bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a selection assay for small guide RNAs that drive efficient site-directed RNA editing
Authors: Diaz Quiroz Juan Felipe , Ojha Namrata , Shayhidin Elnur E , De Silva Dasuni , Dabney Jesse , Lancaster Amy , Coull James , Milstein Stuart , Fraley Andrew W , Brown Christopher R , Rosenthal Joshua J C
Published: February 2023

A major challenge confronting the clinical application of site-directed RNA editing (SDRE) is the design of small guide RNAs (gRNAs) that can drive efficient editing. Although many gRNA designs have effectively recruited endogenous Adenosine Deaminases that Act on RNA (ADARs), most of them exceed the size of currently FDA-approved antisense oligos. We developed an unbiased in vitro selection assay to identify short gRNAs that promote superior RNA editing of a premature termination codon. The selection assay relies on hairpin substrates in which the target sequence is linked to partially randomized gRNAs in the same molecule, so that gRNA sequences that promote editing can be identified by sequencing. These RNA substrates were incubated in vitro with ADAR2 and the edited products were selected using amplification refractory mutation system PCR and used to regenerate the substrates for a new round of selection. After nine repetitions, hairpins which drove superior editing were identified. When gRNAs of these hairpins were delivered in trans, eight of the top ten short gRNAs drove superior editing both in vitro and in cellula. These results show that efficient small gRNAs can be selected using our approach, an important advancement for the clinical application of SDRE.
When translation elongation is impaired, the mRNA is uniformly destabilized by the RNA degradosome, while the concentration of mRNA is altered along the molecule
Authors: Duviau Marie-Pierre , Chen Fan , Emile Anthony , Cocaign-Bousquet Muriel , Girbal Laurence , Nouaille Sébastien
Published: February 2023

mRNA sits at the crossroads of transcription, translation and mRNA degradation. Many questions remain about the coupling of these three processes in Escherichia coli and, in particular, how translation may have an effect on mRNA degradation and transcription. To characterize the interplay between mRNA degradation and translation while accounting for transcription, we altered the translation initiation or elongation and measured the effects on mRNA stability and concentration. Using a mapping method, we analysed mRNA concentration and stability at the local scale all along the transcript. We showed that a decrease in translation initiation efficiency destabilizes the mRNA and leads to a uniform decrease in mRNA concentration throughout the molecule. Prematurely terminating translation elongation by inserting a stop codon is associated with a drop in local mRNA concentration downstream of the stop codon, due to the uncoupling of transcription and translation. In contrast, this translation alteration uniformly destabilizes the coding and ribosome-free regions, in a process triggered by RNase E activity, and its ability to form the RNA degradome. These results demonstrate how ribosomes protect mRNA molecules and highlight how translation, mRNA degradation and transcription are deeply interconnected in the quality control process that avoids unproductive gene expression in cells.
Structural insights into the binding of bS1 to the ribosome
Authors: D’Urso Gaetano , Chat Sophie , Gillet Reynald , Giudice Emmanuel
Published: February 2023

The multidomain ribosomal protein bS1 is the biggest and the most flexible and dynamic protein in the 30S small subunit. Despite being essential for mRNA recruitment and its primary role in the accommodation of the start codon within the decoding centre, there has not yet been a high-resolution description of its structure. Here, we present a 3D atomic model of OB1 and OB2, bS1’s first two N-terminal domains, bound to an elongation-competent 70S ribosome. Our structure reveals that, as previously reported, bS1 is anchored both by a π-stacking to the 30S subunit and via a salt bridge with the Zn2+ pocket of bS1. These contacts are further stabilized by other interactions with additional residues on OB1. Our model also shows a new conformation of OB2, interacting with the Shine–Dalgarno portion of the mRNA. This study confirms that OB1 plays an anchoring role, but also highlights a novel function for OB2, which is directly involved in the modulation and support of mRNA binding and accommodation on the ribosome.
Beyond human capital: how does parents’ direct influence on their sons’ earnings vary across eight OECD countries?
Authors: Bonomi Bezzo Franco , Raitano Michele , Vanhuysse Pieter
Published: February 2023

This article asks to what degree the association between parents’ education and sons’ earnings is mediated by various forms of sons’ human capital across eight large OECD countries. We exploit the OECD Program for the International Assessment of Adult Competencies (PIAAC) database, which provides information on four dimensions of human capital (educational attainment, field of study, cognitive skills, and proxies of non-cognitive skills). We find that the intergenerational transmission process is wholly mediated just by sons’ formal educational attainment in Germany, Norway, and the USA. By contrast, in France, Italy, Spain, Poland, and the UK, a significant residual association remains after we control for all dimensions of sons’ human capital. While we cannot exclude that this residual association is due to unobservable background-related skills sons might have, this also points to family origin factors unrelated to human capital accumulation—such as social ties—that might play a role in the intergenerational transmission of labour market advantages in these countries.
Doing the Job! Expectations of Police Recruits (Pre- and Post- Graduate Entry)
Authors: McCanney John , Taylor Julie
Published: February 2023

