bluuebunny/crossref_metadata_2025 huggingface dataset:
A 7-Month Multidisciplinary Healthy Lifestyle Intervention Effectively Improved Cardiometabolic Risk Profile of Firefighters
Authors: Saint-Martin Daniel Rodrigues Ferreira , Barreto Kevin Alves , Soares Edgard M. K. Von Koenig , Machado Marcelo Serejo , Morais Cristiana Soares dos Santos , Barbosa Adriana Mendonça Bonadio , Nogueira Rosenkranz Maciel , D’Isabel Susanne , Smith Denise L. , Molina Guilherme E. , Grossi Porto Luiz Guilherme
Published: April 2024

Objective

We investigated the effect of a 7-month healthy lifestyle intervention on cardiometabolic risk factors (CMRF) among male career military firefighters (FFs).

Methods

Forty-nine FFs participated in a 7-month workplace multiddisciplinary healthy lifestyle intervention designed to reduce CMRF through exercise, diet, and improved sleep. Medical assessments, accelerometry, and surveys at the beginning and end determined program effectiveness.

Results

At the end of the intervention period, there was a significant improvement in measures of body composition and blood glucose. The prevalence of hypertension also decreased significantly (P < 0.01). The 57% of participants who fully adhered to the program had significantly greater improvements across multiple CMRF. Participants increased their physical activity and improved their diet following the intervention.

Conclusions

This healthy lifestyle intervention was effective in changing behavior and lowering cardiometabolic risk among FFs.
Implementation and Evaluation of a Large Community-Based Colorectal Cancer Screening Program
Authors: Shokar Navkiran K. , Calderón-Mora Jessica , Salaiz Rebekah , Casner Nancy , Zuckerman Marc J. , Byrd Theresa L. , Shokar Gurjeet S. , Dwivedi Alok
Published: April 2024

Context:

Colorectal cancer (CRC) screening can significantly reduce incidence and mortality; however, screening rates are suboptimal. The lowest rates are among those with no usual source of care and the uninsured.

Objective:

We describe the implementation and evaluation of a community-based CRC screening program from 2012 to 2015 designed to increase screening within a predominantly Hispanic US-Mexico border population.

Methods:

The multicomponent, evidence-based program provided in-person, bilingual, culturally tailored health education facilitated by community health workers, no-cost primarily stool-based testing and diagnostic colonoscopy, and navigation. We recruited uninsured individuals due for CRC screening from clinics and community sites. An extensive qualitative and quantitative program process and outcome evaluation was conducted.

Results:

In total, 20 118 individuals were approached, 8361 were eligible for screening; 74.8% completed screening and 74.6% completed diagnostic testing; 14 cancers were diagnosed. The mean age of participants was 56.8 years, and the majority were Hispanic, female, and of low socioeconomic status. The process evaluation gathered information that enabled effective program implementation and demonstrated effective staff training, compliance with processes, and high patient satisfaction.

Conclusions:

This program used a population-based approach focusing on uninsured individuals and proved successful at achieving high fecal immunochemical test kit return rates and colonoscopy completion rates. Key factors related to its success included tailoring the intervention to our priority population, strong partnerships with community-based sites and clinics, expertise in clinical CRC screening, and an active community advisory board. This program can serve as a model for similar populations along the border to increase CRC screening rates among the underserved.
Public Health Response to SARS-CoV-2 in Assisted Living Facilities in New York State: March 2020-December 2022
Authors: D'Ascanio Antonella M. , Hewlett Dial , Davda Karen , Montecalvo Marisa A.
Published: April 2024

Context:

Assisted living facility (ALF) residents are especially vulnerable to SARS-CoV-2 infection due to the age and comorbidities of the resident population and the social nature of these facilities.

Objective:

To collate all New York State Department of Health guidance and regulations to control transmission of SARS-CoV-2 infection within ALFs from March 2020 through December 2022 and to include US Food and Drug Administration COVID-19 testing and vaccine authorizations.

Design:

A narrative chronological review of all New York State Department of Health guidance.

Results:

Documents and associated guidance and regulations are divided into 4 sections: (1) lockdown until COVID-19 vaccine emergency use authorization; (2) COVID-19 vaccine authorization until phased reopening; (3) phased reopening, vaccination requirements, and booster vaccination; (4) the period of the bivalent booster.

Conclusion:

Controlling the spread of SARS-CoV-2 within ALFs required a multifactorial approach that included stringent infection control measures, testing, and vaccination and careful attention to the social structure and support systems within ALFs. The SARS-CoV-2 pandemic highlighted the complexity of controlling spread of an easily transmissible respiratory pathogen in assisted living communities and the need to structure infection control programs within the diverse ALFs that provide care for our aging population.
Prevalence of Burnout Among Public Health Professionals: A Systematic Review
Authors: Spencer-Hwang Rhonda , Cruz Analyn , Ong MY , Chitanda Ashley , Harvey Yolisa , Hwang Jayden , Shah Huma , Tamares Shanalee , Wilber Lori
Published: April 2024

Context:

Since the initial outbreak of COVID-19, health professionals—both clinical health care, as well as public health concentrations—have faced tremendous pressures. A growing body of literature indicates the pandemic has magnified already prevalent burnout rates among clinical health professionals and to what extent for public health professionals remains to be determined.

