bluuebunny/crossref_metadata_2025 huggingface dataset:
Caring Readiness Among Parents of Children Who Have Undergone Liver Transplantation and Are Transitioning From the Intensive Care Unit: A Cross‐Sectional Study
Authors: Wu Jingyun , Lu Fangyan , Li Zhiru , Dai Yanhong , Wang Yan , Zheng Li , Bao Ruijie , Rao Yuxin , Wang Huafen
Published: February 2025

Objective

To investigate the status and influencing factors of caring readiness among parents of children undergoing liver transplantation transitioning from the intensive care unit, and to explore the associations between caring readiness and other variables.

Design

A cross‐sectional study.

Methods

A total of 126 parents of children who underwent liver transplantation at a tertiary hospital in China took a questionnaire survey via convenience sampling. Independent t‐test, ANOVA and correlation analysis were conducted to analyse the data. Multivariable stepwise linear regression was used to analyse the influencing factors of caring readiness. The PROCESS macro (Model 4) was used to verify the mediating effect of caregiver burden between social support and caring readiness.

Reporting Method

The STROBE checklist was used as a guideline in this study.

Results

The mean score of caring readiness among parents of children who had undergone liver transplantation and were transitioning from the intensive care unit was 23.62 ± 5.34. Multivariable stepwise linear regression analysis indicated that experience with caregiving, intensive care unit length of stay, social support and caregiver burden were the factors associated with caring readiness, explaining 18.6% of the variance in caring readiness among parents. Caregiver burden partially moderated the relationship between social support and caring readiness (20.93%).

Conclusion

The study shows caring readiness was moderate among parents of children who have undergone liver transplantation and are transitioning from the intensive care unit. It reveals that lack of caregiving experience and children's short intensive care unit length of stay should be emphasised, preventing inadequate readiness of parents. Furthermore, enhancing social support interventions and burden‐reduction strategies are important for improving parents' caring readiness.

Implications for the Profession and/or Patient Care

The findings demonstrate that health care professionals should provide timely and appropriate intervention strategies to enhance parents' caring readiness, which could potentially be achieved by increasing social support and reducing caregiver burden.

Patient or Public Contribution

Parents of children who underwent liver transplantation participated in this study via a questionnaire survey.
Prognostic Value of Ki‐67 in the Invasive Zone of Oral Squamous Cell Carcinoma
Authors: Li Ke , Wang Shuai , Li Zihui , Yu Qiuya , Liu Lingyun , Li Fuyan , Zhang Lei , Sun Guowen , Ni Yanhong
Published: February 2025

Background

The molecular profile of cells within the tumor invasive zone, where tumor cells interact with surrounding non‐tumor cells, plays a crucial role in defining tumor malignant characteristics, such as the pattern of invasion (POI). Therefore, evaluating the diagnostic value of the proliferation index molecule, Ki‐67, in both tumor cells and adjacent non‐tumor cells at the invasive zone with different POIs, holds significant clinical importance for oral squamous cell carcinoma (OSCC).

Methods

This retrospective study included 133 primary OSCC samples, and the spatial pattern of Ki‐67 in the tumor invasive zone was analyzed by immunohistochemistry (IHC). The prognostic value of tumor cells and stroma proliferative capacity in different POIs were assessed.

Results

Ki‐67 was widely expressed in tumor cells and stroma cells within the invasive zone, and cells in high‐invasiveness POIs exhibit higher proliferation. Elevated Ki‐67 expression in tumor cells was associated with poor overall survival (OS) and disease‐free survival (DFS) in patients, which is independent of POIs. In our study, we identified the expression level of Ki‐67 in tumor cells across high‐invasiveness POIs as an independent risk factor for OS and DFS in OSCC patiens. Additionally, Ki‐67 expression in surrounding non‐tumor cells did not significantly correlate with patient survival.

Conclusion

The remarkable proliferation characteristic of tumor cells in high‐invasiveness POIs of OSCC tumors plays a crucial role in the prognosis of patients.
Capturing Inter and Intra Sectoral Productivity Spillovers in Industrial Filière: A System of Dynamic Spatial Panel Data Models
Authors: Emili Silvia , Galli Federica
Published: February 2025

Given the relevance of spatial and sectoral interactions in shaping the productivity performance of economic systems and filières, in this study, we suggest addressing both aspects by estimating a system of simultaneous dynamic spatial panel data models. This approach allows to consider how the production level of a specific sector is influenced by the performance of other interconnected sectors in the same area (cross‐sectoral spillovers) as well as the role of productivity spillovers originating from the same or other sectors in neighbouring territories (inter and intra sectoral spatial effects). The validity of the proposed approach is confirmed through the estimation of a simultaneous system for the production process of the Italian agribusiness filière. The results indicate the existence of meaningful inter‐dependences within and between sectors and territories that materialises in spillovers of different natures (input factors, internal and external features), offering valuable policy implications for the overall economic growth of the agriculture filière.
Characterisation of nocturnal arrhythmia avalanche dynamics: Insights from generalised linear model analysis
Authors: Shahrbabaki Sobhan Salari , Strong Campbell , Chapman Darius , Tonchev Ivaylo , Jenkins Evan , Lechat Bastien , Nguyen Duc Phuc , Mittinty Murthy , Catcheside Peter , Eckert Danny J. , Baumert Mathias , Ganesan Anand N.
Published: February 2025

