bluuebunny/crossref_metadata_2025 huggingface dataset:
The HSF-DREB-MYB transcriptional regulatory module regulates flavonol biosynthesis and flavonoid B-ring hydroxylation in banana (Musa acuminata)
Authors: Naik Jogindra , Rajput Ruchika , Singh Samar , Stracke Ralf , Pandey Ashutosh
Published: August 2023

Plant flavonols act primarily as ultraviolet radiation absorbers, reactive oxygen species scavengers, and phytoalexins, and they contribute to biotic and abiotic stress tolerance in plants. Banana (Musa acuminata), an herbaceous monocot and important fruit crop, accumulates flavonol derivatives in different organs, including the edible fruit pulp. Although flavonol content varies greatly in different organs, the molecular mechanisms involving transcriptional regulation of flavonol synthesis in banana are not known. Here, we characterized three SG7-R2R3 MYB transcription factors (MaMYBFA1, MaMYBFA2, and MaMYBFA3) and their upstream regulators, heat shock transcription factor (MaHSF11) and dehydration responsive element binding factor (MaDREB1), to elucidate the molecular mechanism involved in transcriptional regulation of flavonol biosynthesis in banana. MaMYBFA positively regulateflavonol synthase2 (MaFLS2)and downregulatesMaFLS1. We show these transcription factors to be weak regulators of flavonol synthesis. Overexpression ofMaHSF11enhances flavonol contents, particularly that of myricetin, and promotes flavonol B-ring hydroxylation, which contributes to the diversity of flavonol derivatives. MaHSF11 directly interacts with theMaFLS1andflavonoid 3′, 5′-hydroxylase1 (MaF3′5′H1)promoters, bothin vitroandin vivo. MaHSF11 activates the expression ofMaDREB1directly, which in turn regulates the expression ofMaMYBFA3. Overall, our study elucidates a novel regulatory mechanism for flavonol synthesis in banana and suggests possible targets for genetic optimization to enhance nutritional value and stress responses in this globally important fruit crop.

Significance statement

Our study reveals that the three stress-responsive SG7 MYB factors, MaMYBFA1-3, are modest regulators of flavonol biosynthesis in banana. In contrast, the drought– and heat-responsive MaHSF11 plays a strong, positive role in this pathway, enhancing flavonol biosynthesis and flavonoid B-ring hydroxylation by upregulating key biosynthetic genes, such asMaFLS1andMaF3’5’H1, as well asMaDREB1, another regulator of flavonol biosynthesis in banana.
Ligand-induced segregation from large cell-surface phosphatases is a critical step in γδ TCR triggering
Authors: Li Fenglei , Roy Sobhan , Niculcea Jacob , Gould Keith , Adams Erin J. , van der Merwe P. Anton , Choudhuri Kaushik
Published: August 2023

Gamma/delta (γδ) T cells are unconventional adaptive lymphocytes that recognize structurally diverse ligandsviasomatically-recombined antigen receptors (γδ TCRs). The molecular mechanism by which ligand recognition initiates γδ TCR signaling, a process known as TCR triggering, remains elusive. Unlike αβ TCRs, γδ TCRs are not mechanosensitive, and do not require coreceptors or typical binding-induced conformational changes for triggering. Here, we show that γδ TCR triggering by nonclassical MHC class Ib antigens, a major class of ligands recognized by γδ T cells, requires steric segregation of the large cell-surface phosphatases CD45 and CD148 from engaged TCRs at synaptic close contact zones. Increasing access of these inhibitory phosphatases to sites of TCR engagement, by elongating MHC class Ib ligands or truncating CD45/148 ectodomains, abrogates TCR triggering and T cell activation. Our results identify a critical step in γδ TCR triggering and provide insight into the core triggering mechanism of endogenous and synthetic tyrosine-phosphorylated immunoreceptors.
PSPire: a machine learning predictor for high-performance screening of phase-separating proteins without intrinsically disordered regions
Authors: Hou Shuang , Hu Jiaojiao , Yu Zhaowei , Liu Cong , Zhang Yong
Published: August 2023

The burgeoning comprehension of protein phase separation (PS) has ushered in a wealth of bioinformatics tools for the prediction of phase-separating proteins (PSPs). These tools often skew towards PSPs with a high content of intrinsically disordered regions (IDRs), thus frequently undervaluing potential PSPs without IDRs. Nonetheless, PS is not only steered by IDRs but also by the structured modular domains and interactions that aren’t necessarily reflected in amino acid sequences. In this work, we introduce PSPire, a unique machine learning predictor designed to incorporate both residue-level and structure-level features for the precise prediction of PSPs. Compared to current PSP predictors, PSPire shows a notable improvement in identifying PSPs without IDRs, which underscores the crucial role of non-IDR, structure-based characteristics in multivalent interactions throughout the PS process. Additionally, our biological validation experiments substantiate the predictive capacity of PSPire, with 6 out of the 8 chosen candidate PSPs confirmed to form condensates within cells. This highlights the considerable potential of structure-based models in the accurate prediction and comprehensive understanding of protein PS.
Protection of β2GPI Deficient Mice from Thrombosis Reflects a Defect in PAR3-facilitated Platelet Activation
Authors: Kulkarni Paresh P , Alluri Ravi Kumar , Godwin Matthew , Forbes Gabriel L , Merkulova Alona , Vijay Aatira , Palihati Maierdan , Kundu Suman , Jun-Shim Young , Schmaier Alvin , Holinstat Michael , Cameron Scott J. , McCrae Keith R
Published: August 2023

Background

Antibodies to β2-glycoprotein I (β2GPI) cause thrombosis in antiphospholipid syndrome, however the role of β2GPI itself in regulation of coagulation pathwaysin vivois not well understood.

