bluuebunny/crossref_metadata_2025 huggingface dataset:
The Massachusetts Department of Public Health Post Overdose Support Team Initiative: A Public Health–Centered Co-Response Model for Post–Overdose Outreach
Authors: Formica Scott W. , Reilly Brittni , Duska MaryKate , Ruiz Sarah C. , Lagasse Peter , Wheeler Mary , Delaney Amy , Walley Alexander Y.
Published: October 2022

Context:

Post–overdose outreach programs have emerged in response to surging overdose deaths amid fentanyl contamination of the illicit opioid supply. Predominantly centered in police departments in collaboration with public health providers, these programs conduct home-based outreach with survivors and their social networks following an overdose.

Approach:

We describe implementation of the Post Overdose Support Team (POST) initiative, an ongoing public health funded and centered approach. Post Overdose Support Team is a person-centered model led by harm reductionists in health and human services agencies in collaboration with municipal first responders. The goal of POST is to engage overdose survivors and their social network to improve general health, connect people to services (including access to treatment, if desired), and reduce risk of subsequent overdose.

Implementation:

Nine agencies in Massachusetts that are part of the state's overdose education and naloxone distribution network implemented POST programs, covering 28 municipalities. The POST teams conduct home-based outreach with individuals who experienced an opioid-related overdose to provide a menu of services, including naloxone rescue kits, overdose response and risk reduction planning, referral to treatment for substance use disorders, including medication for opioid use disorder, and referral to recovery and family supports.

Evaluation:

From October 2017 to October 2021, the POST teams attempted to reach 5634 overdose survivors via 10 536 outreach visits. Teams successfully engaged 3014 survivors, either directly or through contact with their social network (53.5% success rate). Using data from a real-time encounter-level database, monthly peer-sharing calls with program sites, and annual site visits, we describe the implementation of the POST initiative and provide practice-based recommendations and lessons learned.

Discussion:

Early evidence suggests that the POST initiative is meeting its goal to engage overdose survivors, improve general health, and reduce subsequent overdose risk. Future evaluations should examine long-term outcomes among participants, including service linkages and incremental behavior change.
Validation and Improvement of a Machine Learning Model to Predict Interruptions in Antiretroviral Treatment in South Africa
Authors: Esra Rachel , Carstens Jacques , Le Roux Sue , Mabuto Tonderai , Eisenstein Michael , Keiser Olivia , Orel Erol , Merzouki Aziza , De Voux Lucien , Maskew Mhari , Sharpey-Schafer Kieran
Published: October 2022

Introduction:

Machine learning algorithms are increasingly being used to inform HIV prevention and detection strategies. We validated and extended a previously developed machine learning model for patient retention on antiretroviral therapy in a new geographic catchment area in South Africa.

Methods:

We compared the ability of an adaptive boosting algorithm to predict interruption in treatment (IIT) in 2 South African cohorts from the Free State and Mpumalanga and Gauteng and North West (GA/NW) provinces. We developed a novel set of predictive features for the GA/NW cohort using a categorical boosting model. We evaluated the ability of the model to predict IIT over all visits and across different periods within a patient's treatment trajectory.

Results:

When predicting IIT, the GA/NW and Free State and Mpumalanga models demonstrated a sensitivity of 60% and 61%, respectively, able to correctly predict nearly two-thirds of all missed visits with a positive predictive value of 18% and 19%. Using predictive features generated from the GA/NW cohort, the categorical boosting model correctly predicted 22,119 of a total of 35,985 missed next visits, yielding a sensitivity of 62%, specificity of 67%, and positive predictive value of 20%. Model performance was highest when tested on visits within the first 6 months.

Conclusions:

Machine learning algorithms may be useful in informing tools to increase antiretroviral therapy patient retention and efficiency of HIV care interventions. This is particularly relevant in developing countries where health data systems are being strengthened to collect data on a scale that is large enough to apply novel analytical methods.
Radiomics-Based Machine Learning to Predict Recurrence in Glioma Patients Using Magnetic Resonance Imaging
Authors: Hu Guanjie , Hu Xinhua , Yang Kun , Yu Yun , Jiang Zijuan , Liu Yong , Liu Dongming , Hu Xiao , Xiao Hong , Zou Yuanjie , You Yongping , Liu Hongyi , Chen Jiu
Published: October 2022

Objective

Recurrence is a major factor in the poor prognosis of patients with glioma. The aim of this study was to predict glioma recurrence using machine learning based on radiomic features.

Methods

We recruited 77 glioma patients, consisting of 57 newly diagnosed patients and 20 patients with recurrence. After extracting the radiomic features from T2-weighted images, the data set was randomly divided into training (58 patients) and testing (19 patients) cohorts. An automated machine learning method (the Tree-based Pipeline Optimization Tool) was applied to generate 10 independent recurrence prediction models. The final model was determined based on the area under the curve (AUC) and average specificity. Moreover, an independent validation set of 20 patients with glioma was used to verify the model performance.

Results

Recurrence in glioma patients was successfully predicting by machine learning using radiomic features. Among the 10 recurrence prediction models, the best model achieved an accuracy of 0.81, an AUC value of 0.85, and a specificity of 0.69 in the testing cohort, but an accuracy of 0.75 and an AUC value of 0.87 in the independent validation set.

