bluuebunny/crossref_metadata_2025 huggingface dataset:
Translational activity of 80S monosomes varies dramatically across different tissues
Authors: Blandy Albert , Hopes Tayah , Vasconcelos Elton J. R. , Turner Amy , Fatkhullin Bulat , Agapiou Michaela , Fontana Juan , Aspden Julie L.
Published: June 2024

Translational regulation at the stage of initiation can impact the number of ribosomes translating each mRNA molecule. However, the translational activity of single 80S ribosomes (monosomes) on mRNA is less well understood, even though these 80S monosomes represent the dominant ribosomal complexes in vivo. Here, we used cryo-EM to determine the translational activity of 80S monosomes across different tissues inDrosophila melanogaster. We discovered that while head and embryo 80S monosomes are highly translationally active, testis and ovary 80S monosomes are translationally inactive. RNA-Seq analysis of head monosome- and polysome-translated mRNAs, revealed that head 80S monosomes preferentially translate mRNAs with TOP motifs, short 5’-UTRs, short ORFs and are enriched for uORFs. Overall, these findings highlight that regulation of translation initiation, and that protein synthesis is mostly performed by monosomes in head and embryo, whilst polysomes are the main source of protein production in testis and ovary.

Graphical Abstract

Highlights

D. melanogaster80S monosomes and polysomes purified from different tissues exhibit different translational activities

Head and 0-2 hr embryo 80S monosomes are highly translationally active

Testis and ovary 80S monosomes are translationally inactive

Head 80S monosomes preferentially translate mRNAs with TOP motifs, short 5’-UTRs, short ORFs and are enriched for uORFs

Head polysomes preferentially translate mRNAs with neuronal functions
CUT&Tag and DiBioCUT&Tag enable investigation of the AT-rich and dynamic epigenome ofPlasmodium falciparumfrom low input samples
Authors: Gockel Jonas , Ramón-Zamorano Gala , Spielmann Tobias , Bártfai Richárd
Published: June 2024

Phenotypic variation between malaria parasites is one of the major contributors to the pathogens success and is regulated by differences in heterochromatin-mediated gene silencing. Currently, the heterochromatin landscape is mostly profiled utilising chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). However this technique has drawbacks regarding AT-content-related artifacts and requires substantial material and time investment, severely limiting profiling of scarce sample types (e.g. field isolates). In order to facilitate assessments of epigenetic states in low-input samples, we adopted the epigenetic profiling technique Cleavage Under Targets and Tagmentation (CUT&Tag) toPlasmodium falciparumparasites. Performing the reaction with 100,000 or even only 10,000 nuclei yielded reproducible results coherent with bulk-ChIP-seq data while using significantly less material. We also optimised sample preparation, permitting the use of crude saponin lysates, which decreases sample loss due to inefficient nuclei isolation and increases versatility of the protocol. Finally, we developed DiBioCUT&Tag, a novel way of utilising dimerisation-induced recruitment of biotin ligases for signal amplification prior to anti-biotin CUT&Tag, which we successfully deployed to profile both heterochromatin occupancy and a dynamically chromatin-associated protein (BDP5). Methods described here hence provide substantially improved means for epigenetic profiling of (transiently) chromatin-associated proteins from low-input samples in the malaria parasite and beyond.
Natural volatiles causing inhibition of mosquito biting behaviors: development of a virtual screening platform predicting antagonists of ORco function for accelerated discovery
Authors: Kythreoti Georgia , Thireou Trias , Karoussiotis Christos , Georgoussi Zafiroula , Liggri Panagiota GV , Papachristos Dimitrios P , Michaelakis Antonios , Karras Vasileios , Zographos Spyros E , Schulz Stefan , Iatrou Kostas
Published: June 2024

Insect olfactory receptors are heteromeric ligand-gated cation channels composed of an obligatory receptor subunit, ORco, and one of many variable subunits, ORx, in as yet undefined molar ratios. When expressed aloneex vivo, ORco forms homotetrameric channels gated by ORco-specific ligands acting as channel agonists. Using an insect cell-based system as a functional platform for expressing mosquito odorant receptorsex vivo,we identified small molecules of natural origin acting as specific ORco channel antagonists, orthosteric or allosteric relative to a postulated ORco agonist binding site, and causing severe inhibition of olfactory function in mosquitoes. In the present communication, we are reporting on the compilation of common structural features of such orthosteric antagonists and development of a ligand-based pharmacophore whose properties are deemed necessary for binding to the agonist binding site and inhibition of ORco’s biological function.In silicoscreening of an available collection of natural volatile compounds with this pharmacophore resulted in identification of several ORco antagonist hits. Cell-based functional screening of the same compound collection resulted in the identification of several compounds acting as orthosteric and allosteric antagonists of ORco channel functionex vivoand inducing anosmic behaviors toAedes albopictusmosquitoesin vivo.Comparison of thein silicoscreening results with those of the functional assays revealed that the pharmacophore predicted correctly 7 out of the 8 confirmed orthosteric antagonists and none of the allosteric ones. Because the pharmacophore screen also produced additional hits that did not cause inhibition of the ORco channel function, we generated a Support Vector Machine (SVM) model based on two descriptors of all pharmacophore hits. Training of the SVM on theex vivovalidated compound collection resulted in the selection of the confirmed orthosteric antagonists with a very low cross-validation out-of-sample misclassification rate. Employment of the combined pharmacophore-SVM platform forin silicoscreening of a larger collection of olfaction-relevant volatiles produced several new hits. Functional validation of randomly selected hits and rejected compounds from this screen confirmed the power of this virtual screening platform as convenient tool for identifying novel vector control agents. To the best of our knowledge, this study is the first one that combines a pharmacophore with a SVM model for identification of AgamORco antagonists and specifically orthosteric ones.
Sequential intravenous and intracerebroventricular GD2-CAR T-cell therapy for H3K27M-mutated diffuse midline gliomas
Authors: Monje Michelle , Mahdi Jasia , Majzner Robbie , Yeom Kristen , Schultz Liora M. , Richards Rebecca M. , Barsan Valentin , Song Kun-Wei , Kamens Jen , Baggott Christina , Kunicki Michael , Lim Alexandria Sung , Reschke Agnes , Mavroukakis Sharon , Egeler Emily , Moon Jennifer , Patel Shabnum , Chinnasamy Harshini , Erickson Courtney , Jacobs Ashley , Duh Allison K. , Rietberg Skyler P. , Tunuguntla Ramya , Klysz Dorota Danuta , Fowler Carley , Green Sean , Beebe Barbara , Carr Casey , Fujimoto Michelle , Brown Annie Kathleen , Petersen Ann-Louise G. , McIntyre Catherine , Siddiqui Aman , Lepori-Bui Nadia , Villar Katlin , Pham Kymhuynh , Bove Rachel , Musa Eric , Reynolds Warren , Kuo Adam , Prabhu Snehit , Rasmussen Lindsey , Cornell Timothy T. , Partap Sonia , Fisher Paul G. , Campen Cynthia J. , Grant Gerald , Prolo Laura , Ye Xiaobu , Sahaf Bita , Davis Kara L. , Feldman Steven A. , Ramakrishna Sneha , Mackall Crystal
Published: June 2024