Nocturnal arrhythmia avalanche (NAA) episodes, characterised by transient non‐sustained cardiac arrhythmias during sleep, have been demonstrated as a predictor of adverse cardiovascular events. However, their dynamics and association with sleep architecture and events remain unclear. While generalised linear models (GLM) have captured sleep‐disordered breathing (SDB) dynamics, their application to NAA remains underexplored. This study explored whether changes in sleep architecture contribute to nocturnal arrhythmias and if the impact of sleep stages, SDB, and arousal events on these arrhythmias varies by demographic factors. We analysed 7341 ECG recordings from the multi‐ethnic study of atherosclerosis (MESA) and the sleep heart health study (SHHS) datasets. R‐R intervals were divided into 10‐min periods to detect NAA, defined as a 30% drop from baseline followed by recovery to 90% of baseline. A GLM framework was developed to characterise NAA episodes as functions of SDB, sleep arousal events, sleep stages, and prior NAA episodes. The GLM analysis revealed that NAA occurrence was 18% and 30% higher during non‐rapid eye movement (NREM) light sleep compared with deep sleep in SHHS (p < 0.001) and MESA (p < 0.001), respectively. SDB events increased the NAA risk in 34% of participants, and arousals in 29%. In SHHS, the impact of SDB on NAA was 5% greater in men (p = 0.018), while the arousal effects were more pronounced in those over 75, highlighting the role of demographic factors in modulating arrhythmia risk. These findings demonstrate the utility of the GLM framework in modelling the dynamics of nocturnal arrhythmias and their associations with sleep disruptions and architecture.
Conservation Blind Spots: Scenarios for Assessing the Exposure Risk of Brazilian Mammals to Pesticides
Authors: Gomes‐de‐Sá Érica Fernanda Gonçalves , Ferreira Gabriela Fernanda da Silva , de Albuquerque Anna Carolina Figueiredo , Costa Vinícius Araújo , Concone Henrique Villas Boas , de Freitas Natan Diego Alves , Beltrão Mayara Guimarães , da Rocha Patrício Adriano , Cordeiro‐Estrela Pedro
Published: February 2025

Brazil is a large agricultural producer and a megadiverse country. In this context, the use of pesticides poses risks to non‐target species, including wild mammals.

Environmental Risk Assessment (ERA) for pesticides has been adopted by the European Food Safety Authority (EFSA) and the United States Environmental Protection Agency (EPA). Brazil has yet to present a pesticide risk assessment for vertebrates.

To design an ERA for Brazilian mammals, data is needed on the occurrence and distribution of species within and outside crops and agroecosystem types, their biological characteristics and life history traits.

We analyse a comprehensive dataset of mammal occurrences in Brazilian agroecosystems. We identify the main crops studied, review if pesticides were listed as threats for mammals endangered of extinction and discuss mammal traits that lead to pesticide exposure across agroecosystems.

We show that 54% of terrestrial mammals in Brazil occur in agroecosystems (319/716), with 64.3% (205/319) of these found in crop. Most studies registered mammals in large‐scale monocultures, such as annual croplands, tree plantations and pasture grazing. Small farming emerges as an important knowledge gap. We found 25 species threatened with extinction (Critically Endangered, Endangered, and Vulnerable) occurring in crop in Brazilian agroecosystems.

Concerning ERA for Brazilian agricultural scenarios, in the screening tier process, it is suggested to use an indicator model species (IMS) with the following traits: terrestrial, crepuscular, and large body mass for pasture‐grazing, tree plantations and annual croplands. Conversely, in agroforestry and perennial crop agroecosystems, we recommend considering at least one IMS with arboreal habits and a frugivorous and/or nectarivorous diet. Furthermore, in Tier 1, we recommend that a generic model species (GMS) emconpassing carnivorous and herbivorous mammals should be considered in pasture‐grazing systems, tree plantations and annual cropland. In agroforests and perennial croplands, GMS that represent the diet of frugivorous and nectarivorous mammals should be prioritised.
Development of the Team Evaluation and Assessment Measure Quality Improvement (TEAM‐QI) and Proof‐Of‐Concept Testing in Maternity Teams
Authors: Beck Sarah , Harris Jenny , Green James , Lamb Benjamin W. , Aref‐Adib Mehrnoosh , Bick Debra , Taylor Cath
Published: February 2025

Poor teamwork is often implicated in serious healthcare delivery failings, leading to calls for effective team improvement interventions. Taking a complex, adaptive systems perspective, we adapted an oncology team quality improvement program to make it appropriate for other areas of clinical care. Study phases included: (1) meetings with National Health Service, policy and service user representatives (n = 19), a rapid review of existing maternity teamwork interventions, and mapping of the proposed program content to an evidence‐based model of team effectiveness; (2) feasibility and acceptability testing of the team questionnaire component, and content analysis of free‐text responses with four maternity teams within two NHS Trusts (n = 26). Meetings with representatives highlighted the importance of non‐punitive, continuous team‐led assessment, and the ability to compare performance to similar teams while enabling adaptability to different team types. Program content mapped well to known components of team effectiveness. Internal consistency of the questionnaire was acceptable (Cronbach alpha = 0.79–0.92). Most team members (76.9%) reported benefits in identifying priorities for improvement. Preliminary proof of concept was supported but larger‐scale evaluation including testing in other clinical areas is warranted.
Exploring Psychological Factors and Brain Alterations in Functional Anorectal Pain Patients: Insights From Multimodal Magnetic Resonance Imaging Investigations
Authors: Wan Yu , Sun Churan , Fan Mingfeng , Yu Hao , Xu Juan , Zhang Kai , Ji Shanling , Yu Hao , Liu Chuanxin , Zhou Cong , Wang Shuai
Published: February 2025

Background

Functional anorectal pain (FAP) is classified as one of the disorders of gut‐brain interaction (DGBI). It involves the impairments of anorectal afferents and disrupted gut‐brain communication. However, neuroimaging studies focused on FAP are lacking.

