fluid-like phase. When the coupling is stronger, both longitudinal and transverse waves propagate, which is typically seen in solid-like phases. We model the dispersion relations using the spatial distribution of particles and their interaction potential. Finally, we infer the elastic parameters of the granular assembly from equivalent sound velocities, thus realizing the spectroscopy of a granular material.
Whole genome sequencing of a wild yam species Dioscorea tokoro reveals a genomic region associated with sex
Authors: Natsume Satoshi , Yaegashi Hiroki , Sugihara Yu , Abe Akira , Shimizu Motoki , Oikawa Kaori , White Benjamen , Kudoh Aoi , Terauchi Ryohei
Published: June 2022

Dioscorea tokoro is a wild species distributed in East Asia including Japan. Typical of the genus Dioscorea, D. tokoro is dioecious with male and female flowers borne on separate individuals. To understand its sex determination system and to serve as a model species for population genomics of obligate outcrossing wild species, we set out to determine the whole genome sequence of the species. Here we show 443 Mb genome sequence of D. tokoro distributed over 2,931 contigs that were anchored on 10 linkage groups. Linkage analysis of sex in a segregating F1 family revealed a sex determination locus residing on Pseudochromosome 3 with XY-type male heterogametic sex determination system.
Impact of non-pharmaceutical interventions targeted at the COVID-19 pandemic on influenza activity in the UK Armed Forces
Authors: Otieno George , Rawlings Ngwa Niba
Published: June 2022

Introduction

Non-pharmaceutical interventions (NPIs) such as lockdown, social distancing and use of face coverings was adopted by the United Kingdom (UK) Armed Forces (AF) during the COVID-19 pandemic. This study assessed the impact of the use of NPIs on influenza activity in the UK AF.

Methods

A longitudinal study design was adopted, and secondary data was analysed retrospectively. Clinical Read codes for influenza-like illness (ILI) was used to generate data for flu seasons before and during the COVID-19 pandemic (September 2017 to April 2021).

Results

Before the COVID-19 pandemic, the rate of reporting ILI was ∼ 4% across all flu seasons. The count of ILI was 2.9%, 2.2% and 3.1% during 2017-18, 2018-19 and 2019-20 flu seasons respectively. During the COVID-19 pandemic, both the rate of reporting ILI (0.6%) and the count of ILI (0.5%) were significantly smaller (p < .001). The rate of reporting ILI was positively correlated with the count of ILI (r (2) = .97, p = .014). Influenza vaccination rate increased by 1.3% during the COVID-19 pandemic. vaccination rate was negatively correlated with the rate of reporting ILI (r (2) = -.52, p = 0.24) and the count of ILI (r (2) = -.61, p = 0.19). However, this correlation was not significant. The use of NPIs was negatively correlated with the rate of reporting ILI (r (2) = -.99, p = < .001) and the count of ILI (r (2) = -.95, p = 0.026). The overall multiple regression performed was statistically significant (R2= 0.94, F (1, 2) = 33.628, p = 0.028). The rate of reporting ILI significantly predicted the count of ILI (β = 0.609, p = 0.028) while vaccination rate did not significantly predict the count of ILI (β = -0.136, p = 0.677).

Conclusions

Influenza activity in the UK AF was significantly reduced during the COVID-19 pandemic. The use of NPIs and the rate of reporting ILI significantly reduced the count of ILI. Being vaccinated for influenza did not significantly reduce the count of ILI.
BRCA1/BRC-1 and SMC-5/6 regulate DNA repair pathway engagement during C. elegans meiosis
Authors: Toraason Erik , Salagean Alina , Almanzar David E. , Rog Ofer , Libuda Diana E.
Published: June 2022

