bluuebunny/crossref_metadata_2025 huggingface dataset:
Hysterectomy Versus Hysteropexy at the Time of Native Tissue Pelvic Organ Prolapse Repair: A Cost-Effectiveness Analysis
Authors: Chang Olivia H. , Shepherd Jonathan P. , Ridgeway Beri M. , Cadish Lauren A.
Published: June 2020

Objective

The aim of the study was to determine whether a hysterectomy at the time of native tissue pelvic organ prolapse repair is cost-effective for the prevention of endometrial cancer.

Methods

We created a decision analysis model using TreeAge Pro. We modeled prolapse recurrence after total vaginal hysterectomy with uterosacral ligament suspension (TVH-USLS) versus sacrospinous ligament fixation hysteropexy (SSLF-HPXY). We modeled incidence and diagnostic evaluation of postmenopausal bleeding, including risk of endometrial pathology and diagnosis or death from endometrial cancer. Modeled costs included those associated with the index procedure, subsequent prolapse repair, endometrial biopsy, pelvic ultrasound, hysteroscopy, dilation and curettage, and treatment of endometrial cancer.

Results

TVH-USLS costs US $587.61 more than SSLF-HPXY per case of prolapse. TVH-USLS prevents 1.1% of women from experiencing postmenopausal bleeding and its diagnostic workup. It prevents 0.95% of women from undergoing subsequent major surgery for the treatment of either prolapse recurrence or suspected endometrial cancer. Using our model, it costs US $2,698,677 to prevent one cancer death by performing TVH-USLS. As this is lower than the value of a statistical life, it is cost-effective to perform TVH-USLS for cancer prevention. Multiple 1-way sensitivity analyses showed that changes to input variables would not significantly change outcomes.

Conclusions

TVH-USLS increased costs but reduced postmenopausal bleeding and subsequent major surgery compared with SSLF-HPXY. Accounting for these differences, TVH-USLS was a cost-effective approach for the prevention of endometrial cancer. Uterine preservation/removal at the time of prolapse repair should be based on the woman’s history and treatment priorities, but cancer prevention should be one aspect of this decision.
Stimulus valence influences the evaluative processing of action outcome
Authors: Ishii Chikara , Katayama Jun’ichi
Published: June 2020

The aim of the current study is to reveal the influence of prior associations between feedback stimuli and outcomes, in everyday life, on the early and late evaluative processing of outcomes. Participants were subjected to a simple gambling task while their electroencephalograms were recorded. Over two conditions, participants received congruent and incongruent feedback stimuli during the task. Feedback stimuli previously associated with positive outcomes were paired with monetary gain in the congruent condition and paired with monetary loss in the incongruent condition. We analyzed feedback-related negativity and P300 event-related brain potentials, as indices of early and late outcome evaluation. The results show that monetary loss, compared to gain, elicited larger feedback-related negativity, irrespective of congruency. However, the feedback-related negativity effect was delayed in the incongruent condition and an increased P300 amplitude was observed for congruent-loss outcomes. The valence of stimuli formed through experiences differently modulate early and late processes of outcome evaluation. The present study emphasizes the need to consider the stimulus valence to understand processes of outcome evaluation.
Serotonin hyperpolarizes the dorsal raphe nucleus neurons of mice by activating G protein–coupled inward rectifier potassium channels
Authors: Yaman Burak , Bal Ramazan
Published: June 2020

Serotonin (5-HT) has an important role in the pathophysiology of the mood disorders like major depression and anxiety disorders in central nervous system. On the one hand, dorsal raphe nucleus (DRN) neurons send serotonergic projections to almost all brain regions. On the other hand, they affect themselves through 5-HT1A autoreceptors. Many electrophysiological studies have investigated the ionic mechanism of the 5-HTs effect on the DRN neurons of the rat. However, there is no study characterizing the current that mediates the 5-HTs effect on mouse DRN neurons. In the present electrophysiological study, the whole-cell patch-clamp technique was used in the neurons of the DRN from one-month-old Balb/c mice to investigate the effect of 5-HT on the DRN neurons of mice and its ionic mechanism of action. The application of 5-HT resulted in a 14.3 ± 3.1 mV hyperpolarization (n = 9, P < 0.01) of resting membrane potential and 25.7 ± 3.5 pA outward current (n = 7) in the DRN neurons. The reversal potential (E5-HT) of the current induced by 5-HT was close to the potassium equilibrium potential (EK). This current had an inward rectification feature and was blocked by quinine pretreatment (n = 5, P < 0.05). In conclusion, 5-HT inhibits the DRN neurons of mice by inducing a current that is carried by potassium ions through G-protein–coupled inward rectifier potassium channels.
CRISpy-pop: a web tool for designing CRISPR/Cas9-driven genetic modifications in diverse populations
Authors: Stoneman Hayley R. , Wrobel Russell L. , Place Michael , Graham Michael , Krause David J. , De Chiara Matteo , Liti Gianni , Schacherer Joseph , Landick Robert , Gasch Audrey P. , Sato Trey K. , Hittinger Chris Todd
Published: June 2020