Methods

A total of 25 FAP patients and 18 healthy controls (HC) underwent structural magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), resting‐state functional MRI (rs‐fMRI) scans, and collection of demographic data, mental health assessment scales and pain assessment questionnaires. Voxel‐based morphometry (VBM), tract‐based spatial statistics (TBSS), regional homogeneity (ReHo), and amplitude of low‐frequency fluctuations (ALFF) were utilized to analyze the imaging data. Correlation analyses were conducted to explore the relationships between the neuroimaging findings and clinical symptoms.

Key Results

Functional anorectal pain (FAP) patients exhibited higher levels of anxiety, depression scores and lower sleep quality compared to HC. VBM analysis revealed increased gray matter volume (GMV) in the bilateral fusiform, right parahippocampal, bilateral inferior temporal gyrus (ITG), and decreased GMV in the right superior frontal gyrus (SFG), left middle frontal gyrus (MFG), bilateral inferior frontal gyrus (IFG), left Calcarine, bilateral middle occipital gyrus (MOG), left middle temporal gyrus (MTG) in FAP patients. TBSS analysis showed decreased fractional anisotropy (FA) in the superior longitudinal fasciculus (SLF), anterior thalamic radiation (ATR), and forceps minor in the FAP patients. Additionally, increased ALFF in the right cerebellum and increased ReHo in the right MFG were observed in the FAP patients.

Conclusions and Inferences

These findings showed a worse psychological condition and suggested neuroanatomical and neurofunctional alterations associated with pain processing, emotion regulation, and cognitive control in FAP patients.
Weight stigma in the preconception, pregnancy, and postpartum periods: A systematic review of women's perspectives
Authors: Dever Michelle , Skouteris Helen , Incollingo Rodriguez Angela C. , Hailu Haimanot , Galvin Emma , Hill Briony
Published: February 2025

Weight stigma presents a significant challenge for women throughout the preconception, pregnancy, and postpartum (PPP) periods, manifesting in multiple areas of life, including interpersonal relationships, healthcare settings, and broader social contexts. This systematic review investigates weight stigma in women across their reproductive years, examining its impact, and exploring the socioecological factors that contribute to its persistence. We searched Medline, PsycINFO, Embase, Maternity and Infant Care (MIDIRS), and Global Health for peer‐reviewed articles published since 2010. Of the 3486 records identified, 38 were included in a narrative synthesis. Inductive thematic analysis was used to explore women's personal experiences of weight stigma. We then applied a socioecological lens to examine the interrelationships between individual, interpersonal, organizational, and societal factors contributing to weight stigma. Five overarching themes were identified: (1) the impact of weight stigma on PPP women; (2) weight stigma experiences across the socioecological contexts; (3) coping strategies; (4) women's voices as a call to action; and (5) interrelationships of weight stigma contexts. Our findings provide critical insights into the multifaceted nature of weight stigma, highlighting the need for future research, and the development of practical strategies that prioritize women's perspectives, and challenge harmful societal norms for positive change.
An alternative splicing caused by a natural variation in BnaC02.VTE4 gene affects vitamin E and glucosinolate content in rapeseed (Brassica napus L.)
Authors: Wang Furong , Kuang Lieqiong , Xiao Zelin , Tian Ze , Wang Xinfa , Wang Hanzhong , Dun Xiaoling
Published: February 2025

Vitamin E (VE) is essential for plants and animals. Rapeseed oil is rich in α‐tocopherol (α‐T), which is the most bioactive form of VE in human body. This study demonstrated that VE in rapeseed seeds was mainly controlled by embryo genotype through incomplete diallel hybridization. By genome‐wide association study, the QTL‐qVE.C02 associated with VE and α‐T contents was detected in a Brassica napus association population, and the phenotypic contribution rate was up to 18.71%. BnaC02.VTE4, encoding gama‐tocopherol methyltransferase, was proved as the target gene of qVE.C02 by genetic complementation. Two BnaC02.VTE4 haplotypes were identified in the population. Compared with BnaC02.VTE4HapH, a point mutation from A to G at the 3′ splicing site of the second intron were found in BnaC02.VTE4HapL, resulting in alternative splicing and early termination of translation. HapL1052(G‐A), the site‐directed mutagenesis fragment of BnaC02.VTE4HapL, was introduced into Arabidopsis vte4 mutant and 8S088 (a BnaC02.VTE4HapL accession), and the contents of VE and α‐T in atvte4‐4 and 8S088 seeds were increased by 90.10% to 307.29%. These demonstrated the point mutation as the causal for the difference in VE biosynthesis in rapeseed. Further, this variation also led to the significant difference in glucosinolate content between BnaC02.VTE4HapH and BnaC02.VTE4HapL accessions. Multi‐omics analysis suggested that the expression of some genes and the accumulation of several metabolites related to the glucosinolate biosynthesis pathway were significantly increased in BnaC02.VTE4HapL group. Moreover, by functional marker identification, the BnaC02.VTE4HapH was found to be selected during domestication. Our findings offered promising opportunities for enhancing rapeseed quality traits.
Aortic Root Dilatation in Children With End‐Stage Kidney Disease on Regular Hemodialysis and After Kidney Transplantation
Authors: Fadel Fatina I. , Salah Doaa M. , Elnaggar Hend A. , Abdel Wahed Ahmed , Eryan Eman F.
Published: February 2025