Conclusions

Our algorithm that is generated by machine learning exhibits promising power and may predict recurrence noninvasively, thereby offering potential value for the early development of interventions to delay or prevent recurrence in glioma patients.
Using Simulation to Teach Learners in Health Care Behavioral Skills Related to Diversity, Equity, and Inclusion
Authors: Daya Sneha , Illangasekare Tushani , Tahir Peggy , Bochatay Naike , Essakow Jenna , Ju Mindy , van Schaik Sandrijn
Published: October 2022

Summary Statement

Bias is commonplace in the health care environment and can negatively impact patients and their health outcomes. Simulation has long been shown to be an effective teaching tool for communication skills in health care, but it has rarely been used to deliver concrete behavioral skills that address issues of diversity, equity, and inclusion (DEI). This scoping review examines 23 published articles surrounding the use of simulation in health care education to impart behavioral skills that reduce bias and promote DEI. Included articles described various behavioral skills including communication, history-taking, and system/community-level advocacy. The most commonly used simulation modality to teach these skills included the use of simulated participants (16 articles, 70%). The main DEI topics addressed in the trainings included sexual orientation/gender identity, language, and culture/ethnicity. Based on findings from this review, the authors suggest recommendations for educators who are considering teaching DEI-related skills through simulation.
Does Exercise Training Improve Physical Fitness and Health in Adult Liver Transplant Recipients? A Systematic Review and Meta-analysis
Authors: De Smet Stefan , O’Donoghue Katriona , Lormans Maud , Monbaliu Diethard , Pengel Liset
Published: October 2022

Background.

The impaired physical fitness of end-stage liver disease patients often persists after liver transplantation (LT) and compromises posttransplant recovery. This systematic review and meta-analysis evaluated evidence supporting the potential of exercise training to improve physical fitness and health-related quality of life (HRQOL) after LT.

Methods.

Bibliographic searches identified all randomized controlled trials (RCTs) comparing aerobic and strength training versus usual care after LT. Risk of bias was assessed, and study outcomes measuring physical fitness and HRQOL were extracted. Meta-analysis was performed if at least 3 studies reported on an outcome.

Results.

Eight RCTs (n = 334) were identified. Methodological study quality varied and was poorly reported. Meta-analyses showed a trend for favorable effects of exercise on cardiorespiratory fitness (peak oxygen uptake or 6-min walking distance; 6 studies, n = 275; standardized mean difference: 0.23, 95% confidence interval [CI], −0.01 to 0.48) and of strength training either or not combined with aerobic training on muscular fitness (dynamometry-assessed muscle strength or 30-s sit-to-stand test; 3 studies, n = 114; standardized mean difference: 0.34, 95% CI, −0.03 to 0.72). A favorable effect was found for exercise on the Short-Form Health Survey-36 HRQOL physical function subcomponent (3 studies, n = 194; mean difference: 9.1, 95% CI, 0.3-17.8). No exercise-related adverse events were observed.

Conclusions.

RCTs indicate that exercise training in LT recipients is safe, improves physical function aspects of HRQOL, and may benefit cardiorespiratory and muscular fitness. The strength of evidence is, however, limited by the low number of patients and study quality. More adequately powered, high-quality RCTs are warranted.
Impact of the Kidney Transplantation Moratorium in France Because of the COVID-19 Pandemic: A Cohort-based Study
Authors: Bonnemains Vincent , Le Borgne Florent , Savoye Emile , Legeai Camille , Pastural Myriam , Bayat-Makoei Sahar , Lenain Rémi , Ragot Stéphanie , Leffondré Karen , Couchoud Cécile , Foucher Yohann
Published: October 2022

Background.

The COVID-19 pandemic has resulted in worldwide kidney transplantation (KT) moratoriums. The impacts of these moratoriums on the life expectancy of KT candidates remain unclear.

Methods.

We simulated the evolution of several French candidate populations for KT using a multistate semi-Markovian approach and according to moratorium durations ranging from 0 to 24 mo. The transition rates were modeled from the 63 927 French patients who began dialysis or were registered on the waiting list for KT between 2011 and 2019.

Results.

Among the 8350 patients active on the waiting list at the time of the French KT moratorium decided on March 16, 2020, for 2.5 mo, we predicted 4.0 additional months (confidence interval [CI], 2.8-5.0) on the waiting list and 42 additional deaths (CI, –70 to 150) up to March 16, 2030, compared with the scenario without moratorium. In this population, we reported a significant impact for a 9-mo moratorium duration: 135 attributable deaths (CI, 31-257) up to March 16, 2030. Patients who became active on the list after March 2020 were less impacted; there was a significant impact for an 18-mo moratorium (175 additional deaths [CI, 21-359]) in the 10 862 prevalent end-stage renal disease patients on March 16, 2020 and for a 24-mo moratorium (189 additional deaths [CI, 10-367]) in the 16 355 incident end-stage renal disease patients after this date.

Conclusion.

The temporary moratorium of KT during a COVID-19 peak represents a sustainable decision to free up hospitals’ resources if the moratorium does not exceed a prolonged period.
Green spaces for mental disorders
Authors: Wood Carly , Wicks Claire , Barton Jo
Published: October 2022

Purpose of review

Mental illness is a global challenge, exacerbated by the coronavirus pandemic. Research suggests access to local green spaces is associated with better mental health, yet access is not always equitable. Evaluation of how nature-based interventions protect and support mental health is therefore required.

