bluuebunny/crossref_metadata_2025 huggingface dataset:
Weight and Procedural Abortion Complications: A Systematic Review
Authors: McMahon Hayley V. , Moss Regan A. , Pearce Naya , Sehgal Sakshi , He Zeling , Kriete Monica , Lucier-Julian Zoë , Redd Sara K. , Rice Whitney S.
Published: January 2025

OBJECTIVE:

To systematically assess the existing empiric evidence regarding a potential relationship between higher body weight and procedural abortion complications.

DATA SOURCES:

EMBASE, MEDLINE, CINAHL, Web of Science, Google Scholar, and Clinicaltrials.gov were searched.

METHODS OF STUDY SELECTION:

Our search identified 409 studies, which were uploaded to Covidence for review management; 133 duplicates were automatically removed. A team of two reviewers screened 276 studies, and a third reviewer resolved conflicts. Studies were included if they 1) consisted of peer-reviewed research published between 2010 and 2022, 2) were conducted in the United States, 3) included people with a higher body weight (body mass index [BMI] 30 or higher) in the study sample, and 4) assessed at least one outcome of procedural abortion safety stratified by a measure of body weight.

TABULATION, INTEGRATION, AND RESULTS:

We extracted study data using Covidence and calculated an odds ratio for each study to facilitate the synthesis of results. Six studies assessing a total of 38,960 participants were included. No studies found a significant relationship between procedural abortion complications and higher body weight overall. Subgroup analysis from one study identified a significant increase in complications specifically among participants with BMIs higher than 40 who had second-trimester abortions. All studies used a retrospective cohort design and fulfilled Newcastle–Ottawa Scale criteria to be considered good quality. Studies varied in terms of clinical settings, patient populations, gestations assessed, clinician training levels, and care protocols.

CONCLUSION:

Overall, higher body weight was not associated with an increased risk of procedural abortion complications in the included studies. The practice of referring patients undergoing procedural abortion with a higher body weight for hospital-based care is not based on recent safety evidence. On the contrary, this practice threatens the health of people with a higher body weight by potentially delaying their access to abortion care, extending their pregnancies into later gestations, and blocking their ability to access an abortion altogether.
TEMPOUR: A Randomized Controlled Trial Assessing Perioperative Use of An Alpha-1-Blocker to Reduce Postoperative Urinary Retention Following Transanal Endoscopic Microsurgery Procedures
Authors: Couture Thomas , Morin Claudya , Charbonneau Janyssa , Papillon-Dion Émilie , Bouchard Alexandre , Rouleau-Fournier François , Bouchard Philippe , Letarte François , Turgeon Alexis F.
Published: January 2025

BACKGROUND:

Transanal endoscopic microsurgery is a treatment option for a wide range of rectal lesions. Postoperative urinary retention is a frequently associated complication. Some studies have suggested that the use of alpha-1-blockers may reduce the risk of postoperative urinary retention after hernia and colorectal surgery, but evidence is lacking.

OBJECTIVE:

This trial aims to evaluate if prophylactic use of an alpha-1-blocker reduces the rate of postoperative urinary retention following transanal endoscopic microsurgery.

DESIGN:

Double-blind, placebo-controlled trial.

SETTINGS:

Single high-volume Canadian colorectal center.

PATIENTS:

Adult male patients awaiting transanal endoscopic microsurgery and not on alpha-1-blocker were included.

INTERVENTION:

Patients were allocated to either Tamsulosin or placebo from 5 days prior to surgery to 2 days postoperatively.

MAIN OUTCOMES MEASURES:

The primary outcome was the incidence of post-operative urinary retention. Secondary outcomes were urinary retention-related hospitalization, time to removal of bladder catheter and International Prostate Symptom Score, before and after treatment, and adverse events.

RESULTS:

158 patients were randomized between October 2017 and July 2022. There was no significant difference in postoperative urinary retention between groups (23% vs 14%; p = 0.16) respectively in the tamsolusin and placebo groups. Time to removal of bladder catheter was not statistically different between groups (4.8 vs 8.6 days, p = 0.26). No failure of same-day discharge, nor readmissions related to urinary retention occurred. International Prostate Symptom Scores were not significantly different at the time of surgery (3.8 vs 5.4; p = 0.11) and reported adverse events did not differ between groups.

LIMITATIONS:

We cannot exclude a potential type II error.

CONCLUSION:

Prophylactic use of an alpha-1-blocker for patients undergoing transanal endoscopic microsurgery was not associated with a reduction in post-operative urinary retention. See Video Abstract.

TRIAL REGISTRATION:

ClinicalTrials.gov Identifier: NCT03314025.
ESAIC focused guidelines for the management of the failing epidural during labour epidural analgesia
Authors: Brogly Nicolas , Valbuena Gómez Isabel , Afshari Arash , Ekelund Kim , Kranke Peter , Weiniger Carolyn F. , Lucas Nuala , Dewandre Pierre-Yves , Guasch Arevalo Emilia , Ioscovich Alexander , Kollmann Andrea , Lindelof Kim , Orbach-Zinger Sharon , Reis Stephanie , van den Bosch Oscar , Van de Velde Marc , Romero Carolina S.
Published: January 2025

BACKGROUND

Labour epidural analgesia reportedly fails in up to 10 to 25% of cases. A joint taskforce of European Society of Anaesthesiology and Intensive Care (ESAIC) experts was created to develop this focused guideline on the management of failing epidural analgesia in a previously well functioning epidural catheter.