Methods

We developed β2GPI-deficient mice(Apoh-/-)by deleting exon 2 and 3 ofApohusing CRISPR/Cas9 and compared the propensity of wild-type (WT) andApoh-/-mice to develop thrombosis using rose bengal and FeCl3-induced carotid thrombosis, laser-induced cremaster arteriolar injury, and inferior vena cava (IVC) stasis models. We also compared tail bleeding times and assessed platelet activation in WT andApoh-/-mice in the absence and presence of exogenous β2GPI.

Results

Compared to WT littermates,Apoh-/-mice demonstrated a prolonged time to occlusion of the carotid artery after exposure to rose bengal or FeCl3, and reduced platelet and fibrin accumulation in cremasteric arterioles after laser injury. Similarly, significantly smaller thrombi were retrieved from the IVC ofApoh-/-mice 48 hours after IVC occlusion. The activated partial thromboplastin time (aPTT) and prothrombin time, as well as aPTT reagent- and tissue factor-induced thrombin generation times using plasma fromApoh-/-and WT mice revealed no differences. However, we observed significant prolongation of tail bleeding inApoh-/-mice, and reduced P-selectin expression and binding of fibrinogen to the activated α2bβ3 integrin on platelets from these mice after stimulation with low thrombin concentrations; these changes were reversed by exogenous β2GPI. An antibody to PAR3 blocked thrombin-induced activation of WT, but notApoh-/-platelets, as well as the ability of β2GPI to restore the activation response ofApoh-/-platelets to thrombin. β2GPI deficiency did not affect platelet activation by a PAR4-activator peptide, or ADP.

Conclusions

In mice, β2GPI may mediate procoagulant activity by enhancing the ability of PAR3 to present thrombin to PAR4, promoting platelet activation at low thrombin concentrations.

Key Points

β2GPI deficient mice are protected from experimental arterial, venous, and microvascular thrombosis.

β2GPI deficient mice display prolonged tail bleeding times and reduced PAR3-facilitated platelet activation by low concentrations of thrombin.
Predictive evolutionary modelling for influenza virus by site-based dynamics of mutations
Authors: Lou Jingzhi , Liang Weiwen , Cao Lirong , Zhao Shi , Chen Zigui , Yi Chan Renee Wan , Hang Cheung Peter Pak , Zheng Hong , Liu Caiqi , Li Qi , Chun Chong Marc Ka , Zhang Yexian , Yeoh Eng-kiong , Chan Paul Kay-Sheung , Ying Zee Benny Chung , Pun Mok Chris Ka , Wang Maggie Haitian
Published: August 2023

A predictive evolutionary model was developed to forecast representative influenza viral strains and select vaccine strains for upcoming epidemic seasons. Influenza virus continuously evolves to escape human adaptive immunity and generates seasonal epidemics. A computational approach beth-1 that models site-wise mutation dynamics demonstrated remarkable matching of predicted strains to the circulating viruses in subsequent seasons for the influenza A(H1N1)pdm09 and A(H3N2) viruses in both retrospective and prospective validations. The method offers a promising and ready-to-use tool to facilitate vaccine strain selection for the influenza virus, achieved by capturing heterogeneous evolutionary dynamics over genome space-time and linking molecular variants to population immune response.

One-Sentence Summary

A computational model predicts virus evolution and facilitates vaccine strain selection for the influenza virus
Red cabbage juice-mediated gut microbiota modulation improves intestinal epithelial homeostasis and ameliorates colitis
Authors: Jean Wilson Emily , Sirpu Natesh Nagabhishek , Ghadermazi Parsa , Pothuraju Ramesh , Shanmugam Marudhupandiyan , Prajapati Dipakkumar R. , Pandey Sanjit , Kaifi Jussuf T. , Dodam John R. , Bryan Jeffrey , Lorson Christian L. , Watrelot Aude A. , Foster Jason M. , Mansel Thomas J. , Joshua Chan Siu Hung , Batra Surinder K. , Subbiah Jeyamkondan , Rachagani Satyanarayana
Published: August 2023

Gut microbiota plays a crucial role in inflammatory bowel disease (IBD) and has therapeutic benefits. Thus, targeting the gut microbiota is a promising therapeutic approach for IBD treatment. We recently found that red cabbage juice (RCJ) ameliorates dextran sulfate sodium (DSS)-induced colitis in mice. However, the underlying mechanisms remain unknown. The current study investigated the modulation of gut microbiota in response to treatment with RCJ to ameliorate the DSS colitis. The initial results demonstrated that mice treated with DSS + RCJ showed increased body weight and decreased diarrhea and blood in feces compared to the DSS alone group. RCJ ameliorated colitis by regulating the intestinal barrier function by reducing the number of apoptotic cells, improving colonic protective mucin, and increasing tight junction protein in RCJ + DSS groups compared to the DSS group. Short-gun metagenomic analysis revealed significant enrichment of short-chain fatty acid (SCFAs)-producing bacteria(Butyrivibrio, Ruminococcaceae, Acetatifactor muris, Rosburia Sp.CAG:303, Dorea Sp.5-2) increased PPAR-© activation, leading to repression of the nuclear factor κB (NFκB) signaling pathway, thus decreasing the production of crucial inflammatory cytokines and chemokines in the RCJ + DSS groups compared to the DSS group. Pathway abundance analysis showed an increased abundance of the SCFA pathway, reduced histidine degradation (Bacteroides sartorii, and Bacteroides caecimuris), and LCFA production in the RCJ+DSS treated group, suggesting the promotion of good colonic health. Furthermore, increased T-reg (FOXP3+) cells in the colon were due to SCFAs produced by the gut microbiota, which was corroborated by an increase in IL-10, a vital anti-inflammatory cytokine. Thus, our study provides the first evidence that RCJ ameliorates colonic inflammation by modulating the gut microbiota.
Respiration recording for fMRI: breathing belt versus spine coil sensor
Authors: Wilding Marilena , Ischebeck Anja , Zaretskaya Natalia
Published: August 2023