Recent findings

Accessible local green spaces are associated with better mental health. They encourage active behaviours and social interaction, reduce loneliness and stress. Green views from the home are associated with increased self-esteem, life satisfaction and happiness and reduced depression, anxiety and loneliness. Nature-based interventions and green social prescriptions effectively target vulnerable groups, resulting in significant reductions in depression, anxiety and anger alongside positive mental health outcomes.

Although existing evidence is encouraging, robust, high-quality research that strengthens the evidence base and informs future clinical practice and policy decision making is needed. Evidence of the long-term effectiveness in individuals with diagnosed mental illness is also required to ascertain the potential social and wider returns on investment. Barriers to use of green social prescriptions like mental health symptoms and geographical accessibility need to be overcome to increase accessibility and uptake of green social prescriptions for the prevention and treatment of mental illness.
Surfactancy in a tadpole model of proteins
Authors: Dyer O. T. , Ball R. C.
Published: October 2022

We model the environment of eukaryotic nuclei by representing macromolecules by only their entropic properties, with globular molecules represented by spherical colloids and flexible molecules by polymers. We put particular focus on proteins with both globular and intrinsically disordered regions, which we represent with ‘tadpole’ constructed by grafting single polymers and colloids together. In Monte Carlo simulations, we find these tadpoles support phase separation via depletion flocculation, and demonstrate several surfactant behaviours, including being found preferentially at interfaces and forming micelles in single phase solution. Furthermore, the model parameters can be tuned to give a tadpole a preference for either bulk phase. However, we find entropy too weak to drive these behaviours by itself at likely biological concentrations.
Pitfalls in methods to study colocalization of nanoparticles in mouse macrophage lysosomes
Authors: Moreno-Echeverri Aura Maria , Susnik Eva , Vanhecke Dimitri , Taladriz-Blanco Patricia , Balog Sandor , Petri-Fink Alke , Rothen-Rutishauser Barbara
Published: October 2022

Abstract Figure

Background

In the field of nanoscience there is an increasing interest to follow dynamics of nanoparticles (NP) in cells with an emphasis on endo-lysosomal pathways and long-term NP fate. During our research on this topic, we encountered several pitfalls, which can bias the experimental outcome. We address some of these pitfalls and suggest possible solutions. The accuracy of fluorescence microscopy methods has an important role in obtaining insights into NP interactions with lysosomes at the single cell level including quantification of NP uptake in a specific cell type.

Methods

Here we use J774A.1 cells as a model for professional phagocytes. We expose them to fluorescently-labelled amorphous silica NP with different sizes and quantify the colocalization of fluorescently-labelled NP with lysosomes over time. We focus on confocal laser scanning microscopy (CLSM) to obtain 3D spatial information and follow live cell imaging to study NP colocalization with lysosomes.

Results

We evaluate different experimental parameters that can bias the colocalization coefficients (i.e, Pearson’s and Manders’), such as the interference of phenol red in the cell culture medium with the fluorescence intensity and image post-processing (effect of spatial resolution, optical slice thickness, pixel saturation and bit depth). Additionally, we determine the correlation coefficients for NP entering the lysosomes under four different experimental set-ups. First, we found out that not only Pearson’s, but also Manders’ correlation coefficient should be considered in lysosome-NP colocalization studies; second, there is a difference in NP colocalization when using NP of different sizes and fluorescence dyes and last, the correlation coefficients might change depending on live-cell and fixed-cell imaging set-up.

Conclusions

The results summarize detailed steps and recommendations for the experimental design, staining, sample preparation and imaging to improve the reproducibility of colocalization studies between the NP and lysosomes.
Impact of Fluvoxamine on outpatient treatment of COVID-19 in Honduras
Authors: Pineda Estela , Singh Jarmanjeet , Pineda Miguel Vargas , Umanzor Jose Garay , Baires Fernando , Benitez Luis G. , Burgos Cesar , Sekhon Anupamjeet Kaur , Crisp Nicole , Lewis Anita S. , Radwanski Jana , Bermudez Marco , Barjun Karen Sanchez , Diaz Oscar , Palou Elsa , Escalante Rossany E. , Hernandez Carlos Isai , Stevens Mark L. , Eberhard Deke , Sierra Manuel , Alvarado Tito , Videa Omar , Sierra-Hoffman Miguel , Pascua Fernando Valerio
Published: October 2022

Background

COVID-19 pandemic has impacted lives globally. While COVID-19 did not discriminate against developed or developing nations, it has been a significant challenge for third world countries like Honduras to have widespread availability of advanced therapies. The concept of early treatment was almost unheard-of when early outpatient treatment with repurposed drugs in Latin American countries showed promising results. One such drug is fluvoxamine, that has shown tremendous potential in two major studies, following which fluvoxamine was added to the standard of care in Honduras.

Methods

This is a prospective observational study performed at the Hospital Centro Médico Sanpedrano (CEMESA) in San Pedro Sula, Cortes, Honduras in the COVID-19 outpatient clinic. All patients fifteen years of age or older, with mild or moderate signs and symptoms of COVID-19, and a positive SARS-CoV-2 antigen or Reverse Transcription Polymerase Chain Reaction (RT-PCR) were included in the study and prescribed fluvoxamine. Cohort of patients who decided to take fluvoxamine were compared to the cohort who did not take fluvoxamine for mortality risk and risk of hospitalization as primary endpoints. Patient were monitored for 30 days with first follow up at 7 days and second follow up at 10-14 days of symptom onset. Categorical variables were compared by Pearson Chi-square test. The Odds ratio was calculated using univariate and multivariate logistic regression. Continuous variables were compared by t-test and Wilcoxon rank-sum tests.