H3K27M-mutant diffuse midline gliomas (DMGs) express high levels of the GD2 disialoganglioside and chimeric antigen receptor modified T-cells targeting GD2 (GD2-CART) eradicate DMGs in preclinical models. Arm A of the Phase I trialNCT04196413administered one IV dose of autologous GD2-CART to patients with H3K27M-mutant pontine (DIPG) or spinal (sDMG) diffuse midline glioma at two dose levels (DL1=1e6/kg; DL2=3e6/kg) following lymphodepleting (LD) chemotherapy. Patients with clinical or imaging benefit were eligible for subsequent intracerebroventricular (ICV) GD2-CART infusions (10-30e6 GD2-CART). Primary objectives were manufacturing feasibility, tolerability, and identification of a maximally tolerated dose of IV GD2-CART. Secondary objectives included preliminary assessments of benefit. Thirteen patients enrolled and 11 received IV GD2-CART on study [n=3 DL1(3 DIPG); n=8 DL2(6 DIPG/2 sDMG). GD2-CART manufacturing was successful for all patients. No dose-limiting toxicities (DLTs) occurred on DL1, but three patients experienced DLT on DL2 due to grade 4 cytokine release syndrome (CRS). Nine patients received ICV infusions, which were not associated with DLTs. All patients exhibited tumor inflammation-associated neurotoxicity (TIAN). Four patients demonstrated major volumetric tumor reductions (52%, 54%, 91% and 100%). One patient exhibited a complete response ongoing for >30 months since enrollment. Eight patients demonstrated neurological benefit based upon a protocol-directed Clinical Improvement Score. Sequential IV followed by ICV GD2-CART induced tumor regressions and neurological improvements in patients with DIPG and sDMG. DL1 was established as the maximally tolerated IV GD2-CART dose. Neurotoxicity was safely managed with intensive monitoring and close adherence to a management algorithm.
THE ECONOMIC BURDEN OF INVASIVE FORMS OF MENINGOCOCCAL INFECTION
Authors: Sergienko E.N. , Kozhanova I.N. , Romanova O.N. , Solodov A.D. , Scutova P.A.
Published: June 2024

Relevance

Invasive meningococcal infection (IMI) is a significant clinical problem and is associated with a high probability of severe complications and death. Vaccination programs against meningococcus can achieve significant clinical effectiveness and require significant financial costs. This makes it relevant to study the economic burden of meningococcal infection in the conditions of modern healthcare in order to obtain basic data for subsequent research in the field of evaluation of medical technologies.

Aims

To assess the economic burden of IMI in children in the conditions of healthcare in the Republic of Belarus.

Material and methods

a retrospective study using the “cost of illness” method was conducted for 22 children hospitalized in the city children’s infectious clinical diseases hospital in 2018-2019. All values are presented in belarusian rubles. The average ± standard deviation, minimum – maximum values, median [Q1, Q3], cost shares (%) are calculated for the cost values. The minimum– maximum values and median [Q1, Q3] were calculated for the age of the patients.

Results

taking into account the costs of treatment in healthcare organizations of all patients studied, the share of direct costs of hospitalization was 29.0%, the share of direct costs of diagnosis - 7.2%, the share of direct costs of pharmacotherapy - 8.3%. A significant part of the costs accounted for observations after discharge and amounted to 55.4%.