DESIGN

Six clinical questions were defined using a PICO (Population/Intervention/Comparison/Outcome) strategy to conduct a systematic literature search. The questions pertained to clinical management of failing epidural (PICOs 1, 2 and 3), human resource and team training (PICOs 4 and 5) and clinical management of a failing epidural for intrapartum caesarean delivery (PICO 6). The taskforce produced recommendations and clinical practice statements (CPS) and validated them through a Delphi process. The final version of the guideline was submitted to all ESAIC members for critical review and approved by the Guidelines Committee and the ESAIC Board of Directors.

RESULTS

In the initial search, 3737 titles were identified, 93 were retained for complete article analysis and 56 were finally allocated to the PICOs. The full-text analysis of the selected articles precluded extraction of significant data for all PICOs except for PICO 6, for which six articles were identified. Based on the experience, knowledge and opinion of the experts, the task force proposed and validated two recommendations and 11 CPSs.

CONCLUSION

This guideline complemented other recently published expert opinion papers. We hope that this new guidance will serve clinicians to increase parturient safety and quality of care during labour and delivery, while at the same time provide inspiration for further research to fill the current knowledge gaps.
Examining the Recovery Course of Adolescent Concussion Patients With Protracted Recovery Referred to a Specialty Concussion Clinic
Authors: Mathew Abel S. , Datoc Alison E. , Price August M. , Abt John P.
Published: January 2025

Objective:

This study investigated the role of specialty concussion care on the clinical course of recovery in adolescent patients who initiated care beyond 3 weeks from their injury.

Design:

Retrospective analysis of protracted recovery groups was based on the number of days in which a patient presented for care postinjury: early (22-35 days), middle (36-49 days), and late (50+ days).

Setting:

Sports medicine and orthopedics clinic.

Patients:

101 patients aged 12 to 18 years.

Independent variables:

Age, race/ethnicity, sex, concussion or migraine history, neurodevelopmental or psychiatric diagnosis, King-Devick, Trails Making, Vestibular Ocular Motor Screening (VOMS), and Postconcussion Symptom Scale (PCSS).

Main Outcome Measures:

Days since injury to evaluation, recovery days from evaluation, and total recovery days.

Results:

There were no significant differences between groups for PCSS, average K-D scores, and Trails B-A. Vestibular Ocular Motor Screening change score was significantly different between groups such that the late group had less change in VOMS score compared with the early group (F = 3.81, P = 0.03). There were significant differences between groups in terms of days since injury to evaluation (F = 399.74, P < 0.001) and total recovery days (F = 19.06, <0.001). The middle (25.83 ± 34.95) and late group (30.42 ± 33.54) took approximately 1 week and 12 days longer to recover compared with the early group, respectively. Recovery days from evaluation were not significantly different between the 3 groups (F = 1.30; P = 0.28).

Conclusions:

Protracted recovery patients evaluated in a specialty concussion clinic received medical clearance to complete the return-to-play process with an athletic trainer within 1 month from the initial visit. The findings are consistent with previous research suggesting that earlier concussion care can expedite recovery.
Overlooked and underserved: how healthcare fails men in the pursuit of equity
Authors: Schulz Robert J. , Ofner Heidemarie , Nyirády Péter , Rajwa Pawel , Weiss Julia , Shariat Shahrokh F. , Fazekas Tamás
Published: January 2025

Purpose of review

Men face distinctive health-related challenges as a result of biological, behavioral, and sociocultural factors. In addition, the modern healthcare system does not offer men equal opportunities and options to ensure sex-specific access and delivery to health services. Men's health concerns are, indeed, often not addressed or even forgotten. In this review, we wanted to assess the impact of biology and sociocultural effects on sex-specific life-expectancy.

Recent findings

Globally, men have a shorter life expectancy than women. With a 5.8 years gender gap in the USA and 5.4 in the EU-27 (both in 2022). Cardiovascular disease, cancer, and accidents continue to represent the primary causes of mortality for both genders with all having disproportional preponderance in men. In recent years, there has been a notable decline in age-adjusted mortality rates related to cancer, while there has been an increase in deaths from accidental and intentional self-harm. Moreover, in the United States, men are more likely than women to develop and die from nonsex-specific cancers. As a result, men's poor health affects productivity, absenteeism, and employment.

The status of men in healthcare is complex. It is rooted in history, culture, and institutions. To address disparities, we need a comprehensive approach that includes policy reforms, sociocultural changes, and a fair and equitable public discourse. Grassroots and top-down strategies are needed to ensure a value-based societal healthcare system acknowledging the unique health needs of men.
Unusual Causes of Death Due to Constipation
Authors: Byard Roger W. , Tiemensma Marianne
Published: January 2025

Constipation is found in individuals with intellectual disabilities, autism, and cerebral palsy. Although generally a benign condition, it may lead to life-threatening intestinal obstruction, with or without volvulus, or to stercoral ulceration with enteritis and/or perforation. Two unusual cases of lethal chronic constipation are reported to demonstrate other very rare fatal mechanisms that may occur. Case 1: A 17-year-old male with cerebral palsy and autism was found deceased in bed. Death was due to pulmonary thromboembolism arising from compression of pelvic veins by acquired megacolon due to constipation (fecal mass 4.6 kg). Case 2: A second 17-year-old male with intellectual disability, global developmental delay, attention deficit disorder, seizures, and hypotonia collapsed and died during a medical evacuation from a remote community. Death was due to abdominal compartment syndrome in the context of medical air transport (medical retrieval), chronic constipation with acquired megacolon and megarectum (fecal mass 6.5 kg), global developmental delay, intellectual disability, and a suspected underlying genetic syndrome. These cases demonstrate that individuals with constipation may present for medicolegal assessment following sudden collapse/death and that pulmonary thromboembolism and abdominal compartment syndrome should be considered as rare possibilities in the evaluation of vulnerable individuals.
Adherence and forgiveness of two modern ART regimens: lamivudine/dolutegravir and emtricitabine/tenofovir alafenamide/rilpivirine.
Authors: L Taramasso , F Maggiolo , D Valenti , S Blanchi , F Centorrino , L Comi , A Di Biagio
Published: January 2025