The preservation of genome integrity during sperm and egg development is vital for reproductive success. During meiosis, the tumor suppressor BRCA1/BRC-1 and structural maintenance of chromosomes 5/6 (SMC-5/6) complex genetically interact to promote high fidelity DNA double strand break (DSB) repair, but the specific DSB repair outcomes these proteins regulate remain unknown. Here we show that BRCA1/BRC-1 and the SMC-5/6 complex limit intersister crossover recombination as well as error-prone repair pathways during meiotic prophase I. Using genetic and cytological methods to monitor repair of DSBs with different repair partners in Caenorhabditis elegans, we demonstrate that both BRC-1 and SMC-5/6 repress intersister crossover recombination events, with meiotic cells becoming more dependent upon these proteins to repair DSBs in late meiotic prophase I. Sequencing of conversion tracts from homolog-independent DSB repair events indicates that BRC-1 regulates intersister/intrachromatid noncrossover conversion tract length. Moreover, we find that BRC-1 also specifically inhibits error prone repair of DSBs induced at mid-pachytene. Finally, we reveal that functional BRC-1 enhances DSB repair defects in smc-5 mutants by repressing theta-mediated end joining (TMEJ). Taken together, our study illuminates the coordinate interplay of BRC-1 and SMC-5/6 to regulate DSB repair outcomes in the germline.
Distinct airway progenitor cells drive epithelial heterogeneity in the developing human lung
Authors: Conchola Ansley S. , Frum Tristan , Xiao Zhiwei , Hsu Peggy P. , Hein Renee F.C. , Miller Alyssa , Tsai Yu-Hwai , Wu Angeline , Kaur Kamika , Holloway Emily M. , Anand Abhinav , Murthy Preetish K. L. , Glass Ian , Tata Purushothama R. , Spence Jason R.
Published: June 2022

Recent advances using single cell genomic approaches have identified new epithelial cell types and uncovered cellular heterogeneity in the murine and human lung (1). Here, using scRNA-seq and microscopy we identify and describe a secretory-like cell that is enriched in the small airways of the developing human lung and identified by the unique co-expression of SCGB3A2/SFTPB/CFTR. To place these cells in the hierarchy of airway development, we apply a single cell barcode-based lineage tracing method track the fate of SCGB3A2/SFTPB/CFTR cells during airway organoid differentiation in vitro (2). Lineage tracing revealed that these cells have distinct developmental potential from basal cells, giving rise predominantly to pulmonary neuroendocrine cells (PNECs) and a subset of multiciliated cells distinguished by high C6 and low MUC16 expression. We conclude that SCGB3A2/SFTPB/CFTR cells act as a progenitor cell contributing to the cellular diversity and heterogeneity in the developing human airway.

SIGNIFICANCE STATEMENT

The current study identifies a novel secretory cell type that is present predominantly in the small airway of the developing human lung. These secretory cells are defined by co-expression of SCGB3A2/SFTPB/CFTR, and functional studies show that this cell gives rise to pulmonary neuroendocrine cells and a sub-population of multiciliated cells, thereby leading to cellular heterogeneity.
N1-Methylpseudouridine and pseudouridine modifications modulate mRNA decoding during translation
Authors: Monroe Jeremy G. , Mitchell Lili , Deb Indrajit , Roy Bijoyita , Frank Aaron T. , Koutmou Kristin
Published: June 2022

The ribosome relies on hydrogen bonding interactions between mRNA codons and incoming aminoacyl-tRNAs to ensure rapid and accurate protein production. The inclusion of chemically modified bases into mRNAs has the potential to alter the strength and pattern of hydrogen bonding between mRNAs and aminoacyl-tRNAs to alter protein synthesis. We investigated how the Nl-methylpseudouridine (m1Ψ) modification, commonly incorporated into therapeutic and vaccine mRNA sequences, influences the ability of codons to react with cognate and near-cognate tRNAs and release factors. We find that the presence of a single m1Ψ does not substantially change the rate constants for amino acid addition by cognate tRNAs or termination by release factors. However, insertion of m1Ψ can affect the selection of near-cognate tRNAs both in vitro and in human cells. Our observations demonstrate that m1Ψ, and the related naturally occurring pseudouridine (Ψ) modification, exhibit the ability to both increase and decrease the extent of amino acid misincorporation in a codon-position and tRNA dependent manner. To ascertain the chemical logic for our biochemical and cellular observations, we computationally modeled tRNAIle(GAU) bound to unmodified and m1Ψ- or Ψ-modified phenylalanine codons (UUU). Our modeling suggests that changes in the energetics of mRNA:tRNA interactions largely correlate with the context specificity of Ile-miscoding events we observe on Ψ and m1Ψ containing Phe codons. These studies reveal that the sequence context of a given modification within an mRNA plays a large role in determining how (and if) the modification impacts the number and distribution of proteoforms synthesized by the ribosome.
Enzymatic Specificity of Conserved Rho GTPase Deamidases Promotes Invasion ofVibrio parahaemolyticusat the Expense of Infection
Authors: Lafrance Alexander E. , Chimalapati Suneeta , Rodriguez Nalleli Garcia , Kinch Lisa N. , Kaval Karan Gautam , Orth Kim
Published: June 2022