Conclusion

a retrospective study of the economic burden of MI in the Republic of Belarus using the “cost of illness” method in patients hospitalized in a public health organization demonstrates a significant economic burden of this disease, which in the long term is primarily due to the presence of complications in the patient, as well as the impact of the patient’s death on the value of total costs.
Neuronal DNA repair reveals strategies to influence CRISPR editing outcomes
Authors: Ramadoss Gokul N , Namaganda Samali J , Hamilton Jennifer R , Sharma Rohit , Chow Karena G , Macklin Bria L , Sun Mengyuan , Liu Jia-Cheng , Fellmann Christof , Watry Hannah L , Jin Julianne , Perez Barbara S , Sandoval Espinoza Cindy R , Matia Madeline P , Lu Serena H , Judge Luke M , Nussenzweig Andre , Adamson Britt , Murthy Niren , Doudna Jennifer A , Kampmann Martin , Conklin Bruce R
Published: June 2024

Genome editing is poised to revolutionize treatment of genetic diseases, but poor understanding and control of DNA repair outcomes hinders its therapeutic potential. DNA repair is especially understudied in nondividing cells like neurons, which must withstand decades of DNA damage without replicating. This lack of knowledge limits the efficiency and precision of genome editing in clinically relevant cells. To address this, we used induced pluripotent stem cells (iPSCs) and iPSC-derived neurons to examine how postmitotic human neurons repair Cas9-induced DNA damage. We discovered that neurons can take weeks to fully resolve this damage, compared to just days in isogenic iPSCs. Furthermore, Cas9-treated neurons upregulated unexpected DNA repair genes, including factors canonically associated with replication. Manipulating this response with chemical or genetic perturbations allowed us to direct neuronal repair toward desired editing outcomes. By studying DNA repair in postmitotic human cells, we uncovered unforeseen challenges and opportunities for precise therapeutic editing.
Antibiotic Resistance pattern in Bile from Cholecystectomised Patients by Multiplex PCR
Authors: Farhana Nasreen , Uddin Khan Mohammad Ashraf , Shamsuzzaman SM
Published: June 2024

Background

Bile in the biliary tract is normally sterile. Presence of gallstones, ascending infection from duodenum or bacterial translocation from portal vein leads to microfloral colonization in biliary system.

Aim

This study was aimed to evaluate the microbiological profile of bile from gall bladder for determination of the appropriate antibiotics in cholecystectomised patients.

Methods

This cross sectional study included patients who underwent laparoscopic or open cholecystectomy in Dhaka Medical College Hospital, Dhaka, from July, 2013 to December, 2014. Total 246 intraoperative bile were cultured aerobically in Blood agar and MacConkey’s agar media. The identified isolates were tested for their sensitivity pattern according to CLSI guidelines and multiplex PCR was used to detect virulence genes ofSalmonellaTyphi and anaerobic bacteria along with drug resistance genes.

Findings

Out of 246 bile samples, organisms were identified in 171 (69.51%) cases; 119 (48.37%) were aerobic bacteria identified by culture and PCR and 52 (21.14%) were anaerobic bacteria identified by multiplex PCR.Escherichia coli(26.61%) were found predominantly followed byStaphylococcus aureus(19.35%),Clostridium perfringens(13.82%).Salmonella entericaserovar Typhi was detected by culture and PCR in 3 (1.22%) and 8 (3.45%) samples respectively. Prevalence of ESBLs, Carbapenemase producers and MRSA were detected phenotypically in 10.96%, 16.44% and 8.33% samples respectively and the resistance genes blaCTX-M-15 (50.0%), blaOXA-1-group (25.0%), blaNDM-1 (62.50%), OXA-181/OXA-84 (12.5%) and mecA (8.33%) were detected.

Conclusion

Significant proportion of aerobic and anaerobic bacterial infection associated with biliary tract obstruction may warrants serious health risk to cholecystectomised patients in this region.
Multimodal Speech Biomarkers for Remote Monitoring of ALS Disease Progression
Authors: Neumann Michael , Kothare Hardik , Ramanarayanan Vikram
Published: June 2024

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that severely impacts affected persons’ speech and motor functions, yet early detection and tracking of disease progression remain challenging. The current gold standard for monitoring ALS progression, the ALS functional rating scale - revised (ALSFRS-R), is based on subjective ratings of symptom severity, and may not capture subtle but clinically meaningful changes due to a lack of granularity. Multimodal speech measures which can be automatically collected from patients in a remote fashion allow us to bridge this gap because they are continuous-valued and therefore, potentially more granular at capturing disease progression. Here we investigate the responsiveness and sensitivity of multimodal speech measures in persons with ALS (pALS) collected via a remote patient monitoring platform in an effort to quantify how long it takes to detect a clinically-meaningful change associated with disease progression. We recorded audio and video from 278 participants and automatically extracted multimodal speech biomarkers (acoustic, orofacial, linguistic) from the data. We find that the timing alignment of pALS speech relative to a canonical elicitation of the same prompt and the number of words used to describe a picture are the most responsive measures at detecting such change in both pALS with bulbar (n= 36) and non-bulbar onset (n= 107). Interestingly, the responsiveness of these measures is stable even at small sample sizes. We further found that certain speech measures are sensitive enough to track bulbar decline even when there is no patient-reported clinical change, i.e. the ALSFRS-R speech score remains unchanged at 3 out of a total possible score of 4. The findings of this study have the potential to facilitate improved, accelerated and cost-effective clinical trials and care.
Beta Burst-Driven Adaptive Deep Brain Stimulation Improves Gait Impairment and Freezing of Gait in Parkinson’s Disease
Authors: Wilkins K.B. , Petrucci M.N. , Lambert E.F. , Melbourne J.A. , Gala A.S. , Akella P. , Parisi L. , Cui C. , Kehnemouyi Y.M. , Hoffman S.L. , Aditham S. , Diep C. , Dorris H.J. , Parker J.E. , Herron J.A. , Bronte-Stewart H.M
Published: June 2024

Background

Freezing of gait (FOG) is a debilitating symptom of Parkinson’s disease (PD) that is often refractory to medication. Pathological prolonged beta bursts within the subthalamic nucleus (STN) are associated with both worse impairment and freezing behavior in PD, which are improved with deep brain stimulation (DBS). The goal of the current study was to investigate the feasibility, safety, and tolerability of beta burst-driven adaptive DBS (aDBS) for FOG in PD.