CRISPR/Cas9 is a powerful tool for editing genomes, but design decisions are generally made with respect to a single reference genome. With population genomic data becoming available for an increasing number of model organisms, researchers are interested in manipulating multiple strains and lines. CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing for diverse yeast and bacterial strains. The current implementation designs and predicts the activity of guide RNAs against more than 1000Saccharomyces cerevisiaegenomes, including 167 strains frequently used in bioenergy research.Zymomonas mobilis, an increasingly popular bacterial bioenergy research model, is also supported. CRISpy-pop is available as a web application (https://CRISpy-pop.glbrc.org/) with an intuitive graphical user interface. CRISpy-pop also cross-references the human genome to allow users to avoid the selection of sgRNAs with potential biosafety concerns. Additionally, CRISpy-pop predicts the strain coverage of each guide RNA within the supported strain sets, which aids in functional population genetic studies. Finally, we validate how CRISpy-pop can accurately predict the activity of guide RNAs across strains using population genomic data.
Short-Term Corticosteroids in SARS-CoV2 Patients: Hospitalists’ Perspective
Authors: Selvaraj Vijairam , Dapaah-Afriyie Kwame , Finn Arkadiy , Flanigan Timothy
Published: June 2020

Background

Dexamethasone, a synthetic glucocorticoid, has anti-inflammatory and immunosuppressive properties. There is a hyperinflammatory response involved in the clinical course of patients with pneumonia due to SARS-CoV2. To date, there has been no definite therapy for COVID-19. We reviewed the charts of SARS-CoV2 patients with pneumonia and moderate to severely elevated CRP and worsening hypoxemia who were treated with early, short-term dexamethasone.

Methods

We describe a series of 21 patients who tested positive for SARS-CoV2 and were admitted to The Miriam Hospital in Providence and were treated with a short course of dexamethasone, either alone or in addition to current investigative therapies.

Results

CRP levels decreased significantly following the start of dexamethasone from mean initial levels of 129.52 to 40.73 mg/L at time of discharge. 71% percent of the patients were discharged home with a mean length of stay of 7.8 days. None of the patients had escalation of care, leading to mechanical ventilation. Two patients were transferred to inpatient hospice facilities on account of persistent hypoxemia, in line with their documented goals of care.

Conclusions

A short course of systemic corticosteroids among inpatients with SARS-CoV2 with hypoxic respiratory failure was well tolerated, and most patients had improved outcomes. This limited case series may not offer concrete evidence towards the benefit of corticosteroids in COVID-19. However, patients’ positive response to short-term corticosteroids demonstrates that they may help blunt the severity of inflammation and prevent a severe hyperinflammatory phase, in turn reducing the length of stay, ICU admissions, and healthcare costs.

In this series, we demonstrate that timely, short-term use of systemic corticosteroids among hospitalized patients with hypoxic respiratory failure due to SARS-CoV2 was well tolerated with good outcomes. The outcomes were reflected by reductions in inpatient mortality, CRP levels, requirement for mechanical ventilation and escalation of care.
Epigenomics, Genomics, Resistome, Mobilome, Virulome and Evolutionary Phylogenomics of Carbapenem-resistant Klebsiella pneumoniae clinical strains
Authors: Kopotsa Katlego , Mbelle Nontombi M , John Osei Sekyere
Published: June 2020

Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP were characterised.

Methods

CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex-PCR, genotyping by Repetitive Element Palindromic-Polymerase Chain Reaction (REP-PCR), plasmid size, number, incompatibility, and mobility analyses, and PacBio’s SMRT sequencing (n=6).

Results & conclusion

There were 56 multidrug-resistant CRKP, having blaOXA-48-like and blaNDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands and type I and II restriction modification systems (RMS). These plasmids were of close evolutionary relationship to several plasmids globally whilst the strains also clustered with several global clades, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39, and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. The six strains contained at least 41 virulence genes and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II, and III RMS, conferring m6A (GATC, GATGNNNNNNTTG, CAANNNNNNCATC motifs) and m4C (CCWGG) modifications on chromosomes and plasmids, were found.

There is plasmid-mediated, clonal, and multiclonal dissemination of blaOXA-48-like and blaNDM-1 in South Africa, mirroring international epidemiology of similar clones and plasmids. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity, and resistance, threatening infection treatment. RMS influence on antimicrobial and bacteriophage therapy needs urgent investigation.

Highlights/Importance

K. pneumoniae is a major pathogen implicated in numerous nosocomial infections. Worryingly, we show that K. pneumoniae isolates from South Africa, Africa and globally are endowed with rich resistomes and mobilomes that make them almost pandrug resistant. The isolates in this study contained rich virulomes and prophages on both chromosomes and plasmids, with close evolutionary kith or kin to other plasmids identified worldwide. There was a rich diversity of restriction modification systems that regulate virulence, transcription, and plasmid mobility in bacteria, facilitating the epidemiology, resistance, pathogenicity and genomic evolution of the strains, and threatening antimicrobial and bacteriophage therapy.
DNA hypohydroxymethylation in pediatric central nervous system tumors is associated with CTCF binding sites and reduced survival
Authors: Azizgolshani Nasim , Petersen Curtis L. , Chen Youdinghuan , Salas Lucas A. , Perreard Laurent , Nguyen Lananh N. , Christensen Brock C.
Published: June 2020