Results

Of 657 total COVID-19 cases, 594 patients took fluvoxamine and 63 did not. A total of five patients (0.76 percent) died, of which only one death occurred in the fluvoxamine group. Patients who did not receive fluvoxamine had a significantly higher mortality (OR 24, p0.005, CI 2.6 to 233.5). Odds ratio of hospitalization in patients who did not take fluvoxamine was 2.38 (30 vs 10 hospitalizations, p 0.040, CI 1.04-5.47). The odds ratio of requiring oxygen in patients in the non-fluvoxamine group was 5.08 (p<0.001, CI 2.18-11.81). Mean lymphocytes count on the first follow-up visit was significantly higher in the fluvoxamine group (1.72 vs. 1.38, Δ 0.33, p 0.007, CI 0.09 to 0.58).

Conclusion

The results of our study suggest lowers odds of mortality and hospitalization in patients who took fluvoxamine vs fluvoxamine non-takers. Non-fluvoxamine group had higher odds of oxygen requirement than fluvoxamine group as well.
Condition-dependence resolves the paradox of missing plasticity costs
Authors: De Lisle Stephen P. , Rowe Locke
Published: October 2022

Phenotypic plasticity plays a key role in adaptation to changing environments. However, plasticity is neither perfect nor ubiquitous, implying that fitness costs must limit the evolution of phenotypic plasticity in nature. The measurement of such costs of plasticity has proved elusive; decades of experiments show that fitness costs of plasticity are often weak or nonexistent. Here, we show that this paradox can be at least partially explained by condition-dependence. We develop two models differing in their assumptions about how condition-dependence arises; both models show that variation in condition can readily mask costs of plasticity even when such costs are substantial. This can be shown simply in a model where costly plasticity itself evolves condition-dependence. Yet similar effects emerge from an alternative model where trait expression is condition-dependent. In this more complex model, average condition in each environment and genetic covariance in condition across environments both determine when costs of plasticity can be revealed. Analogous to the paradox of missing trade-offs between life history traits, our models show that variation in condition masks costs of plasticity even when costs exist, and suggests this conclusion may be robust to the details of how condition affects trait expression. Our models demonstrate that condition dependence can also account for the often-observed pattern of elevated plasticity costs inferred in stressful environments, the maintenance of genetic variance in plasticity, and provides insight into experimental and biological scenarios ideal for revealing a cost of phenotypic plasticity.
Gains and losses of the epiphytic lifestyle in epidendroid orchids: review and new analyses with succulence traits
Authors: Collobert Géromine , Perez-Lamarque Benoît , Dubuisson Jean-Yves , Martos Florent
Published: October 2022

Background and Aims

Epiphytism has evolved repeatedly in plants and has resulted in a considerable number of species with original characteristics. Succulent forms in particular are thought to have evolved as an adaptation to the epiphytic environment, because the water supply is generally erratic compared to soils’. However, succulent organs also exist in terrestrial plants, and the question of the concomitant evolution of epiphytism and succulence has received little attention, not even in the epidendroid orchids, which account for 68% of vascular epiphytes.

Methods

We reconstructed a new time-calibrated phylogenetic tree of Epidendroideae with 203 genera treated inGenera Orchidacearum, from which we reconstructed the evolution of epiphytism and other traits including stem and leaf succulence, while testing the correlated evolution between lifestyle and morphological traits. Furthermore, we reconstructed the ancestral geographic ranges to interpret major character changes during the Cenozoic.

Key Results

Epiphytism evolved at least 7.1 My ago in the neotropical Sobralieae, 11.5 My ago in the Arethuseae in Southeast Asia and Australia, and 39.0 My ago in the common ancestor of the Dendrobieae and Cymbidieae in the three previous areas, and was notably lost in the Malaxideae, Collabieae, Calypsoeae, Bletiinae, and Eulophiinae. Stem succulence is inferred to have evolved once, in a terrestrial ancestor 43.1 My ago, thus preceding the evolution of epiphytism by at least 4.1 My. If lost, stem succulence was almost systematically replaced by leaf succulence in epiphytic lineages.

Conclusions

Epiphytism probably evolved from terrestrial orchids already possessing succulent stems, which appeared during Eocene climatic cooling. Both epiphytic and secondary terrestrial Epidendroideae may have appeared in seasonally-dry forests. Thus, we believe that the emergence of stem succulence in early epidendroids was a key innovation in the evolution of orchids, facilitating the colonisation of epiphytic environments that led to the greatest diversification of orchids.
A ubiquitous spectrolaminar motif of local field potential power across the primate cortex
Authors: Mendoza-Halliday Diego , Major Alex J. , Lee Noah , Lichtenfeld Maxwell , Carlson Brock , Mitchell Blake , Meng Patrick D. , Xiong Yihan (Sophy) , Westerberg Jacob A. , Maier Alexander , Desimone Robert , Miller Earl K. , Bastos André M.
Published: October 2022