Introduction:

Few data are available about the forgiveness of two-drug (2DR) or low-barrier three-drug antiretroviral regimens. The aim of this study is to evaluate the real-life forgiveness of lamivudine/dolutegravir (3TC/DTG) and emtricitabine/tenofovir alafenamide/rilpivirine (FTC/TAF/RPV).

Methods:

A two center retrospective observational study enrolled all people with HIV (PWH) treated with 3TC/DTG or FTC/TAF/RPV. Adherence was measured as the proportion of days covered (PDC) by drug supply. Binary logistic regression was applied to test the impact of baseline variables and adherence on the achievement of virological suppression.

Results:

1258 adult PWH were enrolled, 368 in 3TC/DTG and 890 in RPV/F/TAF. Most were males (71 %), with median age of 51 years (IQR 43-58 years) and median CD4 nadir of 305 cells/mcL (IQR 132-485). The median cohort follow-up totaled 4558 persons/year. Median adherence, as calculated from PDC, was of 0.98 (IQR 0.93-1). Irrespective of the treatment group, a PDC as low as 0.8 was sufficient to obtain HIV-RNA below 200 copies/mL in almost all study participants. The same adherence value also allowed the achievement of HIV-RNA below 50 copies/mL in > 90% of study participants. PDC (P < 0.0001), Italian origin (P < 0.0001) and male sex (P = 0.038) significantly correlated to the achievement of < 200 copies/mL.

Conclusions:

In this study, we found a similar and high grade of forgiveness in the INSTI-based 2-drug regimen 3TC/DTG and in the NNRTI-based 3-drug regimen FTC/TAF/RPV.
Rare Indocyanine-Induced Anaphylactic Shock During Deep Inferior Epigastric Artery Perforator Breast Reconstruction
Authors: Kang Jung-Min , Park Jin-Woo
Published: January 2025

Indocyanine green (ICG) is a water-soluble green substance that is detectable through infrared cameras and emits greenish light. Approved for medical use in the 1950s, ICG has gained prominence as a real-time visualization tool. Widely recognized as a generally safe substance, ICG is applied in diverse fields. Despite its prevalent use without significant safety concerns, we report a case of anaphylactic shock due to ICG to reflect on its potential risk.

A 46-year-old woman with phyllodes tumor of the breast came to our clinic. She had no significant medical history except dog hair allergy. She underwent nipple-sparing mastectomy, and we planned reconstruction with a deep inferior epigastric perforator free flap. Intraoperatively, we injected ICG to visualize the perfusion area of the abdominal flap. Immediately after injection, her blood pressure dropped to 39/32 from 124/66. Anaphylaxis management included injection of epinephrine, norepinephrine, and steroid. With proper management, her vital signs recovered to normal ranges and the operation proceeded. After discharge, the patient developed no flap-related or internal medical complications.

Despite the widely known safety of ICG, it carries a risk of life-threatening adverse effects. Surgeons should be aware that, although rare, these events can occur in their operations.
The impact of loneliness on healthcare costs and service utilisation and the
cost-effectiveness of loneliness interventions: a systematic review
Authors: Eager Sharon , Baldwin Helen , McCrone Paul , McDaid David , Stefanidou Theodora , Shah Prisha , Jeffreys Stephen , Rojas-Garcia Antonio , Jarvis Ruby , Chipp Beverley , Lloyd-Evans Brynmor , Pitman Alexandra , Barnett Phoebe , Matias Maria Ana , Johnson Sonia
Published: January 2025

Introduction

Loneliness is an unpleasant, subjective experience that can affect
people at all stages of life. Given its association with a range of physical
and mental health problems, it is important to assess the costs of
loneliness to the healthcare system. The current study aimed to: (i) review
literature on the health and social care impacts of loneliness, and (ii)
review economic evaluations of interventions to address loneliness.

Methods

We conducted a systematic review of studies published from 2008 to 2023
by searching five bibliographic databases, two sources of grey literature,
and reference lists of relevant systematic reviews. Studies estimating
health and social care cost and expenditure, and studies on health resource
utilisation were included to assess the impact of loneliness on the health
system. Return on investment, social return on investment, and
cost-effectiveness evaluations were included to assess the economic impact
of loneliness interventions. Studies that reported either mental or physical
health outcomes were included. No limitations were placed on inclusion for
populations, age groups, or language. We conducted quality appraisal and
narrative synthesis of results.

Results

We included 39 eligible studies: Five estimated the healthcare cost or
expenditure of loneliness, 22 reported healthcare resource use, and 18 were
economic evaluations of interventions. Most studies focused on older adult
populations. Findings relating to the cost/expenditure of loneliness and
service use were inconsistent and varied: some studies reported excess
healthcare costs/expenditure and service use associated with loneliness,
while others found lower costs/expenditure and service use associated with
loneliness. Economic evaluation studies covered a wide range of different
intervention types. They generally indicated that loneliness interventions
can be cost-effective, but were less likely to be cost-saving and not
consistently effective in reducing loneliness.