Methods

Seven individuals with PD were implanted with the investigational Summit™ RC+S DBS system (Medtronic, PLC) with leads placed bilaterally in the STN. A PC-in-the-loop architecture was used to adjust stimulation amplitude in real-time based on the observed beta burst durations in the STN. Participants performed either a harnessed stepping-in-place task or a free walking turning and barrier course, as well as clinical motor assessments and instrumented measures of bradykinesia, OFF stimulation, on aDBS, continuous DBS (cDBS), or random intermittent DBS (iDBS).

Results

Beta burst driven aDBS was successfully implemented and deemed safe and tolerable in all seven participants. Gait metrics such as overall percent time freezing and mean peak shank angular velocity improved from OFF to aDBS and showed similar efficacy as cDBS. Similar improvements were also seen for overall clinical motor impairment, including tremor, as well as quantitative metrics of bradykinesia.

Conclusion

Beta burst driven adaptive DBS was feasible, safe, and tolerable in individuals with PD with gait impairment and FOG.
Pseudoscience in Cancer Services; a survey of National Health Service Trusts in England
Authors: Rose Leslie B
Published: June 2024

Background

Scientifically implausible treatments are offered by some hospital cancer departments. Examples are reiki, aromatherapy, and reflexology. Salaried practitioners are employed to deliver these therapies, which are provided as palliative care, although they lack evidence of effectiveness. Such practices seem to conflict with efforts to make health care evidence based.

Aim

To estimate the extent of certain pseudoscientific practices in NHS Trusts, and to evaluate the rationale for such provision.

Design

Relevant documents were requested from NHS Trusts under the Freedom of Information Act 2000 (FOIA). Main outcome measures were: number of trusts offering pseudoscientific practices in cancer departments, time to full FOIA response, presence and content of practice governance documents, and presence and quality of evidence for practices.

Setting/Participants

Cancer care departments in NHS hospitals in England. No patient participants were involved in the survey.

Results

13.6% of eligible NHS trusts were offering pseudoscientific clinical practices. No trust provided a valid business case, or any robust evidence for the practices. The governance documents included claims about chakras, meridians, and invisible “energy”. Ten trusts required that informed consent be obtained from patients. This could not have been obtained because information given was misleading.

Conclusions

Pseudoscientific practices are embedded in the NHS in England, and governance documents show poor understanding of clinical evidence.
Subnational tailoring of malaria interventions to prioritize the malaria response in Guinea
Authors: Diallo Ousmane Oumou , Diallo Abdourahamane , Toh Kok Ben , Diakité Nouman , Dioubaté Mohamed , Runge Manuela , Symons Tasmin , Diallo Elhadj Marouf , Gerardin Jaline , Galatas Beatriz , Camara Alioune
Published: June 2024

Background

In the context of high malaria burden yet limited resources, Guinea’s national malaria program adopted an innovative subnational tailoring (SNT) approach, including engagement of stakeholders, data review, and data analytics, to update their malaria operational plan for 2024-2026 and identify the most appropriate interventions for each district considering the resources available.

Methods

Guinea’s malaria program triggered the SNT exercise with a list of decisions that could be informed with local data. The program established an SNT team, which determined intervention targeting criteria; identified, assembled, and reviewed relevant data sources; stratified malaria risk and its determinants to inform geographical targeting for each intervention; and used mathematical modeling to predict the impact of different intervention mix scenarios. The SNT analysis was performed at the district level, excluding the urban area of Conakry.

Results

Malaria incidence, malaria prevalence, and all-cause under-5 mortality were used for the epidemiological stratification of Guinea. Additional indicators relevant for decisions-making including seasonality patterns, insecticide resistance or malaria interventions and vaccine coverage were also stratified. Stratified layers were used to inform the targeting criteria for each intervention to identify districts to prioritize for indoor residual spray, dual-action insecticide-treated nets, seasonal malaria chemoprevention (SMC) including number of cycles for each eligible district, malaria vaccine, and perennial malaria chemoprevention. Results of the SNT analysis were used to mobilize funding from the Global Fund for scale-up of dual-action nets and expansion of SMC.

Conclusions

SNT allowed Guinea’s national malaria program to adapt their intervention strategy at the health district level, an unprecedented approach in the country. The use of local data to inform eligibility and prioritization allowed the program to identify the optimal mix of interventions for each district and to successfully mobilize resources to support their plans.
Establishment of Reference Values of Markers of Non-Thyroidal Illness Syndrome on a State-of-the-Art Fully Automated ABEI-Based Chemiluminescence System
Authors: Ijaz Aamir , Anjum Muhammad Usman , Ahmed Farhan , Paracha Shamila Najeeb , Habib Farzana , Shaukat Muhammad Bilal , Najeeb Sara , Hafeez Najma
Published: June 2024

Background

Non-Thyroidal Illness Syndrome (NTIS), previously called Euthyroid Sick Syndrome has always been a diagnostic dilemma for Chemical Pathologists and treating physicians. Combination of four test i.e. Reverse Triiodothyronine (rT3), Free Triiodothyronine (fT3), Free Thyroxine (fT4) and Thyroid Stimulating Hormone (TSH) can be helpful to diagnose NTIS in critically ill patients. We need, however, to determine the reference values found in a reference population, free of any thyroidal as well as non-thyroidal illness.