Physiological signals such as pulse and respiration strongly contribute to non-neuronal signal change of the blood oxygenation level-dependent (BOLD) contrast in functional magnetic resonance imaging (fMRI). This has been observed not only during task-based but also during resting-state fMRI measurements, where the confounding influence of physiological signals is most pronounced. Over the last decades, a variety of techniques evolved, aiming at detecting and removing physiological artifacts in fMRI time series. These follow either a solely data-driven approach or rely on externally recorded physiological data. To record cardiac and respiratory signals, typically pulse oximetry or electrocardiography (ECG) and a respiration belt are used, respectively. New technologies allow to capture respiratory signal directly with a sensor placed within the spine coil in the patient table, eliminating the need of a respiration belt, which considerably increases participants’ comfort. However, little is known about the effectiveness of these new technologies and how they compare to the standard respiration belt recording. In the current study, we compared the two devices, respiration belt and spine coil sensor, in their suitability for physiological noise removal during a visual perception task and during rest. We did not find any differences in resting-state functional connectivity (RSFC) or stimulus-related activity between data corrected with the two recording devices. However, we did find reduced residual noise in the time series corrected with spine coil-derived respiration signals compared to belt-based corrected data in the task dataset. Our results show that spine coil-derived respiration recordings are slightly superior to belt respiration recordings for physiological noise removal in task-induced activity, with spine coil recordings having an additional advantage in terms of subject comfort.
Disparities in adherence to antiretroviral therapy of the selected subpopulations among adults living with HIV/AIDS in Tanzania. Analysis of a population-based survey 2016-17
Authors: Adam Dayani , Balan Ramkumar T. , Ismail Abbas
Published: August 2023

Adherence is a critical component of successful HIV treatment among people living with HIV/AIDS. It is essential for achieving and maintaining viral suppression, which is the primary goal of HIV care and treatment. The objective of this study was to assess the disparity of the treatment adherence of selected subpopulations among HIV adult patients in Tanzania. The study used a cross-sectional survey of 792 adults living with HIV/AIDS from 31 regions in Tanzania. A two-stage stratified cluster design was used in this survey and included jackknife replicate sampling weights. Frequency tables displaying frequencies, weighted proportions, and confidence intervals were employed to depict socio-demographics by treatment adherence. Treatment adherence was calculated by subtracting missed doses from prescribed doses, dividing the result by the prescribed dosage, and multiplying by 100 to establish a percentage. Rao-Scott chi-square was used to produce the weighted proportions of the adherence within subpopulations. Also, the Adjusted Wald Test was used to examine whether or not the subpopulations are similar to or different in terms of their level of treatment adherence. The results showed that there was a significant difference in treatment adherence between the selected subpopulations. The majority of the selected subpopulations, including those based on age, sex, marital status, and level of education, were found to have disparities in the level of treatment adherence. However, the study also revealed no disparities in treatment adherence between urban and rural settings, married and widowed, age groups of 25 to 34, and those of 55 and over. The study’s findings revealed considerable disparities in treatment adherence between various subpopulations, emphasizing the necessity for specifically developed interventions to address these disparities to attain better health outcomes among adults living with HIV/AIDS.
Prevalence of Modifiable Risk Factors for Cardiovascular Disease among School-going Children and Adolescents in Eldoret, Kenya
Authors: Magutah Karani , Mbuthia Grace Wambura , Osengo Gilbert , Odhiambo Dancun , Meiring Rebecca
Published: August 2023

Cardiovascular disease (CVD) prevalence in Kenya is rising. Overweight, pre-hypertension and physical inactivity in younger ages is contributory. These risk factors are inadequately documented among Kenyan children and adolescents, hampering CVD prevention.

This cross-sectional study randomly sampled 384 school children and adolescents. After obtaining assent and consent, global physical activity (PA) questionnaire was used to assess PA. Body mass index (BMI), Waist-Hip Ratio (WHR) and Waist-Height Ratio (WHtR) were determined. Blood pressure (BP) was also measured.

Participants were 14.6±2.7 years, and 62.6% were female. Overall BMI was 19.8±3.9 kg/m2with 8% having ≥25.0 kg/m2, 87% of whom were in secondary schools. Using SBP, 27.9% were at risk of CVD. For age ≥13 years old, males and females proportions were 42.5% and 20% respectively while that for <13 years old, it was 26.5% and 27% respectively. For DBP, 12.8% had elevated- to-hypertensive BP. For ages ≥ 13 years old, this was 13.2% and 8.3% for males and females respectively and for the <13 years old, the respective percentages were 11.8 and 25.4. Combining SBP and DBP, 8.1% of participants, mostly males, had elevated-to-hypertensive BP. Thirty-one percent of boys and 15.6% of girls were at CVD risk using respective WHR cutoffs of 0.90 and 0.85 (males, 0.93±0.02; females, 0.89±0.03). For WHtR, 39.6% of boys had values >0.463 cut-off (0.493±0.02), with 52.6% in secondary schools against 32.4% for girls having >0.469 cut-off (0.517±0.05), 69.7% being in secondary schools. Overall, 45% of participants were sports-inactive and 77.2% did minimal PA.