Discussion

Inconsistent and varied findings on the impact of loneliness on the
healthcare system and on economic evaluations of loneliness interventions
meant it was difficult to synthesise the results. Therefore, we cannot
derive confident conclusions about the impact of loneliness on
costs/expenditure related to the health and social care system from this
review. Future research should prioritise studies relating to social care,
the direct healthcare costs of loneliness, and randomised controlled trials
with long-term follow-ups to appropriately address these evidence gaps.
Research on younger populations should also be considered a
priority.
An inverse correlation between linguistic and genetic diversity
Authors: Graff Anna , Ringen Erik J. , Zakharko Taras , Stoneking Mark , Shimizu Kentaro K. , Bickel Balthasar , Barbieri Chiara
Published: January 2025

Human population history, as traced by our genome, has shaped the
distribution of languages around the world. While case studies suggest that
population history can also affect specific structures of languages, such as
patterns in their sound systems and grammars, results are conflicting, and it
remains unknown whether such effects hold globally. Here we show that, adjusting
for geography, phylogeny, and environment, genetic diversity is inversely
correlated with diversity in linguistic structures. Low genetic diversity (i.e.
excess homozygosity) results from relative isolation, and this promotes
diversification in language. High genetic diversity results from contact and
migration, and this promotes homogenization in language. These effects are
particularly pronounced in Asia and, under some conditions, also in a few other
areas, suggesting sociocultural factors contributing to differences in how
strongly isolation favors linguistic diversity and how strongly contact promotes
linguistic homogenization. Our results suggest that present-day hotspots of
linguistic diversity, which are characterized by relative isolation, may provide
a privileged window on the dynamics of linguistic evolution as they are less
affected by the vast demographic expansions, migrations, and extinctions that
characterize the Neolithic age.
Recombinant B3 clade enterovirus D68 strains are efficiently rescued in 293T
cells and infect human spinal cord organoids
Authors: Jones Jennifer E. , Maya Sarah , Yovel Gal , Ciomperlik-Patton Jessica , Anstadt Jennifer , Freeman Megan Culler
Published: January 2025

Enterovirus D68 (EV-D68) is associated with respiratory disease in children.
Between 2014 and 2018, biennial EV-D68 outbreaks coincided with peaks of a
polio-like neurologic condition called acute flaccid myelitis (AFM). We
hypothesized that specific mutations within the currently circulating B3 clade
of EV-D68 impacted neurovirulence. However, recovery of these strains from
infectious clones by published methods proved unsuccessful. Therefore, we tested
different cell lines, reagents, and conditions to enhance efficiency of
recombinant (r)EV-D68 rescue. In this study, we present a tractable rescue
system to define virulence determinants in B3 clade strains. Using this
approach, we successfully rescued historic and contemporary rEV-D68 strains to
high titer after limited cell culture passage. All strains in our study
replicated efficiently in the parental RD cell line and in human respiratory
epithelial cell lines, with BEAS-2B cells exhibiting greater permissivity than
A549 cells. While B2 and B3 clade strains could infect the SH-SY5Y neuroblastoma
cell line, the neurovirulent B2 clade strain rUSA/IL/2014-18952 was more
dependent on neuron differentiation than B3 clade strains and replication was
not sustained under multi-cycle growth conditions. Conversely, replication of
rUSA/IL/2014-18952 was more efficient in human spinal cord organoids, which
model the cellular heterogeneity of the spinal cord, while replication of B3
clade strains was more modest. Immunofluorescence staining confirmed infection,
with viral antigen colocalized with neurons. These findings suggest shifting
dynamics of EV-D68 neurovirulence and provide a critical platform for further
assessment of viral determinants of neurovirulence in B3 clade strains.

IMPORTANCE

Enterovirus D68 (EV-D68) can cause acute flaccid myelitis (AFM), a
debilitating neurological condition of the spinal cord in children.
Identifying viral determinants of EV- D68 neuropathogenesis is critical to
understanding recent shifts in AFM prevalence; however, these investigations
are limited to a small subset of infectious clones distantly related to
currently circulating B3 clade strains. In this study, we leverage improved
rescue strategies to characterize recombinant (r)EV-D68 strains from the
dominant B3 clade. While all rEV-D68 replicate efficiently in the parental
cell line and in human respiratory epithelial cells, B3 clade strains
achieved greater titers in cultured neurons than a neurovirulent B2 clade
strain, with less dependence on neuronal differentiation state. All B3 clade
strains established infection in human spinal cord organoids, but
replication varied between strains. Therefore, our study presents a
tractable rescue system to begin to dissect viral determinants of shifting
neurotropism within contemporary EV-D68 clades.
Retinal vascular dysfunction in theMthfr677C>Tmouse model of cerebrovascular disease
Authors: Reagan Alaina M. , MacLean Michael , Cossette Travis L. , Howell Gareth R.
Published: January 2025

Introduction

Investigating retinal biomarkers for Alzheimer’s disease (AD) and related dementias (RD), has increased significantly. We examine retinal vascular health in a mouse containing the ADRD risk variantMthfr677C>Tto determine if changes in retina mirror similar changes in cerebrovasculature.

Methods

Morphology and function of retinal vasculature and neurons were assessed usingin vivoimaging, immunohistochemistry and pattern electroretinography. RNAscope and proteomics were employed to determineMthfrgene expression and differential protein expression in mice carryingMthfr677C>T.