Nucleotide-specific 5-hydroxymethylcytosine (5hmC) remains understudied in pediatric central nervous system tumors. We measured genome-scale 5hmC in glioma, ependymoma, and embryonal tumors from children, as well as control pediatric brain tissues using oxidative and bisulfite treatments. Tumor 5hmC localized to regulatory elements crucial to cell identity, including transcription factor binding sites and super-enhancers. A linear model tested the CpG-specific differences in 5hmC between tumor and non-tumor samples, as well as between tumor subtypes. Compared to non-tumor samples, tumors were hypohydroxymethylated across the epigenome. Differentially hydroxymethylated loci among tumor subtypes tended to be hypermethylated and disproportionally found in CTCF binding sites and genes related to posttranscriptional RNA regulation, such as DICER1. Model-based clustering results indicated that patients with low 5hmC patterns have poorer overall survival and increased risk of recurrence. These results have implications for emerging molecular neuropathology classification approaches and epigenetic therapeutic strategies in childhood brain tumors.
Space-time conditional autoregressive modeling to estimate neighborhood-level risks for dengue fever in Cali, Colombia
Authors: Desjardins M.R. , Eastin M.D. , Paul R. , Casas I. , Delmelle E.M.
Published: June 2020

Vector-borne diseases (VBDs) affect more than 1 billion people a year worldwide, cause over 1 million deaths, and cost hundreds of billions of dollars in societal costs. Mosquitoes are the most common vectors, responsible for transmitting a variety of arboviruses. Dengue fever (DENF) has been responsible for nearly 400 million infections annually. Dengue fever is primarily transmitted by female Aedes aegypti and Aedes albopictus mosquitoes. Since both Aedes species are peri-domestic and container-breeding mosquitoes, dengue surveillance should begin at the local level - where a variety of local factors may increase the risk of transmission. Dengue has been endemic in Colombia for decades and is notably hyperendemic in the city of Cali. For this study, we use weekly cases of DENF in Cali, Colombia from 2015-2016; and develop space-time conditional autoregressive models to quantify how DENF risk is influenced by socioeconomic, environmental, and accessibility risk factors, and lagged weather variables. Our models identify high-risk neighborhoods for DENF throughout Cali. Statistical inference is drawn under Bayesian paradigm using Markov Chain Monte Carlo techniques. The results provide detailed insight about the spatial heterogeneity of DENF risk and the associated risk factors (such as weather, proximity to Aedes habitats, and socioeconomic classification) at a fine-level, informing public health officials to motivate at-risk neighborhoods to take an active role in vector surveillance and control, and improving educational and surveillance resources throughout the city of Cali.
COVID-19 lockdown: if, when and how
Authors: Mayorga Lía , García Samartino Clara , Flores Gabriel , Masuelli Sofía , Sánchez María V. , Sánchez Cristián G. , Mayorga Luis S.
Published: June 2020

Background

With the lack of an effective SARS-CoV-2 vaccine, mathematical modeling has stepped up in the COVID-19 management to guide non-pharmaceutical intervention (NPI) policies. Complete lockdown has been characterized as the most powerful strategy for the epidemic; anyhow, it is associated with undeniable negative consequences. Not aware that global panic could make countries adopt premature and lengthy lockdowns, previous studies only warned about the inefficacy of late quarantine sets. Therefore, we proposed ourselves to find the optimal timing and lasting for COVID-19 suppressive measures.

Methods

We used our previously elaborated compartmental SEIR (Susceptible-Exposed-Infected-Recovered) model to scan different timings for lockdown set and various lockdown lengths under different reproduction number (R0) scenarios. We explored healthcare parameters focusing on ICU occupation and deaths since they condition the sanitary system and reflect the severity of the epidemic.

Results

The timing for the lockdown trigger varies according to the original R0and has great impact on ICU usage and fatalities. The less the R0the later the lockdown should be for it to be effective. The lockdown length is also something to consider. Too short lockdowns (∼15 days) have minimal effect on healthcare parameters, but too long quarantines (>45 days) do not benefit healthcare parameters proportionally when compared to more reasonable 30 to 45-day lockdowns. We explored the outcome of the combination of a 45-day lockdown followed by strict mitigation measures sustained in time, and interestingly, it outperformed the lengthy quarantine. Additionally, we show that if strict mitigation actions were to be installed from the very beginning of the epidemic, lockdown would not benefit substantially regarding healthcare parameters.