Vibrio parahaemolyticusis among the leading causes of bacterial seafood-borne acute gastroenteritis. Like many intracellular pathogens,V. parahaemolyticusinvades host cells during infection by deamidating host small Rho GTPases. The Rho GTPase deamidating activity of VopC, a type three secretion system (T3SS) translocated effector, drivesV. parahaemolyticusinvasion. The intracellular pathogen uropathogenicEscherichia coli(UPEC) invades host cells by secreting a VopC homolog, the secreted toxin cytotoxic necrotizing factor one (CNF1). Because of the homology between VopC and CNF1, we hypothesized topical application of CNF1 duringV. parahaemolyticusinfection could supplement VopC activity. Here, we demonstrate that CNF1 improves the efficiency ofV. parahaemolyticusinvasion, a bottleneck inV. parahaemolyticusinfection, across a range of doses. CNF1 increasesV. parahaemolyticusinvasion independent of both VopC and the T3SS altogether, but leaves a disproportionate fraction of intracellular bacteria unable to escape the endosome and complete their infection cycle. This phenomenon holds true in the presence or absence of VopC, but is particularly pronounced in the absence of a T3SS. The native VopC, by contrast, promotes a far less efficient invasion, but permits the majority of internalized bacteria to escape the endosome and complete their infection cycle. These studies highlight the significance of enzymatic specificity during infection, as virulence factors (VopC and CNF1 in this instance) with similarities in function (bacterial uptake), catalytic activity (deamidation), and substrates (Rho GTPases) are not sufficiently interchangeable for mediating a successful invasion for neighboring bacterial pathogens.

IMPORTANCE

Many species of intracellular bacterial pathogens target host small Rho-GTPases to initiate invasion, including the human pathogensVibrio parahaemolyticusand uropathogenicEschericia coli(UPEC). The type three secretion system (T3SS) effector VopC ofV. parahaemolyticuspromotes invasion through the deamidation of Rac1 and CDC42 in the host, whereas the secreted toxin cytotoxic necrotizing factor one (CNF1) drives UPEC’s internalization through the deamidation of Rac1, CDC42, and RhoA. Despite these similarities in the catalytic activity of CNF1 and VopC, we observed the two enzymes were not interchangeable. Although CNF1 increasedV. parahaemolyticusendosomal invasion, most intracellularV. parahaemolyticusaborted their infection cycle and remained trapped in endosomes. Our findings illuminate how the precise biochemical fine-tuning of T3SS effectors is essential for efficacious pathogenesis. They moreover pave the way for future investigations into the biochemical mechanisms underpinningV. parahaemolyticusendosomal escape, and more broadly, the regulation of successful pathogenesis.
Helicobacter pylori chronic infection selects for effective colonizers of metaplastic glands
Authors: O’Brien VP , Jackson LK , Frick JP , Rodriguez Martinez AE , Jones DS , Johnston CD , Salama NR
Published: June 2022

Chronic gastric infection with Helicobacter pylori can lead to progressive tissue changes that culminate in cancer, but how H. pylori adapts to the changing tissue environment during disease development is not fully understood. In a transgenic mouse gastric metaplasia model, we found that strains from unrelated individuals differed in their ability to infect the stomach, to colonize metaplastic glands, and to induce proliferation and alter the expression of metaplasia-associated proteins. H. pylori isolates from different stages of disease from a single individual had differential ability to colonize healthy and metaplastic gastric glands. Exposure to the metaplastic environment selected for high gastric colonization by one of these strains. Complete genome sequencing revealed a unique alteration in the frequency of a variant allele of the putative adhesin sabB, arising from a recombination event with the related sialic acid binding adhesin (SabA) gene. Mutation of sabB strongly reduced adherence to both normal and metaplastic gastric tissue in multiple strain backgrounds and highly attenuated stomach colonization. Thus, the changing gastric environment during disease development promotes bacterial adhesin gene variation associated with enhanced gastric colonization.