Results

Mice show reduced retinal vascular density and reduced perfusion rate in aging mice, mirroring previously published brain data.Mthfris widely expressed and colocalizes with vascular cell markers. Proteomics identified common molecular signatures across brain and retina.

Discussion

Results demonstrate thatMthfr-dependent vascular phenotypes occur in brain and retina similarly. These data suggest that assessing age and genetic-driven changes within retinal vasculature represents a minimally invasive method to predict AD-related cerebrovascular damage.
Sequestration of SerRS through LLPS Impairs Localized Translation and Contributes to Antibiotic Persistence
Authors: Zhang Ziyin , Li Daqian , Zheng Bo , Liu Jiafeng
Published: January 2025

Antibiotic-tolerant persisters contribute to the emergence of resistance, posing a significant challenge to the efficacy of antibiotic therapies. Despite extensive research, the mechanisms underlying persistence remain inadequately understood. By tracking the evolution of exponential-phase bacterial populations subjected to intermittent high-dose ertapenem exposure, we characterized the evolved strains in terms of tolerance. Mutant strains, harboring mutations in the seryl-tRNA synthetase gene (serS), exhibited abrupt growth arrest upon serine depletion during exponential growth, resembling the persistence phenotype induced by serine hydroxamate (SHX). Under serine starvation, the mutated SerRS protein was sequestrated into liquid-liquid phase separation (LLPS)-driven condensates, disrupting their composition and impairing localized translation. This event precipitated growth arrest and dormancy in theSerSTstrain, triggering persistence. Our findings reveal an unrecognized role for aminoacyl-tRNA synthetases (aaRSs) in modulating bacterial condensates and provide insights into the molecular mechanisms underlying bacterial persistence.

Graphic abstract

SerRS Recruitment Disrupts Localized Translation in DeaD-marked Condensates.

Upon serine starvation, SerRSTpartitions into LLPS-driven DeaD-marked condensates, impairing their localized translation activity and suggesting mechanisms underlying persistence arising during exponential phase. These evolutionarily conserved condensates orchestrate a robust translation program to enable stress responses and instruct cell fate decisions in bacterial populations.
Flaviviruses Hijack HuR to Suppress CNPY3: A Novel Pathway for Immune Evasion and Therapeutic Intervention
Authors: Ding Xiaoyan , He Jiuxiang , Zhao Jing , Zhou Yuxin , Chen Xiaozhong , Tong Jun , Quan Wenxuan , Qiu Minyue , Hua Dong , Liu Minchi , Guan Shan , Li Jintao
Published: January 2025

Flaviviruses represent a serious global health threat, infecting millions annually with high rates of cross-infection among different flaviviruses, yet no broad-spectrum antiviral therapy currently targets these pathogens. Through biological big data analysis, we observed a significant downregulation of Canopy FGF Signaling Regulator 3 (CNPY3), a positive regulator of defense responses, in flavivirus-infected patients, with the level of downregulation correlating with infection severity. This observation was validated in cellular and animal models. Mechanistically, we demonstrate that flaviviruses hijack the RNA-binding protein Human antigen R (HuR) to destabilize CNPY3 mRNA via adenine-uridine-rich elements (AREs), thus downregulating CNPY3 expression and promoting viral replication. Our findings identify CNPY3 as a novel antiviral mediator essential for the TLR-mediated type I interferon (IFN-I) pathway in defense against flaviviruses. In vitro, CNPY3 overexpression reduced DENV and ZIKV replication, confirming its antiviral role. To explore therapeutic potential, we developed lipid nanoparticles (LNPs) encapsulating CNPY3 mRNA (LNP-CNPY3), and early administration in flavivirus-infected mice improved survival, reduced viral loads, and attenuated neuroinflammation by enhancing antiviral and interferon responses. Together, these findings establish CNPY3 as a critical antiviral target and support LNP-CNPY3 as a promising therapeutic approach against flavivirus infections.
Efficient searches in protein sequence space through AI-driven iterative learning
Authors: Suarez-Martin Ignacio , Risso Valeria A. , Romero-Zaliz Rocío , Sanchez-Ruiz Jose M.
Published: January 2025

Protein sequence space is vast. This fact, together with the prevalence of epistasis, hampers the engineering of novel enzymes through library screening and is a major obstacle to any attempt to predict natural protein evolution. Recently, specialized methodologies have been used to determine fitness data on ∼260000 sequences for the gene of the enzyme dihydrofolate reductase and antibody affinity data for all combinations of the mutations present in the receptor binding domain (RBD) of the Omicron strain of SARS-CoV-2 (∼30000 variants). We show that, upon iterative training on a total of just a few hundred variants, various state-of-the-art AI tools (multi-layer perceptron, random forest and XGBoost algorithms) find very high fitness variants of the enzyme and predict the antibody-evasion patterns of the RBD. This work provides a basis for efficient, widely applicable, low-throughput experimental approaches to assess viral protein evolution and to engineer enzymes for biotechnological applications.
Non-nucleosomal (CENP-A/H4)2- DNA complexes as a possible platform for centromere organization
Authors: Ali-Ahmad Ahmad , Mors Mira , Carrer Manuel , Li Xinmeng , Bilokapić Silvija , Halić Mario , Cascella Michele , Sekulić Nikolina
Published: January 2025

The centromere is a part of the chromosome that is essential for the even segregation of duplicated chromosomes during cell division. It is epigenetically defined by the presence of the histone H3 variant CENP-A. CENP-A associates specifically with a group of 16 proteins that form the centromere-associated network of proteins (CCAN). In mitosis, the kinetochore forms on the CCAN to connect the duplicated chromosomes to the microtubules protruding from the cell poles. Previous studies have shown that CENP-A replaces H3 in nucleosomes, and recently the structures of CENP-A-containing nucleosomes in complex with CCANs have been revealed, but they show only a limited interaction between CCANs and CENP-A. Here, we report the cryoEM structure of 2x(CENP-A/H4)2-di-tetramers assembled on DNA in the absence of H2A/H2B histone dimer and speculate how (CENP-A/H4)2-tetramers and -di-tetramers might serve as a platform for CCAN organization.