Conclusion

Lockdown settiming and lastingare non-trivial variables to COVID-19 management.
Behavioral changes before lockdown, and decreased retail and recreation mobility during lockdown, contributed most to the successful control of the COVID-19 epidemic in 35 Western countries
Authors: Deforche Koen , Vercauteren Jurgen , Müller Viktor , Vandamme Anne-Mieke
Published: June 2020

The COVID-19 pandemic has prompted a lockdown in many countries to control the exponential spread of the SARS-CoV-2 virus (1, 2). This resulted in curbing the epidemic by reducing the time-varying basic reproduction number (Rt) to below one (3, 4). Governments are looking for evidence to balance the demand of their citizens to ease some of the restriction, against the fear of a second peak in infections. More details on the specific circumstances that promote exponential spread (i.e. Rt> 1) and the measures that contributed most to a reduction in Rt are needed. Here we show that in 33 of 35 Western countries (32 European, plus Israel, USA and Canada), Rt fell to around or below one during lockdown (March – May 2020). One third of the effect happened already on average 6 days before the lockdown, with lockdown itself causing another major drop in transmission. Country-wide compulsory usage of masks was implemented only in Slovakia 10 days into lockdown, and on its own reduced transmission by half. During lockdown, decreased mobility in retail and recreation was an independent predictor of lower Rt during lockdown, while changes in other types of mobility were not. These results are consistent with anecdotal evidence that large recreational gatherings are super-spreading events (5, 6), and may even suggest that infections during day-to-day contact at work are not sufficient to spark exponential growth. Our data suggest measures that will contribute to avoiding a second peak include a tight control on circumstances that facilitate massive spread such as large gatherings especially indoors, physical distancing, and mask use.
Mathematical modeling explains differential SARS CoV-2 kinetics in lung and nasal passages in remdesivir treated rhesus macaques
Authors: Goyal Ashish , Duke Elizabeth R. , Cardozo-Ojeda E. Fabian , Schiffer Joshua T.
Published: June 2020

Remdesivir was recently demonstrated to decrease recovery time in hospitalized patients with SARS-CoV-2 infection. In rhesus macaques, early initiation of remdesivir therapy prevented pneumonia and lowered viral loads in the lung, but viral loads increased in the nasal passages five days after therapy. We developed mathematical models to explain these results. We identified that 1) drug potency is slightly higher in nasal passages than in lungs, 2) viral load decrease in lungs relative to nasal passages during therapy because of infection-dependent generation of refractory cells in the lung, 3) incomplete drug potency in the lung that decreases viral loads even slightly may allow substantially less lung damage, and 4) increases in nasal viral load may occur due to a slight blunting of peak viral load and subsequent decrease of the intensity of the innate immune response, as well as a lack of refractory cells. We also hypothesize that direct inoculation of the trachea in rhesus macaques may not recapitulate natural infection as lung damage occurs more abruptly in this model than in human infection. We demonstrate with sensitivity analysis that a drug with higher potency could completely suppress viral replication and lower viral loads abruptly in the nasal passages as well as the lung.

One Sentence Summary

We developed a mathematical model to explain why remdesivir has a greater antiviral effect on SARS CoV-2 in lung versus nasal passages in rhesus macaques.
Recovery-associated resting-state activity and connectivity alterations in Anorexia nervosa
Authors: Lotter Leon D. , von Polier Georg , Offermann Jan , Buettgen Kimberly , Stanetzky Lukas , Eickhoff Simon B. , Konrad Kerstin , Seitz Jochen , Dukart Juergen
Published: June 2020

Background

Previous studies provided controversial insight on the impact of starvation, disease status and underlying grey matter volume (GMV) changes on resting-state functional magnetic resonance imaging (rsfMRI) alterations in Anorexia nervosa (AN). Here we adapt a combined longitudinal and cross-sectional approach to disentangle the effects of these factors on resting-state alterations in AN.

Methods

Overall, 87 female subjects were included in the study: adolescent patients with acute AN scanned at inpatient admission (N = 22, mean age 15.3 years) and at discharge (N = 21), 21 patients recovered from AN (22.3 years) and two groups of healthy age-matched controls (both N = 22, 16.0 and 22.5 years). Whole-brain measures of resting-state activity and functional connectivity were computed (Network Based Statistics, Global Correlation, Integrated Local Correlation, fractional Amplitude of Low Frequency Fluctuations) to assess rsfMRI alterations over the course of AN treatment before and after controlling for underlying GMV.

Results

Patients with acute AN displayed strong and widespread prefrontal, sensorimotor, parietal, temporal, precuneal and insular reductions of resting-state connectivity and activity. All alterations were independent of GMV and were largely normalized in short- and absent in long-term recovered AN.

Conclusions

Resting-state fMRI alterations in AN constitute acute and GMV independent presumably starvation-related phenomena. The majority of alterations found here normalized over the course of recovery without evidence for possible preexisting trait- or remaining “scar”-effects.
Analysis and Prediction of the COVID-19 outbreak in Pakistan
Authors: Ali Mohsin , Imran Mudassar , Khan Adnan
Published: June 2020

In this study we estimate the severity of the COVID-19 outbreak in Pakistan prior to and after lock down restrictions were eased. We also project the epidemic curve considering realistic quarantine, social distancing and possible medication scenarios. We use a deterministic epidemic model that includes asymptomatic, quarantined, isolated and medicated population compartments for our analysis. We calculate the basic reproduction number ℛ0 for the pre and post lock down periods, noting that during this time no medication was available.1 The pre-lock down value of ℛ0 is estimated to be 1.07 and the post lock down value is estimated to be 1.86. We use this analysis to project the epidemic curve for a variety of lock down, social distancing and medication scenarios. We note that if no substantial efforts are made to contain the epidemic, it will peak in mid of September, with the maximum projected active cases being close to 700,000. In a realistic, best case scenario, we project that the epidemic peaks in early to mid July with the maximum active cases being around 120000.We note that social distancing measures and medication if available will help flatten the curve, however without the reintroduction of further lock down it would be very difficult to bring ℛ0 below 1. Our study strongly supports the recent WHO recommendation of reintroducing lock downs to control the epidemic.
The COVID-19 Spread Patterns in Italy and India: A Comparison of the Current Situations
Authors: Barauh Hemanta K.
Published: June 2020