Importance

Chronic infection with Helicobacter pylori is the primary risk factor for developing stomach cancer. As disease progresses H. pylori must adapt to a changing host tissue environment that includes induction of new cell fates in the cells that line the stomach. We tested representative H. pylori isolates collected from the same patient during early and later stages of disease in a mouse model where we can rapidly induce disease-associated tissue changes. Only the later-stage H. pylori strains could robustly colonize the diseased stomach environment. We also found that the ability to colonize the diseased stomach was associated with genetic variation in a putative cell surface adhesin gene called sabB. Additional experiments revealed that SabB promotes binding to stomach tissue and is critical for stomach colonization by the late-stage strains. Thus, H. pylori diversifies its genome during disease progression and these genomic changes highlight critical factors for bacterial persistence.
A data-driven approach to identify clusters of HbA1c longitudinal trajectories and associated outcomes in type 2 diabetes mellitus: a large population-based cohort study
Authors: la Torre Adrian Martinez-De , Faquetti Maria Luisa , Perez-Cruz Fernando , Meier Christian , Weiler Stefan , Burden Andrea M.
Published: June 2022

Background

We aimed to identify and characterize common patterns of HbA1c progression among type 2 diabetes mellitus patients who initiate a non-insulin antidiabetic drug (NIAD).

Methods

The IQVIA Medical Research Data incorporating data from THIN, a Cegedim database of anonymized electronic health records, was used to identify a cohort of patients with a first-ever prescription for a NIAD between 2006 and 2019. Trajectory clusters were identified using an Expectation-Maximization algorithm by iteratively fitting k thin-plate splines and reassigning each patient to the nearest cluster. Cox proportional hazards models calculated the hazard ratios (HR) and 95% confidence intervals (CI) for the estimated risk of microvascular (e.g., retinopathy, diabetic polyneuropathy [DPN]) and macrovascular events.

Findings

Among 116,251 new users of NIADs we found five distinct clusters of HbA1c progression, which were characterized as: optimally controlled (OC), adequately controlled (AC), sub-optimally controlled (SOC), poorly controlled (PC), and uncontrolled (UC). The UC and AC clusters had similar index HbA1C (>9%) but the AC cluster achieved HbA1c control (HbA1C <7.5%), while the UC cluster HbA1c remained >9.0%. Compared to the OC cluster, there was a 21% (HR: 1.21, 95% CI: 1.14-1.28) and 30% (HR: 1.30, 95% CI: 1.21-1.40) elevated risk of retinopathy in the AC and UC clusters, respectively. While the PC and UC clusters had a significant 23% (HR 1.23, 95% CI 1.12 – 1.35) and 45% (HR 1.45, 95% CI: 1.27 – 1.64) increased risk of DPN, respectively.

Interpretation

The five identified HbA1c trajectory clusters had different risk profiles. Despite achieving diabetic control, patients categorized in the AC cluster had similar outcomes to the UC cluster, suggesting baseline HbA1c is an important indicator of health outcomes.

Funding

The Swiss Data Science Centre
Genetic mining of newly isolated Salmophages for phage therapy
Authors: Gendre J. , Ansaldi M. , Olivenza D.R. , Denis Y. , Casadesús J. , Ginet N.
Published: June 2022

I.

Salmonella enterica - a Gram negative zoonotic bacterium – is mainly a food-borne pathogen and the main cause of diarrhea in humans worldwide. Main reservoirs are found in poultry farms but also in wild birds. The development of antibiotic resistance in S. enterica species raises concerns about the future of efficient therapies against this pathogen and revives the interest in bacteriophages as a useful therapy against bacterial infections. Here we aimed at deciphering and functionally annotate 10 new Salmonella phage genomes isolated in Spain in the light of phage therapy. We designed a bioinformatic pipeline using available building blocks to de novo assemble genomes and perform syntaxic annotation. We then used genome-wide analyses for taxonomic annotation enabled by vContact2 and VICTOR. We were also particularly interested in improving functional annotation using remote homologies detection and comparisons with the recently published phage-specific PHROG protein database. We finally searched for useful functions for phage therapy such as systems encoded by the phage to circumvent cellular defenses with a particular focus on anti-CRIPSR proteins. We thus were able to genetically characterized nine virulent phages and one temperate phage and identified putative functions relevant to the formulation of phage cocktails for Salmonella biocontrol.
Dual role of Pectin Methyl Esterase activity in the regulation of plant cell wall biophysical properties
Authors: Gallemí Marçal , Montesinos Juan Carlos , Zarevski Nikola , Pribyl Jan , Skládal Petr , Hannezo Edouard , Benková Eva
Published: June 2022