This research explores the views of police recruits from cohorts pre and post the introduction of the graduate entry scheme. Recruits at the end of their initial training period were asked about their role and their expectations of policing. The views of recruits from these different cohorts are compared to understand whether the new graduate programme inculcated different views than the previous training programme. This research suggests that there are few differences between student officers who have completed the graduate training programme and those that did not. The findings suggest that there are deeply entrenched barriers and resistance to the change process. If change is to be achieved, it will require that the commitment of several stakeholders including the graduate officers themselves.
Trust in the police in Latin America: A multilevel analysis of institutional and experiential models
Authors: Salazar-Tobar Felipe , Rengifo Andres F
Published: February 2023

This paper explores two models of preference-formation of trust in the police in Latin America and the Caribbean: An institutional model that highlights the role of broad assessments of government performance and legitimacy and an experiential approach focussed on more narrow experiences of victimization and police contact. We examine these frameworks based on theory and analysis of administrative data and surveys from the Americas Barometer 2014 (N = 34,798 respondents T = 22 countries). Findings show that respondents with higher confidence in their government also indicate higher ratings of trust in the police. Similarly, trust is higher among individuals who had not experienced victimization or bribery or who anticipated faster police response times. At the country level, our results suggest that trust is negatively related to economic development but positively related to rule of law. We draw on these findings to outline an integrative model that combines both institutional and experiential perspectives.
Central nervous system manifestations of dengue infection: data from a tertiary care Centre in South India
Authors: George John Titus , Lenin Audrin , Koshy Maria , Vignesh C V , Sathyendra Sowmya
Published: February 2023

Background

Dengue fever is the second most common mosquito-borne disease affecting human beings and neurological manifestations (NMs) of this arboviral infection are increasingly being reported.

Methods

In this retrospective study, conducted in a tertiary care centre in south India, we sought to describe the spectrum of NMs of dengue fever. The records of all patients admitted in the Department of Internal Medicine over 8 years, with a diagnosis of dengue—based on clinical symptoms and the detection of dengue IgM antibodies or detection of NS1 antigen or nucleic acid by reverse transcriptase–polymerase chain reaction (RT-PCR); with Glasgow coma score (GCS) ≤14, neck stiffness, focal neurological signs, seizures, or visual disturbances—were explored.

Results

Of 1121 patients admitted with dengue fever, 341 (30%) had severe dengue and 23 (2%) had NMs. Encephalopathy was seen in 9 patients (39%), encephalitis in 6 (27%), cerebellitis in 4 (17%), acute disseminated encephalomyelitis (ADEM) in 2 (9%), ischaemic stroke in 1 (4%) patient, and neuro-ophthalmological manifestations in 1 (4%) patient. The median duration of hospital stay was 7 days. Nine (39% of) patients required intensive care unit (ICU) admission and 5 (22%) had fatal outcomes. There was no association between thrombocytopenia, metabolic acidosis, transaminitis, hyponatremia, the type of dengue infection, and the various NMs described.

Conclusions

The NMs of dengue infection are varied, and a high index of suspicion is needed to identify them in patients who present with lethargy or altered sensorium on the background of an acute febrile illness suggestive of dengue.
Increased rhinovirus/enterovirus infections including Ev-D68 in the United States, a challenge for healthcare providers amidst influenza virus infection and the COVID-19 pandemic
Authors: Abdul-Rahman Toufik , Nazir Abubakar , Khater Bashar , Pyrpyris Nikolaos , Wireko Awuah A , Miteu David G , Patel Heli , Sikora Vladyslav
Published: February 2023

In March 2020, WHO declared SARS-CoV-2 a global pandemic and lockdowns were enforced in most of the United States. Self-protective measures and travel restrictions were implemented, and schools/universities initiated online learning. Consequently, the global incidence and hospitalization rates of seasonal respiratory infections decreased significantly up to early 2021. Despite the decrease in hospitalization rates due to respiratory illnesses other than Covid-19, hospitals and healthcare providers faced huge stressors regarding workload dueto the pandemic. Furthermore, higher vaccination rates across the United States decreased non pharmaceutical interventions (NPI) implementation increasing the risk of major seasonal viral outbreaks. This editorial discusses the increased Rhinovirus/Enterovirus infections in the United States, challenges faced by healthcare providers and provides recommendations to address the issue.
The effect of a 5-minute body scan mindfulness intervention on healthier food choices
Authors: Hopfer Kaylea B , Fang Di , Zabelina Darya L , Hung Yung , Upshaw Joshua D , Nayga Rodolfo M
Published: February 2023

The effects of mindfulness interventions on food purchases and consumption are popular topics. Recent studies focus on mindfulness interventions that target overweight and obese populations. We measure the effects of a guided 5-minute body scan mindfulness intervention on ‘healthier’ food purchases in an online experiment. Specifically, we use a choice experiment approach with a between-subject design to evaluate participants’ choices of unhealthy/healthier foods. Results revealed the mindfulness intervention effectively increased state mindfulness in the treatment group. The treatment had a positive and significant effect on the overweight subsample. Additionally, we found nutrition knowledge to have a positive and significant effect on ‘healthier’ food choices across three regression models and various subsamples. Our findings suggest that mindfulness interventions may be a useful, low-cost alternative to current weight loss strategies, especially for overweight and obese individuals. In addition, our findings point to the importance of nutrition knowledge in promoting ‘healthier’ food choices.
EVALUATION OF EXISTING PUBLIC DOSE LIMITS APPLIED TO RECREATIONAL SPACEFLIGHT
Authors: Long Michael A , Hayes Robert B
Published: February 2023

