bluuebunny/crossref_metadata_2025 huggingface dataset:
CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments
Authors: Qu Yuanhao , Huang Kaixuan , Cousins Henry , Johnson William A. , Yin Di , Shah Mihir , Zhou Denny , Altman Russ , Wang Mengdi , Cong Le
Published: April 2024

The introduction of genome engineering technology has transformed biomedical research, making it possible to make precise changes to genetic information. However, creating an efficient gene-editing system requires a deep understanding of CRISPR technology, and the complex experimental systems under investigation. While Large Language Models (LLMs) have shown promise in various tasks, they often lack specific knowledge and struggle to accurately solve biological design problems. In this work, we introduce CRISPR-GPT, an LLM agent augmented with domain knowledge and external tools to automate and enhance the design process of CRISPR-based gene-editing experiments. CRISPR-GPT leverages the reasoning ability of LLMs to facilitate the process of selecting CRISPR systems, designing guide RNAs, recommending cellular delivery methods, drafting protocols, and designing validation experiments to confirm editing outcomes. We showcase the potential of CRISPR-GPT for assisting non-expert researchers with gene-editing experiments from scratch and validate the agent’s effectiveness in a real-world use case. Furthermore, we explore the ethical and regulatory considerations associated with automated gene-editing design, highlighting the need for responsible and transparent use of these tools. Our work aims to bridge the gap between biological researchers across various fields with CRISPR genome engineering technology and demonstrate the potential of LLM agents in facilitating complex biological discovery tasks.
Discovery and characterization of unusual O-link glycosylation of IgG4 antibody using LC-MS
Authors: Janecki Dariusz J. , Kao-Scharf Chi-Ya , Hoffmann Andreas
Published: April 2024

4

The analysis of several batches of commercial biopharmaceutical product Dupixent using top-down intact mass spectrometry revealed that this immunoglobulin IgG4 features a small amount of O-link glycosylation in Fab region. This is the first report of an O-link glycosylation in IgG4 antibody. The paper describes most likely structure of the O-link glycosylation as well as probable location(s). The relative quantification showed only small quantity of the modification but appearing consistently in several batches of Dupixent. The O-link glycosylation site was characterized by standard tryptic peptide digestion and LC-MS analysis approach.
Estrogen Receptor α/14-3-3 molecular glues as alternative treatment strategy for endocrine resistant breast cancer
Authors: Visser Emira J. , Collier Maria Donaldson , Siefert Joseph C. , Konstantinidou Markella , Paul Susana N. , Berkhout Jari B. , Virta Johanna M. , Somsen Bente A. , Cossar Peter , Miley Galen , Luzietti Lara , Young Leonie , Vareslija Damir , Buluwela Lakjaya , Ali Simak , Meijer Onno C. , Arkin Michelle R. , Ottmann Christian , Zwart Wilbert , Brunsveld Luc
Published: April 2024

Endocrine resistance in breast cancer treatment is a major clinical hurdle, causing an urgent need for alternative treatment modalities. The suppressive protein-protein interaction (PPI) between Estrogen Receptor alpha (ERα) and the adaptor protein 14-3-3 offers such a strategy. Here, we report the biological impact of small-molecule ‘molecular glues’ of this ERα/14-3-3 PPI by using both fusicoccin-derived semi-synthetic natural products and fully synthetic covalent drug-like molecules. We show that the ERα/14-3-3 PPI is stabilized by both the natural- and synthetic glues, resulting in a suppression of ERα transcriptional activity and a blockade of breast cancer cell proliferation, both in cell lines and in organoids derived from endocrine therapy resistant breast cancer patients. Importantly, the molecular glues effectively blocked ERα action even in case of constitutively active clinical ERα mutations, providing the foundations for developing alternative classes of ERα targeting compounds to improve treatment of patients with endocrine-therapy resistant breast cancer.