Objective:

This study purpose is to conduct a systematic review of literature examining burnout prevalence among public health professionals before and during the COVID-19 pandemic—nationally and internationally—with identification of potential risk factors.

Design:

We conducted a literature search in PubMed, EMBASE, PsycINFO, SocINDEX, and ClinicalKey since inception through April 4, 2023. Inclusion criteria included peer-reviewed, original research studies (qualitative or quantitative), in English, assessing prevalence of, or risk factors for, burnout in public health professionals. Two authors independently screened abstracts, titles, full report of studies and abstracted data related to burnout. This review was conducted using Joanna Briggs Institute Systematic Reviews guidelines and Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines with narrative synthesis. Protocol for this review registered on PROSPERO (CRD42023424468).

Results:

Of 3327 health-related articles mentioning burnout, 15 met inclusion criteria (11 quantitative and 4 qualitative) with 10 in international settings and 5 in US majority of quantitative studies were from international settings and only 1 in United States. Seventy-eight percent of studies that included prevalence data, exhibited a burnout prevalence greater than 50% (with a range of 19%-81%). The pandemic likely heightened (13% increase) already elevated burnout prevalence. Major risk factors identified included overwork, lack of support, changing roles, and full-time employment status, though many risk factors had not been studied in the United States.

Conclusions:

Burnout is prevalent among public health professionals, nationally and internationally, and likely heightened by the COVID-19 pandemic. More research is warranted assessing burnout among differing public health concentrations and interventions developed. Public health is an essential framework for protecting and promoting health nationally and internationally, and we need to ensure and support solidity of that framework.
Latent Profiles of Coronavirus-Related Health Literacy in Chinese Residents and Its Related Predictors
Authors: Du Yawen , Wang Xiaokang , Bu Xiaoou , Hu Fawen , Long Junwei , Wang Pei
Published: April 2024

Objectives:

This study aimed to explore the latent profiles of coronavirus-related health literacy among Chinese residents and investigate whether some predictive factors are linked with different latent subgroups of coronavirus-related health literacy.

Design/Setting:

This study was a cross-sectional survey conducted among Chinese residents beginning in April 2020.

Participants:

A total of 1610 Chinese residents aged 15 to 69 years were involved and were asked to complete the questionnaire about coronavirus-related health literacy, demographic information, and COVID-19 pandemic-related information.

Main Outcome Measure:

Examined the latent profiles of coronavirus-related health literacy and explored the influencing factors of different profiles of coronavirus-related health literacy.

Results:

The results showed that there were 3 latent subgroups, namely, high coronavirus-related health literacy (45.53%), medium coronavirus-related health literacy (47.76%), and low coronavirus-related health literacy (6.71%). Logistic regression analysis showed that gender, education, and the frequency of exposure to news about the pandemic could predict group membership.

Conclusions:

Most Chinese residents have medium coronavirus-related health literacy. Education is an important factor that has a long-term stable influence on coronavirus-related health literacy, and the frequency of exposure to news about the pandemic is a factor that can improve coronavirus-related health literacy in a short time.
Solid organ transplant-related central nervous system infections
Authors: Morado-Aramburo Oscar , Hasbun Rodrigo
Published: April 2024

Purpose of review

Central nervous system (CNS) infections in solid organ transplant (SOT) recipients may present atypical or nonspecific symptoms. Due to a wider range of infectious agents compared with immunocompetent hosts, diagnosis is challenging. This review categorizes CNS infections in SOT recipients by cause.

Recent findings

New studies have reported new data on the epidemiology and the risk factors associated with each specific pathogen described in this review. Additionally, we included the treatment recommendations.

The latest findings give us an insight into the different pathogens causing infectious neurologic complications in SOT recipients.
Benchmark Outcomes in Deceased Donor Kidney Transplantation: A Multicenter Analysis of 80 996 Transplants From 126 Centers
Authors: Rompianesi Gianluca , Montalti Roberto , Vrakas Georgios , Zarrinpar Ali , Warren Curtis , Loiaco Giuseppe , Rubba Fabiana , Troisi Roberto I.
Published: April 2024

Background.

We defined clinically relevant benchmark values in deceased donor kidney transplantation (KT), to assess the best achievable results in low-risk patient cohorts from experienced centers.

Methods.

We identified the “ideal” cases from the United Network for Organ Sharing Standard Transplant Analysis and Research files from centers performing ≥50 KT per year between 2010 and 2018. Cases have been selected based on the kidney donor profile index values (<35%), a cold ischemia time (CIT) ≤18 h, a HLA mismatch ≤4, and excluding blood group (ABO) incompatible, dual and combined transplants. The outcomes of the benchmark cohort have been compared with a group of patients excluded from the benchmark cohort because but not meeting 1 or more of the abovementioned criteria.

Results.

The 171 424 KT patients in the United Network for Organ Sharing Standard Transplant Analysis and Research files were screened and 8694 benchmark cases of a total of 80 996 KT (10.7%) from 126 centers meeting the selection criteria were identified. The benchmarks for 1-, 3-, and 5-y patient survival are ≥97%, ≥92.5%, and ≥86.7%, and ≥95.4%, ≥87.8%, and ≥79.6% for graft survival. Benchmark cutoff for hospital length of stay is ≤5 d, ≤23.6% for delayed graft function, and ≤7.5% and ≤9.1% for 6-mo and 1-y incidence of acute rejection. Overall 1-, 3-, and 5-y actuarial graft survivals were 96.6%, 91.1%, and 84.2% versus 93.5%, 85.4%, and 75.5% in the benchmark and comparison groups, respectively (P < 0.001). Overall 1-, 3-, and 5-y actuarial patient survivals were 98.1%, 94.8%, and 90.0% versus 96.6%, 91.1%, and 83.0% in the benchmark and comparison groups, respectively (P < 0.001).