Background

Cardiovascular disease (CVD) is the major cause of mortality in end‐stage kidney disease (ESKD) patients. Aortic root dilatation (ARD) was recently recognized as a cardiovascular (CV) sequela in these patients. This study aims to evaluate the prevalence, risk factors, and progression of ARD in children with ESKD on regular hemodialysis (HD) and after kidney transplantation (KT).

Methods

Seventy children in HD (HD group) and 80 pediatric kidney transplant recipients (KTR) (KT group) were included. The echocardiographic assessment was done twice at intervals of more than 6 months (6–14 months) except for 3 patients who died before the second assessment.

Results

ARD's overall prevalence was higher in HD than in KT groups (71.4% and 40%). ARD was more prominent in patients with increased duration of ESKD, EDW, normalized IDWG%, and normalized UF vol%. In the KTR group, underweight was more prevalent among the ARD group than the non‐ARD group. Patients with ARD had higher BP than patients without ARD. Most of the patients with ARD were on classic triple immunosuppressive therapy. ARD patients of both groups had lower HB, higher PLTS, Ph, Ca × Ph levels, and lower e‐GFR than non‐ARD patients.

Conclusion

ARD is prevalent among ESKD children, with furthermore prevalence in HD than in KT patients. Younger age, lower BMI Z‐scores, hypertension (HTN), and increased Ca × Ph are risk factors for ARD. Aortic root measures and ARD frequency decrease on ≥ 6‐month follow‐up of patients.
Social Movements, Public Policy, and Informal Institutions: The Role of Patronage in Chile (2006–2022)
Authors: Barozet Emmanuelle , Espinoza Vicente , Moya Emilio
Published: February 2025

The article analyzes how mobilization and public policy meet and shape one another in Chile over almost two decades, characterized by an intensive cycle of collective action (2006–2022). By examining the interrelationship between mobilization and public policy, we argue that patronage is the glue that binds the two issues. Using descriptive data from the Conflict Observatory of the Center for Social Cohesion and Conflict Studies, as well as secondary information produced by state agencies in Chile and primary information comprising fieldwork conducted in six regions between 2003 and 2021, we show that until 2019, patronage channeled and attenuated social conflict in specific areas, enabling the rapid delivery of social benefits and jobs that public policies should transparently manage but do not.
Endogenous H2S promotes Arabidopsis flowering through the regulation of GA20ox4 in the gibberellin pathway
Authors: Xuan Lijuan , Tian Yongke , Chen Xiaoyan , Gao Le , Wang Meng , Wu Haijun
Published: February 2025

Flowering time is a critical determinant of plant reproductive success and agricultural yield. Hydrogen sulfide (H₂S), as a signaling molecule, regulates various aspects of plant growth and development. In this study, we examined the role of endogenous H₂S in regulating flowering time in Arabidopsis. The O‐acetylserine thiol lyase a1 (oasa1) mutant, which has elevated H₂S levels due to impaired OASA1 activity that catalyzes the synthesis of Cys from H2S, flowers earlier than wild type (WT). The OASA1 overexpression lines (OE‐OASA1‐#33/#142), characterized by reduced H₂S levels, show delayed flowering, accompanied by decreased expression of key flowering regulators, FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), and AGAMOUS‐LIKE24 (AGL24). Notably, vernalization and short‐day (SD) conditions did not affect their flowering patterns. Exogenous H₂S and GA₃ treatment rescued the delayed flowering phenotype of OE‐OASA1‐#33/#142. In oasa1, levels of GA intermediates (GA15 and GA53) were elevated, while their levels were reduced in OE‐OASA1‐#33/#142. RT‐qPCR analysis showed a significant reduction in the expression of GIBBERELLIN 20‐OXIDASE 4 (GA20ox4) in OE‐OASA1‐#33/#142 compared to WT. Overexpression of GA20ox4 (OE‐GA20ox4‐#20/#30) resulted in earlier flowering and partially rescued the delayed flowering phenotype of OE‐OASA1‐#33/#142. Additionally, the expression of age pathway‐related genes, including miRNA172b and SQUAMOSA PROMOTER BINDING PROTEIN‐LIKE 3/4/5/9/15 (SPL3/4/5/9/15), was significantly reduced in OE‐OASA1‐#33/#142 seedlings. These findings suggest that endogenous H₂S positively regulates GA20ox4 expression, thereby promoting gibberellin synthesis and advancing flowering in Arabidopsis through the GA pathway. Furthermore, the promotion of flowering by H₂S appears to be linked to the age pathway.
GAI1 underlines the antagonism between gibberellin and jasmonic acid in modulating disease resistance
Authors: Xu Haoran , Tan Mengting , Zhang Bowen , Yan Wenlei , Zeng Hongqiu
Published: February 2025