Establishing realistic radiation dose limits with a solid scientific basis is a key component of the ‘as low as reasonably achievable’ (ALARA) principle. Although existing occupational dose limits have been established for civil astronauts, with the rise in popularity and technological maturation of the ‘space tourism’ sector, there does not appear to be considerable discussion on the subject of non-occupational astronaut dose limits. The necessity to come to a collective decision on dose limits and radiation safety procedures for recreational spaceflight is urgent and imperative to maintain ALARA goals, as existing federal dose limits to the public cannot be adequately or universally applied to the space tourism sector. Development of an entirely new set of regulations and guidelines should also provide long-term benefits in public perception as evidence of safety commitments from decision makers and the community in protecting passengers from radiological risks balanced with other spaceflight hazards.
Cross-cultural Differences in Hallucinations: A Comparison Between Middle Eastern and European Community-Based Samples
Authors: Khaled Salma M , Brederoo Sanne G , Yehya Arij , Alabdulla Majid , Woodruff Peter W , Sommer Iris E C
Published: February 2023

Background and Hypothesis

While literature indicates that culture modulates phenomenological characteristics of hallucinations in schizophrenia-spectrum disorders, little is known about the extent culture modulates these characteristics in nonclinical samples.

Study Design

We compared lifetime prevalence, age of onset, and phenomenology of hallucinations as assessed with the Questionnaire for Psychotic Experiences between samples of nonclinical participants used from the Netherlands (N = 2999) and Qatar (N = 2999). While participant recruitment differed between the 2 countries, the samples were relatively equal in terms of demographic factors.

Study Results

Our findings indicate that the lifetime prevalence of tactile and olfactory hallucinations are the same across countries. However, the prevalence of auditory hallucinations (AH) and visual hallucinations (VH) were twice as high in the Dutch sample. The reported age of onset for auditory and tactile hallucinations was younger for the Dutch sample. Findings from the measurement invariance supported cross-cultural comparisons with exception for duration, distress, and insight. Qatar’s and Dutch participants reported similar valence and extent of interaction with AH and VH. However, compared to those in the Netherlands, participants from Qatar reported significantly more impact on daily functioning and a higher prevalence of receiving commands from hallucinations in the past week.

Conclusions

While AH and VH were more often reported in the Dutch sample, participants in Qatar generally had higher mean factor scores for past week AH and VH than in the Netherlands. The phenomenology of hallucinations in the Qatar sample was of greater clinical relevance, with potentially important implications for early screening and prevention.
Oxytocin mediated excitation of hypoglossal motoneurons: implications for treating obstructive sleep apnea
Authors: Dergacheva Olga , Polotsky Vsevolod Y , Mendelowitz David
Published: February 2023

Clinical studies have shown that oxytocin administered intranasally (IN) decreased the incidence and duration of obstructive events in patients with obstructive sleep apnea (OSA). Although the mechanisms by which oxytocin promotes these beneficial effects are unknown, one possible target of oxytocin could be the excitation of tongue-projecting hypoglossal motoneurons in the medulla, that exert central control of upper airway patency. This study tested the hypothesis that IN oxytocin enhances tongue muscle activity via the excitation of hypoglossal motoneurons projecting to tongue protrudor muscles (PMNs). To test this hypothesis we performed in vivo and in vitro electrophysiological studies in C57BL6/J mice as well as fluorescent imaging studies in transgenic mice in which neurons that express oxytocin receptors co-express fluorescent protein. IN oxytocin significantly increased the amplitude of inspiratory-related tongue muscle activity. This effect was abolished by severing the medial branch of hypoglossal nerve that innervates PMNs of the tongue. Oxytocin receptor-positive neurons were more prevalent in the population of PMNs than in retractor-projecting hypoglossal motoneurons (RMNs). Oxytocin administration increased action potential firing in PMNs, but had no significant effect on firing activity in RMNs. In conclusion, IN oxytocin stimulates respiratory-relating tongue muscle activity likely acting on central hypoglossal motoneurons that provide tongue protrusion and upper airway opening. This mechanism may play a role in oxytocin-induced reductions in upper airway obstructions in patients with OSA.
Factors Influencing the Efficacy of Umbilical Cord Blood-Derived Cell Therapy for Perinatal Brain Injury
Authors: Purcell Elisha , Nguyen Timothy , Smith Madeleine , Penny Tayla , Paton Madison C B , Zhou Lindsay , Jenkin Graham , Miller Suzanne L , McDonald Courtney A , Malhotra Atul
Published: February 2023

Introduction

We have previously described preclinical literature which supports umbilical cord blood-derived cell (UCBC) therapy as an efficacious treatment for perinatal brain injury. However, efficacy of UCBCs may be influenced by different patient population and intervention characteristics.

Objectives

To systematically review the effects of UCBCs on brain outcomes in animal models of perinatal brain injury across subgroups to better understand the contribution of model type (preterm versus term), brain injury type, UCB cell type, route of administration, timing of intervention, cell dosage, and number of doses.