Main points

CENP-A/H4 in the absence of H2A/H2B dimers associate on DNA to form di-tetrasomes

CENP-A/H4 di-tetrasomes are stable but highly flexible structures resembling nucleosomes

CENP-A/H4 tetrasomes bind CENP-N/L and can serve as platform for centromere organisation
A third type of PETase from the marineHalopseudomonaslineage
Authors: Turak Onur , Gagsteiger Andreas , Upadhyay Ashank , Kriegel Mark , Salein Peter , Agarwal Seema , Borchert Erik , Höcker Birte
Published: January 2025

The enzymatic degradation of polyethylene terephthalate (PET) offers a sustainable solution for PET recycling. Over the past two decades, more than 100 PETases have been characterized, primarily exhibiting similar sequences and structures. Here, we report new PET-degrading α/β hydrolases, includingHaloPETase1 from the marineHalopseudomonaslineage, thereby extending the narrow sequence space by novel features at the active site. The crystal structure ofHaloPETase1 was determined to a resolution of 1.16 Å, revealing a unique active site architecture and a lack of the canonical π-stacking clamp found in PETases so far. Further, variations in active site composition and loop structures were observed. Additionally, we found five more enzymes from the same lineage, two of which have a high similarity to type IIa bacterial PETases, while the other three resembleHaloPETase1. All these enzymes exhibited high salt tolerance ranging from 2.5 to 5 M NaCl leading to higher total product releases upon PET degradation at 40 or 50 °C. Based on these findings, we propose an extension of the existing PETase classification system to include type III PETases.
Persistent virulent phages exist in bacterial isolates
Authors: Dougherty Peter Erdmann , Bernard Charles , Carstens Alexander Byth , Stanford Kim , McAllister Tim A. , Rocha Eduardo P. C. , Hansen Lars Hestbjerg
Published: January 2025

Despite the immense diversity of tailed bacteriophages, they are traditionally classified as either virulent or temperate, with only the latter thought capable of long-term persistence in bacterial cells through lysogeny. Virulent phages, characterized by their obligatory lytic cycle, are assumed to lack the ability to persist within bacterial colonies, and their infection is expected to decimate the host population underin-vitroconditions. Consequently, when bacterial isolates are cultured for sequencing, the resulting assemblies are not expected to contain virulent phage genomes. To test this assumption on a large scale, we analyzed over 267,000 publicly availableEscherichiaassemblies. Surprisingly, we identified 373 genomes corresponding to virulent phages within the bacterial genomes. These viral genomes are associated with specific phage groups and especially with jumbo phages with very large genomes (>200 kb). Chimallin was a core gene in two of these jumbo phage clusters, the major protein used by some jumbo phages to form a protective phage nucleus during infection. We found multiple lines of evidence suggesting that these virulent phage genomes in bacterial assemblies arise from persistent infections rather than contamination. Supporting this, we experimentally demonstrated the coexistence of non-temperate jumbo phages with their bacterial hosts. In a targeted follow-up search for three clades of persistent jumbo phages, we identified 285 additional jumbo phage genomes in bacterial taxa beyondEscherichia,highlighting that there are many more undiscovered persistent phages in bacterial assemblies. Our findings challenge the traditional virulent-temperate dichotomy, highlighting the overlooked diversity and prevalence of non-canonical phage lifestyles.
Protection of photosynthesis by UVR8 and cryptochromes in Arabidopsis under blue and UV radiation
Authors: Morales Luis Orlando , Shapiguzov Alexey , Rai Neha , Aphalo Pedro José , Brosché Mikael
Published: January 2025

Photosynthesis in plants is negatively affected by high light intensity and UV radiation. The photoreceptors UV RESISTANCE LOCUS 8 (UVR8) and CRYPTOCHROMES (CRYs) mediate perception and acclimation of plants to UV-B/UV-A2 (290–340 nm) and UV-A1/blue light (350–500 nm), respectively. However, their roles in photoprotection of photosynthesis across different wavebands of the spectrum remain unclear. Using chlorophyll fluorescence and LED lighting we studied the roles of UVR8 and CRYs in maintaining photosynthetic capacity in Arabidopsis exposed to UV-B, UV-A1, and blue light. Analysis of quantum yield of Photosystem II, non-photochemical quenching, and LHCII phosphorylation demonstrated that CRYs preserve photosynthetic performance in plants exposed to UV-B, UV-A1, and blue light. UVR8 and CRYs exhibit partially redundant functions in maintaining photosynthetic activity under UV-B, UV-A1, and blue light, and in preventing photodamage under high UV-A1 irradiance. Impaired UVR8 and CRY signaling reduced epidermal flavonol accumulation in leaves, which further compromised photoprotection. These findings provide valuable insights into how UV and blue light perception contribute to photoprotection, with broad implications for plant performance both in natural and managed environments.
Mechanisms of chromatin remodeling by an Snf2-type ATPase
Authors: Malik Deepshikha , Deshmukh Ashish , Bilokapic Silvija , Halic Mario
Published: January 2025