Methods and Materials

Initially, 266 adult volunteers were included in the study from Mohi Uddin Islamic Medical College Mirpur AJ&K (MIMC) and Mohi Uddin Teaching Hospital Mirpur AJ&K (MOTH) after taking written informed consent. About 124 volunteers were selected (males 61; females 63) after exclusion of the volunteers with one or more of the exclusion criteria. Blood specimens were collected and analyzed for rT3, fT3, fT4 and TSH using Maglumi X8 (S nibe, China), an ABEI (N-(aminobutil)-N-(ethyl)-isoluminol) based analyzer at Pathology Laboratory MOTH.

Results

Reference values of rT3, fT3, fT4 and TSH were found to be 13.3 – 19.8 ng/dL (0.2 – 0.30 nmol/L); 2.65 - 4.15 pg/mL (4.08 - 6.39 pmol/L);10.6 - 16.2 pg/mL (13.64–20.84 pmol/L) and 0.43 - 3.98 μIU/mL (0.43 – 3.98 mIU/L), respectively.

Conclusion

Reference values determined in our own population should be used when diagnosing and monitoring NTIS and other thyroid disorders
Could the Inflation Reduction Act Maximum Fair Price Hurt Patients?
Authors: Rivera Esteban , Sydor Anne M. , Popovian Robert
Published: June 2024

Background

The Inflation Reduction Act’s Medicare Drug Price Negotiation Program allows the federal government to negotiate caps for select medications. These price caps may reduce revenue for the pharmacy benefit managers (PBMs) that negotiate the actual price paid for medicines in the US. To offset the resulting pressure on their profit margins, it is possible that PBMs would, in turn, increase patient’s out-of-pocket costs for medicines with capped prices. The model presented here evaluates how such increased out-of-pocket costs for the anticoagulants Eliquis (apixaban) and Xarelto (rivaroxaban) could impact patients financially and clinically.

Methods

Copay distributions for all 2023 prescription fills for Eliquis and Xarelto managed by the three largest PBMs were used to approximate current copay costs. Increased out-of-pocket costs were modeled as a shift of all Eliquis and Xarelto prescriptions to the highest copay tier. The known linear relationship between copay costs and treatment abandonment was used to calculate the potential resulting increase in treatment abandonment. Known rates of morbidity and mortality due to abandoning anticoagulants were used to estimate resulting increases in morbidity and mortality.

Results

If the three largest PBMs all shifted costs onto patients by moving all Eliquis and Xarelto prescriptions to the highest formulary tier, Tier 6, patients’ copay amount would increase by $235 to $482 million for Eliquis and $105 to $206 million for Xarelto. Such an increase could lead to 169,000 to 228,000 patients abandoning Eliquis and 71,000 to 93,000 abandoning Xarelto. The resulting morbidity and mortality could include up to an additional 145,000 major cardiovascular events and up to 97,000 more deaths.

Conclusion

The Medicare Price Negotiation Program could impact patients negatively if it causes PBMs to increase patients’ out-of-pocket costs for medicines. Policymakers should closely monitor changes in overall affordability, including all patient out-of-pocket expenditures, for medications in the program. Preemptive measures to ensure that the most vulnerable citizens are not placed in precarious situations leading to poorer health outcomes should be considered.
A qualitative study on factors influencing health workers’ uptake of a pilot surgical antibiotic prophylaxis stewardship programme in selected Georgian hospitals
Authors: Narayan Sideeka , Warsi Sahil Khan , Kachkachishvili Iago , Kontselidze Osiko , Jibuti Mariam , Esebua Nino , Papiashvili Ana , Wong Danilo Lo Fo , Kandelaki Ketevan
Published: June 2024

Antimicrobial misuse in surgical antibiotic prophylaxis (SAP) can include the inappropriate use of broad-spectrum antibiotics or prolonged dosing. In 2021, a pilot antimicrobial stewardship programme (ASP) was launched in Georgia, which involved developing and adapting SAP guidelines, establishing an interprofessional SAP prescribing approach, collecting surgical site infection (SSI) data via routinely collected data and telephonic patient follow-ups, and providing surgical unit staff with prescribing feedback and training on antimicrobial resistance (AMR) and antimicrobial stewardship (AMS). ASP introduction was staggered across ten hospitals over three years.

This study explored behavioural determinants of surgical teams’ ASP uptake in five hospitals where the ASP was introduced or about to be introduced. Findings primarily concerned epidemiologists’ and nurses’ ASP-related behaviour. Those at ASP non-introduced hospitals were less involved in the SAP prescribing process, had lower AMR awareness, and lacked professional development opportunities. Those at ASP-introduced hospitals exhibited higher AMR knowledge and felt ASP participation boosted confidence, facilitated work, and furnished key professional development.

Results indicate interprofessional collaboration on SAP prescribing supported ASP uptake across teams, and investment in health worker training and administrative encouragement ensured effective ASP participation and implementation. Findings highlight the crucial role of epidemiologists in SAP and illustrate a need for developing Georgian nurses’ AMR competencies as a vehicle to address public AMR knowledge gaps. Longer-term ASP uptake will need to consider the regulatory context in which hospitals lack access to national-level SSI data and feedback on SSI reporting but are fined for reporting non-compliance.