Methods

A systematic search of MEDLINE and Embase databases was performed to identify studies using UCBC therapy in animal models of perinatal brain injury. Subgroup differences were measured by chi2 test where possible.

Results

Differential benefits of UCBCs were seen across a number of subgroup analyses including intraventricular hemorrhage (IVH) vs. hypoxia ischemia (HI) model (apoptosis white matter (WM): chi2 = 4.07; P = .04, neuroinflammation-TNF-α: chi2 = 5.99; P = .01), UCB-derived mesenchymal stromal cells (MSCs) vs. UCB-derived mononuclear cells (MNCs) (oligodendrocyte WM: chi2 = 5.01; P = .03, neuroinflammation-TNF-α: chi2 = 3.93; P = .05, apoptosis grey matter (GM), astrogliosis WM), and intraventricular/intrathecal vs. systemic routes of administration (microglial activation GM: chi2 = 7.51; P = .02, astrogliosis WM: chi2 = 12.44; P = .002). We identified a serious risk of bias and overall low certainty of evidence.

Conclusions

Preclinical evidence suggests UCBCs to show greater efficacy in the injury model of IVH compared to HI, the use of UCB-MSCs compared to UCB-MNCs and the use of local administrative routes compared to systemic routes in animal models of perinatal brain injury. Further research is needed to improve certainty of evidence and address knowledge gaps.
Cigarette smoke and tumor microenvironment copromote aggressiveness of human breast cancer cells
Authors: Benoit Louise , Tomkiewicz Celine , Delit Maxime , Khider Hanna , Audouze Karine , Kowandy Flavie , Bortoli Sylvie , Barouki Robert , Coumoul Xavier , Koual Meriem
Published: February 2023

Breast cancer is a major public health issue and the role of pollutants in promoting breast cancer progression has recently been suggested. We aimed to assess if a mixture of pollutants, cigarette smoke, could favor the aggressivity of breast cancer cells. We also evaluated the impact of the tumor microenvironment, largely represented by adipocytes, in mediating this modification of cell phenotype. Breast cancer cells lines, MCF-7 were cultured using a transwell coculture model with preadipocytes hMADS cells or were cultured alone. Cells were treated with cigarette smoke extract (CSE) and the four conditions: control, treated by CSE, coculture, and coexposure (coculture and CSE) were compared. We analyzed morphological changes, cell migration, resistance to anoikis, stemness, epithelial-to-mesenchymal transition (EMT), and the presence of hormonal receptors in each condition. A complete transcriptomic analysis was carried out to highlight certain pathways. We also assessed whether the aryl hydrocarbon receptor (AhR), a receptor involved in the metabolism of xenobiotics, could mediate these modifications. Several hallmarks of metastasis were specific to the coexposure condition (cell migration, resistance to anoikis, stemness characterized by CD24/CD44 ratios and ALDH1A1 and ALDH1A3 rates) whereas others (morphological changes, EMT, loss of hormonal receptors) could be seen in the coculture condition and were aggravated by CSE (coexposure). Moreover, MCF-7 cells presented a decrease in hormonal receptors, suggesting an endocrine treatment resistance. These results were confirmed by the transcriptomic analysis. We suggest that the AhR could mediate the loss of hormonal receptor and the increase in cell migration
H9N2 avian influenza virus dispersal along Bangladeshi poultry trading networks
Authors: Carnegie L , Hasan M , Mahmud R , Hoque M A , Debnath N , Uddin M H , Lewis N S , Brown I , Essen S , Giasuddin Md , Pfeiffer D U , Samad M A , Biswas P , Raghwani J , Fournié G , Hill S C
Published: February 2023

Avian influenza virus subtype H9N2 is endemic in Bangladesh’s poultry population. The subtype affects poultry production and poses a potential zoonotic risk. Insufficient understanding of how the poultry trading network shapes the dissemination of avian influenza viruses has hindered the design of targeted interventions to reduce their spread. Here, we use phylodynamic analyses of haemagglutinin sequences to investigate the spatial spread and dispersal patterns of H9N2 viruses in Bangladesh’s poultry population, focusing on its two largest cities (Dhaka and Chattogram) and their poultry production and distribution networks. Our analyses suggest that H9N2 subtype avian influenza virus lineage movement occurs relatively less frequently between Bangladesh’s two largest cities than within each city. H9N2 viruses detected in single markets are often more closely related to viruses from other markets in the same city than to each other, consistent with close epidemiological connectivity between markets. Our analyses also suggest that H9N2 viruses may spread more frequently between chickens of the three most commonly sold types (sunali—a cross-bred of Fayoumi hen and Rhode Island Red cock, deshi—local indigenous, and exotic broiler) in Dhaka than in Chattogram. Overall, this study improves our understanding of how Bangladesh’s poultry trading system impacts avian influenza virus spread and should contribute to the design of tailored surveillance that accommodates local heterogeneity in virus dispersal patterns.
Provider-To-Provider Communication About Care Transitions: Considering Different Health Technology Tools
Authors: Beal Eliza W. , Kurien Natasha , DePuccio Matthew J. , Tsung Allan , McAlearney Ann Scheck
Published: February 2023