Abstract Figure
A deoxynucleoside triphosphate triphosphohydrolase promotes cell cycle progression inCaulobacter crescentus
Authors: Hellenbrand Chandler N. , Stevenson David M. , Gromek Katarzyna A. , Amador-Noguez Daniel , Hershey David M.
Published: April 2024

Intracellular pools of deoxynucleoside triphosphates (dNTPs) are strictly maintained throughout the cell cycle to ensure accurate and efficient DNA replication. DNA synthesis requires an abundance of dNTPs, but elevated dNTP concentrations in nonreplicating cells delay entry into S phase. Enzymes known as deoxyguanosine triphosphate triphosphohydrolases (Dgts) hydrolyze dNTPs into deoxynucleosides and triphosphates, and we propose that Dgts restrict dNTP concentrations to promote the G1 to S phase transition. We characterized a Dgt from the bacteriumCaulobacter crescentustermedflagellar signaling suppressor C(fssC) to clarify the role of Dgts in cell cycle regulation. DeletingfssCincreases dNTP levels and extends the G1 phase of the cell cycle. We determined that the segregation and duplication of the origin of replication (oriC) is delayed in ΔfssC, but the rate of replication elongation is unchanged. We conclude that dNTP hydrolysis by FssC promotes the initiation of DNA replication through a novel nucleotide signaling pathway. This work further establishes Dgts as important regulators of the G1 to S phase transition, and the high conservation of Dgts across all domains of life implies that Dgt-dependent cell cycle control may be widespread in both prokaryotic and eukaryotic organisms.

Importance

Cells must faithfully replicate their genetic material in order to proliferate. Studying the regulatory pathways that determine when a cell initiates DNA replication is important for understanding fundamental biological processes, and it can also improve the strategies used to treat diseases that affect the cell cycle. Here, we describe a nucleotide signaling pathway that regulates when cells will begin DNA replication. We show that this pathway promotes the transition from the G1 to the S phase of the cell cycle in the bacteriumCaulobacter crescentusand propose that this pathway is prevalent in all domains of life.
Multiple Omics Find New Cecal Microbial Features Associated with Feed Efficiency in Ducks
Authors: Guo Rongbing , Chang Yuguang , Wang Dandan , Sun Hanxue , Zhao Ayong , Gu Tiantian , Zong Yibo , Zhou Shiheng , Huang Zhizhou , Chen Li , Tian Yong , Xu Wenwu , Lu Lizhi , Zeng Tao
Published: April 2024

As the global population continues to grow exponentially, the competition for resources between livestock and humans has become increasingly intense. Breeding efficient animal breeds, fully utilizing feed resources, and reducing environmental damage are major challenges facing the livestock industry. To address these issues, enhancing the feed utilization efficiency in the poultry industry is crucial. Recent studies have elucidated the pivotal role of gut microbiota in modulating the feeding behavior of their host organisms. Thus, we used metagenomics, transcriptomics, and metabolomics to explore how the intestinal microbiome affects the feed utilization efficiency in ducks. Our metagenomic analysis revealed a significant up-regulation ofElusimicrobiotaat the phylum level within the high residual feed intake (HRFI) group, in comparison to the low residual feed intake (LRFI) group. Additionally, functional analysis using Clusters of Orthologous Groups of proteins (COG) indicated prominent disparities in the category of secondary metabolites biosynthesis, transport, and catabolism between the HRFI and LRFI groups. Furthermore, our metabolomics investigation identified an upregulated expression of the secondary metabolite 15-deoxy-Δ12,14-prostaglandin J2 (15d-PGJ2) in the HRFI group compared to the LRFI group. Liver transcriptome analysis identified prostaglandin-endoperoxide synthase 2 (PTGS2) as a key hub gene, exerting significant regulatory influence within the arachidonic acid pathway. Notably, the metabolite 15d-PGJ2 is a terminal product in the metabolic pathway of arachidonic acid. The correlation analysis between the cecal microbiota and differential metabolites revealed a significant negative correlation betweenElusimicrobiotaand the metabolite 15d-PGJ2. In summary, we assumed that the intestinal microbiomeElusimicrobiotaregulates the expression of thePTGS2gene, consequently inducing variations inPTGS2efficiency between the HRFI and LRFI groups, ultimately leading to diverse residual feed intake levels in ducks.