Despite resource limitations and a small sample size, the study engaged all pilot ASP health workers. Respondents’ inexperience of qualitative research participation and ensuant hesitation limited exploration of motivational factors supporting health workers’ ASP uptake, which could be explored in further research.
TheO-Fucosyltransferase SPINDLY Attenuates Auxin-Induced Fruit Growth by Inhibiting ARF6 and ARF8 binding to Coactivator Mediator Complex inArabidopsis
Authors: Wang Yan , Kelley Seamus , Zentella Rodolfo , Hu Jianhong , Wei Hua , Wang Lei , Shabanowitz Jeffrey , Hunt Donald F. , Sun Tai-ping
Published: June 2024

The phytohormone auxin plays a pivotal role in promoting fruit initiation and growth upon fertilization in flowering plants. Upregulation of auxin signaling by genetic mutations or exogenous auxin treatment can induce seedless fruit formation from unpollinated ovaries, termed parthenocarpy. Recent studies suggested that the class A AUXIN RESPONSE FACTOR6 (ARF6) and ARF8 inArabidopsisplay dual functions by first inhibiting fruit initiation when complexed with unidentified corepressor IAA protein(s) before pollination, and later promoting fruit growth after fertilization as ARF dimers. However, whether and how posttranslational modification(s) regulate ARF6- and ARF8-mediated fruit growth were unknown. In this study, we reveal that both ARF6 and ARF8 areO-fucosylated in their middle region (MR) by SPINDLY (SPY), a novel nucleocytoplasmic proteinO-fucosyltransferase, which catalyzes the addition of a fucose moiety to specific Ser/Thr residues of target proteins. Epistasis, biochemical and transcriptome analyses indicated that ARF6 and ARF8 are downstream of SPY, but ARF8 plays a more predominant role in parthenocarpic fruit growth. Intriguingly, two ARF6/8-interacting proteins, the co-repressor IAA9 and MED8, a subunit of the coactivator Mediator complex, were alsoO-fucosylated by SPY. Biochemical assays demonstrated that SPY-mediatedO-fucosylation of these proteins reduced ARF-MED8 interaction, which led to enhanced transcription repression activity of the ARF6/8-IAA9 complex but impaired transactivation activities of ARF6/8. Our study unveils the role of proteinO-fucosylation by SPY in attenuating auxin-triggered fruit growth through modulation of activities of key transcription factors, a co-repressor and the coactivator MED complex.
Optimization of an improved, time-saving, and scalable, protocol for the extraction of DNA from diverse viromes
Authors: Shamash Michael , Kapoor Saniya , Maurice Corinne F.
Published: June 2024

Introduction

The virome, composed of viruses inhabiting diverse ecosystems, significantly influences microbial community dynamics and host health. The phenol-chloroform DNA extraction protocol for viromes, though effective, is time-intensive and requires the use of multiple toxic chemicals.

Methods

This study introduces a streamlined, scalable protocol for DNA extraction using a commercially-available kit as an alternative, assessing its performance against the phenol-chloroform method across human fecal, mouse fecal, and soil samples.

Results

No significant differences in virome diversity or community composition were seen between methods. Most viral operational taxonomic units (vOTUs) were common to both methods, with only a small percentage unique to either approach. Alpha- and beta-diversity analyses showed no significant impact of the extraction method on virome composition, confirming the kit’s efficacy and versatility.

Conclusions

While the kit approach offers benefits like reduced toxicity and increased throughput, it has limitations such as higher costs and potential issues reliably capturing low-abundance taxa. This protocol provides a viable option for large-scale virome studies, although the phenol-chloroform approach may still be preferable for specific sample types.
Speech-reception-threshold estimation via EEG-based continuous speech envelope reconstruction
Authors: Borges Heidi B. , Zaar Johannes , Alickovic Emina , Christensen Christian B. , Kidmose Preben
Published: June 2024

This study investigates the potential of speech-reception-threshold (SRT) estimation through electroencephalography (EEG) based envelope reconstruction techniques with continuous speech. Additionally, we investigate the influence of the stimuli’s signal-to-noise ratio (SNR) on the temporal response function (TRF). Twenty young normal-hearing participants listened to audiobook excerpts with varying background noise levels while EEG was recorded. A linear decoder was trained to reconstruct the speech envelope from the EEG data. The reconstruction accuracy was calculated as the Pearson’s correlation between the reconstructed and actual speech envelopes. An EEG SRT estimate (SRTneuro) was obtained as the midpoint of a sigmoid function fitted to the reconstruction accuracy versus SNR data points. Additionally, the TRF was estimated at each SNR level, followed by a statistical analysis to reveal significant effects of SNR levels on the latencies and amplitudes of the most prominent components. The SRTneurowas within 3 dB of the behavioral SRT for all participants. The TRF analysis showed a significant latency decrease for N1 and P2 and a significant amplitude magnitude increase for N1 and P2 with increasing SNR. The results suggest that both envelope reconstruction accuracy and the TRF components are influenced by changes in SNR, indicating they may be linked to the same underlying neural process.
Responses to ligand binding in the bacterial DNA sliding clamp β-clamp manifest in dynamic allosteric effects
Authors: Simonsen Signe , Prestel Andreas , Østerlund Eva C. , Otterlei Marit , Jørgensen Thomas J.D. , Kragelund Birthe B.
Published: June 2024

The homo-dimeric, ring-shaped bacterial DNA sliding clamp, β-clamp, is a central hub in DNA replication and repair. It interacts with a plethora of proteins via short linear motifs, which bind to the same hydrophobic binding pocket on β-clamp. Although the structure, functions and interactions of β-clamp have been amply studied, less focus has been on understanding its dynamics and how this is influenced by ligand binding. In this work, we have made a backbone nuclear magnetic resonance (NMR) assignment of the 83 kDa dimeric β-clamp and used NMR in combination with hydrogen-deuterium exchange mass spectrometry to scrutinize the dynamics of β-clamp and how different ligands affect this. We found that binding of a small peptide from the polymerase III α subunit affects the dynamics and stability of β-clamp. This effect not only appears locally around the binding pocket, but also globally through dynamic allosteric connections to distant regions of the protein, including the dimer interface. This dissipated dynamic effect is likely a consequence of the binding pocket architecture and may reflect a common mechanism of structural plasticity, where different ligands impose differential responses in the structure and dynamics of β-clamp.