Transitions in patient care require exchanges of information between providers. This period of transition presents a range of challenges, and inadequate transitions can have serious consequences for patients. Our objective was to understand providers' perspectives about patient care transitions, especially around communication between providers and the role of health information technology in provider-to-provider communication. Semi-structured interviews were conducted. Deductive-dominant thematic analysis was used to allow categorization of data based on general themes derived from the interview guides, as well as identification of emergent themes. We characterized three main themes involving providers' perspectives about care transitions. Themes included communication challenges, communication preferences, and suggestions for improving the care transition processes. With respect to challenges around communication, providers highlighted four main concerns. These concerns included the existence of too many methods of communication, high volume of communication, challenges with involvement of multiple providers delivering longitudinal care, and difficulty communicating with providers outside the health system. Providers noted opportunities to improve transitions including improving standardization, enhancing the specialty to primary care transition process, and increasing communication back to the referring provider. Implementation and evaluation of these improvements could be considered by health systems to enhance care transitions.
Peripheral Blood Monocytosis Is Associated With Long-Term Disease Severity in Pediatric-Onset Inflammatory Bowel Disease
Authors: Zhang Xiaoyi , Ramos-Rivers Claudia , Prathapan Krishnapriya , Wang Xianling , Tang Gong , Kim Sandra , Binion David G.
Published: February 2023

Objectives:

Peripheral blood monocytosis (PBM) is a marker of increased disease severity in adults with inflammatory bowel diseases (IBDs). We sought to determine whether PBM serves as a prognostic biomarker in patients with pediatric-onset IBD for a more aggressive long-term disease course when followed into adulthood.

Methods:

Patients with pediatric-onset inflammatory bowel disease were identified within an adult tertiary care center, within a consented, prospectively collected natural history disease registry, to compare clinical outcomes between patients with and without PBM from the years 2009 to 2019. Patients demonstrating elevation in PBM at any time defined membership and long-term clinical trajectories were compared with pediatric-onset patients without PBM.

Results:

A total of 581 patients with IBD, diagnosed by 18 years of age, were identified for inclusion, of which 440 patients were diagnosed with Crohn disease and 141 with ulcerative colitis. Monocytosis was detected by complete blood cell counts in 40.1% of patients. PBM was associated with steroid and biologic exposure, number of IBD-related surgeries, and increased health care utilization. Multivariate logistic regression analyses, accounting for elevation of inflammatory markers and other values associated with acute disease activity as well as steroid use, showed persistently increased odds of biologic exposure, emergency department visits, and hospitalizations, but not surgeries, after detection of monocytosis.

Conclusions:

Within patients with pediatric-onset IBD, the sub-cohort with PBM had associated worse clinical outcomes and other markers of increased disease severity.
Estrogen alleviates post-hemorrhagic shock mesenteric lymph-mediated lung injury through autophagy inhibition
Authors: Sun Qi , Zhang Hong , Du Hui-Bo , Zhao Zhen-Ao , Li Cai-Juan , Chen Si-Jie , Li Yi-Ming , Zhang Sen-Lu , Liu Jun-Chao , Niu Chun-Yu , Zhao Zi-Gang
Published: February 2023

Background

Hemorrhagic shock-induced acute lung injury (ALI) is commonly associated with the post-hemorrhagic shock mesenteric lymph (PHSML) return. Whether excessive autophagy is involved in PHSML-mediated ALI remains unclear. The relationship between estrogen treatment and PHSML or autophagy needs to verify. The current study will clarify the role of estrogen in reducing PHSML-mediated ALI through inhibition of autophagy.

Methods

Firstly, a hemorrhagic shock model in conscious rats was employed to observe the effects of 17β-estradiol (E2) on intestinal blood flow, pulmonary function, intestinal and pulmonary morphology, and expression of autophagy marker proteins. Meanwhile, the effect of PHSML and autophagy agonist during E2 treatment was also investigated. Secondly, rat primary pulmonary microvascular endothelial cells (PMVECs) were used to observe the effect of PHSML, PHSML plus E2, and E2-PHSML (PHSML obtained from rats treated by E2) on the cell viability.

Results

Hemorrhagic shock induced intestinal and pulmonary tissue damage and increased wet/dry ratio, reduced intestinal blood flow, along with pulmonary dysfunction characterized by increased functional residual capacity and lung resistance and decreased inspiratory capacity and peak expiratory flow. Hemorrhagic shock also enhanced the autophagy levels in intestinal and pulmonary tissue, which was characterized by increased expressions of LC3 II/I and Beclin-1 and decreased expression of p62. E2 treatment significantly attenuated these adverse changes following hemorrhagic shock, which was reversed by PHSML or rapamycin administration. Importantly, PHSML incubation decreased the viability of PMVECs, while E2 co-incubation or E2-treated lymph counteracted the adverse roles of PHSML.