Epidemiological mathematical models and time series models can be used to forecast about the spread of an infectious disease. In this article, without using such models, we are going to show how exactly the pattern evolves day by day once a pattern is seen to be approximately followed by the data. Although in Italy as well as in India the novel corona virus appeared on the same day, in Italy the spread is nearly logarithmic by now and in India it is nearly exponential even now.
Health Condition and Test Availability as Predictors of Adults’ Mental Health during the COVID-19 Pandemic
Authors: Dai Huiyang , Zhang Stephen X. , Looi Kim Hoe , Su Rui , Li Jizhen
Published: June 2020

Background

Research identifying adults’ mental health during the COVID-19 pandemic relies solely on demographic predictors without examining adults’ health status during the COVID-19 pandemic as a potential predictor.

Methods

An online survey of 669 adults in Malaysia was conducted during May 2–8, 2020, six weeks after a Movement Control Order (MCO) was issued.

Findings

Adults’ health condition had curvilinear relationships (horizontally reversed J-shaped) with insomnia, anxiety, depression and distress. Reported test availability for COVID-19 (from “strongly disagree” to “strongly agree”) also had curvilinear relationships (horizontally reversed J-shaped) with anxiety and depression. Younger adults reported worse mental health, but people from various religions and ethnic groups did not differ significantly in reported mental health.

Interpretation

Adults with worse health conditions had more mental health problems, especially adults at the lower end of the health spectrum. Test availability negatively predicted anxiety and depression, especially for adults experiencing poor COVID-19 test availability. The significant predictions of health condition and COVID-19 test availability suggest a new direction for the literature to identify psychiatric risk factors directly from health related variables during a pandemic.

Funding

Tsinghua University-INDITEX Sustainable Development Fund (Project No. TISD201904).
An interferon lambda 4-associated variant in the hepatitis C virus RNA polymerase affects viral replication in infected cells
Authors: Bamford Connor G G , McLauchlan John
Published: June 2020

HostIFNL4haplotype status contributes to the development of chronic hepatitis C virus infection in individuals who are acutely infected with the virus.In silicostudies revealed that specific amino acid variants at multiple sites on the HCV polyprotein correlate with functional single nucleotide polymorphisms (SNPs) in theIFNL4locus. Thus, SNPs at theIFNL4locus may select variants that influence virus replication and thereby outcome of infection. Here, we examine the most significantlyIFNL4-associated amino acid variants that lie in the ‘Lambda (L) 2 loop’ of the HCV NS5B RNA polymerase. L2 loop variants were introduced into both sub-genomic replicon and full-length infectious clones of HCV and viral replication examined in the presence and absence of exogenous IFNλ4. Our data demonstrate that while mutation of NS5B L2 loop affects replication, individualIFNL4-associated variants have modest but consistent effects on replication both in the presence and absence of IFNλ4. Given the strong genetic association between these variants andIFNL4, these data suggest a nuanced effect of each individual position on viral replication, the combined effect of which might mediate resistance to the effects of IFNλ4.
Transcription repressor protein ZBTB25 interacts with HDAC1 in macrophages infected withMycobacterium tuberculosis,and its inhibition leads to autophagy and killing of the intracellular pathogen
Authors: Madhavan Aravind , Arun K B , Pushparajan Akhil Raj , Balaji M , Kumar R Ajay
Published: June 2020

Downregulation of host gene expression is one of the key strategies adopted by intracellular pathogens such asMycobacterium tuberculosis(MTB) for their survival and subsequent pathogenesis. In a previous study, we have shown that HDAC1 levels go up in macrophages infected with MTB and it hypoacetylates histone H3 at the promoter ofIL-12Bgene leading to its downregulation. Here we show that after infection with MTB, the levels of the phosphorylated form of HDAC1 increase significantly in macrophages. Employing immunoprecipitation and LC-MS/MS, we found transcriptional repressor protein ZBTB25 associates with HDAC1 silencing complex along with transcriptional corepressor Sin3a. By chromatin immunoprecipitation and PCR analyses, we found that phosphorylated HDAC1, Sin3a, and ZBTB25 are recruited to the promoter ofIL-12Bto downregulate its expression in infected macrophages. Knocking down ofZBTB25enhanced release of IL-12p40 from infected macrophages. Interestingly, the treatment of infected macrophages with CI994 (inhibitor of HDAC1) or dithiopyridine (inhibitor of ZBTB25) promoted the colocalization of LC3 (microtubule-associated protein 1A/1B-light chain 3, a marker for autophagy) and MTB in autophagosomes. Induction of autophagy resulted in the killing of intracellular MTB. Enhanced phosphorylation of JAK2 and STAT4 was observed in macrophages upon CI994 and dithiopyridine treatment, and inhibition of JAK2/STAT4 negated the killing of intracellular mycobacteria suggesting a possible role of these proteins in the autophagy-mediated killing of intracellular MTB.
Functional characterization of SARS-CoV-2 infection suggests a complex inflammatory response and metabolic alterations
Authors: Trilla-Fuertes Lucía , Ramos Ricardo , Blanca-López Natalia , López-Camacho Elena , Martín-Pedraza Laura , Ryan Murua Pablo , Díaz-Almirón Mariana , Llorens Carlos , Gabaldón Toni , Moya Andrés , Fresno Vara Juan Ángel , Gámez-Pozo Angelo
Published: June 2020