Acid-growth theory has been postulated in the 70s to explain the rapid elongation of cells in response to plant hormone auxin. More recently, it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting acidification of the apoplast is the principal mechanism through which hormones like auxin as well as brassinosteroids (BR) induce cell elongation. However, the impact of this acidification on the mechanical properties of the cell wall remained largely unexplored. Here, we use Atomic Force Microscopy (AFM) to demonstrate that acidification of apoplast is necessary and sufficient to induce cell elongation through cell wall relaxation. Moreover, we demonstrate that Pectin Methyl Esterase (PME) can induce both cell wall softening or stiffening in extracellular calcium dependent-manner and that tight control of PME activity is required for hypocotyl elongation.
Genomic, transcriptomic, and metabolomic analysis of Traditional Chinese Medicine plantOldenlandia corymbosareveals the biosynthesis and mode of action of anti-cancer metabolites
Authors: Julca Irene , Mutwil-Anderwald Daniela , Manoj Vaishnervi , Khan Zahra , Lai Soak Kuan , Yang Lay Kien , Beh Ing Tsyr , Dziekan Jerzy , Lim Yoon Pin , Lim Shen Kiat , Low Yee Wen , Lam Yuen In , Mu Yuguang , Tan Qiao Wen , Nuc Przemyslaw , Choo Le Min , Khew Gillian , Shining Loo , Kam Antony , Tam James P. , Bozdech Zbynek , Schmidt Maximilian , Usadel Bjoern , Kanagasundaram Yoganathan s/o , Alseekh Saleh , Fernie Alisdair , Yeung Li Hoi , Mutwil Marek
Published: June 2022

Natural products from traditional medicinal plants are valuable candidates for clinical cancer therapy. Plants from the Oldenlandia-Hedyotis complex are popular ingredients of Traditional Chinese Medicine (TCM), however a major hurdle in the plant bioprospecting process of TCM plants is that the active metabolites, their biosynthetic pathways, and mode of action are often unknown. We show thatOldenlandia corymbosaextracts are active against breast cancer cell lines. To study the genes involved in the biosynthesis of active compounds in this medicinal plant, we assembled a high-quality genome. We show that the main active compound is ursolic acid and that abiotic stresses cause changes in anti-cancer activity, metabolite composition, and gene expression of plants. To reveal the mode of action of ursolic acid, we show that cancer cells undergo mitotic catastrophe, and we identify three high-confidence protein binding targets by Cellular Thermal Shift Assay (CETSA) and reverse docking.
Synaptic vesicle proteins and ATG9A self-organize in distinct vesicle phases within synapsin condensates
Authors: Park Daehun , Wu Yumei , Baublis Aaron , De Camilli Pietro
Published: June 2022

Ectopic expression in fibroblasts of synapsin 1 and synaptophysin is sufficient to generate condensates of vesicles highly reminiscent of synaptic vesicle (SV) clusters and with liquid-like properties. We show that unlike synaptophysin, other major integral SV membrane proteins fail to form condensates with synapsin, but coassemble into the clusters formed by synaptophysin and synapsin in this ectopic expression system. Another vesicle membrane protein, ATG9A, undergoes activity-dependent exo-endocytosis at synapses, raising questions about the relation of ATG9A traffic to the traffic of SVs. We have found that both in fibroblasts and in nerve terminals ATG9A does not coassemble into synaptophysin-positive vesicle condensates but localizes on a distinct class of vesicles that also assembles with synapsin but into a distinct phase. Our findings suggest that ATG9A undergoes differential sorting relative to SV proteins and also point to a dual role of synapsin in controlling clustering at synapses of SVs and ATG9A vesicles.
Nutrient limitation mimics artemisinin tolerance in malaria
Authors: Brown Audrey , Warthan Michelle D , Aryal Anush , Liu Shiwei , Guler Jennifer L
Published: June 2022