IMPORTANCE

This investigation utilizes metabolomics to elucidate the interplay between genes and microbiome communities. We present evidence of disparities in the composition of microbial consortia among ducks RFI, alongside identification of pivotal genes within the liver that potentially modulate RFI. These results provide novel perspectives on the processes through which the cecum and liver influence RFI.
ELUCIDATION OF THE ROLE OF miRNA 4263 IN DYSREGULATED MITOCHONDRIAL ENERGETICS AND CARCINOGENESIS
Authors: Maurya Ashutosh Kumar , Sruthi TV. , Kumar V.B. Sameer
Published: April 2024

Dysfunctional mitochondria have been reported to be associated with several pathological conditions and in cancer, dysregulated mitochondrial metabolism is considered as an important hallmark of the disease. Cancer cells alter their mitochondrial machinery and activate glycolytic pathway as an alternate source of continuous energy, required for their indefinite growth. This modulation of the mitochondria could be due to the dysrupted expression of important mitochondrial genes involved in the normal functioning of the mitochondria. MicroRNAs are known to regulate the expression pattern of a variety of genes. With our in-silico analysis, we found that miR 4263 has targets on important mitochondrial genes, involved in mitochondrial energetics. Next, we checked the role of miR 4263 in modulating the mitochondrial metabolism and impact of this alteration on carcinogenesis. The results revealed that miR 4263 contributes to carcinogenesis in hepatic cells by altering the mitochondrial energetics.
In-silico analysis of important mitochondrial microRNAs and their differential expression in mitochondria
Authors: Maurya Ashutosh Kumar , Rabina P , Kumar V.B. Sameer
Published: April 2024

Mitochondria, often called as the power house of cell, serves important role in cellular physiology and survivability. It plays crucial role in the normal functioning of the cell. Dysfunctional mitochondria have been found to be associated with various pathological conditions including cancer. The modulation of mitochondrial machinery could be due to the suppression of the expression pattern of important mitochondrial genes and microRNAs could be considered as the key player in reprograming of the mitochondrial metabolism. Apart from the microRNAs coded by mitochondrial genome, nuclear coded microRNAs gets localized to the mitochondria and they influence the mitochondrial machinery by targeting the important mitochondrial genes. This group of microRNAs are called mitochondrial miRNAs or MitomiRs. In this study we selected 10 important candidate mitochondrial microRNAs and checked their abundance in the cancerous and non cancerous hepatic cell line (HepG2 and WRL68), followed by their differential expression in the mitochondria of the respective cell line. The results shown an inverse relation in the expression pattern of the candidate microRNAs with mitochondrial target genes, suggesting their direct targeting, as predicted by our in-silico data.
Mild Hyperthermia Enhanced Liposomal Doxorubicin Delivery and CD8+T cell Infiltration in Triple Negative Breast Cancer
Authors: Rezazadeh Farzaneh , Saadat Wajfa , Smith Ryan , Pattyn Alexander , Malik Mohammad , Yazdani Fuad , Saliganan Allen-Dexter , Mehrmohammadi Mohammad , Viola Nerissa T.
Published: April 2024

Mild hyperthermia (MHTh) is often used in combination with chemotherapy and radiotherapy for cancer treatment. In the current study, the effect of MHTh on the enhanced uptake of the FDA-approved chemotherapy drug, liposomal doxorubicin (dox) in syngeneic 4T1 tumors was investigated. Doxorubicin has inherent fluorescence properties having an emission signal at 590 nm upon excitation with a 480 nm laser. A group of mice administered with doxorubicin (dox) were exposed to MHTh (42 °C) for 30 minutes whereas control group given dox did not receive MHTh.Ex vivooptical imaging of harvested tumors confirmed higher uptake of dox in treated versus the control untreated tumors. Confocal microscopy of tumor sections indicates higher fluorescent intensity due to increased accumulation of dox in MHTh-treated compared to untreated tumors. We examined the effect of MHTh to enhance CD8 tumor infiltration, production of interferon-γ (IFN-γ) and expression of programmed death ligand-1 (PD-L1). mRNAin situhybridization was performed to test for transcripts of CD8, IFN-γ and PD-L1. Results showed that higher expression of CD8 mRNA was observed in MHTh-administered tumors versus untreated cohorts. The signal for IFN-γ and PD-L1 in both groups were not significantly different. Taken together, our findings imply that MHTh can improve tumor uptake of dox. Importantly, our data suggests that MHTh can boost CD8+T cell infiltration.
From Web to RheumaLpack: Creating a Linguistic Corpus for Exploitation and Knowledge Discovery in Rheumatology
Authors: Madrid-García Alfredo , Merino-Barbancho Beatriz , Freites-Núñez Dalifer , Rodríguez-Rodríguez Luis , Menasalvas-Ruíz Ernestina , Rodríguez-González Alejandro , Peñas Anselmo
Published: April 2024