Cassava bacterial blight (CBB) is a devastating disease affecting cassava production worldwide. Although phytohormones are important in regulating defense responses, their roles and the possible crosstalk in cassava remain elusive. Here, we illustrate the antagonistic effects of gibberellin (GA) and jasmonic acid (JA) in modulating disease resistance to CBB. Notably, we found that GIBBERELLIN INSENSITIVE1 (GAI1), a critical repressor of GA signaling, physically interacted with JASMONATE ZIM DOMAIN2.2 (JAZ2.2). JAZ2.2 negatively regulates cassava disease resistance by interfering with JA signaling through its direct interaction with MYELOCYTOMATOSIS2.2 (MYC2.2), thereby inhibiting the transcription of several resistant genes, including MeSERK1, MeLYK3, MeZAR1, MeADR2, MePR1, MePR4.1, MePR5. Interestingly, the interaction between GAI1 and JAZ2.2 releases the MYC2.2 and then activates the transcription of downstream resistant genes, resulting the antagonistic effects of GA and JA. In summary, this study clarifies the antagonism between GA and JA in modulating cassava disease resistance, which is underlined by the interaction between GAI1 and JAZ2.2. The GAI1‐JAZ2.2‐MYC2.2 gene network not only extends the our understanding of the phytohormone signaling pathway, but also provides new clues for the genetic improvement of cassava disease resistance.
The impact of wild-boar-derived microbiota transplantation on piglet microbiota, metabolite profile, and gut proinflammatory cytokine production differs from sow-derived microbiota
Authors: Rahman Rajibur , Fouhse Janelle M. , Ju Tingting , Fan Yi , Bhardwaj Tulika , Brook Ryan K. , Nosach Roman , Harding John , Willing Benjamin P.
Published: February 2025

Colonization of co-evolved, species-specific microbes in early life plays a crucial role in gastrointestinal development and immune function. This study hypothesized that modern pig production practices have resulted in the loss of co-evolved species and critical symbiotic host-microbe interactions. To test this, we reintroduced microbes from wild boars (WB) into conventional piglets to explore their colonization dynamics and effects on gut microbial communities, metabolite profiles, and immune responses. At postnatal day (PND) 21, 48 piglets were assigned to four treatment groups: (i) WB-derived mixed microbial community (MMC), (ii) sow-derived MMC, (iii) a combination of WB and sow MMC (Mix), or (iv) Control (PBS). Post-transplantation analyses at PND 48 revealed distinct microbial communities in WB-inoculated piglets compared with Controls, with trends toward differentiation from Sow but not Mix groups. WB-derived microbes were more successful in colonizing piglets, particularly in the Mix group, where they competed with Sow-derived microbes. WB group cecal digesta enriched with
Lactobacillus helveticus
,
Lactobacillus mucosae
, and
Lactobacillus pontis
. Cecal metabolite analysis showed that WB piglets were enriched in histamine, acetyl-ornithine, ornithine, citrulline, and other metabolites, with higher histamine levels linked to
Lactobacillus
abundance. WB piglets exhibited lower cecal IL-1β and IL-6 levels compared with Control and Sow groups, whereas the Mix group showed reduced IFN-γ, IL-2, and IL-6 compared with the Sow group. No differences in weight gain, fecal scores, or plasma cytokines were observed, indicating no adverse effects. These findings support that missing WB microbes effectively colonize domestic piglets and may positively impact metabolite production and immune responses.

IMPORTANCE

This study addresses the growing concern over losing co-evolved, species-specific microbes in modern agricultural practices, particularly in pig production. The implementation of strict biosecurity measures and widespread antibiotic use in conventional farming systems may disrupt crucial host-microbe interactions that are essential for gastrointestinal development and immune function. Our research demonstrates that by reintroducing wild boar-derived microbes into domestic piglets, these microbes can successfully colonize the gut, influence microbial community composition, and alter metabolite profiles and immune responses without causing adverse effects. These findings also suggest that these native microbes can fill an intestinal niche, positively impacting immune activation. This research lays the groundwork for future strategies to enhance livestock health and performance by restoring natural microbial populations that produce immune-modulating metabolites.
Robust and highly efficient transformation method for a minimal mycoplasma cell
Authors: Mizutani Masaki , Glass John I. , Fukatsu Takema , Suzuki Yo , Kakizawa Shigeyuki
Published: February 2025

Mycoplasmas have been widely investigated for their pathogenicity, as well as for genomics and synthetic biology. Conventionally, transformation of mycoplasmas was not highly efficient, and due to the low transformation efficiency, large amounts of DNA and recipient cells were required for that purpose. Here, we report a robust and highly efficient transformation method for the minimal cell JCVI-syn3B, which was created through streamlining the genome of
Mycoplasma mycoides
. When the growth states of JCVI-syn3B were examined in detail by focusing on such factors as pH, color, absorbance, colony forming unit, and transformation efficiency, it was found that the growth phase after the lag phase can be divided into three distinct phases, of which the highest transformation efficiency was observed during the early exponential growth phase. Notably, the transformation efficiency of up to 4.4 × 10
−2
transformants per cell per microgram of plasmid DNA was obtained. A method to obtain several hundred to several thousand transformants with less than 0.2 mL of culture with approximately 1 × 10
7
–10
8
cells and 10 ng of plasmid DNA was developed. Moreover, a transformation method using a frozen stock of transformation-ready cells was established. These procedures and information could simplify and enhance the transformation process of minimal cells, facilitating advanced genetic engineering and biological research using minimal cells.