Conclusions.

For the first time, we quantified the best achievable postoperative results in an ideal scenario in deceased donor KT, aimed at improving the clinical practice guided by the comparison of center performances with the ideal outcomes defined.
Current Status of Contralateral Prophylactic Mastectomy: Investigating Structural Racial Disparity
Authors: Vadlakonda Amulya , Curry Joanna , Gao Zihan , Chervu Nikhil , Ali Konmal , Lee Hanjoo , Thompson Carlie K , Benharash Peyman
Published: April 2024

BACKGROUND:

Contralateral prophylactic mastectomy (CPM) remains a personal decision, influenced by psychosocial factors, including cosmesis and peace of mind. Although use of CPM is disproportionately low among Black patients, the degree to which these disparities are driven by patient- vs hospital-level factors remains unknown.

STUDY DESIGN:

Patients undergoing mastectomy for nonmetastatic ductal or lobular breast cancer were tabulated using the National Cancer Database from 2004 to 2020. The primary endpoint was receipt of CPM. Multivariable logistic regression models were constructed with interaction terms between Black-serving hospital (BSH) status and patient race to evaluate associations with CPM. Cox proportional hazard models were used to evaluate long-term survival.

RESULTS:

Of 597,845 women studied, 70,911 (11.9%) were Black. After multivariable adjustment, Black race (adjusted odds ratio 0.65, 95% CI 0.64 to 0.67) and treatment at BSH (adjusted odds ratio 0.84, 95% CI 0.83 to 0.85) were independently linked to lower odds of CPM. Although predicted probability of CPM was universally lower at higher BSH, Black patients faced a steeper reduction compared with White patients. Receipt of CPM was linked to improved survival (hazard ratio [HR] 0.84, 95% CI 0.83 to 0.86), whereas Black race was associated with a greater HR of 10-year mortality (HR 1.14, 95% CI 1.12 to 1.17).

CONCLUSIONS:

Hospitals serving a greater proportion of Black patients are less likely to use CPM, suggestive of disparities in access to CPM at the institutional level. Further research and education are needed to characterize surgeon-specific and institutional practices in patient counseling and shared decision-making that shape disparities in access to CPM.
Identification and biological characteristics of Enterococcus casseliflavus TN-47 isolated from Monochamus alternatus
Authors: Peng Zi-Ran , Zhang Jian-Gang , Zhang Jia-Bao , Lin Xiao-Qi , Chen Wei , Yang Yong-Jun , Liu Zhen-Zhen
Published: April 2024

With the widespread use of antibiotics, the incidence of antibiotic resistance in microorganisms has increased. Monochamus alternatus is a trunk borer of pine trees. This study aimed to investigate the in vitro antimicrobial and biological characteristics of Enterococcus casseliflavus TN-47 (PP411196), isolated from the gastrointestinal tract of M. alternatus in Jilin Province, PR China. Among 13 isolates obtained from the insects, five were preliminarily screened for antimicrobial activity. E. casseliflavus TN-47, which exhibited the strongest antimicrobial activity, was identified. E. casseliflavus TN-47 possessed antimicrobial activity against Staphylococcus aureus USA300 and Salmonella enterica serovar Pullorum ATCC 19945. Furthermore, E. casseliflavus TN-47 was sensitive to tetracyclines, penicillins (ampicillin, carbenicillin, and piperacillin), quinolones and nitrofuran antibiotics, and resistant to certain beta-lactam antibiotics (oxacillin, cefradine and cephalexin), macrolide antibiotics, sulfonamides and aminoglycosides. E. casseliflavus TN-47 could tolerate low pH and pepsin-rich conditions in the stomach and grow in the presence of bile acids. E. casseliflavus TN-47 retained its strong auto-aggregating ability and hydrophobicity. This strain did not exhibit any haemolytic activity. These results indicate that E. casseliflavus TN-47 has potential as a probiotic. This study provides a theoretical foundation for the future applications of E. casseliflavus TN-47 and its secondary metabolites in animal nutrition and feed.
In vivoAuto-tuning of Antibody-Drug Conjugate Delivery for Effective Immunotherapy using High-Avidity, Low-Affinity Antibodies
Authors: Kopp Anna , Dong Shujun , Kwon Hyeyoung , Wang Tiexin , Desai Alec A. , Linderman Jennifer J. , Tessier Peter , Thurber Greg M.
Published: April 2024