Abstract

This study introducesRheumaLinguisticpack(RheumaLpack), the first specialised linguistic web corpus designed for the field of musculoskeletal disorders. By combining web mining (i.e., web scraping) and natural language processing (NLP) techniques, as well as clinical expertise,RheumaLpacksystematically captures and curates structured and unstructured data across a spectrum of web sources including clinical trials registers (i.e.,ClinicalTrials.gov), bibliographic databases (i.e., PubMed), medical agencies (i.e. EMA), social media (i.e., Reddit), and accredited health websites (i.e., MedlinePlus, Harvard Health Publishing, and Cleveland Clinic). Given the complexity of rheumatic and musculoskeletal diseases (RMDs) and their significant impact on quality of life, this resource can be proposed as a useful tool to train algorithms that could mitigate the diseases’ effects. Therefore, the corpus aims to improve the training of artificial intelligence (AI) algorithms and facilitate knowledge discovery in RMDs. The development ofRheumaLpackinvolved a systematic six-step methodology covering data identification, characterisation, selection, collection, processing, and corpus description. The result is a non-annotated, monolingual, and dynamic corpus, featuring almost 3 million records spanning from 2000 to 2023.RheumaLpackrepresents a pioneering contribution to rheumatology research, providing a useful resource for the development of advanced AI and NLP applications. This corpus highlights the value of web data to address the challenges posed by musculoskeletal diseases, illustrating the corpus’s potential to improve research and treatment paradigms in rheumatology. Finally, the methodology shown can be replicated to obtain data from other medical specialities. The code and details on how to buildRheumaL(inguistic)packare also provided to facilitate the dissemination of such resource.
Vitamin D, acute respiratory infections, and Covid-19: the curse of small-size randomised trials. A critical review with meta-analysis of randomised trials
Authors: Autier Philippe , Doi Giulia , Mullie Patrick , Vankrunkelsven Patrick , D’Ecclesiis Oriana , Gandini Sara
Published: April 2024

Background

Randomised trials conducted before 2021 indicated that vitamin D supplementation (VDS) was able to prevent severe COVID-19 and acute respiratory infections (ARI). However, these health benefits were not confirmed by larger randomised trials published after 2021.

Objective

To examine the characteristics of randomised trials on VDS to COVID-19 patients and admission to intensive care unit (ICU), and on VDS for the prevention of ARI.

Method

A systematic search retrieved randomised trials on VDS to COVID-19 patients and admission to ICU. Data on VDS and ARI were extracted from the meta-analysis of Jolliffe et al., 2021. The associations between VDS vs no VDS, and admission to ICU were evaluated using random effect models. Meta-analyses were done for all trials and by groups trial size. Publication bias was assessed using the LFK index (no bias if index between -1 and +1) and the Trim and Fill method.

Results

Nine trials on VDS for preventing admission to ICU were identified. The summary odds ratio (SOR) was 0.61 (95%CI: 0.39-0.95) for all trials, 0.34 (0.13-0.93) for trials including 50 to <106 patients and 0.88 (0.62-1.24) for trials including 106 to 548 patients (effect modification: p=0.04). The LFK index was -3.79, and after Trim and Fill, the SOR was 0.80 (0.40-1.61). The SOR for the 37 trials on VDS for ARI prevention was 0.92 (0.86-0.99) for all trials, 0.69 (0.57-0.83) for trials including 25 to <248 patients and 0.98 (0.94-1.03) for trials including 248 to 16,000 patients (effect modification p=0.0001). The LFK index was -3.11, and after Trim and Fill, the SOR was 0.96 (0.88-1.05).