IMPORTANCE

Mycoplasmas are parasitic and pathogenic bacteria for many animals. They are also useful bacteria to understand the cellular process of life and for bioengineering because of their simple metabolism, small genomes, and cultivability. Genetic manipulation is crucial for these purposes, but transformation efficiency in mycoplasmas is typically quite low. Here, we report a highly efficient transformation method for the minimal genome mycoplasma JCVI-syn3B. Using this method, transformants can be obtained with only 10 ng of plasmid DNA, which is around one-thousandth of the amount required for traditional mycoplasma transformations. Moreover, a convenient method using frozen stocks of transformation-ready cells was established. These improved methods play a crucial role in further studies using minimal cells.
Not just passengers: effectors contribute to the assembly of the type VI secretion system as structural building blocks
Authors: Dyrma Sherina , Pei Tong-Tong , Liang Xiaoye , Dong Tao
Published: February 2025

Protein secretion systems are critical macromolecular machines employed by bacteria to interact with diverse environments and hosts during their life cycle. Cytosolically produced protein effectors are translocated across at least one membrane to the outside of the cells or directly into target cells. In most secretion systems, these effectors are mere passengers in unfolded or folded states. However, the type VI secretion system (T6SS) stands out as a powerful contractile device that requires some of its effectors as structural components. This review aims to provide an updated view of the diverse functions of effectors, especially focusing on their roles in T6SS assembly, the implications for T6SS engineering, and the potential of recently developed T6SS models to study effector-T6SS association.
Development and evaluation of a next-generation sequencing methodology for measles virus using Oxford Nanopore Technology
Authors: Zubach Vanessa , Osahan Gurasis , Kolsun Kurt , Pfeifer Claudia , Severini Alberto , Hiebert Joanne
Published: February 2025

We report the development of a bench protocol and evaluation of bioinformatics pipelines for the whole genome sequence (WGS) of measles virus (MeV) genotype D8. We established a bench protocol using 1 kb amplicons tiling the MeV WGS. Four different pipeline parameters were assessed based on two basecallers and two quality thresholds: Guppy simplex with Q-score thresholds of 20 and 25 (G20 and G25), and Dorado duplex with Q-score thresholds of 20 and 25 (D20 and D25). Using a reference genome, we determined that complete genomes were obtained down to 10 copies/µL with all four parameters; however, errors began to be detected in the consensus sequence at 100 copies/µL. A panel of specimens from 32 measles cases, for which measles WGS had been obtained by other methods (reference sequences), was used to assess the utility and accuracy of the Oxford Nanopore Technologies (ONT) for the purposes of measles surveillance. We found that a crossing point (Cp) value of 31 (corresponding to approximately 100 copies/µL) or less could be considered a predictor for the generation of accurate and complete WGS. The GQ20 parameter achieved the most complete genomes (75%) and had the most identical sequences (84.4%). Error rates compared with the reference sequences for all parameters were below one nucleotide per whole genome. After assessing the reproducibility, GQ20 had the most identical sequences (97.4%). Finally, we inserted ONT-generated WGS and reference sequences into outbreaks with known epidemiological links, and our results show that the ONT WGS matches the epidemiological data. This evaluation establishes that NGS generated by ONT produces accurate and reliable MeV WGS.

IMPORTANCE

The use of ONT-sequencing platforms has the potential to expand the availability of measles sequencing as a result of its relatively lower cost and portability. This study establishes that measles sequences generated by ONT are accurate and reliable. This will enable sequencing in global regions where there is a lack of sequence data (which also tend to be the measles exporting regions) and more timely sequencing in low incidence settings, due also to the lower number of samples needed for the ONT platform. More timely generation of these data enables better investigation of cases, which informs public health response and outbreak management in measles-eliminated countries.
YTHDF1 and YTHDC1 m
6
A reader proteins regulate HTLV-1
tax
and
hbz
activity
Authors: King Emily M. , Midkiff Amanda , McClain Karsyn , Kim Sanggu , Panfil Amanda R.
Published: February 2025

Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus responsible for adult T-cell leukemia/lymphoma (ATLL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), a progressive neurodegenerative disease. Regulation of viral gene expression plays a key role in viral persistence and pathogenesis. However, the molecular mechanisms underlying this fine-tuned regulation remain poorly understood. Little is known regarding RNA chemical modifications of HTLV-1 RNA and how these affect viral biology and disease development. Post-transcriptional chemical modification of RNA is common in eukaryotes, with N
6
-methyladenosine (m
6
A) being the most prevalent. In this study, we investigated the role of m
6
A RNA modifications on HTLV-1 gene expression. Using MeRIP-Seq, we mapped the sites of m
6
A modification to the 3’ end of the viral genome. We found HTLV-1 RNA, as well as viral oncogene transcripts
tax
and
hbz
, contained m
6
A modifications. m
6
A-depletion in HTLV-1-transformed cells decreased sense-derived viral genes (
Tax, Gag,
and
Env
) and increased antisense-derived
Hbz
expression.
Tax
and
hbz
transcripts were bound by reader proteins YTHDF1 and YTHDC1 in a panel of HTLV-1 T-cell lines. Using expression vectors and shRNA-mediated knockdown, we found that YTHDF1 had opposing effects on viral gene expression, decreasing sense-derived viral genes and increasing antisense-derived
Hbz
. Upon further study, the YTHDF1 effects on
tax
abundance were dependent on
tax
m
6
A deposition. The nuclear m
6
A reader protein YTHDC1 affected the abundance of both sense- and antisense-derived viral transcripts and specifically enhanced the nuclear export of
tax
transcript. Collectively, our results demonstrate global m
6
A levels and m
6
A reader proteins YTHDF1 and YTHDC1 regulate HTLV-1 gene expression.