Conclusions

The role of estrogen reducing PHSML-mediated ALI is associated with the inhibition of autophagy.
Identification of further variation at the lipooligosaccharide outer core locus inAcinetobacter baumanniigenomes and extension of the OCL reference sequence database forKaptive
Authors: Sorbello Bianca , Cahill Sarah M. , Kenyon Johanna J.
Published: February 2023

The outer core locus (OCL) that includes genes for the synthesis of the variable outer core region of the lipooligosaccharide (LOS) is one of the key epidemiological markers used for tracing the spread ofAcinetobacter baumannii, a bacterial pathogen of global concern. In this study, we screened 12476 publicly availableA. baumanniigenome assemblies for novel OCL sequences, detecting six new OCL types that were designated OCL17-OCL22. These were compiled with previously characterised OCL to create an updated version of theA. baumanniiOCL reference database, providing a total of 22 OCL reference sequences for use with the bioinformatics tool,Kaptive. Use of this database against the 12476 downloaded assemblies found OCL1 to be the most common locus, present in 73.6% of sequenced genomes assigned byKaptivewith a match confidence score of ‘Good’ or above. OCL1 was most common amongst isolates belonging to sequence types, ST1, ST2, ST3 and ST78, all of which are over-represented clonal lineages associated with extensive antibiotic resistance. The highest level of diversity in OCL types was found in ST2, with eight different OCL identified. The updated OCL reference database is available for download from GitHub (https://github.com/katholt/Kaptive; under versionv 2.0.5), and has been integrated for use onKaptive-Web (https://kaptive-web.erc.monash.edu/) and PathogenWatch (https://pathogen.watch/), enhancing current methods forA. baumanniistrain identification, classification and surveillance.

IMPACT STATEMENT

In the absence of effective treatment options for multi-drug resistantAcinetobacter baumannii, the highest-ranking critical priority bacterial pathogen of global concern, national and global surveillance is necessary to detect, track and subsequently curb the spread of isolates that resist current therapies. Several epidemiological markers are used to characteriseA. baumanniistrains by detecting genetic differences in specific regions of the genome. One of these is the chromosomal OC locus (OCL) responsible for the synthesis of the outer core (OC) component of the lipooligosaccharide (LOS). Here, we provide an update to the internationalA. baumanniiOCL reference sequence database, extending the number of known OCL types to assist with clinical surveillance of important strains or clonal lineages.

Data summary

The updatedA. baumanniiOCL reference sequence database including 22 annotated OCL sequences is available for download underKaptive v. 2.0.5athttps://github.com/katholt/Kaptive.

Genome assemblies or GenBank records used as representative reference sequences are listed in Table 1 and acknowledged in each record in the database.
The pluripotency factor Tex10 finetunes Wnt signaling for PGC and male germline development
Authors: Li Dan , Yang Jihong , Ma Fanglin , Malik Vikas , Zang Ruge , Shi Xianle , Huang Xin , Zhou Hongwei , Wang Jianlong
Published: February 2023

Testis-specific transcript 10 (Tex10) is a critical factor for pluripotent stem cell maintenance and preimplantation development. Here, we dissect its late developmental roles in primordial germ cell (PGC) specification and spermatogenesis using cellular and animal models. We discover that Tex10 binds the Wnt negative regulator genes, marked by H3K4me3, at the PGC-like cell (PGCLC) stage in restraining Wnt signaling. Depletion and overexpression of Tex10 hyperactivate and attenuate the Wnt signaling, resulting in compromised and enhanced PGCLC specification efficiency, respectively. Using the Tex10 conditional knockout mouse models combined with single-cell RNA sequencing, we further uncover critical roles of Tex10 in spermatogenesis with Tex10 loss causing reduced sperm number and motility associated with compromised round spermatid formation. Notably, defective spermatogenesis in Tex10 knockout mice correlates with aberrant Wnt signaling upregulation. Therefore, our study establishes Tex10 as a previously unappreciated player in PGC specification and male germline development by fine-tuning Wnt signaling.
Pharmacometric assessment of primaquine induced haemolysis in glucose-6-phosphate dehydrogenase deficiency
Authors: Pukrittayakamee Sasithon , Jittamala Podjanee , Watson James A , Hanboonkunupakarn Borimas , Leungsinsiri Pawanrat , Poovorawan Kittiyod , Chotivanich Kesinee , Bancone Germana , Chu Cindy S , Imwong Mallika , Day Nicholas PJ , Taylor Walter RJ , White Nicholas J
Published: February 2023

Background

Primaquine is an 8-aminoquinoline antimalarial. It is the only widely available treatment to prevent relapses ofPlasmodium vivaxmalaria. The 8-aminoquinolines cause dose dependent haemolysis in glucose-6-phosphate dehydrogenase deficient (G6PDd) individuals. G6PDd is common in malaria endemic areas but testing is often not available. As a consequence primaquine is underused.

Methods

We conducted a pharmacometric study to characterise the relationship between primaquine dose and haemolysis in G6PDd. The aim was to explore shorter and safer primaquine radical cure regimens compared to the currently recommended 8-weekly regimen (0.75 mg/kg once weekly), potentially obviating the need for G6PD testing. Hemizygous G6PDd healthy adult Thai and Burmese male volunteers were admitted to the Hospital for Tropical Diseases in Bangkok. In Part 1, volunteers were given ascending dose primaquine regimens whereby daily doses were increased from 7.5 mg up to 45 mg over 15 to 20 days. In Part 2, a single primaquine 45 mg dose was given.