Antibody-drug conjugates (ADCs) have experienced a surge in clinical approvals in the past five years. Despite this success, a major limitation to ADC efficacy in solid tumors is poor tumor penetration, which leaves many cancer cells untargeted. Increasing antibody doses or co-administering ADC with an unconjugated antibody can improve tumor penetration and increase efficacy when target receptor expression is high. However, it can also reduce efficacy in low-expression tumors where ADC delivery is limited by cellular uptake. This creates an intrinsic problem because many patients express different levels of target between tumors and even within the same tumor. Here, we generated High-Avidity, Low-Affinity (HALA) antibodies that can automatically tune the cellular ADC delivery to match the local expression level. Using HER2 ADCs as a model, HALA antibodies were identified with the desired HER2 expression-dependent competitive binding with ADCsin vitro. Multi-scale distribution of trastuzumab emtansine and trastuzumab deruxtecan co-administered with the HALA antibody were analyzedin vivo, revealing that the HALA antibody increased ADC tumor penetration in high-expression systems with minimal reduction in ADC uptake in low-expression tumors. This translated to greater ADC efficacy in immunodeficient mouse models across a range of HER2 expression levels. Furthermore, Fc-enhanced HALA antibodies showed improved Fc-effector function at both high and low expression levels and elicited a strong response in an immunocompetent mouse model. These results demonstrate that HALA antibodies can expand treatment ranges beyond high expression targets and leverage strong immune responses.
The growth rate of senile plaques is determined by the competition between the rate of deposition of free Aβ aggregates into plaques and the autocatalytic production of free Aβ aggregates
Authors: Kuznetsov Andrey V.
Published: April 2024

The formation of amyloid beta (Aβ) deposits (senile plaques) is one of the hallmarks of Alzheimer’s disease (AD). This study investigates what processes are primarily responsible for their formation. A model is developed to simulate the diffusion of amyloid beta (Aβ) monomers, the production of free Aβ aggregates through nucleation and autocatalytic processes, and the deposition of these aggregates into senile plaques. The model suggests that efficient degradation of Aβ monomers alone may suffice to prevent the growth of senile plaques, even without degrading Aβ aggregates and existing plaques. This is because the degradation of Aβ monomers interrupts the supply of reactants needed for plaque formation. The impact of Aβ monomer diffusivity is demonstrated to be small, enabling the application of the lumped capacitance approximation and the derivation of approximate analytical solutions for limiting cases with both small and large rates of Aβ aggregate deposition into plaques. It is found that the rate of plaque growth is governed by two competing processes. One is the deposition rate of free Aβ aggregates into senile plaques. If this rate is small, the plaque grows slowly. However, if the rate of deposition of Aβ aggregates into senile plaques is very large, the free Aβ aggregates are removed from the intracellular fluid by deposition into the plaques, leaving insufficient free Aβ aggregates to catalyze the production of new aggregates. This suggests that under certain conditions, Aβ plaques may offer neuroprotection and impede their own growth. Additionally, it indicates that there exists an optimal rate of deposition of free Aβ aggregates into the plaques, at which the plaques attain their maximum size.
Loss of precise auditory sampling as a sign of value-driven visual attentional capture
Authors: Harcevnicow Rodrigo Caramés , Sánchez-Costa Thaiz , Carboni Alejandra , Constantino Francisco Cervantes
Published: April 2024

By linking with rewards, sensory signals gain salience and the ability to influence selective attention even when they have become irrelevant. The dynamics of reward-driven distraction in the brain remains unclear, particularly at the time of shaping multisensory associations. It is unknown whether reward-driven distraction by visual signals interferes with the robust ability of the brain to phase-lock to auditory modulations. In a dynamic audiovisual (AV) coherence task, we investigated how visual reward associations affect performance and modulate auditory encoding precision. Participants were presented with dual visual object streams flickering at different rates, accompanied by an amplitude-modulated sound matching one of the flicker periods, for subjects to identify the matching visual object. At the periphery, an irrelevant color feature flickers in sync with the target and may capture observers’ attention, due to a prior color-reward association training regime. Electroencephalography (EEG) recordings assessed participants’ sensitivity to the audiovisual task. The findings indicate that target discrimination was impoverished in the presence of colors that had previously been associated with reward. The phase locking of auditory responses also decreased, evidencing an attentional shift away from auditory modulation representations. Moreover, down-modulations of auditory phase locking predicted the effect size of participants’ reward-driven distraction. These findings highlight how value-driven attentional capture fundamentally alters multimodal processing in the temporal domain. They suggest that less precise neural representations of unisensory streams not connected to reward-associated cues undermine the processing of temporal coherence relationships between multisensory streams. Momentary inter-modal competition, induced by reward-driven distraction, appears consistent with the systematic exploit of gaps in active attentional sampling strategies that unfold over time.
Callose Deficiency Modulates Plasmodesmata frequency and the intercellular space In Rice Anthers
Authors: Somashekar Harsha , Takanami Keiko , Benitez-Alfonso Yoselin , Oishi Akane , Hiratsuka Rie , Nonomura Ken-Ichi
Published: April 2024

Fertilization relies on pollen mother cells able to transit from mitosis-to-meiosis to supply gametes. This process involves remarkable changes at the molecular, cellular and physiological levels including (but not limited to) remodelling of cell wall. During meiosis onset, cellulose content at the pollen mother cell walls gradually declines with the concurrent deposition of the polysaccharide callose in anther locules. We aim to understand the biological significance of cellulose-to-callose turnover in pollen mother cells walls using electron microscopic analyses of rice flowers. Our observations indicate that in wild type anthers, the mitosis-to-meiosis transition coincides with a gradual reduction in the number of cytoplasmic connections called plasmodesmata. A mutant in theOryza sativacallose synthase GSL5, impaired in callose accumulation in premeiotic and meiotic anthers, displayed a reduction in plasmodesmata frequency among pollen mother cells and tapetal cells suggesting a role for callose in plasmodesmata maintenance. In addition, a significant increase in cell-cell distance between pollen mother cells and impaired premeiotic cell shaping was observed in the mutant. The results suggest that cellulose-to-callose turnover during mitosis-meiosis transition is necessary to maintain cell-to-cell connections and optimal intercellular spacing among anther locular cells explaining the regulatory influence of callose metabolism during meiosis in flowering plants.