Chromatin remodeling enzymes play a crucial role in the organization of chromatin, enabling both stability and plasticity of genome regulation. These enzymes use a Snf2-type ATPase motor to move nucleosomes, but how they translocate DNA around the histone octamer is unclear. Here we use cryo-EM to visualize the continuous motion of nucleosomal DNA induced by human chromatin remodeler SNF2H, an ISWI family member. Our work reveals conformational changes in SNF2H, DNA and histones during nucleosome sliding and provides the structural basis for DNA translocation. ATP hydrolysis induces conformational changes in SNF2H that pull the DNA tracking strand, distorting DNA and histones at SHL2. This is followed by SNF2H rotation on the nucleosome, which first pulls the DNA guide strand and creates one-base pair bulge at SHL2, and then releases the pulled DNA. Given the high conservation of the catalytic motors among ATP-dependent chromatin remodelers, the mechanisms we describe likely apply to other families.
Transcription Machinery Anchors ecDNAs to Mitotic Chromosomes for Segregation
Authors: Xie Yipeng , Lim Jun Yi Stanley , Liu Wenyue , Gilbreath Collin , Kim Yoon Jung , Wu Sihan
Published: January 2025

Extrachromosomal DNA (ecDNA) is a prevalent driver of cancer, whose random segregation promotes aggressive tumors. Acentric ecDNAs attach to chromosomes during mitosis for segregation. However, the molecular mechanism governing ecDNA-chromosome mitotic interactions remains poorly understood. This study shows that ecDNAs attach to histone 3 lysine 27 acetylation (H3K27ac)-marked chromatin during mitosis. H3K27ac depletion resulted in ecDNA detachment from mitotic chromosomes. Diverse bromodomain proteins, which are known readers of H3K27ac, stabilize ecDNAs’ mitotic interaction, exhibiting context-dependent and mutually complementary roles. Furthermore, disruptions of the Mediator complex and RNA polymerase II transcription activity both dissociate ecDNAs from mitotic chromosomes, suggesting that the transcription machinery mediates ecDNA segregation. Mis-segregated ecDNAs were expelled into the cytosol and degraded, leading to diminished oncogene expression and a reversal of therapy resistance. Our research provides new insights into the interplay between RNA transcription and acentric ecDNA inheritance in cancer, offering a novel avenue for disrupting ecDNA-driven oncogenesis.
LIN-67 functionally interacts with heterochronic miRNAs and regulates developmental timing inCaenorhabditis elegans
Authors: Medley Jeffrey C. , Perales Roberto , Humada Belén Gaete , Doerfel Katja , Levine Ariana , Panzade Ganesh , Hammell Christopher M. , Zinovyeva Anna
Published: January 2025

Temporal regulation of gene expression is required for developmental transitions, including differentiation, proliferation, and morphogenesis. In the nematodeCaenorhabditis elegans, heterochronic microRNAs (miRNAs) regulate the temporal expression of genes that promote animal development. The heterochronic miRNAs lin-4 and let-7 are required during different stages of larval development and are associated with the miRNA-specific Argonaute ALG-1. In this study, we have identifiedlin-67as a heterochronic gene that negatively regulateslin-4,let-7,andalg-1. Loss oflin-67function restores proper developmental timing and stage-specific gene expression to hypomorphiclin-4andlet-7mutants. We found that loss oflin-67resulted in a reduced number of seam cells, defects in alae formation, precocious expression of an adult-specific gene reporter, and sterility. LIN-67 contains a K homology (KH) RNA-binding domain and is a homolog of the Sam68-like splicing factor KHDRBS2. We show that LIN-67 localizes to the nucleus throughout animal development and is enriched in nuclear foci. Mutating the KH domain of LIN-67 abolished the nuclear localization of LIN-67, suggesting that the localization of LIN-67 is likely dependent on RNA-binding activity. We show that LIN-67 negatively regulateslin-4miRNA levels and restores normal levels oflet-7toalg-1mutants, which can, at least in part, explain howlin-67suppressesalg-1. Our data indicate thatlin-67is a novel heterochronic gene that regulates developmental timing and miRNA-dependent gene regulation inC. elegans.
SSARP: An R Package for Easily Creating Species- and Speciation- Area Relationships Using Web Databases
Authors: Martinet Kristen M. , Román-Palacios Cristian , Harmon Luke J.
Published: January 2025

A universal method of quantifying patterns of biodiversity on islands is the species-area relationship (SAR). SARs visualize the relationship between species richness (the number of species) and the area of the land mass on which they live. An extension of this visualization, the speciation-area relationship (SpAR), helps researchers determine trends in speciation rate over a set of land masses. Comparing these relationships across island systems globally is an extremely difficult task because gathering and processing a large amount of species occurrence data and island data often requires researchers to conduct lengthy literature searches and combine datasets from several different sources. Here we presentSSARP(Species/Speciation-Area Relationship Projector), an R package that provides a simple workflow for creating SARs and SpARs. TheSSARPworkflow allows users to gather occurrence data from GBIF, use mapping tools to determine whether the GPS points in the occurrence data refer to valid land masses, associate those land masses with their areas using a built-in dataset of island names and areas, and create SARs using linear and segmented regression.SSARPalso provides multiple functions for estimating speciation rates for use in creating a SpAR. UsingSSARPallows researchers to dramatically increase the scope of their biodiversity research through the creation of SARs and SpARs with data from island systems across the globe.
Identification and characterization of shifted G•U wobble pairs resulting from alternative protonation of RNA
Authors: Saon Md. Sharear , Douds Catherine A. , Veenis Andrew J. , Pearson Ashley N. , Yennawar Neela H. , Bevilacqua Philip C.
Published: January 2025