Results

24 volunteers were enrolled in Part 1, and 16 in Part 2 (13 participated in both studies). In three volunteers, the ascending dose regimen was stopped because of haemolysis (n=1) and asymptomatic increases in transaminases (n=2; one was hepatitis E positive). Otherwise the ascending regimens were well tolerated with no drug-related serious adverse events. In Part 1, the median haemoglobin concentration decline was 3.7 g/dL (range: 2.1 to 5.9; relative decline of 26% [range: 15 to 40%]). Primaquine doses up to 0.87 mg/kg/day were tolerated subsequently without clinically significant further falls in haemoglobin. In Part 2, the median haemoglobin concentration decline was 1.7 g/dL (range 0.9 to 4.1; relative fall of 12% [range: 7 to 30% decrease]). The ascending dose primaquine regimens gave 7 times more drug but resulted in only double the haemoglobin decline.

Conclusions and Interpretation

In patients with Southeast Asian G6PDd variants full radical cure treatment can be given in under three weeks compared with the current 8 week regimen.
Ecogenomics reveals distinctive viral-bacterial communities in the surface microlayer of a natural surface slick
Authors: Rahlff Janina , Wietz Matthias , Giebel Helge-Ansgar , Bayfield Oliver , Nilsson Emelie , Bergström Kristofer , Kieft Kristopher , Anantharaman Karthik , Ribas-Ribas Mariana , Wurl Oliver , Hoetzinger Matthias , Antson Alfred , Holmfeldt Karin
Published: February 2023

Visible surface films, termed slicks, can extensively cover the sea surface, particularly in coastal regions. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (slick SML) harbors a distinctive bacterial community, but little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we investigated viruses and the bacterial community from a brackish slick SML in comparison to non-slick SML as well as the seawater below (SSW). We conducted size-fractionated filtration of all samples to distinguish viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. The distinctness was underlined by specific metabolic profiles of bacterial metagenome assembled genomes and isolates, which revealed prevalence of motility genes and diversity of CAZymes in the slick SML. Despite overall lower diversity, several vOTUs were enriched in slick SML over slick SSW. Nine vOTUs were only found in slick SML and six of them were targeted by slick SML-specific CRISPR spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages forAlishewanellasp. andPseudoalteromonas tunicata, representing abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks can contribute to biogeochemical cycling in coastal ecosystems.
Combining biophysical models and machine learning to optimize implant geometry and stimulation protocol for intraneural electrodes
Authors: Romeni Simone , Losanno Elena , Koert Elisabeth , Pierantoni Luca , Delgado-Martinez Ignacio , Navarro Xavier , Micera Silvestro
Published: February 2023

Objective

Peripheral nerve interfaces have the potential to restore sensory, motor, and visceral functions. In particular, intraneural interfaces allow targeting deep neural structures with high selectivity, even if their performance strongly depends upon the implantation procedure and the subject’s anatomy. Currently, few alternatives exist for the determination of the target subject structural and functional anatomy, and statistical characterizations from cadaveric samples are limited because of their high cost. We propose an optimization workflow that can guide both the pre-surgical planning and the determination of maximally selective multisite stimulation protocols for implants consisting of several intraneural electrodes, and we characterize its performance in silico. We show that the availability of structural and functional information leads to very high performances and allows taking informed decisions on neuroprosthetic design.

Approach

We employ hybrid models (HMs) of neuromodulation in conjunction with a machine learning-based surrogate model to determine fiber activation under electrical stimulation, and two steps of optimization through particle swarm optimization (PSO) to optimize in silico implant geometry, implantation and stimulation protocols using morphological data from the human median nerve at a reduced computational cost.

Main results

Our method allows establishing the optimal geometry of multi-electrode transverse intra-fascicular multichannel electrode (TIME) implants, the optimal number of electrodes to implant, their optimal insertion, and a set of multipolar stimulation protocols that lead in silico to selective activation of all the muscles innervated by the human median nerve.

Significance

We show how to use effectively HMs for optimizing personalized neuroprostheses for motor function restoration. We provide in-silico evidences about the potential of multipolar stimulation to increase greatly selectivity. We also show that the knowledge of structural and functional anatomies of the target subject leads to very high selectivity and motivate the development of methods for their in vivo characterization.
Inhibiting mitochondrial translation overcomes multidrug resistance in MYC-driven neuroblastoma via OMA1-mediated integrated stress response
Authors: Borankova Karolina , Krchniakova Maria , Leck Lionel YW , Neradil Jakub , Kubistova Adela , Jansson Patric J , Hogarty Michael D , Skoda Jan
Published: February 2023