Highlights

Cellulose-to-callose switch during meiosis onset in pollen mother cell walls correlates with changes in cytoplasmic connections called plasmodesmata, among meiocytes and between meiocytes and surrounding somatic cells.

A mutant in GSL5 (glucan synthase like 5) affects callose deposition but no other cell wall component (e.g., cellulose) in premeiotic and meiotic anthers, except at dyad stage.

Impaired callose synthesis is proposed to alter plasmodesmata frequency, the extracellular spacing and the shaping of pollen mother cells during mitosis-to-meiosis transition.

Increase in plasmodesmata frequency negatively correlates with cell-cell distance between pollen mother cells in both wildtype and a callose mutant.
TRIP12 governs DNA Polymerase β involvement in DNA damage response and repair
Authors: Inanc Burcu , Fang Qingming , Andrews Joel F. , Zeng Xuemei , Clark Jennifer , Li Jianfeng , Dey Nupur B. , Ibrahim Md , Sykora Peter , Yu Zhongxun , Braganza Andrea , Verheij Marcel , Jonkers Jos , Yates Nathan A. , Vens Conchita , Sobol Robert W.
Published: April 2024

The multitude of DNA lesion types, and the nuclear dynamic context in which they occur, present a challenge for genome integrity maintenance as this requires the engagement of different DNA repair pathways. Specific ‘repair controllers’ that facilitate DNA repair pathway crosstalk between double strand break (DSB) repair and base excision repair (BER), and regulate BER protein trafficking at lesion sites, have yet to be identified. We find that DNA polymerase β (Polβ), crucial for BER, is ubiquitylated in a BER complex-dependent manner by TRIP12, an E3 ligase that partners with UBR5 and restrains DSB repair signaling. Here we find that, TRIP12, but not UBR5, controls cellular levels and chromatin loading of Polβ. Required for Polβ foci formation, TRIP12 regulates Polβ involvement after DNA damage. Notably, excessive TRIP12-mediated shuttling of Polβ affects DSB formation and radiation sensitivity, underscoring its precedence for BER. We conclude that the herein discovered trafficking function at the nexus of DNA repair signaling pathways, towards Polβ-directed BER, optimizes DNA repair pathway choice at complex lesion sites.

Graphical Abstract
Interplay of geometry and mechanics in epithelial wound healing
Authors: Babu Nandhu Krishna , Sreepadmanabh M , Dutta Sayantan , Bhattacharjee Tapomoy
Published: April 2024

Wound healing is a complex biological process critical for maintaining an organism’s structural integrity and tissue repair following an infection or injury. Recent studies have unveiled the mechanisms involving the coordination of biochemical and mechanical responses in the tissue in wound healing. In this article, we focus on the healing property of an epithelial tissue as a material while the effects of biological mechanisms such as cell crawling and tissue proliferation is minimal. We present a mathematical framework that predicts the fate of a wounded tissue based on the wound’s geometrical features and the tissue’s mechanical properties. Precisely, adapting the vertex model of tissue mechanics, we predict whether a wound of a specific size in an epithelial monolayer characterized by certain levels of acto-myosin contractility and cell-cell adhesion will heal (i.e., close), shrink in size, or rupture the tissue further. Moreover, we show how tissue-mediated mechanisms such as purse-string tension at the wound boundary facilitate wound healing. Finally, we validate the predictions of our model by designing an experimental setup that enables us to create wounds of specific sizes in MDCK monolayers. Altogether, this work sets up a basis for interpreting the interplay of mechanical and geometrical features of a tissue in the process of wound healing.
Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations
Authors: Nallapareddy Mohan Vamsi , Craighero Francesco , Gobet Cédric , Naef Felix , Vandergheynst Pierre
Published: April 2024

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, and in turn, predict the speed of translation. The proposed method, RiboGL, combines graph and recurrent neural networks to account for both graph and sequence-based features. The model takes a graph representing the secondary structure of the mRNA sequence as input, which incorporates both sequence and structural codon neighbors. In our experiments, RiboGL greatly outperforms the state-of-the-art RiboMIMO model for ribosome density prediction. We also conduct ablation studies to justify the design choices made in building the pipeline. Additionally, we use gradient-based interpretability to understand how the codon context and the structural neighbors affect the ribosome density at the A-site. By individually analyzing the genes in the dataset, we elucidate how structural neighbors could also potentially play a role in defining the ribosome density. Importantly, since these neighbors can be far away in the sequence, a recurrent model alone could not easily extract this information. This study lays the foundation for understanding how the mRNA secondary structure can be exploited for ribosome density prediction, and how in the future other graph modalities such as features from the nascent polypeptide can be used to further our understanding of translation in general.
3D-printing fabrication of microwave-microfluidic device for droplets network formation and characterisation
Authors: Silver Kai , Li Jin , Dimitriou Pantelitsa , Kallnik Colin , Porch Adrian , Barrow David
Published: April 2024