Conclusion

Strong publication bias affected randomised trials on VDS for the prevention of severe COVID-19 and of ARI. Systematic reviews should beware of small-size randomised trials that generally exaggerate health benefits.
Radiomic analysis of patient and inter-organ heterogeneity in response to immunotherapies and BRAF targeted therapy in metastatic melanoma
Authors: Tompkins Alexandra , Gray Zane N. , Dadey Rebekah E. , Zenkin Serafettin , Batavani Nasim , Newman Sarah , Amouzegar Afsaneh , Ak Murat , Ak Nursima , Pak Taha Yasin , Peddagangireddy Vishal , Mamindla Priyadarshini , Behr Sarah , Goodman Amy , Ploucha Darcy L. , Kirkwood John M. , Zarour Hassane M. , Najjar Yana G. , Davar Diwakar , Colen Rivka , Luke Jason J. , Bao Riyue
Published: April 2024

Background

Variability in treatment response may be attributable to organ-level heterogeneity in tumor lesions. Radiomic analysis of medical images can elucidate non-invasive biomarkers of clinical outcome. Organ-specific radiomic comparison across immunotherapies and targeted therapies has not been previously reported.

Methods

We queried UPMC Hillman Cancer Center registry for patients with metastatic melanoma (MEL) treated with immune checkpoint inhibitors (ICI) (anti-PD1/CTLA4 [ipilimumab+nivolumab; I+N] or anti-PD1 monotherapy) or BRAF targeted therapy. Best overall response was measured using RECIST v1.1. Lesions were segmented into discrete volume-of-interest with 400 radiomics features extracted. Overall and organ-specific machine-learning models were constructed to predict disease control (DC)versusprogressive disease (PD) using XGBoost.

Results

291 MEL patients were identified, including 242 ICI (91 I+N, 151 PD1) and 49 BRAF. 667 metastases were analyzed, including 541 ICI (236 I+N, 305 PD1) and 126 BRAF. Across cohorts, baseline demographics included 39-47% female, 24-29% M1C, 24-46% M1D, and 61-80% with elevated LDH. Among patients experiencing DC, the organs with the greatest reduction were liver (−88%±12%, I+N; mean±S.E.M.) and lung (−72%±8%, I+N). For patients with multiple same-organ target lesions, the highest inter-lesion heterogeneity was observed in brain among patients who received ICI while no intra-organ heterogeneity was observed in BRAF. 267 patients were kept for radiomic modeling, including 221 ICI (86 I+N, 135 PD1) and 46 BRAF. Models consisting of optimized radiomic signatures classified DC/PD across I+N (AUC=0.85) and PD1 (0.71) and within individual organ sites (AUC=0.72∼0.94). Integration of clinical variables improved the models’ performance. Comparison of models between treatments and across organ sites suggested mostly non-overlapping DC or PD features. Skewness, kurtosis, and informational measure of correlation (IMC) were among the radiomic features shared between overall response models. Kurtosis and IMC were also utilized by multiple organ-site models.

Conclusions

Differential organ-specific response was observed across BRAF and ICI with within organ heterogeneity observed for ICI but not for BRAF. Radiomic features of organ-specific response demonstrated little overlap. Integrating clinical factors with radiomics improves the prediction of disease course outcome and prediction of tumor heterogeneity.
Investigation of the sero-epidemiology of vaccine preventable diseases and common viral infections in French populations using a multiplex serological assay
Authors: Bloch Emma , Baudemont Gaëlle , Donnadieu Françoise , Garcia Laura , Pelleau Stephane ,   SeroPed Study Consortium,   Milieu Interieur Consortium, Quintana-Murci Lluis , Duffy Darragh , Fontanet Arnaud , White Michael
Published: April 2024