The mammalian cerebral cortex is anatomically organized into a six-layer motif. It is currently unknown whether a corresponding laminar motif of neuronal activity exists across the cortex. Here, we report such a motif in the power of local field potentials (LFP). We implanted multicontact laminar probes in five macaque monkeys and recorded activity across layers in 14 cortical areas at various hierarchical processing stages in all cortical lobes. The anatomical laminar locations of recordings were histologically identified via electrolytic lesions. In all areas, we found a common spectrolaminar pattern characterized by an increasing deep-to-superficial layer gradient of gamma frequency LFP power peaking in layers 2/3, and an increasing superficial-to-deep gradient of alpha-beta power peaking in layers 5/6. Our results show an electrophysiological dissociation between superficial and deep layers that is preserved across the cortex, suggesting a ubiquitous layer and frequency-based mechanism for cortical computation.
TCRi: Information theoretic metrics for single cell RNA and TCR sequencing in cancer
Authors: Ceglia Nicholas , Sethna Zachary M. , Elhanati Yuval , Burman Bharat , Chow Andrew , Zamarin Dmitriy , DeWolf Susan , Shahid Sanam , Bojilova Viktoria , Rusk Nicole , Balachandran Vinod P. , McPherson Andrew , Shah Sohrab P. , Greenbaum Benjamin D.
Published: October 2022

Single-cell T cell repertoire sequencing can pair both T cell receptor (TCR) and gene expression sequence data, providing an enriched view of T cell behavior. This powerful tool can identify and characterize specific clonotypes and phenotypes as well as track their changes in response to therapy, such as immune checkpoint blockade (ICB). We present a novel information theoretic framework called TCRi for characterizing single cell T cell repertoires by formalizing the relationship between clonotype and phenotype in a joint probability distribution. Our strategy allows for the identification of subpopulations of T cells and jointly quantifies their TCR and expression profiles in response to stimuli, in addition the framework tracks the phenotypic changes in individual T cell clones over time. We applied this framework to four datasets of T cells sequenced from cancer patients treated with anti-PD-(L)1 ICB immunotherapies and examined evolution of T cell responses pre- and post-treatment. Quantitative of phenotypic and clonotypic entropy analysis with TCRi demonstrated improvements in characterization of the transcriptional signature of clonotypes. Furthermore, TCRi highlighted the importance of phenotypic flux and specific T-cell phenotypes as determinants of therapeutic response.
The PTEX pore component EXP2 is important for intrahepatic development during the Plasmodium liver stage
Authors: Hussain Tahir , Linera-Gonzalez Jose , Beck John M , Fierro Manuel A , Mair Gunnar R , Smith Ryan C , Beck Josh R
Published: October 2022

During vertebrate infection, obligate intracellular malaria parasites develop within a parasitophorous vacuole which constitutes the interface between the parasite and its hepatocyte or erythrocyte host cells. To transcend this barrier, Plasmodium spp. utilize a dual-function pore formed by EXP2 for nutrient transport and, in the context of the PTEX translocon, effector protein export across the vacuole membrane. While critical to blood stage survival, less is known about EXP2/PTEX function in the liver stage, although major differences in the export mechanism are indicated by absence of the PTEX unfoldase HSP101 in the intrahepatic vacuole. Here, we employed the glucosamine-activated glmS ribozyme to study the role of EXP2 during Plasmodium berghei liver stage development in hepatoma cells. Insertion of the glmS sequence into the exp2 3’UTR enabled glucosamine-dependent depletion of EXP2 after hepatocyte invasion, allowing separation of EXP2 function during intrahepatic development from a recently reported role in hepatocyte invasion. Post-invasion EXP2 knockdown reduced parasite size and largely abolished expression of the mid to late liver stage marker LISP2. As an orthogonal approach to monitor development, EXP2-glmS parasites and controls were engineered to express nanoluciferase. Activation of glmS after invasion substantially decreased luminescence in hepatoma monolayers and in culture supernatants at later time points corresponding with merosome detachment that marks the culmination of liver stage development. Collectively, our findings extend the utility of the glmS ribozyme to study protein function in the liver stage and reveal EXP2 is important for intrahepatic parasite development, indicating PTEX components also function at the hepatocyte-parasite interface.
Human HelQ and DNA polymerase δ interact to halt DNA synthesis and stimulate DNA single-strand annealing
Authors: He Liu , Lever Rebecca , Cubbon Andrew , Tehseen Muhammad , Jenkins Tabitha , Nottingham Alice O. , Horton Anya , Betts Hannah , Fisher Martin , Hamdan Samir M. , Soultanas Panos , Bolt Edward L.
Published: October 2022

DNA strand breaks can be repaired by base-pairing with unbroken homologous DNA, forming a template for new DNA synthesis that patches over the break site. In eukaryotes multiple DNA break repair pathways utilize DNA polymerase δ (Pol δ) to synthesise new DNA from the available 3’OH at the strand break. Here we show that DNA synthesis by human Pol δ is halted by the HelQ DNA repair protein directly targeting isolated Pol δ or Pol δ in complex with PCNA and RPA. The mechanism is independent of DNA binding by HelQ or Pol δ, maps to a region of HelQ that also modulates RPA, and requires multiple Pol δ subunits. Interaction of HelQ with the POLD3 subunit of Pol δ stimulated DNA single-strand annealing activity of HelQ. The data implicates HelQ in preventing genetic instability by restraining DNA synthesis in multiple DNA break repair pathways.
The scaffold proteins Tanc1 and Tanc2 are required for myoblast fusion
Authors: El-Khoury Michelle , Lalonde Andréane , Hipfner David , Côté Jean-François
Published: October 2022