RNA can serve as an enzyme, small molecule sensor, and vaccine, and it may have been a conduit for the origin of life. Despite these profound functions, RNA is thought to have quite limited molecular diversity. A pressing question, therefore, is whether RNA can adopt novel molecular states that enhance its function. Covalent modifications of RNA have been demonstrated to augment biological function, but much less is known about non-covalent alterations such as novel protonated or tautomeric forms. Conventionally, a G•U wobble has the U shifted into the major groove. We used a cheminformatic approach to identify four structural families of shifted G•U wobbles in which the G instead resides in the major groove of RNA, which requires alternative tautomeric states of either base, or an anionic state of the U. We provide experimental support for these shifted G•U wobbles via the potent, and unconventional,in vivoreactivity of the U with dimethylsulfate (DMS) in three organisms. These shifted wobbles may play important functional roles and could serve as drug targets. Our cheminformatics approach is general and can be applied to identify alternative protonation states in other RNA motifs, as well as in DNA and proteins.

Graphical Abstract
Conformational dynamics and multi-modal interaction of Paxillin with the Focal Adhesion Targeting Domain
Authors: Bhattacharya Supriyo , He Yanan , Chen Yihong , Mohanty Atish , Grishaev Alexander , Kulkarni Prakash , Salgia Ravi , Orban John
Published: January 2025

Paxillin (PXN) and focal adhesion kinase (FAK) are two major components of the focal adhesion complex, a multiprotein structure linking the intracellular cytoskeleton to the cell exterior. PXN interacts directly with the C-terminal targeting domain of FAK (FAT) via its intrinsically disordered N-terminal domain. This interaction is necessary and sufficient for localizing FAK to focal adhesions. Furthermore, PXN serves as a platform for recruiting other proteins that together control the dynamic changes needed for cell migration and survival. Here, we show that the PXN disordered region undergoes large-scale conformational restriction upon binding to FAT, forming a 48-kDa multi-modal complex consisting of four major interconverting states. Although the complex is flexible, each state has unique sets of contacts involving disordered regions that are both highly represented in ensembles and conserved. Moreover, conserved intramolecular contacts from glutamine-rich regions in PXN contribute to high entropy and thus stability of the FAT bound complex. As PXN is a hub protein, the results provide a structural basis for understanding how perturbations that lead to cellular network rewiring, such as ligand binding and phosphorylation, may lead to shifts in the multi-state equilibrium and phenotypic switching.
The role of MYB46 in modulating polysaccharide acetylation by mediating the transcriptional regulation of cell wall-related genes in Arabidopsis
Authors: Rastogi Lavi , Deshpande Sanjay , Pawar Prashant Anupama-Mohan
Published: January 2025

Understanding the mechanism behind the transcriptional regulation of polysaccharideO-acetylation remains a key challenge that might be regulated through transcription factors. Our earlier work revealed the upregulation ofAtGELP7 in MYB46 overexpression lines, prompting us to investigate how MYB46 transcriptionally controlsAtGELP7 including other cell wall acetylation pathway genes in Arabidopsis. In MYB46 overexpression lines, we observed alteration in acetylation levels on xylan, xyloglucan and pectin in different tissue types, which suggests complex and tight regulation of acetylation homeostasis in the cell wall. Further, our transcriptomic data revealed the simultaneous upregulation of bothAtGELP7 (acetyl xylan esterase) and xylan-specific TBLs (xylanO-acetyltransferases) indicating sophisticated regulation of cell wall acetylation homeostasis. Using transactivation studies in Nicotiana andpAtGELP7::GUSstable lines, we found that MYB46 enhancesAtGELP7 expression probably through downstream regulators which could be either MYB103 or other MYBs. In addition, extensive cell wall analysis of MYB46 overexpression lines showed differential sugar distribution, preferably to major cell wall components such as cellulose, xyloglucan, and xylan across different tissue types of different developmental stages. Moreover, the integration of RNA-sequencing and ChIP-sequencing data uncovered previously unknown, novel probable direct gene targets of MYB46 that may be involved in polysaccharide acetylation and cell wall remodeling.
GPNMB is a biomarker for lysosomal dysfunction and is secreted via LRRK2-modulated lysosomal exocytosis
Authors: Bogacki Erin C. , Longmore George , Lewis Patrick A. , Herbst Susanne
Published: January 2025

Genome-wide association studies have identifiedGlycoprotein Nmb(GPNMB) as a risk factor for Parkinson’s Disease. The risk allele increasesGPNMBtranscription and GPNMB protein levels in the CSF highlighting GPMNB as a potential biomarker for Parkinson’s Disease. However, a lack of knowledge of GPNMB’s function and mechanism of secretion have hindered an interpretation of secreted GPNMB levels. In this study, we assessed the mechanism of GPNMB secretion by macrophages, the primary cell type expressing GPNMB in the brain. We show that GPNMB is secreted in response to lysosomal stress via lysosomal exocytosis and highlight the Parkinson’s Disease risk factor LRRK2 as a strong modulator of GPNMB secretion.