Vaccine-preventable diseases (VPDs) and common viral infections (CVIs) pose substantial public health challenges. Despite data collected through routine vaccination programs and through hospital-based case reporting systems, the understanding of population-level immunity to VPDs and CVIs remains limited. To address this challenge, this study focuses on the development and application of a high-throughput multiplex serological assay to assess IgG levels against a large panel of eight VPDs (e.g., tetanus, diphtheria, measles, mumps, rubella) and 18 CVIs that typically occur in early childhood (e.g., adenovirus, cytomegalovirus, respiratory syncytial virus). A cross-sectional study of 2,032 serum samples from French children and adults was used to optimize and validate a 47-plex assay. These antibody measurements allowed us to enhance our understanding of immunity, vaccination and booster dose effect, as well as antibody waning over time. Preliminary results demonstrate the importance of age-stratified IgG level measurements, revealing notable variation in seroprevalence patterns among different age groups. These findings suggest that there are variations in immunity and exposure to the targeted pathogens across these groups. These findings highlight the potential of high-throughput multiplex serology assays for routine surveillance of common viral infections and assessment of vaccine coverage.
Patients with Achilles Tendinopathy use compensation strategies to reduce tendon load during rehabilitation exercises
Authors: Deroost Frea , Petrella Davide , Mylle Ine , Vanwanseele Benedicte
Published: April 2024

Purpose

This study aimed to determine differences in the Achilles tendon loading during rehabilitation exercises for Achilles tendinopathy (AT), and the ranking of these exercises in patients with AT and controls.

Methods

Sixteen patients with AT (5F & 11M, 44.1 ± 12.9yr) and sixteen controls (4F & 12M, 39.4 ± 15.6yr) performed rehabilitation exercises while 3D motion and ground reaction forces were measured. Musculoskeletal modeling was used to compute joint kinematics and triceps surae muscle forces. Individual triceps surae muscle forces were summed to estimate Achilles tendon load. Subsequently, peak Achilles tendon loading, loading impulse, loading rate, loading indexes (combining the different loading parameters), and ankle and knee angles at the time of peak loading were determined.

Results

Patients with AT have a significantly reduced peak loading of the Achilles tendon compared to controls during the exercises with the highest peak loading: unilateral heel drop with flexed knee (3.66 ± 0.90BW [AT] vs. 4.65 ± 1.10BW [Control], p=0.003, d=0.979) and walking (3.37 ± 0.49BW [AT] vs. 3.68 ± 0.33BW [Control], p=0.044, d=0.742). Furthermore, ankle dorsiflexion and knee flexion were reduced during unilateral heel drop with a flexed knee for the AT group. The ranking of exercises by peak loading or loading index was similar for people with and without AT. However, the ranking of exercises depends on the parameter used to define Achilles tendon loading.

Conclusion

During the highest load-imposing exercises, patients with AT employ compensatory strategies to reduce the load on their Achilles tendon. Clear instructions and feedback on the patient’s performance are crucial as altered exercise execution influences Achilles tendon loading.
Do Sleep Quality Can Be the Intervening Factors of Personality Data to Occupational Fatigue?
Authors: Izhar Doddy , Kusmawan David , Aswin Budi
Published: April 2024

Fatigue during work among oil and gas employees can have dangerous effects on wellbeing, economics, safety, and health. This cross-sectional survey was conducted in July and August of 2022 at two national oil and gas companies located in Muara Jambi and Jambi City. A convenience sample of 116 respondents was selected in total. To address the study hypotheses, partial least square-structural equation modeling (PLS-SEM) was employed. This study aims to determine the relationship between the risk of job weariness among Indonesian oil and gas workers in Jambi Province and the direct and indirect impacts of mental workload, sociodemographic characteristics, and sleep quality. Personality data has a significant and negative direct impact on occupational weariness at alpha 5% and with a path value of -0.203 (p-value: 0.047), corroborating the earlier hypothesis. For the second hypothesis, the path coefficient value of 0.462 (p-value: 0.000) clearly shows that sleep quality has an impact on occupational weariness. In order to improve sleep hygiene and address personality factors like age and length of employment, fatigue risk management strategies can be combined with those that are currently being used to control job tiredness.
Day 3 parasitemia andPlasmodium falciparum Kelch 13mutations among uncomplicated malaria patients treated with artemether-lumefantrine in Adjumani district, Uganda
Authors: Angwe Martin Kamilo , Mwebaza Norah , Nsobya Sam Lubwama , Vudriko Patrick , Dralabu Savior , Omali Denis , Tumwebaze Maria Agnes , Ocan Moses
Published: April 2024