Myoblast fusion is a crucial step in myogenesis during embryogenesis and adulthood. In Drosophila, the scaffold protein Antisocial (Ants)/Rols7 plays is essential in myoblast fusion by connecting the cell adhesion surface proteins to the cytoskeleton. Most molecular pathways governing fusion are evolutionary conserved between mammals and flies, but the relative contributions of Tanc1 and Tanc2, mammalian orthologs of Ants/Rols7, in myoblast fusion have not been established. We used the myoblast C2C12 cell line as a model for differentiation and fusion to assess the contributions of Tanc1 and Tanc2 in fusion. We found that Tanc1 and Tanc2 expressions are not modulated during differentiation, but that both proteins are enriched at the cell cortex in proliferating myoblasts. The knockdown of either Tanc1 or Tanc2 in either of the fusing myoblasts impaired fusion. Notably, the expression of human Tanc1 or Tanc2 restored fusion defects observed in Tanc1- or Tanc2-depleted cells. We found that neither Tanc1 nor Tanc2 could substitute for Ants/Rols7 during Drosophila myoblast fusion. We conclude that both Tanc1 and Tanc2 play a role in mammalian myoblast fusion, but there may be some mechanistic differences with the functions of the Drosophila orthologous protein.
Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene
Authors: Yui Anna , Kuroda Daisuke , Maruno Takahiro , Nakakido Makoto , Nagatoishi Satoru , Uchiyama Susumu , Tsumoto Kouhei
Published: October 2022

LI-cadherin is a member of the cadherin superfamily. LI-cadherin mediates Ca2+-dependent cell-cell adhesion by forming a homodimer. A previous study reported two single nucleotide polymorphisms (SNPs) in the LI-cadherin-coding gene (CDH17). These SNPs correspond to the amino acid changes of Lys115 to Glu and Glu739 to Ala. Patients with colorectal cancer carrying these SNPs are reported to have a higher risk of lymph node metastasis than patients without the SNPs. Although proteins associated with metastasis have been identified, the molecular mechanisms underlying the functions of these proteins remain unclear, making it difficult to develop effective strategies to prevent metastasis. In this study, we employed biochemical assays and molecular dynamics (MD) simulations to elucidate the molecular mechanisms by which the amino acid changes caused by SNPs in the LI-cadherin-coding gene increase the risk of cancer metastasis. Cell aggregation assays showed that the amino acid changes weakened the LI-cadherin-dependent cell-cell adhesion. In vitro assays demonstrated a decrease in homodimerization tendency due to the mutation of Lys115, and MD simulations suggested an alteration in the intramolecular hydrogen bond network due to the amino acid change. Taken together, our results indicate that the increased risk of lymph node metastasis is due to weakened cell-cell adhesion caused by the decrease in homodimerization tendency.
Differential requirement for BRCA1-BARD1 E3 ubiquitin ligase activity in DNA damage repair and meiosis in theCaenorhabditis elegansgerm line
Authors: Li Qianyan , Kaur Arshdeep , Okada Kyoko , McKenney Richard J. , Engebrecht JoAnne
Published: October 2022

The tumor suppressor BRCA1-BARD1 complex functions in many cellular processes; of critical importance to its tumor suppressor function is its role in genome integrity. Although RING E3 ubiquitin ligase activity is the only known enzymatic activity of the complex, thein vivorequirement for BRCA1-BARD1 E3 ubiquitin ligase activity has been controversial. Here we probe the role of BRCA1-BARD1 E3 ubiquitin ligase activityin vivousingC. elegans. Genetic, cell biological, and biochemical analyses of mutants defective for E3 ligase activity reveal both E3 ligase-dependent and independent functions of the complex in the context of DNA damage repair and meiosis. We show that E3 ligase activity is essential for BRCA1-BARD1 to concentrate at both DNA damage and recombination sites in meiotic germ cells, but not at DNA damage sites in proliferating germ cells. While BRCA1 alone is capable of monoubiquitylation, BARD1 is required with BRCA1 to promote polyubiquitylation. We find that the requirement for E3 ligase activity and BARD1 in DNA damage signaling and repair can be partially alleviated by driving the nuclear accumulation and self-association of BRCA1. Our data suggest that in addition to E3 ligase activity, BRC-1 serves a structural role for DNA damage signaling and repair while BRD-1 plays an accessory role to enhance BRC-1 function.