Highlights

NMR spectroscopy of β-clamp revealed its inherent dynamics

A peptide ligand from polymerase III stabilizes β-clamp from global unfolding

Peptide binding causes allosteric effects that manifest in changes in dynamics

Dynamic changes occur distant to the binding pocket in the dimer interface

Allostery may be a mechanism for differential responses to interaction partners

Graphical abstract
Anhedonic behaviour in a TLR7-driven neuroinflammation mouse model is associated with impaired thalamostriatal signalling and immune cell ingress into the brain
Authors: Sharma Deepika , Andrianova Lilya , McGonigal Rhona , Gardner-Stephen Kirstyn , al Fadhel Hassan , Barrie Jennifer A , Hohne Richard , Saathoff Megan , Karabalci Yaprak , Bourgognon Julie-Myrtille , Cole John J , Craig Michael T , Cavanagh Jonathan T
Published: June 2024

Depression is a heterogenous condition driven by multiple aetiologies, which make its pathophysiology challenging to map. Stratifying depression by underlying biological causes may allow for more effective, targeted treatments. Immune-mediated inflammation is present in around 20% of individuals with depression and provides a potential mechanistic pathway for some key symptoms such as reward / hedonic impairment. Here we used a non-invasive model of neuroinflammation, topical application of Aldara (a TLR7/8 agonist) for 3 days in mice, to explore relationships between the intracerebral immune response, neural circuitry and behaviours closely linked to depression: motivation, reward and anxiety.

Mice that were treated with Aldara exhibited anhedonia-like behaviour and impairments in intrinsic motivational behaviours (measured through assays such as sucrose preference and nest-building tests) relative to untreated controls, but displayed little anxiety-like behaviour. Aldara-driven neuroinflammation was associated with evidence of immune cell (including lymphoid and myeloid cells) ingression into the brain, and both microglia and astrocytes showed evidence of activation. Within 4 to 6 hours of Aldara treatment, neurons in midline thalamus showed strongly increased Fos immunoreactivity relative to controls. Optogenetic activation of midline thalamic projections onto ventral striatum medium spiny neurons (MSNs) revealed that Aldara treatment substantially reduced the magnitude of the evoked thalamic AMPA receptor-mediated EPSC, but with no change to the AMPA/NMDA ratio nor change in the frequency of amplitude of spontaneous EPSP. Finally, whole brain transcriptome overrepresentation analysis revealed that Aldara treatment led to significant upregulation of genes associated with immune response and downregulation of genes associated with glutamate metabolism and synaptic transmission.

Altogether, our data suggest potential, testable mechanisms through which neuroinflammation can drive anhedonic-like behaviour through activation of resident neural cells, infiltrating activated immune cells and functional changes in thalamostriatal circuitry consistent with increased extrasynaptic glutamate.
Post-retrieval noradrenergic activation impairs subsequent memory depending on cortico-hippocampal reactivation
Authors: Heinbockel Hendrik , Leicht Gregor , Wagner Anthony D. , Schwabe Lars
Published: June 2024

When retrieved, seemingly stable memories can become sensitive to significant events, such as acute stress. The mechanisms underlying these memory dynamics remain poorly understood. Here we show that noradrenergic stimulation after memory retrieval impairs subsequent remembering, depending on hippocampal and cortical signals emerging during retrieval. In a three-day study, we measured brain activity using fMRI during initial encoding, 24h-delayed memory cueing followed by pharmacological elevations of glucocorticoid or noradrenergic activity, and final recall. While post-retrieval glucocorticoids did not affect subsequent memory, the impairing effect of noradrenergic arousal on final recall depended on hippocampal reactivation and category-level reinstatement in ventral temporal cortex during memory cueing. These effects did not require a reactivation of the original memory trace and did not interact with offline reinstatement during rest. Our findings demonstrate that, depending on the retrieval-related neural reactivation of memories, noradrenergic arousal after retrieval can alter the future accessibility of consolidated memories.
A small RNA derived from the 5’ end of the IS200tnpAtranscript regulates multiple virulence regulons inSalmonellaTyphimurium
Authors: Trussler Ryan S. , Scherba Naomi-Jean Q. , Ellis Michael J. , Förstner Konrad U. , Albert Matthew , Westermann Alexander J. , Haniford David B.
Published: June 2024