Among school-going children and adolescents in Eldoret, Kenya, prevalence of CVD risk-factors was high especially among boys and in high schools. Large proportions had elevated BP, BMI, WHR and WHtR, and, further, were sedentary, posing high CVD risk. Lifestyle interventions to mitigate this public health concern among children and adolescent are urgently needed.
Improving diagnosis of non-malarial fevers in Senegal:Borreliaand the contribution of tick-borne bacteria
Authors: Levine Zoë C. , Sene Aita , Mkandawire Winnie , Deme Awa B. , Ndiaye Tolla , Sy Mouhamad , Gaye Amy , Diedhiou Younouss , Mbaye Amadou M. , Ndiaye Ibrahima , Gomis Jules , Ndiop Médoune , Sene Doudou , Paye Marietou Faye , MacInnis Bronwyn , Schaffner Stephen F. , Park Daniel J. , Badiane Aida S. , Colubri Andres , Ndiaye Mouhamadou , Sy Ngayo , Sabeti Pardis C. , Ndiaye Daouda , Siddle Katherine J.
Published: August 2023

The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata from febrile patients and healthy controls in a low malaria burden area. Using 16S and unbiased sequencing, we detected viral, bacterial, or eukaryotic pathogens in 29% of NMFI cases. Bacteria were the most common, with relapsing feverBorreliaand spotted feverRickettsiafound in 15% and 3.7% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosedPlasmodium, including one putativeP. ovaleinfection. We developed a logistic regression model to distinguishBorreliafrom NMFIs with similar presentation based on symptoms and vital signs. These results highlight the challenge and importance of improved diagnostics, especially forBorrelia, to support diagnosis and surveillance.
Breast cancer epidemiology in women from colombian caribbean region during 2018-2021
Authors: Pérez Bravo Valentina Vanessa , Vásquez Serge Valentina Alexandra , Norwood Lobo George , Alcocer Olaciregui Adalgisa , Vargas Moranth Rusvelt
Published: August 2023

Background

Breast cancer is a global public health problem, representing a significant burden at the personal, collective, economic and quality of life level. It is necessary to consider the incidence, prevalence and mortality of this disease with a regional approach, so the objective of this work is to describe the epidemiological behavior of this tumor in the departments of the Colombian Caribbean Region during the period 2018 to 2021.

Methodology

Descriptive, retrospective study. Data from a secondary source (Cuenta de Alto Costo) was taken through the Higia platform. Rates x 100,000 of proportion of new cases reported, prevalence and incidence, by departments are analyzed. Data was imported from a downloadable.csv file into Excel and then into SPSS V22.

Results

The indicators analyzed showed a heterogeneous behavior in the 8 departments of the Region. Atlántico and Bolívar were the departments with similar and higher figures in the 4 years observed than those of the country and there were atypical values in San Andrés. La Guajira was the only department with a sustained tendency to increase in incidence, prevalence and mortality.
Nutritional traits in the prodromal phase of Parkinson’s disease in community-dwelling older adults in Japan
Authors: Yamaguchi Takashi , Nozaki Ryota , Taguchi Keita , Suzuki Yoshio , Takahashi Kai , Takahashi Kenta , Iwaoka Kazuhiro , Sato Yuriko , Terauchi Takahiro , Akasaka Hiroshi , Ishizuka Naoki , Uchida Kazuhiro , Ninomiya Toshiharu , Maeda Tetsuya
Published: August 2023

The growing aging population means that increasing numbers of people are living with Parkinson’s disease (PD). Although dopamine replacement is effective, there are currently no curative or disease-modifying treatments. Nutrition is a well-known environmental risk factor of PD. This study aimed to clarify the relationship between nutritional traits and the prodromal phase of PD.

Subjects were enrolled from community-dwelling older adults. To identify individuals with prodromal PD (PPD), probability of PPD (PPP) and mild parkinsonian sign (MPS) assessments were used. Nutritional status was evaluated using a self-administered food frequency questionnaire form. Intakes of total energy, the three major nutrients (fat, protein, and carbohydrate), B vitamins, water, and dietary fiber were calculated. Nutrient intake in PPD was analyzed using analysis of covariance with age and sex as covariates.

We enrolled 305 subjects. The prevalence of older adults living with PPD was 4.1% by PPP ≥ 0.3 and 21.0% by MPS criteria. Compared with subjects without PPD, individuals with PPP ≥ 0.3 had significantly higher fat intake (33.4 ± 8.8 vs. 29.3 ± 6.7 g/1000 kcal/day, p=0.037) and lower carbohydrate intake (121.4 ± 19.0 vs. 132.1 ± 17.7 g/1000 kcal/day, p=0.039), and MPS-positive subjects had significantly lower total energy intake (1817.5 ± 384.7 vs. 1933.7 ± 433.7 kcal/day, p=0.012).