Covid-19, caused by the SARS-CoV-2 virus, has reached the category of a worldwide pandemic. Even though intensive efforts, no effective treatments or a vaccine are available. Molecular characterization of the transcriptional response in Covid-19 patients could be helpful to identify therapeutic targets. In this study, RNAseq data from peripheral blood mononuclear cell samples from Covid-19 patients and healthy controls was analyzed from a functional point of view using probabilistic graphical models. Two networks were built: one based on genes differentially expressed between healthy and infected individuals and another one based on the 2,000 most variable genes in terms of expression in order to make a functional characterization. In the network based on differentially expressed genes, two inflammatory response nodes with different tendencies were identified, one related to cytokines and chemokines, and another one related to bacterial infections. In addition, differences in metabolism, which were studied in depth using Flux Balance Analysis, were identified. SARS-CoV2-infection caused alterations in glutamate, methionine and cysteine, and tetrahydrobiopterin metabolism. In the network based on 2,000 most variable genes, also two inflammatory nodes with different tendencies between healthy individuals and patients were identified. Similar to the other network, one was related to cytokines and chemokines. However, the other one, lower in Covid-19 patients, was related to allergic processes and self-regulation of the immune response. Also, we identified a decrease in T cell node activity and an increase in cell division node activity. In the current absence of treatments for these patients, functional characterization of the transcriptional response to SARS-CoV-2 infection could be helpful to define targetable processes. Therefore, these results may be relevant to propose new treatments.
Modeling Heterogeneity of Triple-Negative Breast Cancer Uncovers a Novel Combinatorial Treatment Overcoming Primary Drug Resistance
Authors: Lamballe Fabienne , Ahmad Fahmida , Vinik Yaron , Castellanet Olivier , Daian Fabrice , Müller Anna-Katharina , Köhler Ulrike A. , Bailly Anne-Laure , Josselin Emmanuelle , Castellano Rémy , Cayrou Christelle , Charafe-Jauffret Emmanuelle , Mills Gordon B. , Géli Vincent , Borg Jean-Paul , Lev Sima , Maina Flavio
Published: June 2020

Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype characterized by a remarkable molecular heterogeneity. Currently, there are no effective druggable targets and advanced preclinical models of the human disease. Here, we generated a unique mouse model (MMTV-R26Metmice) of mammary tumors driven by a subtle increase in the expression of the wild-type MET receptor.MMTV-R26Metmice develop spontaneous, exclusive TNBC tumors, recapitulating primary resistance to treatment of patients. Proteomic profiling ofMMTV-R26Mettumors and machine learning approach showed that the model faithfully recapitulates inter-tumoral heterogeneity of human TNBC. Further signaling network analysis highlighted potential druggable targets, of which co-targeting of WEE1 and BCL-XL synergistically killed TNBC cells and efficiently induced tumor regression. Mechanistically, BCL-XL inhibition exacerbates the dependency of TNBC cells on WEE1 function, leading to Histone H3 and phosphoS33RPA32 upregulation, RRM2 downregulation, cell cycle perturbation, mitotic catastrophe and apoptosis. Our study introduces a unique, powerful mouse model for studying TNBC formation and evolution, its heterogeneity, and for identifying efficient therapeutic targets.
C. elegansmethionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor
Authors: Giese Gabrielle E. , Walker Melissa D. , Ponomarova Olga , Zhang Hefei , Li Xuhang , Minevich Gregory , Walhout Albertha J.M.
Published: June 2020

Vitamin B12 is an essential micronutrient that functions in two metabolic pathways: the canonical propionate breakdown pathway and the methionine/S-adenosylmethionine (Met/SAM) cycle. InCaenorhabditis elegans, low vitamin B12, or genetic perturbation of the canonical propionate breakdown pathway results in propionate accumulation and the transcriptional activation of a propionate shunt pathway. This propionate-dependent mechanism requiresnhr-10and is referred to as “B12-mechanism-I”. Here, we report that vitamin B12 represses the expression of Met/SAM cycle genes by a propionate-independent mechanism we refer to as “B12-mechanism-II”. This mechanism is activated by perturbations in the Met/SAM cycle, genetically or due to low dietary vitamin B12. B12-mechanism-II requiresnhr-114to activate Met/SAM cycle gene expression, the vitamin B12 transporter,pmp-5, and adjust influx and efflux of the cycle by activating msra-1 and repressingcbs-1, respectively. Taken together, Met/SAM cycle activity is sensed and transcriptionally adjusted to be in a tight metabolic regime.
Can colony size of honeybees (Apis mellifera) be used as predictor for colony losses due toVarroa destructorduring winter?
Authors: van Dooremalen Coby , van Langevelde Frank
Published: June 2020