High-risk neuroblastoma remains a clinically challenging childhood tumor with a 5-year survival of only 50%. Tumors overexpressing N-MYC or c-MYC oncoproteins define a group of MYC-driven high-risk neuroblastoma with the most dismal outcomes, mainly caused by treatment failure due to the emergence and regrowth of multidrug-resistant cancer cells. Specific mitochondrial processes have been implicated in the maintenance of aggressive stem-like phenotypes in various cancers. We have recently identified a novel mitochondria-mediated mechanism of neuroblastoma multidrug resistance. However, the potential of pharmacological targeting of mitochondria to overcome therapy resistance and stemness in neuroblastoma remains unclear. Here, we show that c-MYC/N-MYC-driven multidrug-resistant neuroblastoma cells are highly vulnerable to cell death induced by the inhibition of mitochondrial translation. In contrast with normal fibroblasts, doxycycline (DOXY)-mediated inhibition of mitochondrial ribosomes efficiently impaired the survival of neuroblastoma cells regardless of their multidrug resistance and stem-like phenotypes. Mechanistically, inhibiting mitochondrial translation induced the mitochondrial stress-activated integrated stress response (ISR) via the OMA1-eIF2α axis, which preceded neuroblastoma cell death. Strikingly, several oncoproteins associated with poor neuroblastoma prognosis, including c-MYC and N-MYC, were markedly downregulated upon ISR activation. Comparing models of various neuroectodermal tumors and normal fibroblasts, we identified high levels of phosphorylated c-MYC and N-MYC (indicating their activity and rapid turnover) as a factor that predetermines susceptibility of neuroblastoma cells to DOXY-induced cell death. Neuroblastoma cells failed to develop significant DOXY resistance over a long-term repeated (pulsed) selection pressure, further demonstrating mitochondrial protein balance as a clinically relevant vulnerability of cancer cells that rely on high MYC activity. Together, our findings provide insight into mitochondrial retrograde regulatory networks in the context of MYC dependence and demonstrate the mitochondrial translation machinery as a promising therapeutic target in multidrug-resistant MYC-driven neuroblastoma.
Neisseria leonissp. nov. isolated from rabbits, reclassification ofUruburuella suis, Uruburuella testudinis, Kingella potus, Bergeriella denitrificansandMorococcus cerebrosusintoNeisseriagenus and reclassification ofNeisseria shayeganiiintoEikenellagenus
Authors: Boutroux M. , Favre-Rochex S. , Gorgette O. , Touak G. , Muhle E. , Chesneau O. , Clermont D. , Rahi P.
Published: February 2023

Genome sequence-based identification of two strains (3986Tand 51.81) isolated from rabbits in France in 1972 and 1981 and deposited in the Collection of Institut Pasteur (CIP) has led to the description of a novel species in the genusNeisseria. The cells of both strains were non-motile, Gram-stain-negative and diplococcobacilli. Optimal growth on trypticase soy agar was recorded at 37°C and pH 8.5 in aerobic conditions. Phylogeny based on 16S rRNA gene placed the strains close toNeisseria bacilliformisATCC BAA-1200T(96.38%) nesting with the members of Neisseriaceae family. Furthermore, the phylogenetic analysis based onbac120gene set from the Genome Taxonomy Database (GTDB) placed both strains within the monophyleticNeisseriaclade, which also included type strains ofMorococcus cerebrosus, Bergeriella denitrificans,Kingella potus, Uruburuella suisandUruburuella testudinis. However,Neisseria shayeganiistrain 871Twas placed outsideNeisseriaclade and close to the members ofEikenellagenus. Strains 3986Tand 51.81 were placed in a branch distinct from all species of the genusNeisseriaand exhibited the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values below the species demarcation values. In contrast, ANI value within the two strains was 96.9% confirming that they represent same species. The genomic DNA G+C content of strain 3986Twas 56.92%. Based on the phylogenetic and phenotypic data, the strains 3986Tand 51.81 represent a novel species of the genusNeisseria, for which the nameNeisseria leonissp. nov. is proposed (type strain 3986T= CIP 109994T= LMG 32907T). Additionally, based on phylogenetic analysis, DUS dialect and average amino acid identity (AAI) values, we also proposed the reclassification ofMorococcus cerebrosus,Bergeriella denitrificans,Kingella potus, Uruburuella suisandUruburuella testudinisintoNeisseriagenus andNeisseria shayeganiiintoEikenellagenus.

Author Notes

The GenBank accession numbers for the 16S rRNA gene sequence of strains 3986Tand 51.81 are respectively OQ121838.1 and OQ428162.1. The draft genome sequences have been deposited in GenBank under the accession numbers JAPQFK000000000 (strain 3986T) and JAPQFL000000000 (strain 51.81).

Further explanations mentioned in the article as well as 7 supplementary tables and 7 supplementary figures are available with the online version of this article.
IFN-λ is protective against lethal oralToxoplasma gondiiinfection
Authors: Murillo-León Mateo , Bastidas-Quintero Aura M. , Endres Niklas S. , Schnepf Daniel , Delgado-Betancourt Estefanía , Ohnemus Annette , Taylor Gregory A. , Schwemmle Martin , Staeheli Peter , Steinfeldt Tobias
Published: February 2023

Interferons are essential for innate and adaptive immune responses against a wide variety of pathogens. Interferon lambda (IFN-λ) protects mucosal barriers during pathogen exposure. The intestinal epithelium is the first contact site forToxoplasma gondii(T. gondii) with its hosts and the first defense line that limits parasite infection. Knowledge of very earlyT. gondiiinfection events in the gut tissue is limited and a possible contribution of IFN-λ has not been investigated so far. Here, we demonstrate with systemic interferon lambda receptor (IFNLR1) and conditional (Villin-Cre) knockout mouse models and bone marrow chimeras of oralT. gondiiinfection and mouse intestinal organoids a significant impact of IFN-λ signaling in intestinal epithelial cells and neutrophils toT. gondiicontrol in the gastrointestinal tract. Our results expand the repertoire of interferons that contribute to the control ofT. gondiiand may lead to novel therapeutic approaches against this world-wide zoonotic pathogen.