Mounting evidence demonstrates that nutritional environment can alter pathogen drug sensitivity. While the nutrient-rich media used for standard in vitro culture contains supra-physiological nutrient concentrations, pathogens encounter a relatively restrictive environment in vivo. We assessed the effect of nutrient limitation on the protozoan parasite that causes malaria and demonstrated that short-term growth under physiologically-relevant mild nutrient stress (or “metabolic priming”) triggers increased tolerance of the potent antimalarial drug dihydroartemisinin (DHA). We observed beneficial effects using both short-term survival assays and longer-term proliferation studies, where metabolic priming increases parasite survival to a level previously defined as DHA resistant (>1% survival). We performed these assessments by either decreasing single nutrients that have distinct roles in parasite metabolism or using a media formulation with reductions in many nutrients that simulates the human plasma environment. We determined that priming-induced DHA tolerance was restricted to parasites that had newly invaded the host red blood cell but the effect was not dependent on genetic background. The molecular mechanisms of this intrinsic effect mimic aspects of genetic artemisinin tolerance, including translational repression, autophagy, and protein export. This finding suggests regardless of the impact on survival rates, environmental stress could stimulate changes that ultimately directly contribute to drug tolerance. Because metabolic stress is likely to occur more frequently in vivo compared to the stable in vitro environment, priming-induced drug tolerance has ramifications for how in vitro results translate to in vivo studies. Improving our understanding of how pathogens adjust their metabolism to impact survival of current and future drugs is an important avenue of research to prevent and slow the spread of resistance.
A choline-releasing glycerophosphodiesterase essential for phosphatidylcholine biosynthesis and blood stage development in the malaria parasite
Authors: Ramaprasad Abhinay , Burda Paul-Christian , Calvani Enrica , Sait Aaron , Palma-Duran Susana Alejandra , Withers-Martinez Chrislaine , Hackett Fiona , MacRae James , Collinson Lucy , Gilberger Tim-Wolf , Blackman Michael J
Published: June 2022

The malaria parasite Plasmodium falciparum synthesizes significant amounts of phospholipids to meet the demands of replication within red blood cells. De novo phosphatidylcholine (PC) biosynthesis via the Kennedy pathway is essential, requiring choline that is primarily sourced from host serum lysophosphatidylcholine (lysoPC). LysoPC also acts as an environmental sensor to regulate parasite sexual differentiation. Despite these critical roles for host lysoPC, the enzyme(s) involved in its breakdown to free choline for PC synthesis are unknown. Here we show that a parasite glycerophosphodiesterase (PfGDPD) is indispensable for blood stage parasite proliferation. Exogenous choline rescues growth of PfGDPD-null parasites, directly linking PfGDPD function to choline incorporation. Loss of PfGDPD reduces choline uptake from lysoPC, resulting in depletion of several PC species in the parasite, whilst purified PfGDPD releases choline from glycerophosphocholine in vitro. Our results identify PfGDPD as a choline-releasing glycerophosphodiesterase that mediates a critical step in PC biosynthesis and parasite survival.
Crystal structure and functional peculiarities of a primordial Orange Carotenoid Protein (OCPX)
Authors: Slonimskiy Yury B. , Zupnik Andrey O. , Varfolomeeva Larisa A. , Boyko Konstantin M. , Maksimov Eugene G. , Sluchanko Nikolai N.
Published: June 2022

The two-domain photoactive Orange Carotenoid Protein (OCP) confers photoprotection in cyanobacteria and presumably stems from domain fusion. Yet, the primitive thylakoid-less cyanobacteria Gloeobacter encodes a complete OCP. Its photosynthesis regulation lacks the so-called Fluorescence Recovery Protein (FRP), which in Synechocystis inhibits OCP-mediated phycobilisome fluorescence quenching, and Gloeobacter OCP belongs to the recently defined, heterogeneous clade OCPX (GlOCPX), the least characterized compared to OCP2 and especially OCP1 clades. Here we describe the first crystal structure of OCPX and provide its detailed structural and functional comparison with OCP1 from Synechocystis. Monomeric GlOCPX quenches Synechocystis phycobilisomes but displays drastically accelerated, less temperature-dependent recovery after photoactivation, evades regulation by FRP from other species and reveals numerous structural features reflecting its functional peculiarities. Our detailed description of a primordial OCPX sheds light on the evolution of the OCP-dependent photoprotection mechanism, rationalizing subdivision of the OCPX clade into subclades.
Cdc42 prevents precocious Rho1 activation during cytokinesis in a Pak1-dependent manner
Authors: Onwubiko Udo N. , Koory Emma , Pokharel Sahara , Roberts Hayden , Mitoubsi Ahmad , Das Maitreyi
Published: June 2022