Microwave-microfluidic devices (MMDs) have emerged as precision tools for the rapid, accurate, sensitive, and non-invasive characterisation of low-volume liquids. However, the fabrication of MMDs remains a significant challenge due to the complexities associated with integrating fluidic ducts and electronic components. Herein, we present a versatile and economical 3D-printing approach for MMD fabrication, using liquid metal as an electrical conductor. Cyclic olefin copolymer, polylactic acid and polypropylene were identified as potential printable dielectric materials for MMD fabrication. 3D-printed cyclic olefin copolymer substrates exhibited the lowest loss tangent of 0.002 at 2.7GHz, making it an ideal material for high frequency engineering. Liquid metal, specifically gallium indium eutectic, was injected into the printed ducts to form conductive microwave structures. Exemplar MMDs were fabricated to integrate split-ring type microwave resonators and droplet-forming fluidic junctions. These devices were applied in the formation and characterisation of water-in-oil emulsions for constructing definable lipid-segregated droplet interface bilayer (DIB) networks. This work not only indicates the feasibility of using 3D-printing for rapid prototyping of customised MMDs but also demonstrates the potential of MMDs as a new research tool for biochemistry and synthetic biology.
RGF1 controls PLT2 protein stability through ROS-dependent regulation of a cysteine residue in root meristem development
Authors: Hsiao Yu-Chun , Shiue Shiau-Yu , Yen Ming-Ren , Lai Joon-Keat , Yamada Masashi
Published: April 2024

The protein concentration gradients of the master regulators of the root meristem, named the PLETHORA proteins, modulate the root meristem size. Root meristem growth factor 1 (RGF1) peptide extends the PLETHORA2 (PLT2) protein gradients by altering reactive oxygen species (ROS) distributions. However, the underlying mechanism through which the ROS alterations regulate PLT2 remains unknown. Here, we demonstrate that the 212thcysteine of the PLT2 protein plays a pivotal role in modulating PLT2 stability through the ROS altered by RGF1. The substitution of the 212thcysteine of PLT2 with serine (PLT2C212S) enhanced the PLT2 protein stability upon RGF1 and resulted in robust resistance to ROS relative to the native PLT2. Accordingly, PLT2C212Smodulated expressions of certain specific root development-related genes to a greater extent than native PLT2. In summary, these findings show that the PLT2 concentration gradient formation through ROS, modulated by RGF1, is dependent on a mechanism involving the 212thcysteine of PLT2.
Natural variation in salt-induced changes in root:shoot ratio reveals SR3G as a negative regulator of root suberization and salt resilience in Arabidopsis
Authors: Ishka Maryam Rahmati , Sussman Hayley , Hu Yunfei , Alqahtani Mashael Daghash , Craft Eric , Sicat Ronell , Wang Minmin , Yu Li’ang , Ait-Haddou Rashid , Li Bo , Drakakaki Georgia , Nelson Andrew , Pineros Miguel , Korte Arthur , Jaremko Lukasz , Testerink Christa , Tester Mark , Julkowska Magdalena M.
Published: April 2024

Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoot growth rates, thereby affecting overall plant performance. While past studies have extensively documented the effect of salt stress on root elongation and shoot development separately, here we take an innovative approach by examining the coordination of root and shoot growth under salt stress conditions. Utilizing a newly developed tool for quantifying the root:shoot ratio in agar-grown Arabidopsis seedlings, we found that salt stress results in a loss of coordination between root and shoot growth rates. We identify a specific gene cluster encoding domain-of-unknown-function 247 (DUF247), and characterize one of these genes asSaltRoot:shootRatioRegulatorGene (SR3G). Further analysis elucidates the role of SR3G as a negative regulator of salt stress tolerance, revealing its function in regulating shoot growth, root suberization, and sodium accumulation. We further characterize thatSR3Gexpression is modulated byWRKY75transcription factor, known as a positive regulator of salt stress tolerance. Finally, we show that the salt stress sensitivity ofwrky75mutant is completely diminished when it is combined withsr3gmutation. Together, our results demonstrate that utilizing root:shoot ratio as an architectural feature leads to the discovery of new stress resilience gene. The study’s innovative approach and findings not only contribute to our understanding of plant stress tolerance mechanisms but also open new avenues for genetic and agronomic strategies to enhance crop environmental resilience.
Quantification of tissue creatine content using capillary electrophoresis
Authors: Choi Y. Jane , Bautista Angelo P , Terrill Jessica R , Pillow J. Jane , Arthur Peter G
Published: April 2024