IMPORTANCE

Human T-cell leukemia virus type 1 (HTLV-1) persistence and pathogenesis are controlled through tight regulation of viral gene expression. The fate of RNA can be controlled by epigenetic modifications that impact gene expression without altering the DNA sequence. Our study details the impact of N6-methyladenosine (m
6
A) RNA chemical modifications on HTLV-1 gene expression. We found that reductions in global m
6
A levels affected viral gene expression, decreasing
Tax
and other sense-derived viral genes, whereas increasing the antisense-derived
Hbz
. Our results suggest the oncogenic viral transcripts,
tax
and
hbz
, are m
6
A-modified in cells. We found that these viral RNA modifications are interpreted by reader proteins YTHDF1 and YTHDC1, which dictate the fate of the viral RNA. Understanding HTLV-1 RNA chemical modifications offers potential insights into novel therapeutic strategies for HTLV-1-associated diseases.
Enhancing the solubility of SARS-CoV-2 inhibitors to increase future prospects for clinical development
Authors: Kuhn Ariel J. , Outlaw Victor K. , Marcink Tara C. , Yu Zhen , Mears Megan C. , Cajimat Maria N. , Kreitler Dale F. , Cleven Payton R. , Mook Jee Ching , Bente Dennis A. , Porotto Matteo , Gellman Samuel H. , Moscona Anne
Published: February 2025

SARS-CoV-2 poses an ongoing threat to human health as variants continue to emerge. Several effective vaccines are available, but a diminishing number of Americans receive the updated vaccines (only 22% received the 2023 update). Public hesitancy towards vaccines and common occurrence of “breakthrough” infections (i.e.
,
infections of vaccinated individuals) highlight the need for alternative methods to reduce viral transmission. SARS-CoV-2 enters cells by fusing its envelope with the target cell membrane in a process mediated by the viral spike protein, S. The S protein operates via a Class I fusion mechanism in which fusion between the viral envelope and host cell membrane is mediated by structural rearrangements of the S trimer. We previously reported lipopeptides derived from the C-terminal heptad repeat (HRC) domain of SARS-CoV-2 S that potently inhibit fusion by SARS-CoV-2, both
in vitro
and
in vivo
. These lipopeptides bear an attached cholesterol unit to anchor them in the membrane. Here, to improve prospects for experimental development and future clinical utility, we employed structure-guided design to incorporate charged residues at specific sites in the peptide to enhance aqueous solubility. This effort resulted in two new, potent lipopeptide inhibitors.

IMPORTANCE

Despite the existence of vaccines for SARS-CoV-2, the constant evolution of new variants and the occurrence of breakthrough infections highlight the need for new and effective antiviral approaches. We have shown that lipopeptides designed to bind a conserved region on the SARS-CoV-2 spike protein can effectively block viral entry into cells and thereby block infection. To support the feasibility of using this approach in humans, we re-designed these lipopeptides to be more soluble, using information about the structure of the spike protein interacting with the peptides to modify the peptide chain. The new peptides are effective against both SARS-CoV-2 and MERS. The lipopeptides described here could serve as treatment for people who are unvaccinated or who experience breakthrough infections, and the approach to increasing solubility can be applied in a broad spectrum approach to treating infections with emerging viruses.
MeJA inhibits fungal growth and DON toxin production by interfering with the cAMP-PKA signaling pathway in the wheat scab fungus
Fusarium graminearum
Authors: Duan Kaili , Qin Shaozhe , Cui Fangling , Zhao Liangyuan , Huang Yongqing , Xu Jin-Rong , Wang Guanghui
Published: February 2025

Deoxynivalenol (DON), a mycotoxin primarily produced by
Fusarium
species, is commonly found in cereal grains and poses risks to human and animal health, as well as global grain trade. This study demonstrates that methyl jasmonate (MeJA), a natural plant hormone, inhibits the growth and conidiation of
Fusarium graminearum
. Importantly, MeJA significantly reduces DON production by suppressing
TRI
gene expression and toxisome formation. To explore the molecular mechanism, we identified MeJA-tolerant mutants, including a transcription factor
MRT1
and cAMP-PKA pathway-related genes (
FgGPA1
and
FgSNT1
). MeJA treatment reduced PKA activity and intracellular cAMP levels in
F. graminearum
, suggesting it targets the cAMP-PKA pathway. Notably, the MeJA-resistant mutant
FgGPA1
R178H
enhanced fungal growth, DON production, and cAMP levels in the presence of MeJA. Exogenous cAMP alleviated MeJA’s inhibitory effects on DON production, further supporting this pathway’s involvement. Interestingly, MeJA had no effect on all three MAP kinase pathways (Mgv1, Gpmk1, and FgHog1). Truncated and phospho-mimicking mutations in Mrt1 or FgSnt1 conferred MeJA resistance, suggesting they may act downstream of the cAMP-PKA pathway. In conclusion, MeJA presents a promising approach to control
F. graminearum
growth and DON production.