Cytokinesis consists of a series of coordinated multi-step events that partition a dividing cell. Accurate regulation of cytokinesis is essential for proliferation and genome integrity. In fission yeast, these coordinated events ensure that the actomyosin ring and septum start ingressing only after chromosome segregation. How cytokinetic events are coordinated remains unclear. The GTPase Cdc42 is required for the delivery of certain cell wall-building enzymes while the GTPase Rho1 is required for activation of these enzymes. Here we show that Cdc42 prevents early Rho1 activation during cytokinesis. Using an active Rho-probe, we show that even though the Rho1 activators Rgf1 and Rgf3 localize to the division site in early anaphase, Rho1 is not activated until late anaphase, just before the onset of ring constriction. We find that loss of Cdc42 activation enables precocious Rho1 activation in early anaphase. Furthermore, this inhibition of Rho1 activation is dependent on the downstream Cdc42 effector Pak1 kinase. Disrupting pak1 function results in early Rho1 activation accompanied by precocious septum deposition and ring constriction. We provide functional and genetic evidence which indicates that Pak1 regulates Rho1 activation likely via the regulation of its GEF Rgf1. Our work proposes a mechanism of Rho1 regulation by active Cdc42 to coordinate timely septum formation and cytokinesis fidelity.
Design principles of dose-response alignment in coupled GTPase switches
Authors: Qiao Lingxia , Ghosh Pradipta , Rangamani Padmini
Published: June 2022

“Dose-response alignment” (DoRA), where the downstream response of cellular signaling path-ways closely matches the fraction of activated receptor, can improve the fidelity of dose information transmission. It is believed that a key component for DoRA is negative feedback and thus a natural question that arises is whether there exist design principles for signaling motifs within such negative feedback loops, which may enable these motifs to attain near-perfect DoRA. Here, we investigated several model formulations of an experimentally validated circuit that couples two molecular switches—mGTPase (monomeric GTPase) and tGTPase (heterotrimeric GTPases) — with negative feedback loops. We find that, in the absence of feedback, the low and intermediate mGTPase activation levels benefit DoRA in the mass action and Hill-function models, respectively. In other cases, where the mass action model with a high mGTPase activation level or the Hill-function model with a non-intermediate mGTPase activation level, the DoRA can be improved by adding negative feedback loops. Furthermore, we found that DoRA in a longer cascade (i.e., tGTPase) can be obtained using Hill-function kinetics under certain conditions. In summary, we show how ranges of activity of mGTPase, reaction kinetics, the negative feedback, and the cascade length affect DoRA. This work provides a framework for improving the DoRA performance in signaling motifs with negative feedback loops.

Significance Statement

Dose-response alignment helps cells faithfully transmit dose information; how this alignment is achieved in motifs with negative feedback is unclear. Through rigorous studies interrogating a naturally occurring motif comprised of two species of GTPases coupled by negative feedback loops, this work reveals the versatile roles of negative feedback loops and GTPase regulators on DoRA. We find that the negative feedback can enhance DoRA only with specific kinetic forms and with certain ranges of GTPases activation levels. This knowledge advances our understanding of the role of negative feedback on DoRA and sheds light on the importance of dynamic range of signaling processes as an essential determinant of how cells transfer information about stimuli. Findings can help design signaling circuits with better DoRA behavior, and ultimately augment cell signaling studies.
Assessment of endocytic traffic and Ocrl function in the developing zebrafish neuroepithelium
Authors: Williams Daniel M. , Gungordu Lale , Jackson-Crawford Anthony , Lowe Martin
Published: June 2022

Endocytosis is a vital process, required during development and for maintenance of tissue homeostasis, that allows cells to internalize a wide range of molecules from their environment as well maintain their plasma membrane composition. The ability to visualise endocytosis in vivo requires suitable assays to monitor the process. Here, we describe imaging-based assays to visualize endocytosis in the neuroepithelium of living zebrafish embryos. These assays rely on injection of fluorescent tracers into the brain ventricles followed by live imaging and can be used to study fluid-phase or receptor-mediated endocytosis, for which we use receptor-associated protein (RAP) as a ligand for LDL receptor-related protein (LRP) receptors expressed at the neuroepithelium. Using dual colour imaging combined with transient or stable expression of endocytic markers, it is possible to track the progression of endocytosed tracers and to monitor trafficking dynamics. Using these assays, we reveal a role for the Lowe syndrome protein Ocrl in endocytic trafficking within the neuroepithelium. We also find that the RAP binding receptor Lrp2 appears to only partially contribute to neuroepithelial RAP endocytosis. Altogether, our results provide a basis to track endocytosis within the neuroepithelium in vivo, and support a role for Ocrl in this process.