Creatine plays a fundamental role in cellular energy homeostasis. The current protocol describes an alternative method for creatine quantification in biological tissue samples using capillary electrophoresis, with high separation efficiency that enables rapid analysis with low sample volumes. The protocol involves homogenization of snap-frozen tissue in phosphate buffer, followed by electrophoresis through a bare-fused capillary (75 µm internal diameter) and measurement at 200 nm on the Agilent 7100 CE system. Under the optimised conditions, there was excellent linearity in creatine standards between 6.3 – 100 µM. The overall intra-assay variability for concentrations between 6.3 – 100 µM was 1.5 %, and the inter-assay variability was 6.4 %, with a limit of detection at 6 nmol/mg protein. The protocol was further benchmarked against a commercially available enzyme assay kit using lung samples from lambs that received continuous creatine or saline supplementation. There was good agreement between the two methods (mean difference = 0.42 [-0.26-1.1] nmol/mg protein). Importantly, capillary electrophoresis enables reliable detection of creatine in biological samples from just ∼1.5 mg of wet-weight lung tissue. Capillary electrophoresis enables rapid (<10 minutes) and highly efficient analysis of tissue samples and avoids challenges faced with traditional enzymatic assays. The current protocol was developed and optimised with ovine lung tissue, but it can be easily adapted to analyse various tissue types. For tissues with higher baseline creatine content, such as the skeletal muscles or brain, <1 mg wet weight tissue would be sufficient to detect creatine using capillary electrophoresis.
Artificial Intelligence-Enabled AlphaFold II Pipeline Guides Functional Fluorescence Labeling of Tubulin Across Species
Authors: Xu Kaiming , Li Zhiyuan , Mao Linfan , Guo Zhengyang , Chen Zhe , Chai Yongping , Xie Chao , Yang Xuerui , Na Jie , Li Wei , Ou Guangshuo
Published: April 2024

Dynamic properties are essential for microtubule (MT) physiology. Current techniques forin vivoimaging of MTs present intrinsic limitations in elucidating the isotype-specific nuances of tubulins, which contribute to their versatile functions. Harnessing the power of AlphaFold II pipeline, we engineered a strategy for the minimally invasive fluorescence labeling of endogenous tubulin isotypes or those harboring missense mutations. We demonstrated that a specifically designed 16-amino acid linker, coupled with sfGFP11 from the split-sfGFP system and integration into the H1-S2 loop of tubulin, facilitated tubulin labeling without compromising MT dynamics, embryonic development, or ciliogenesis inC. elegans. Extending this technique to human cells and murine oocytes, we visualized MTs with the minimal background fluorescence and a pathogenic tubulin isoform with fidelity. The utility of our approach across biological contexts and species set an additional paradigm for studying tubulin dynamics and functional specificity, with implications for understanding tubulin-related diseases known as tubulinopathies.
Two-ended recombination at a Flp-nickase-broken replication fork
Authors: Elango Rajula , Nilavar Namrata , Li Andrew G. , Duffey Erin E. , Jiang Yuning , Nguyen Daniel , Abakir Abdulkadir , Willis Nicholas A. , Houseley Jonathan , Scully Ralph
Published: April 2024

Collision of a replication fork with a DNA nick is thought to generate a one-ended break, fostering genomic instability. Collision of the opposing converging fork with the nick could, in principle, form a second DNA end, enabling conservative repair by homologous recombination (HR). To study mechanisms of nickase-induced HR, we developed the Flp recombinase “step arrest” nickase in mammalian cells. Flp-nickase-induced HR entails two-ended, BRCA2/RAD51-dependent short tract gene conversion (STGC), BRCA2/RAD51-independent long tract gene conversion, and discoordinated two-ended invasions. HR induced by a replication-independent break and by the Flp-nickase differ in their dependence onBRCA1. To determine the origin of the second DNA end during Flp-nickase-induced STGC, we blocked the opposing fork using a site-specific Tus/Terreplication fork barrier. Flp-nickase-induced STGC remained robust and two-ended. Thus, collision of a single replication fork with a Flp-nick can trigger two-ended HR, possibly reflecting replicative bypass of lagging strand nicks. This response may limit genomic instability during replication of a nicked DNA template.
Efficient Generation of Human Pluripotent Stem Cells from Frozen Cord Tissue via Chemical Reprogramming
Authors: Nansubuga Coneria , Mahnke Donna K. , Li Siqi , Multerer Abigail , Minx Jake , Miller Bradley , Shen Mengcheng , Beyer Andreas , Han Lu , Lincoln Joy , Liu Chun
Published: April 2024

Chemical reprogramming presents an innovative approach for generating induced pluripotent stem cells (iPSCs), bypassing the genetic instability and safe concern associated with viral vector approach. We describe a novel, efficient chemical method for reprogramming human umbilical cord tissue-derived mesenchymal stem cells (MSCs) into induced pluripotent stem cells (iPSCs). Compared to previous sources like adipose tissue and skin, frozen umbilical cord tissue offers an abundant, non-invasive, long-term storable, and ethically sound cell source. Our findings not only showcase the feasibility and safety of utilizing chemical reprogramming on cells from frozen umbilical cords but also underscore its potential in regenerative medicine, especially for developing safer and more effective therapies for cardiovascular diseases.
Profiling microRNA expression during senescence and aging: mining for a diagnostic tool of senescent-cell burden
Authors: Weigl Moritz , Krammer Teresa L. , Pultar Marianne , Wieser Matthias , Chaib Selim , Suda Masayoshi , Diendorfer Andreas , Khamina-Kotisch Kseniya , Giorgadze Nino , Pirtskhalava Tamar , Johnson Kurt O , Inman Christina L. , Xue Ailing , Lämmermann Ingo , Meixner Barbara , Wang Lichao , Xu Ming , Grillari Regina , Ogrodnik Mikolaj , Tchkonia Tamar , Hackl Matthias , Kirkland James L , Grillari Johannes
Published: April 2024