For more than three decades, honeybee colonies (Apis mellifera) experience high losses during winter, and these losses are still continuing. It is crucial that beekeepers monitor their colonies closely and anticipate losses early enough to apply mitigating actions. We tested whether colony size can be used as early predictor for potential colony losses, in particular due to the parasitic miteVarroa destructor. V. destructoris one of the most important causes for these losses. Such early predictor for potentialV. destructorinduced losses is especially relevant as measuringV. destructorload in colonies is difficult and cumbersome. During three years, we monitored colonies with high and lowV. destructorload from July until March of the next year. We found that differences in colony size were only visible after November, even though we lost almost all colonies every winter in the group with highV. destructorload. In the Northern hemisphere, November is considered to be too late for beekeepers to strengthen colonies in preparation for winter. We therefore argue that early-warning signs for potential colony losses due toV. destructorare urgently needed to allow beekeepers preventing winter losses. We discuss the role of precision apiculture to monitor the health and productivity of honeybee colonies.
The small RNA ErsA plays a role in the regulatory network ofPseudomonas aeruginosapathogenicity in airways infection
Authors: Ferrara Silvia , Rossi Alice , Ranucci Serena , De Fino Ida , Bragonzi Alessandra , Cigana Cristina , Bertoni Giovanni
Published: June 2020

Bacterial small RNAs play a remarkable role in the regulation of functions involved in host-pathogen interaction. ErsA is a small RNA ofPseudomonas aeruginosathat contributes to the regulation of bacterial virulence traits such as biofilm formation and motility. Shown to take part in a regulatory circuit under the control of the envelope stress response sigma factor σ22, ErsA targets post-transcriptionally the key virulence-associated genealgC. Moreover, ErsA contributes to biofilm development and motility through the post-transcriptional modulation of the transcription factor AmrZ. Intending to evaluate the regulatory relevance of ErsA in the pathogenesis of respiratory infections, we analyzed the impact of ErsA-mediated regulation on the virulence potential ofP. aeruginosaand the stimulation of the inflammatory response during the infection of bronchial epithelial cells and a murine model. Furthermore, we assessed ErsA expression in a collection ofP. aeruginosaclinical pulmonary isolates and investigated the link of ErsA with acquired antibiotic resistance by generating anersAgene deletion mutant in a multidrug-resistantP. aeruginosastrain which has long been adapted in the airways of a cystic fibrosis (CF) patient. Our results show that the ErsA-mediated regulation is relevant for theP. aeruginosapathogenicity during acute infection and contributes to the stimulation of the host inflammatory response. Besides, ErsA could be subjected to selective pressure forP. aeruginosapatho-adaptation and acquirement of resistance to antibiotics commonly used in clinical practice during chronic CF infections. Our findings establish the role of ErsA as an important regulatory element in the host-pathogen interaction.

Author summary

Pseudomonas aeruginosais one of the most critical multi-drug resistant opportunistic pathogen in humans, able to cause both lethal acute and chronic lung infections. Thorough knowledge of the regulatory mechanisms involved in the establishment and persistence of the airways infections byP. aeruginosaremains elusive. Emerging candidates as molecular regulators of pathogenesis inP. aeruginosaare small RNAs, which act post-transcriptionally as signal transducers of host cues. Known for being involved in the regulation of biofilm formation and responsive to envelope stress response, we show that the small RNA ErsA can play regulatory roles in acute infection, stimulation of host inflammatory response, mechanisms of acquirement of antibiotic resistance and adaptation during the chronic lung infections of cystic fibrosis patients. Elucidating the complexity of the networks regulating host-pathogen interaction is crucial to identify novel targets for future therapeutic applications.
Phosphoproteomics after nitrate treatments reveal an important role for PIN2 phosphorylation in control of root system architecture
Authors: Vega Andrea , Fredes Isabel , O’Brien José , Shen Zhouxin , Ötvös Krisztina , Benkova Eva , Briggs Steven P. , Gutiérrez Rodrigo A.
Published: June 2020

Nitrate is an important signaling molecule that commands genome-wide gene expression changes that impact metabolism, physiology, plant growth and development. Although gene expression responses to nitrate at the mRNA level have been characterized in great detail, the impact of nitrate signaling at the proteome level has been much less explored. Most signaling pathways involve post-translational modifications of key protein factors and chiefly among these modifications is protein phosphorylation. In an effort to identify new components involved in nitrate responses in plants, we performed analyses of theArabidopsis thalianaroot phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. We identified 268 phosphoproteins that show significant changes at 5 min or 20 min after nitrate treatments. The large majority of these proteins (96%) are coded by genes that are not modulated at the expression level in response to nitrate treatments in publicly available transcriptome data. Proteins identified by 5 min include potential signaling-components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with protein binding, transporter activity or hormone metabolism functions. Interestingly, the phosphorylation profile ofNITRATE TRANSPORTER 1.1(NRT1.1)mutant plants in response to nitrate at 5 min was significantly different (95%) as compared to wild-type plants. This result is consistent with the role of NRT1.1 as a key component of a nitrate signaling pathway that involves phosphoproteomic changes. Our integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post-translational level. We experimentally validated the role of PIN2 phosphorylation in both primary and lateral root growth responses to nitrate. Our data provide new insights into the phosphoproteome and identifies novel protein components that are regulated post-translationally, such as PIN2, in nitrate responses inArabidopsis thalianaroots.
Generation of SARS-CoV-2 S1 spike glycoprotein putative antigenic epitopes in vitro by intracellular aminopeptidases
Authors: Stamatakis George , Samiotaki Martina , Mpakali Anastasia , Panayotou George , Stratikos Efstratios
Published: June 2020