In this community-based cross-sectional study, nutritional traits differed between older individuals with and without PPD; these differences were more pronounced when the PPP was used to evaluate PPD. Nutrition and diet may thus modify PD incidence.
Personalized Machine Learning using Passive Sensing and Ecological Momentary Assessments for Meth Users in Hawaii: A Research Protocol
Authors: Washington Peter
Published: August 2023

Background

Artificial intelligence (AI)-powered digital therapies which detect meth cravings delivered on consumer devices have the potential to reduce these disparities by providing remote and accessible care solutions to Native Hawaiians, Filipinos, and Pacific Islanders (NHFPI) communities with limited care solutions. However, NHFPI are fully understudied with respect to digital therapeutics and AI health sensing despite using technology at the same rates as other races.

Objective

We seek to fulfill two research aims: (1) Understand the feasibility of continuous remote digital monitoring and ecological momentary assessments (EMAs) in NHFPI in Hawaii by curating a novel dataset of longitudinal FitBit biosignals with corresponding craving and substance use labels. (2) Develop personalized AI models which predict meth craving events in real time using wearable sensor data.

Methods

We will develop personalized AI/ML (artificial intelligence/machine learning) models for meth use and craving prediction in 40 NHFPI individuals by curating a novel dataset of real-time FitBit biosensor readings and corresponding participant annotations (i.e., raw self-reported substance use data) of their meth use and cravings. In the process of collecting this dataset, we will glean insights about cultural and other human factors which can challenge the proper acquisition of precise annotations. With the resulting dataset, we will employ self-supervised learning (SSL) AI approaches, which are a new family of ML methods that allow a neural network to be trained without labels by being optimized to make predictions about the data itself. The inputs to the proposed AI models are FitBit biosensor readings and the outputs are predictions of meth use or craving. This paradigm is gaining increased attention in AI for healthcare.

Conclusions

We expect to develop models which significantly outperform traditional supervised methods by fine-tuning to an individual subject’s data. Such methods will enable AI solutions which work with the limited data available from NHFPI populations and which are inherently unbiased due to their personalized nature. Such models can support future AI-powered digital therapeutics for substance abuse.
Multimodal Data Hybrid Fusion and Natural Language Processing for Clinical Prediction Models
Authors: Ye Jiancheng , Hai Jiarui , Song Jiacheng , Wang Zidan
Published: August 2023

Objective

To propose a novel approach for enhancing clinical prediction models by combining structured and unstructured data with multimodal data fusion.

Methods

We presented a comprehensive framework that integrated multimodal data sources, including textual clinical notes, structured electronic health records (EHRs), and relevant clinical data from National Electronic Injury Surveillance System (NEISS) datasets. We proposed a novel hybrid fusion method, which incorporated state-of-the-art pre-trained language model, to integrate unstructured clinical text with structured EHR data and other multimodal sources, thereby capturing a more comprehensive representation of patient information.

Results

The experimental results demonstrated that the hybrid fusion approach significantly improved the performance of clinical prediction models compared to traditional fusion frameworks and unimodal models that rely solely on structured data or text information alone. The proposed hybrid fusion system with RoBERTa language encoder achieved the best prediction of the Top 1 injury with an accuracy of 75.00% and Top 3 injuries with an accuracy of 93.54%.

Conclusion

Our study highlights the potential of integrating natural language processing (NLP) techniques with multimodal data fusion for enhancing clinical prediction models’ performances. By leveraging the rich information present in clinical text and combining it with structured EHR data, the proposed approach can improve the accuracy and robustness of predictive models. The approach has the potential to advance clinical decision support systems, enable personalized medicine, and facilitate evidence-based health care practices. Future research can further explore the application of this hybrid fusion approach in real-world clinical settings and investigate its impact on improving patient outcomes.
Protozoan predation enhances stress resistance and antibiotic tolerance in the opportunistic pathogenBurkholderia cenocepaciaby triggering the SOS response
Authors: Morón Álvaro , Belinchón Iván , Tarhouchi Alaa E. , Valenzuela Juan M. , de Francisco Patricia , Martín-González Ana , Amaro Francisco
Published: August 2023

Bacterivorous protists are thought to serve as training grounds for bacterial pathogens by subjecting them to the same hostile conditions that they will encounter in the human host. Bacteria that survive intracellular digestion exhibit enhanced virulence and stress resistance after successful passage through protozoa but the underlying mechanisms remain to be clarified. Here we show that the opportunistic pathogenBurkholderia cenocepaciasurvives phagocytosis by ciliates found in domestic and hospital sink drains, and viable bacteria are expelled packaged in respirable membrane vesicles with enhanced resistance to oxidative stress, desiccation and antibiotics, thereby contributing to bacterial dissemination in the environment. By using diverse methodological approaches, we demonstrate that reactive oxygen species generated within the protozoan phagosome promote the formation of persisters tolerant to ciprofloxacin by activating the bacterial SOS response. Besides, we show that genes encoding antioxidant enzymes are upregulated during passage through ciliates increasing bacterial resistance to oxidative radicals. We prove that suppression of the SOS response impairs bacterial intracellular survival and persister formation within protists. This study highlights the significance of protozoan food vacuoles as niches that foster bacterial adaptation in natural and built environments and suggests that persister switch within phagosomes may be a widespread phenomenon in bacteria surviving intracellular digestion.
Age and obesity-driven changes in the extracellular matrix of the primary tumor and metastatic site influence tumor invasion and metastatic outgrowth
Authors: Conner Sydney J. , Guarin Justinne R. , Borges Hannah B. , Salhany Kenneth J. , Mensah Diamond N. , Hamilton Grace A. , Le Giang H. , Oudin Madeleine J.
Published: August 2023