Summary statement

We describe live imaging assays to analyse endocytosis in the zebrafish neuroepithelium and show involvement of the inositol phosphatase OCRL in this process
Decoding gene regulation in the mouse embryo using single-cell multi-omics
Authors: Argelaguet Ricard , Lohoff Tim , Li Jingyu Gavin , Nakhuda Asif , Drage Deborah , Krueger Felix , Velten Lars , Clark Stephen J. , Reik Wolf
Published: June 2022

Following gastrulation, the three primary germ layers develop into the major organs in a process known as organogenesis. Single-cell RNA sequencing has enabled the profiling of the gene expression dynamics of these cell fate decisions, yet a comprehensive map of the interplay between transcription factors and cis-regulatory elements is lacking, as are the underlying gene regulatory networks. Here we generate a multi-omics atlas of mouse early organogenesis by simultaneously profiling gene expression and chromatin accessibility from tens of thousands of single cells. We develop a computational method to leverage the multimodal readouts to predict transcription factor binding events in cis-regulatory elements, which we then use to infer gene regulatory networks that underpin lineage commitment events. Finally, we show that these models can be used to generatein silicopredictions of the effect of transcription factor perturbations. We validate this experimentally by showing that Brachyury is essential for the differentiation of neuromesodermal progenitors to somitic mesoderm fate by priming cis-regulatory elements. The data set can be interactively explored athttps://www.bioinformatics.babraham.ac.uk/shiny/shiny_multiome_organogenesis/
Proinsulin dependent interaction between ENPL-1/GRP94 and ASNA-1 in neurons is required to maintain insulin secretion in C. elegans
Authors: Podraza-Farhanieh Agnieszka , Raj Dorota , Kao Gautam , Naredi Peter
Published: June 2022

Maturation of insulin is crucial for insulin secretion and function. ENPL-1/GRP94/HSP90B1 plays an important role in this process. ASNA-1/TRC40/GET3 and ENPL-1/GRP94 are conserved insulin secretion regulators in Caenorhabditis elegans and mammals and mouse mutants display type 2 diabetes. ENPL-1 and GRP94 bind proinsulin and regulate proinsulin levels in C. elegans and cultured cells. Here we found that ASNA-1 and ENPL-1 co-operated to regulate insulin secretion in worms via a physical interaction that required pro-DAF-28/insulin but occurred independently of the insulin binding site of ENPL-1. ASNA-1 acted in neurons to promote DAF-28/insulin secretion. The interaction occurred in insulin expressing neurons and was sensitive to changes in pro-DAF-28 levels. The chaperone form of ASNA-1 is likely bound to ENPL-1. Loss of asna-1 disrupted Golgi trafficking pathways. ASNA-1 localization was affected in enpl-1 mutants and ENPL-1 overexpression partially bypassed ASNA-1 requirement. Taken together, we find a functional interaction between ENPL-1 and ASNA-1 which is necessary to maintain proper insulin secretion in C. elegans and provides insights about how their loss might produce diabetes in mammals.
Automated matching of two-time X-ray photon correlation maps from phase-separating proteins with Cahn–Hilliard-type simulations using auto-encoder networks
Authors: Timmermann Sonja , Starostin Vladimir , Girelli Anita , Ragulskaya Anastasia , Rahmann Hendrik , Reiser Mario , Begam Nafisa , Randolph Lisa , Sprung Michael , Westermeier Fabian , Zhang Fajun , Schreiber Frank , Gutt Christian
Published: June 2022

Machine learning methods are used for an automated classification of experimental two-time X-ray photon correlation maps from an arrested liquid–liquid phase separation of a protein solution. The correlation maps are matched with correlation maps generated with Cahn–Hilliard-type simulations of liquid–liquid phase separations according to two simulation parameters and in the last step interpreted in the framework of the simulation. The matching routine employs an auto-encoder network and a differential evolution based algorithm. The method presented here is a first step towards handling large amounts of dynamic data measured at high-brilliance synchrotron and X-ray free-electron laser sources, facilitating fast comparison with phase field models of phase separation.