Author Summary

BRCA1-BARD1 is a E3 ubiquitin ligase, which modifies proteins by the addition of the small protein ubiquitin. While mutations that disrupt E3 ligase activity and stability of the BRCA1-BARD1 complex lead to a predisposition for breast and ovarian cancer, the specific requirement for E3 ligase activity in tumor suppression is not known. Here we probe the function of E3 ligase activity and BARD1 in the maintenance of genome integrity by engineering point mutations that disrupt E3 ligase activity inC. elegansBRCA1 as well as a null mutation in BARD1. We find that while E3 ligase activity is important for genome integrity, the complex plays additional roles besides ubiquitylating proteins. Further, our data suggest that BRCA1 is the key functional unit of the complex while BARD1 is an accessory partner that enhances BRCA1’s function. These findings may help explain why there is a higher prevalence of cancer-causing mutations in BRCA1 compared to BARD1.
Observed Kinetics of Enterovirus Inactivation by Free Chlorine Is Host Cell-Dependent
Authors: Torii Shotaro , David Shannon Christa , Larivé Odile , Cariti Federica , Kohn Tamar
Published: October 2022

The virucidal efficacy of disinfectants is typically assessed by infectivity assay utilizing a single type of host cell. Enteroviruses infect multiple host cells via different entry routes, and each entry route may be impaired to a varying extent by a given disinfectant. Yet, it is not known how the choice of host cells for titration affects the observed inactivation kinetics. Here, we evaluated the inactivation kinetics of echovirus 11 (E11) by free chlorine, ultraviolet (UV) irradiation, and heat, using three different host cells (BGMK, RD, and A549). E11 inactivation by free chlorine occurred at a two-fold greater rate when enumerated on BGMK cells compared to RD and A549 cells. Conversely, a comparable inactivation rate was observed for UV and heat independent of the host cell used. Host cell-dependent inactivation kinetics by free chlorine were also observed for echovirus 7, 9 and 13, and coxsackievirus A9, confirming that this phenomenon is not serotype-specific. Inactivation of E11 was partly caused by a loss in host cell attachment, which was most pronounced for BGMK cells, and which may be promoted by a lack of CD55 attachment receptors on this cell type. Additionally, BGMK cells lack a key subunit of the uncoating receptor, β2M, which may further contribute to the differential inactivation kinetic for this cell type. Consequently, inactivation kinetics of enteroviruses should be assessed using host cells with different receptor profiles. This will yield a more complete understanding of the inactivating power of disinfectants targeting the viral attachment and/or uncoating.

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RNA-sensing pattern-recognition receptors synergize with TLR2 or dectin-1 to trigger high production of IL-12p70 by human dendritic cells
Authors: Gilmour Brian C. , Corthay Alexandre , Øynebråten Inger
Published: October 2022

IL-12p70 is crucial for T helper 1 polarization and the generation of type 1 immunity that is required to fight cancer and intracellular pathogens. Therefore, strategies to optimize the production of IL-12p70 by dendritic cells (DCs) may significantly improve the efficacy of vaccines and immunotherapies for cancer. However, the rules governing the production of IL-12p70 remain obscure. Here, we stimulated pattern recognition receptors (PRRs) representing all five families of PRRs, to evaluate their ability to elicit high production of IL-12p70 by human DCs. We used ten well-characterized agonists and stimulated human monocyte-derived DCsin vitrowith either single agonists or 26 different combinations. We found that poly(I:C), which engages the RNA-sensing PRRs TLR3 and/or MDA5, was the only agonist that could elicit IL-12p70 production when used alone. Combinations of agonists of cell surface and intracellular PRRs were found to synergize to induce high IL-12p70 production, given that the combination included poly(I:C) or resiquimod, which both are agonists of intracellular, RNA sensing PRRs (TLR3/MDA5 and TLR7/8, respectively). Our data show that production of high IL-12p70 is strictly controlled, which is different from what we observed for IFNβ, whose production could be elicited by several intracellular PRRs. In conclusion, we identified six different combinations of PRR ligands able to induce high IL-12p70 production by human DCs. The identified synergistic PRR ligand combinations may represent strong adjuvant candidates in particular for therapeutic cancer vaccines.
More than mcr: Canonical Plasmid- and Transposon-Encoded Mobilized Colistin Resistance (mcr) Genes Represent a Subset of Phosphoethanolamine Transferases
Authors: Gaballa Ahmed , Wiedmann Martin , Carroll Laura M.
Published: October 2022

Mobilized colistin resistance genes (mcr) may confer resistance to colistin, a last-resort, critically important antimicrobial for human health. mcr can often be transmitted horizontally (e.g., via mobile genetic elements); however, mcr encode phosphoethanolamine transferases (PET) closely related to chromosomally encoded, intrinsic lipid modification enzymes (e.g., EptA, EptB, CptA). To explore the genetic diversity of mcr within the context of intrinsic lipid modification PET, we identified 9,836 non-redundant protein accession numbers associated with mcr-like genes, representing a total of 69,814 mcr-like genes present across 256 bacterial genera. We subsequently identified 125 unique, putative novel mcr-like genes encoded on the same contig as a plasmid replicon and other antimicrobial resistance genes. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like genes, and intrinsic lipid modification PET-encoding genes indicated that sequence similarity is insufficient to discriminate between genes involved in colistin resistance and genes encoding intrinsic lipid modification PET. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific diversifying positive selection might have played a role in the evolution of subvariants within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. These residues were found to be differentially conserved in different mcr families and thus may play a role in mcr subvariant phenotypic diversity. Moreover, we found that eptA and mcr are localized within different genomic contexts. Canonical eptA are typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. In contrast, mcr are encoded as single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to “colistin resistance genes” through various mechanisms, including selection and diversification of the genomic context, regulatory pathways, and mobilization. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.
The cellular states and fates of shed intestinal cells
Authors: Halpern Keren Bahar , Kohanim Yael Korem , Biram Adi , Egozi Adi , Shulman Ziv , Itzkovitz Shalev
Published: October 2022