In the last decade cellular senescence, a hallmark of aging, has come into focus for pharmacologically targeting aging processes. Senolytics are one of these interventive strategies that have advanced into clinical trials, creating an unmet need for minimally invasive biomarkers of senescent cell load to identify patients at need for senotherapy. We created a landscape of miRNA and mRNA expression in five human cell types induced to senescencein-vitroand provide proof-of-principle evidence that miRNA expression can track senescence burden dynamicallyin-vivousing transgenic p21highsenescent cell clearance in HFD fed mice. Finally, we profiled miRNA expression in seven different tissues, total plasma, and plasma derived EVs of young and 25 months old mice. In a systematic analysis, we identified 22 candidate senomiRs with potential to serve as circulating biomarkers of senescence not only in rodents, but also in upcoming human clinical senolytic trials.
Ergothioneine boosts mitochondrial respiration and exercise performance via direct activation of MPST
Authors: Sprenger Hans-Georg , Mittenbühler Melanie J. , Sun Yizhi , Van Vranken Jonathan G. , Schindler Sebastian , Jayaraj Abhilash , Khetarpal Sumeet A. , Vargas-Castillo Ariana , Puszynska Anna M. , Spinelli Jessica B. , Armani Andrea , Kunchok Tenzin , Ryback Birgitta , Seo Hyuk-Soo , Song Kijun , Sebastian Luke , O’Young Coby , Braithwaite Chelsea , Dhe-Paganon Sirano , Burger Nils , Mills Evanna L. , Gygi Steven P. , Arthanari Haribabu , Chouchani Edward T. , Sabatini David M. , Spiegelman Bruce M.
Published: April 2024

Ergothioneine (EGT) is a diet-derived, atypical amino acid that accumulates to high levels in human tissues. Reduced EGT levels have been linked to age-related disorders, including neurodegenerative and cardiovascular diseases, while EGT supplementation is protective in a broad range of disease and aging models in mice. Despite these promising data, the direct and physiologically relevant molecular target of EGT has remained elusive. Here we use a systematic approach to identify how mitochondria remodel their metabolome in response to exercise training. From this data, we find that EGT accumulates in muscle mitochondria upon exercise training. Proteome-wide thermal stability studies identify 3-mercaptopyruvate sulfurtransferase (MPST) as a direct molecular target of EGT; EGT binds to and activates MPST, thereby boosting mitochondrial respiration and exercise training performance in mice. Together, these data identify the first physiologically relevant EGT target and establish the EGT-MPST axis as a molecular mechanism for regulating mitochondrial function and exercise performance.
Delivering large genes using adeno-associated virus and the CRE-lox DNA recombination system
Authors: Datta Poppy , Rhee Kun Do , Staudt Rylee J , Thompson Jacob M , Hsu Ying , Hassan Salma , Drack Arlene V. , Seo Seongjin
Published: April 2024

Adeno-associated virus (AAV) is a safe and efficient gene delivery vehicle for gene therapies. However, its relatively small packaging capacity limits its use as a gene transfer vector. Here, we describe a strategy to deliver large genes that exceed the AAV’s packaging capacity using up to four AAV vectors and the CRE-lox DNA recombination system. We devised novel lox sites by combining non-compatible and reaction equilibrium-modifying lox site variants. These lox sites facilitate sequence-specific and near-unidirectional recombination of AAV vector genomes, enabling efficient reconstitution of up to 16 kb of therapeutic genes in a pre-determined configuration. Using this strategy, we have developed AAV gene therapy vectors to deliverIFT140,PCDH15,CEP290, andCDH23and demonstrate efficient production of full-length proteins in cultured mammalian cells and mouse retinas. Notably, this approach significantly surpasses the trans-splicing and split-intein-based reconstitution methods in efficiency, requiring lower doses, minimizing or eliminating the production of truncated protein products, and offering flexibility in selecting splitting positions. The CRE-lox approach described here provides a simple and effective platform for producing AAV gene therapy vectors beyond AAV’s packaging capacity.
Microbial Metabolite Trimethylamine N-Oxide PromotesCampylobacter jejuniInfection by Escalating Intestinal Inflammation, Epithelial Damage, and Barrier Disruption
Authors: Smith Caitlyn B. , Gao Angela , Bravo Paloma , Alam Ashfaqul
Published: April 2024

The interactions betweenCampylobacter jejuni, a critical foodborne cause of gastroenteritis, and the intestinal microbiota during infection are not completely understood. The crosstalk betweenC. jejuniand its host is impacted by the gut microbiota through mechanisms of competitive exclusion, microbial metabolites, or immune response. To investigate the role of gut microbiota onC. jejunipathogenesis, we examined campylobacteriosis in the IL10KO mouse model, which was characterized by an increase in the relative abundance of intestinal proteobacteria,E. coli, and inflammatory cytokines duringC. jejuniinfection. We also found a significantly increased abundance of microbial metabolite Trimethylamine N-Oxide (TMAO) in the colonic lumens of IL10KO mice. We further investigated the effects of TMAO onC. jejunipathogenesis. We determined thatC. jejunisenses TMAO as a chemoattractant and the administration of TMAO promotesC. jejuniinvasion into Caco-2 monolayers. TMAO also increased the transmigration ofC. jejuniacross polarized monolayers of Caco-2 cells, decreased TEER, and increasedC. jejuni-mediated intestinal barrier damage. Interestingly, TMAO treatment and presence duringC. jejuniinfection of Caco-2 cells synergistically caused an increased inflammatory cytokine expression, specifically IL-1β and IL-8. These results establish thatC. jejuniutilizes microbial metabolite TMAO for increased virulence during infection.