Younger age and obesity increase the incidence and metastasis of triple-negative breast cancer (TNBC), an aggressive subtype of breast cancer. The extracellular matrix (ECM) promotes tumor invasion and metastasis. We characterized the effect of age and obesity on the ECM of mammary fat pads, lungs, and liver using a diet-induced obesity (DIO) model. At 4 week intervals, we either injected the mammary fat pads with allograft tumor cells to characterize tumor growth and metastasis or isolated the mammary fat pads and livers to characterize the ECM. Age had no effect on tumor growth but increased lung and liver metastasis after 16 weeks. Obesity increased tumor growth starting at 12 weeks, increased liver metastasis only at 4 weeks, and weight gain correlated to increased lung but not liver metastasis. Utilizing whole decellularized ECM coupled with proteomics, we found that early stages of obesity were sufficient to induce changes in the ECM composition and invasive potential of mammary fat pads with increased abundance of pro-invasive ECM proteins Collagen IV and Collagen VI. We identified cells of stromal vascular fraction and adipose stem and progenitor cells as primarily responsible for secreting Collagen IV and VI, not adipocytes. We characterized the changes in ECM in the lungs and liver, and determined that older age decreases the metastatic potential of lung and liver ECM while later-stage obesity increases the metastatic potential. These data implicate ECM changes in the primary tumor and metastatic microenvironment as mechanisms by which age and obesity contribute to breast cancer progression.

Significance

Younger age and obesity increase the incidence and metastasis of triple-negative breast cancer. Our data suggest that changes in the breast, lung and liver ECM are driving some of these effects.
VapC12 ribonuclease toxin modulates host immune response duringMycobacterium tuberculosisinfection
Authors: Tyagi Shaifali , Sadhu Srikanth , Sharma Taruna , Paul Abhijit , Pandey Manitosh , Nain Vaibhav , Rathore Deepak , Chatterjee Samrat , Awasthi Amit , Pandey Amit Kumar
Published: August 2023

Mechanistic understanding of antibiotic persistence is a prerequisite in controlling the emergence of MDR cases in Tuberculosis (TB). We have reported that the cholesterol-induced activation of VapC12 ribonuclease is critical for disease persistence in TB. In this study, we observed that relative to the wild type, mice infected with ΔvapC12induced a proinflammatory response, had a higher pathogen load, and responded better to the anti-TB treatment. In a high-dose infection model, all the mice infected with ΔvapC12succumbed early to the disease. Finally, we reported that the above phenotype of ΔvapC12was dependent on the presence of the TLR4 receptor. Overall, the data suggest that the inability of ΔvapC12to resolve neutrophil-mediated inflammation reduced bacterial killing by altering the T-cell response. In conclusion, our findings suggest the role of the VapC12 toxin in modulating the host’s innate immune response in ways that favor the long-term survival of the pathogen inside the host.
Remote sensing of emperor penguin abundance and breeding success
Authors: Winterl Alexander , Richter Sebastian , Houstin Aymeric , Barracho Téo , Boureau Matthieu , Cornec Clément , Couet Douglas , Cristofari Robin , Eiselt Claire , Fabry Ben , Krellenstein Adélie , Mark Christoph , Mainka Astrid , Ménard Delphine , Morinay Jennifer , Pottier Susie , Schloesing Elodie , Bohec Céline Le , Zitterbart Daniel P.
Published: August 2023

Emperor penguins (Aptenodytes forsteri) are under increasing environmental pressure. Monitoring colony size and trends of this Antarctic seabird relies primarily on satellite imagery recorded near the end of the breeding season, when illumination levels are sufficient to capture images, but colony occupancy is highly variable. To correct population estimates for this variability, we develop a phenological model that accurately predicts the number of breeding pairs and fledging chicks, as well as key phenological events such as arrival, hatching and foraging times, from as few as six data points from a single season. The ability to extrapolate occupancy from sparse data makes the model particularly useful for monitoring remotely sensed animal colonies where ground-based population estimates are very rare or unavailable.

Teaser

The Emperor penguin becomes the Southern Ocean’s canary in a coal mine through remote sensing its annual breeding success.
Role of protonation states in stability of molecular dynamics simulations of high-resolution membrane protein structures
Authors: Lasham Jonathan , Djurabekova Amina , Zickermann Volker , Vonck Janet , Sharma Vivek
Published: August 2023

Classical molecular dynamics (MD) simulations provide unmatched spatial and time resolution of protein structure and function. However, accuracy of MD simulations often depends on the quality of force field parameters and the time scale of sampling. Another limitation of conventional MD simulations is that the protonation states of titratable amino acid residues remain fixed during simulations, even though protonation state changes coupled to conformational dynamics are central to protein function. Due to the uncertainty in selecting protonation states, classical MD simulations are sometimes performed with all amino acids modeled in their standard charged states at pH 7. Here we performed and analyzed classical MD simulations on high-resolution cryo-EM structures of two membrane proteins that transfer protons by catalyzing protonation/deprotonation reactions. In simulations performed with amino acids modeled in their standard protonation state the structure diverges far from its starting conformation. In comparison, MD simulations performed with pre-determined protonation states of amino acid residues reproduce the structural conformation, protein hydration, and protein-water and protein-protein interactions of the structure much better. The results suggest it is crucial to perform basic protonation state calculations, especially on structures where protonation changes play an important functional role, prior to launching any MD simulations. Furthermore, the combined approach of protonation state prediction and MD simulations can provide valuable information on the charge states of amino acids in the cryo-EM sample. Even though accurate prediction of protonation states currently remains a challenge, we introduce an approach of combining pKa prediction with cryo-EM density map analysis that helps in improving not only the protonation state predictions, but also the atomic modeling of density data.
Understanding Author Choices in the Current Conservation Publishing Landscape
Authors: Yoh Natalie , Holle Mukhlish Jamal Musa , Willis Jasmin , Rudd Lauren F , Fraser Iain M , Verissimo Diogo
Published: August 2023