The intestinal epithelium is replaced every few days1. Enterocytes are shed into the gut lumen predominantly from the tips of villi3,4, and are believed to rapidly die upon their dissociation from the tissue. However, technical limitations prohibited studying the cellular states and fates of shed intestinal cells. Here, we used bulk and single cell RNA sequencing of mouse intestinal fecal washes to demonstrate that shed epithelial cells remain viable and up-regulate distinct anti-microbial programs upon shedding. We further identify abundant shedding of immune cells, a process that is elevated in DSS-induced colitis. We find that fecal host transcriptomics mirrors changes in the intestinal tissue following perturbations. Our study suggests potential functions of shed cells in the intestinal lumen and demonstrates that host cell transcriptomes in intestinal washes can be used to probe tissue states.
Midbody proteins display distinct temporal dynamics during cytokinesis
Authors: Halcrow Ella F.J. , Mazza Riccardo , Diversi Anna , Enright Anton , D’Avino Pier Paolo
Published: October 2022

The midbody is an organelle that forms between the two daughter cells during cytokinesis. It co-ordinates the abscission of the nascent daughter cells and is composed of a multitude of proteins that are meticulously arranged into distinct temporal and spatial localization patterns. However, very little is known about the mechanisms that regulate the localization and function of midbody proteins. Here, we analyzed the temporal and spatial profiles of key midbody proteins during mitotic exit under normal conditions and after treatment with drugs that affect phosphorylation and proteasome-mediated degradation to decipher the impacts of post-translational modifications on midbody protein dynamics. Our results highlighted that midbody proteins show distinct spatio-temporal dynamics during mitotic exit and cytokinesis that depend on both ubiquitin-mediated proteasome degradation and phosphorylation/de-phosphorylation. They also identified two discrete classes of midbody proteins: ‘transient’ midbody proteins - including Anillin, Aurora B and PRC1- which rapidly accumulate at the midbody after anaphase onset and then slowly disappear, and ‘stable’ midbody proteins - including CIT-K, KIF14 and KIF23- which instead persist at the midbody throughout cytokinesis and also post abscission. These two classes of midbody proteins display distinct interaction networks with ubiquitylation factors, which could potentially explain their different dynamics and stability during cytokinesis.
Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast
Authors: Schindler Daniel , Walker Roy S.K. , Jiang Shuangying , Brooks Aaron N. , Wang Yun , Müller Carolin A. , Cockram Charlotte , Luo Yisha , García Alicia , Schraivogel Daniel , Mozziconacci Julien , Blount Benjamin A. , Cai Jitong , Ogunlana Lois , Liu Wei , Jönsson Katarina , Abramczyk Dariusz , Garcia-Ruiz Eva , Turowski Tomasz W. , Swidah Reem , Ellis Tom , Antequera Francisco , Shen Yue , Nieduszynski Conrad A. , Koszul Romain , Dai Junbiao , Steinmetz Lars M. , Boeke Jef D. , Cai Yizhi
Published: October 2022

Here we report the design, construction and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190 kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporated orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enable an orthogonal SCRaMbLE system capable of adjusting tRNA abundance. Following construction, we obtained evidence of a potent selective force once the neochromosome was introduced into yeast cells, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up new opportunities to directly test hypotheses surrounding these essential non-coding RNAs.

Highlights

De novo design, construction and functional characterization of a neochromosome containing all 275 nuclear tRNA genes of Saccharomyces cerevisiae.

Increasing the copy number of the 275 highly expressed tRNA genes causes cellular burden, which the host cell likely buffers either by selecting for partial tRNA neochromosome deletions or by increasing its ploidy.

The tRNA neochromosome can be chemically extracted and transformed into new strain backgrounds, enabling its transplantation into multi-synthetic chromosome strains to finalize the Sc2.0 strain.

Comprehensive functional characterization does not pinpoint a singular cause for the cellular burden caused by the tRNA neochromosome, but does reveal novel insights into its tRNA and structural chromosome biology.
EngineeringEscherichia colito utilize erythritol as sole carbon source
Authors: Ba Fang , Ji Xiangyang , Huang Shuhui , Zhang Yufei , Liu Wan-Qiu , Liu Yifan , Ling Shengjie , Li Jian
Published: October 2022

Erythritol, one of the natural sugar alcohols, is widely used as a sugar substitute sweetener in food industries. Human themselves are not able to catabolize erythritol and their gut microbes lack related catabolic pathways either to metabolize erythritol. Here, we engineerEscherichia colito utilize erythritol as sole carbon source aiming for defined applications. First, we isolate the erythritol metabolic gene cluster and experimentally characterize the erythritol-binding transcriptional repressor and its DNA-binding site. Transcriptome analysis suggests that carbohydrate metabolism-related genes in the engineeredE. coliare overall upregulated, which then guides the selection of four genes for overexpression that notably enhances cell growth. Finally, engineeredE. colistrains can be used as a living detector to distinguish erythritol-containing soda soft drinks and can grow in the simulated intestinal fluid supplemented with erythritol. We expect our work will inspire the engineering of more hosts to respond and utilize erythritol for broad applications in metabolic engineering, synthetic biology, and biomedical engineering.