The insertion sequence IS200 is widely distributed in Eubacteria. Despite its wide-ranging occurrence, IS200 does not appear to be mobile and as such is considered an ancestral component of bacterial genomes. Previous work inSalmonella entericarevealed that the IS200tnpAtranscript is processed to form a small highly structured RNA (5’tnpA) that participates in the post-transcriptional control ofinvFexpression, encoding a key transcription factor in this enteropathogen’s invasion regulon. To further examine the scope of5’tnpAtranscript integration intoSalmonellagene expression networks, we performed comparative RNA-seq revealing the differential expression of over 200 genes in aSalmonellaSL13445’tnpAdisruption strain. This includes the genes for the master regulators of both invasion and flagellar regulons (HilD and FlhDC, respectively), plus genes involved in cysteine biosynthesis (cysteine regulon) and an operon (phsABC) encoding a thiosulfate reductase complex. These expression changes were accompanied by an 80-fold increase inSalmonellainvasion of HeLa cells. Likewise, aphsABCdisruption strain was associated with an increased invasion specifically under anaerobic growth conditions. Based on these findings, we propose that early induction of invasion and motility regulons in the absence of5’tnpAcauses a metabolic stress resulting in cysteine limitation and activation of CysB, which turns down expression of thephsABCoperon to increase the flux of thiosulfate in the media towards cysteine production. Taken together, this study provides a powerful new example of bacterial transposon domestication that is based not on the production of a regulatory protein, but of a transposon-derived small RNA.
Inhibition of SF3B1 affects recruitment of P-TEFb to chromatin through multiple mechanisms
Authors: Ansa Gilbert , Murphy Shona , Tellier Michael
Published: June 2024

Processing of nascent pre-mRNAs is tightly coupled to transcription by RNA polymerase II (RNAPII) through reversible phosphorylation of the polymerase and associated factors by transcriptional kinases. P-TEFb, comprising cyclin-dependent kinase (CDK)9 and cyclin T1, is a key transcription elongation kinase, which also regulates co-transcriptional splicing and mRNA cleavage and polyadenylation. Chemical inhibition of SF3B1, a component of the splicing factor U2 snRNP, decreases P-TEFb recruitment to chromatin and mirrors the effect of P-TEFb inhibition on transcription. However, the mechanism of this effect of SF3B1 inhibitors was unclear. Here we show that SF3B1 inhibition causes rapid nuclear export of P-TEFb and loss of SF3B1 phosphorylation. SF3B1 is in complex with P-TEFb on chromatin with the elongation/splicing factor HTATSF1 and the splicing factor SNW1. SF3B1 inhibition causes the nuclear export of SNW1, but not of HTATSF1. The chromatin association of AFF4, an interaction partner of P-TEFb, is also affected by SF3B1 inhibition. Surprisingly, SF3B1 inhibition promotes degradation of SRSF2, a splicing factor known to help recruit P-TEFb to chromatin. Our results indicate that SF3B1 inhibition affects P-TEFb recruitment to genes via multiple pathways. Together, these interactions ensure efficient coupling of transcription and splicing.
Beyond Histones: Unveiling the Functional Roles of Protein Acetylation in Prokaryotes and Eukaryotes
Authors: Sousa Bonifácio Bruno , Barbosa Leite Ariely , de Castro Nascimento Sousa Ana Caroline , Rodrigues Maran Suellen , Severo Gomes Antoniel Augusto , Vasconcelos Elton J. R. , Silvio Moretti Nilmar
Published: June 2024

Lysine acetylation plays a crucial role in cellular processes and is found across various evolutionary organisms. Recent advancements in proteomic techniques revealed the presence of acetylation in thousands of non-histone proteins. Here, we conducted extensive meta-analysis of 48 acetylomes spanning diverse organisms, including archaea, bacteria, fungi, protozoa, worms, plants, insects, crustacea, fish, and mammals. Our analyzes revealed a predominance of a single acetylation site in a protein detected in all studied organisms, and proteins heavily acetylated, with >5-10 acetylated-sites, were represented by Hsp70, histone or transcription GTP-biding domain. Moreover, using gene enrichment approaches we found that ATP metabolic processes, glycolysis, aminoacyl-tRNA synthetase pathways and oxidative stress response are among the most acetylated cellular processes. Finally, to better explore the regulatory function of acetylation in glycolysis and oxidative stress we used aldolase and superoxide dismutase A (SODA) enzymes as model. For aldolase, we found that K147 acetylation, responsible to regulate human enzyme, conserved in all phylogenic clade, suggesting that this acetylation might play the same role in other species; while for SODA, we identified many lysine residues in different species present in the tunnel region, which was demonstrated for human andTrypanosoma cruzi,as negative regulator, also suggesting a conserved regulatory mechanism. In conclusion, this study provides insights into the conservation and functional significance of lysine acetylation in different organisms emphasizing its roles in cellular processes, metabolic pathways, and molecular regulation, shedding light in the extensive function of non-histone lysine acetylation.
A KIF1C-CNBP motor-adaptor complex for trafficking mRNAs to cell protrusions
Authors: Moissoglu Konstadinos , Wang Tianhong , Gasparski Alexander N. , Stueland Michael , Paine Elliott L. , Jenkins Lisa , Mili Stavroula
Published: June 2024

mRNA localization to subcellular compartments is a widely used mechanism that functionally contributes to numerous processes. mRNA targeting can be achieved upon recognition of RNA cargo by molecular motors. However, our molecular understanding of how this is accomplished is limited, especially in higher organisms. We focus on a pathway that targets mRNAs to peripheral protrusions of mammalian cells and is important for cell migration. Trafficking occurs through active transport on microtubules, mediated by the KIF1C kinesin. Here, we identify the RNA-binding protein CNBP, as a factor required for mRNA localization to protrusions. CNBP binds directly to GA-rich sequences in the 3’UTR of protrusion targeted mRNAs. CNBP also interacts with KIF1C and is required for KIF1C recruitment to mRNAs and for their trafficking on microtubules to the periphery. This work provides a molecular mechanism for KIF1C recruitment to mRNA cargo and reveals a motor-adaptor complex for mRNA transport to cell protrusions.