Conservation literature addresses a broad spectrum of interdisciplinary questions and benefits most by representing a diverse range of authors, particularly those from countries where much conservation work is focused. In other disciplines, it is well known that barriers and biases exist in the academic publishing sphere, which can impact research dissemination and an author’s career development. Here, we used a Discrete Choice Experiment to determine how different journal attributes impact authors’ choices of where to publish in conservation. We identified three demographic groups across 1038 respondents who have previously published in conservation journals, each exhibiting different publishing preferences. Only two attributes showed a consistent response across groups: cost to publish negatively impacted journal choice, including for those in high-income countries, and authors had a consistent preference for double-blind review. Authors from middle-income countries were willing to pay more for society-owned journals, unlike authors from higher-income countries. Journals with a broad geographical scope, which were Open Access, and which had higher impact factors were preferable to two of the three demographic groups. However, we found journal scope and Open Access were more important in dictating journal choice than impact factor. Overall, our findings demonstrate that different demographics experience different preferences or limitations depending on attributes such as a journal’s Open Access policy. However, the scarcity of published authors from low-income countries highlights further, pervasive barriers to representation in conservation research. Based on our findings, we provide recommendations to conservation-related journals to reduce barriers to publishing and ultimately benefit conservation science.
A General Framework to Interpret Hydrogen-Deuterium Exchange Native Mass Spectrometry of G-Quadruplex DNA
Authors: Largy Eric , Ranz Matthieu , Gabelica Valérie
Published: August 2023

G-quadruplexes (G4s) are secondary structures formed by guanine-rich oligonucleotides involved in various biological processes. However, characterizing G4s is challenging because of their structural polymorphism. Here, we establish how hydrogen-deuterium exchange native mass spectrometry (HDX/MS) can help to characterize G4 structures and dynamics in solution. We correlated the time range of G4 exchange to the number of guanines involved in inner and outer tetrads. We also established relationships between exchange rates, number of tetrads, bound cations, and stability. The use of HDX/native MS allows for the determination of tetrads formed and assessment of G4 stability at a constant temperature. A key finding is that stable G4s exchange through local fluctuations (EX2 exchange), whereas less stable G4s also undergo exchange through partial or complete unfolding (EX1 exchange). Deconvolution of the bimodal isotope distributions resulting from EX1 exchange provides valuable insight into the kinetics of folding and unfolding processes, and allows one to detect and characterize transiently unfolded intermediates, even if scarcely populated. HDX/native MS thus represents a powerful tool for a more comprehensive exploration of the folding landscapes of G4s.

TOC graphic
Targeted lipid A modification ofShigellavaccine strains reduced endotoxicity without compromising immunogenicity or invasiveness
Authors: Sherman Matthew E , Michalski Jane , Das Sayan , Yang Hyojik , Barnoy Shoshana , Chandrasekaran Lakshmi , Venkatesan Malabi , Ernst Robert K
Published: August 2023

Shigellainfection contributes significantly to the global disease burden, especially affecting young children in developing countries. Currently, a vaccine againstShigellais unavailable and the prevalence of antibiotic resistance amongstShigellaspecies is continually rising. Live-attenuatedShigellavaccine candidates developed at Walter Reed Army Institute of Research have shown remarkable immunogenicity but exhibit adverse reactogenicity, most likely due to the highly toxic lipid A moiety present on the bacterial membrane. Previous attempts at reducing the endotoxicity have focused on deletion of intrinsic lipid A biosynthesis enzymes. In this study, we instead introduce exogenous lipid A modifying enzymes, generating targeted modifications in the lipid A structure, leading to a dampened TLR4 response within the host. In doing so, we generated vaccine candidates with detoxified lipid A and unaltered O-antigen structure thereby preserving the serotype-specific immunity while reducing endotoxicity.
Prolonging the Delivery of Influenza Virus Vaccine Improves the Quantity and Quality of the Induced Immune Responses in Mice
Authors: Beukema M. , Gong S. , Al-Jaawni K. , de Vries-Idema J. J. , Krammer F. , Zhou F. , Cox R. J. , Huckriede A. L. W.
Published: August 2023

Influenza vaccines play a vital role in protecting individuals from influenza virus infection and severe illness. However, current influenza vaccines have suboptimal efficacy, which is further reduced in cases where the vaccine strains do not match the circulating strains. One strategy to enhance the efficacy of influenza vaccines is by extended antigen delivery, thereby mimicking the antigen kinetics of a natural infection. Prolonging antigen availability was shown to quantitatively enhance influenza virus-specific immune responses but how it affects the quality of the induced immune response is unknown. Therefore, the current study aimed to investigate whether prolongation of the delivery of influenza vaccine improves the quality of the induced immune responses over that induced by prime-boost immunization. To study this, mice were given daily doses of whole inactivated influenza virus vaccine for periods of 14, 21, or 28 days; the control group received prime-boost immunization with a 28 days interval. Our data show that the highest levels of cellular and humoral immune responses were induced by 28 days of extended antigen delivery, followed by 21, and 14 days of delivery, and prime-boost immunization. Moreover, prolonging vaccine delivery also improved the quality of the induced antibody response, as indicated by higher level of high avidity antibodies, a balanced IgG subclass profile, and a higher level of cross-reactive antibodies. Overall, our findings contribute to a better understanding of the immune response to influenza vaccination and have important implications for the design and development of future slow-release influenza vaccines.
Lineage tracing of newly accrued nuclei in skeletal myofibers uncovers distinct transcripts and interplay between nuclear populations
Authors: Sun Chengyi , Swoboda Casey O. , Petrany Michael J. , Parameswaran Sreeja , VonHandorf Andrew , Weirauch Matthew T. , Lepper Christoph , Millay Douglas P.
Published: August 2023