Presentation of antigenic peptides by MHCI is central to cellular immune responses against viral pathogens. While adaptive immune responses versus SARS-CoV-2 can be of critical importance to both recovery and vaccine efficacy, how protein antigens from this pathogen are processed to generate antigenic peptides is largely unknown. Here, we analyzed the proteolytic processing of overlapping precursor peptides spanning the entire sequence of the S1 spike glycoprotein of SARS-CoV-2, by three key enzymes that generate antigenic peptides, aminopeptidases ERAP1, ERAP2 and IRAP. All enzymes generated shorter peptides with sequences suitable for binding onto HLA alleles, but with distinct specificity fingerprints. ERAP1 was the most efficient in generating peptides 8-11 residues long, the optimal length for HLA binding, while IRAP was the least efficient. The combination of ERAP1 with ERAP2 greatly limited the variability of peptide sequences produced. Less than 7% of computationally predicted epitopes were found to be produced experimentally, suggesting that aminopeptidase processing may constitute a significant filter to epitope presentation. These experimentally generated putative epitopes could be prioritized for SARS-CoV-2 immunogenicity studies and vaccine design. We furthermore propose that this in vitro trimming approach could constitute a general filtering method to enhance the prediction robustness for viral antigenic epitopes.
Ferric Heme as a CO/NO Sensor in the Nuclear Receptor Reverbβ by Coupling Gas binding to Electron Transfer
Authors: Sarkar Anindita , Carter Eric L. , Harland Jill B. , Speelman Amy L. , Lehnert Nicolai , Ragsdale Stephen W.
Published: June 2020

Rev-Erbβ is a nuclear receptor that couples circadian rhythm, metabolism, and inflammation.1-7Heme binding to the protein modulates its function as a repressor, its stability, its ability to bind other proteins, and its activity in gas sensing.8-11Rev-Erbβ binds Fe3+-heme tighter than Fe2+-heme, suggesting its activities may be regulated by the heme redox state.9Yet, this critical role of heme redox chemistry in defining the protein’s resting state and function is unknown. We demonstrate by electrochemical and whole-cell electron paramagnetic resonance experiments that Rev-Erbβ exists in the Fe3+form within the cell essentially allowing the protein to be heme-replete even at low concentrations of labile heme in the nucleus. However, being in the Fe3+redox state contradicts Rev-Erb’s known function as a gas sensor, which dogma asserts must be a Fe2+protein This paper explains why the resting Fe3+-state is congruent both with heme-binding and cellular gas sensing. We show that the binding of CO/NO elicits a striking increase in the redox potential of the Fe3+/Fe2+couple, characteristic of an EC mechanism in which the unfavorableElectrochemical reduction of heme is coupled to the highly favorableChemical reaction of gas binding, making the reduction spontaneous. Thus, Fe3+-Rev-Erbβ remains heme-loaded, crucial for its repressor activity, and only undergoes reduction when diatomic gases are present. This work has broad implications for hemoproteins where ligand-triggered redox changes cause conformational changes influencing protein’s function or inter-protein interactions, like NCoR1 for Rev-Erbβ. This study opens up the possibility of CO/NO-mediated regulation of the circadian rhythm through redox changes in Rev-Erbβ.
Movement signaling in ventral pallidum and dopaminergic midbrain is gated by behavioral state in singing birds
Authors: Chen Ruidong , Gadagkar Vikram , Roeser Andrea C. , Puzerey Pavel A. , Goldberg Jesse H.
Published: June 2020

Movement-related neuronal discharge in ventral tegmental area (VTA) and ventral pallidum (VP) is inconsistently observed across studies. One possibility is that some neurons are movement-related and others are not. Another possibility is that the precise behavioral conditions matter - that a single neuron can be movement related under certain behavioral states but not others. We recorded single VTA and VP neurons in birds transitioning between singing and non-singing states, while monitoring body movement with microdrive-mounted accelerometers. Many VP and VTA neurons exhibited body movement-locked activity exclusively when the bird was not singing. During singing, VP and VTA neurons could switch off their tuning to body movement and become instead precisely time-locked to specific song syllables. These changes in neuronal tuning occurred rapidly at state boundaries. Our findings show that movement-related activity in limbic circuits can be gated by behavioral context.

Significance statement

Neural signals in the limbic system have long been known to represent body movements as well as reward. Here we show that single neurons dramatically change their tuning to movements when a bird starts to sing.