IMPORTANCE

Deoxynivalenol (DON) poses significant risks to both human and animal health and severely disrupts the global grain trade due to its prevalence as a common contaminant in wheat grains. With rising public concern over food safety, finding effective and sustainable methods to reduce DON contamination becomes increasingly urgent. In our study, we found that methyl jasmonate (MeJA), a natural plant hormone, can effectively inhibit the vegetative growth of
F. graminearum
and significantly reduce its DON toxin production. To explore the underlying molecular mechanism, we identified the mutations in MeJA-tolerant mutants and revealed that MeJA effectively exerts its antifungal activities by inhibiting the cAMP-PKA signaling pathway in
F. graminearum
. Our work provides a promising natural solution to reduce DON toxin contamination in cereal grains, enhancing food safety while decreasing the reliance on chemical fungicides and their associated environmental impact.
Industrialization drives the gut microbiome and resistome of the Chinese populations
Authors: Tian Chen , Zhang Tongzuo , Zhuang Daohua , Luo Yu , Li Teng , Zhao Fangfang , Sang Jianan , Tang Zecheng , Jiang Peicheng , Zhang Tao , Liu Pengfei , Zhu Lei , Zhang Zhigang
Published: February 2025

Industrialization has driven lifestyle changes in eastern and western Chinese populations, yet we have a poor understanding of the dynamic changes in their gut microbiome and resistome under industrialization, which is essential for the scientific management of public health. Here, this study employed metagenomics to analyze the gut microbiota of 1,382 healthy individuals from China, including 415 individuals from the eastern region of advanced industrialization and 967 individuals from the western region of developing industrialization. Compared with western populations, eastern populations show a significant increase in interindividual dissimilarity of microbial species composition and metabolic pathways but a significant decrease in intraindividual species and functional diversity. Furthermore, our results found significantly less abundance and richness of antibiotic resistance genes (ARGs) in the gut microbiota of eastern populations, alongside a lower prevalence of unique core ARG subtypes. For the 12 core ARG types shared between eastern and western populations, the mean relative abundance of two types was notably higher in the eastern populations, while eight core ARG types had significantly higher mean relative abundance in the western populations. Based on the reconstruction of metagenomic assembled genomes, we found that
Escherichia coli
genomes from western populations carried more virulence factor genes (VFGs) and mobile genetic elements (MGEs) compared to those from eastern populations. This large-scale study for the first time revealed industrialization potentially led to unexpected alterations of the gut microbiome and resistome between eastern and western populations that provide a vital implication for Chinese public health and may aid in the development of region-specific strategies for managing pathogenic infections.

IMPORTANCE

As China experiences rapid but uneven industrialization, understanding its effect on people’s gut bacteria is critical for public health. This study reveals how industrialization may reshape the health risks related to gut bacteria and antibiotic resistance. This work provides crucial information to help create customized public health policies for different regions.
Resilience of human gut microbiomes in autism spectrum disorder: measured using stiffness network analysis
Authors: Chen Hongju (Daisy) , Yi Bin , Ma Zhanshan (Sam)
Published: February 2025

Autism spectrum disorder (ASD) affects an estimated 1%–2% of children worldwide, but its specific etiology remains unclear. In recent years, the gut microbiome’s role in ASD pathogenesis has garnered increasing attention. However, the exact relationship between microbiota and ASD—such as which microbial species significantly impact disease onset and progression—remains unresolved, and effective methods to measure microbial interactions are still lacking. In this study, we introduce an innovative stiffness network analysis (SNA) method to quantify changes in microbial network structure and identify disease-specific microbial bacteria theoretically. The SNA method was applied to reanalyze eight ASD gut microbiome data sets, encompassing 898 ASD samples and 467 healthy control (HC) samples from 16S-rRNA sequencing data. Key findings include the following: (i) an “allies” biomarker subgroup consisting of
Bacteroides plebeius
,
Sutterella
,
Lachnospira
, and
Prevotella copri
was identified; (ii) a profile monitoring score of 0.72 for the biomarker subgroup, indicating significant relationship changes between HC and ASD states, and (iii) a P/N ratio of biomarker subgroup in ASD-associated gut bacteria that was three times higher than that of HC microbiomes. Additionally, we discuss the non-monotonic relationship alterations within microbial sub-communities in the ASD gut microbiome.

IMPORTANCE

It is crucial to assess alterations in network structure in different biological states in order to promote health. The stiffness network allows for the exploration of species interactions and the measurement of resilience in complex microbial networks. The objective of this study was to develop a stiffness network analysis (SNA) method for evaluating the contribution of microbial bacteria in differentiating disease samples from healthy control samples by examining changes in network stiffness parameters. Furthermore, the SNA method was employed on both simulated and real autism spectrum disorder gut microbiome data sets to identify potential microbial biomarker subgroups, with a particular focus on the relationship alterations within microbial networks.