Multinucleated skeletal muscle cells have an obligatory need to acquire additional nuclei through fusion with activated skeletal muscle stem cells when responding to both developmental and adaptive growth stimuli. A fundamental question in skeletal muscle biology has been the reason underlying this need for new nuclei in syncytial cells that already harbor hundreds of nuclei. To begin to answer this long-standing question, we utilized nuclear RNA-sequencing approaches and developed a lineage tracing strategy capable of defining the transcriptional state of recently fused nuclei and distinguishing this state from that of pre-existing nuclei. Our findings reveal the presence of conserved markers of newly fused nuclei both during development and after a hypertrophic stimulus in the adult. However, newly fused nuclei also exhibit divergent gene expression that is determined by the myogenic environment to which they fuse. Moreover, accrual of new nuclei through fusion is required for nuclei already resident in adult myofibers to mount a normal transcriptional response to a load-inducing stimulus. We propose a model of mutual regulation in the control of skeletal muscle development and adaptations, where newly fused and pre-existing myonuclear populations influence each other to maintain optimal functional growth.
Conservation of affinity rather than sequence underlies a dynamic evolution of the motif-mediated p53/MDM2 interaction in teleosts
Authors: Mihalič Filip , Arcila Dahiana , Pettersson Mats E. , Farkhondehkish Pouria , Andersson Eva , Andersson Leif , Betancur-R Ricardo , Jemth Per
Published: August 2023

The transcription factor and cell cycle regulator p53 is marked for degradation by the ubiquitin ligase MDM2. The interaction between these two proteins is mediated by a conserved binding motif in the disordered p53 transactivation domain (p53TAD) and the folded SWIB domain in MDM2. The conserved motif in p53TAD from zebrafish displays a 20-fold weaker interaction with MDM2, compared to the interaction in human and chicken. To investigate this apparent difference, we tracked the molecular evolution of the p53TAD/MDM2 interaction among ray- finned fishes (Actinopterygii), the largest vertebrate clade. Intriguingly, phylogenetic analyses, ancestral sequence reconstructions, and binding experiments showed that different loss-of- affinity changes in the canonical binding motif within p53TAD have occurred repeatedly and convergently in different fish lineages, resulting in relatively low extant affinities (KD= 0.5-5 μM). However, for eleven different fish p53TAD/MDM2 interactions, non-conserved regions flanking the canonical motif increased the affinity 4 to 73-fold to be on par with the human interaction. Our findings suggest that compensating changes at conserved and non-conserved positions within the motif, as well as in flanking regions of low conservation, underlie a stabilizing selection of “functional affinity” in the p53TAD/MDM2 interaction. Such interplay complicates bioinformatic prediction of binding and call for experimental validation. Motif- mediated protein-protein interactions involving short binding motifs and folded interaction domains are very common across multicellular life. It is likely that evolution of affinity in motif- mediated interactions often involves an interplay between specific interactions made by conserved motif residues and non-specific interactions by non-conserved disordered regions.
iATPSnFR2: a high dynamic range fluorescent sensor for monitoring intracellular ATP
Authors: Marvin Jonathan S. , Kokotos Alexandros C. , Kumar Mukesh , Pulido Camila , Tkachuk Ariana N. , Yao Jocelyn Shuxin , Brown Timothy A. , Ryan Timothy A.
Published: August 2023

We developed a significantly improved genetically encoded quantitative adenosine triphosphate (ATP) sensor to provide real-time dynamics of ATP levels in subcellular compartments. iATPSnFR2 is a variant of iATPSnFR1, a previously developed sensor that has circularly permuted super-folder GFP inserted between the ATP-binding helices of theε-subunit of a bacterial F0-F1ATPase. Optimizing the linkers joining the two domains resulted in a ∼ 5-6 fold improvement in the dynamic range compared to the previous generation sensor, with excellent discrimination against other analytes and affinity variants varying from 4 μM to 500 μM. A chimeric version of this sensor fused to either the HaloTag protein or a suitably spectrally separated fluorescent protein, provides a ratiometric readout allowing comparisons of ATP across cellular regions. Subcellular targeting of the sensor to nerve terminals reveals previously uncharacterized single synapse metabolic signatures, while targeting to the mitochondrial matrix allowed direct quantitative probing of oxidative phosphorylation dynamics.

Significance Statement

Adenosine triphosphate (ATP) is a key metabolite necessary for cellular life. Here we develop a next-generation genetically encoded ratiometric fluorescent ATP sensor that allows subcellular tracking of ATP levels in living cells. The large dynamic range makes it possible to follow the dynamics of this metabolite across cells and subcellular regions under different metabolic stressors. We expect that iATPSnFR2 will provide researchers with exciting new opportunities to study ATP dynamics with temporal and spatial resolution that has, until now, been unavailable.