Artemisinin resistance threatens malaria control and elimination efforts globally. Recent studies have reported the emergence ofPlasmodium falciparumparasites tolerant to artemisinin agents in sub-Saharan Africa, including Uganda. The current study assessed the day 3 parasite clearance and its correlation withP. falciparum K13propeller gene (pfkelch13) mutations inP. falciparumparasites isolated from patients with uncomplicated malaria under artemether-lumefantrine (AL) treatment. This study enrolled 100P. falciparum-positive patients to whom AL was prescribed between 09/September/2022 and 06/November/2022. Blood samples were collected in EDTA tubes before treatment initiation (day 0) and on day 3. Parasitemia was assessed by microscopy from blood smears and quantitative polymerase chain reaction (qPCR) from the DNA extracted. The day 0 parasiteK13gene was sequenced using Sanger sequencing. Sequence data were analysed using MEGAversion11 software. The data were analysed using STATAversion15, and the Mann‒Whitney U test was used to compare PCR parasite clearance on day 3 using the comparative CT value method andpfkelch13mutations.

The prevalence of day 3 parasitaemia was 24% (24/100) by microscopy and 63% (63/100) by qPCR from the AL-treated patients.P. falciparum K13-propeller gene polymorphism was detected in 18.8% (15/80) of the day 0 DNA samples. TheK13mutations found were C469Y, 12.5% (10/80); A675V, 2.5% (2/80); A569S, 1.25%, (1/80), A578S, 1.25%, (1/80) and; F491S, 1.25%, (1/80) a new allele not reported anywhere. The C469Y mutation, compared to the wild-type, was associated with delayed parasite clearancep=0.0278, Hodges-Lehmann estimation 3.2108 on the log scale, (95%CI 1.7076, 4.4730).

There was a high prevalence of day 3P. falciparumamong malaria patients treated using artemether-lumefantrine. We conclude that theK13mutation associated with artemisinin resistance byP. falciparumis present in Adjumani district, Uganda. This necessitates regular surveillance of the effectiveness and efficacy of artemether-lumefantrine in the country.
Time spent in outdoor light is associated with increased blood pressure, higher hypertension risk, and lower hypotension risk
Authors: Li Sicheng , Lu Liyong , Xian Wenpan , Li Jiawei , Xu Shuaiming , Chen Jiajin , Wang Yan
Published: April 2024

Objective

Light exposure is considered to be associated with reduced blood pressure (BP). However, longitudinal epidemiological studies concerning the light‒BP association with large samples are still limited.

Methods

This cohort study enrolled over 300,000 participants from the UK Biobank. Information on time spent in outdoor light during typical summer or winter days was obtained through questionnaires. Cases of hypertension and hypotension were identified using the 10th edition of International Classification of Diseases codes. Cox proportional hazard regression models were employed to estimate the light‒BP associations, restricted cubic splines were utilized to detect potential nonlinear associations, subgroup analyses were conducted to identify effect modifiers, and causal mediation analyses were performed to explore potential mechanisms.

Results

Using summer light exposure as an illustration, after a median follow-up of 13.4 years, each additional hour of summer light exposure was associated with an increased risk of hypertension (hazard ratio [HR] 1.011, 95% confidence interval [CI] 1.006‒1.017,P-nonlinear=0.803) and a decreased risk of hypotension (0.988, 0.977‒ 0.998,P-nonlinear=0.109). The light‒BP association is stronger in females (P=0.022), those with short sleep duration (P=0.049), and those with high genetic risk of hypertension (P<0.001). Potential mechanisms included increasing biological age (proportion mediated, 24.1%,P<0.001), neutrophil count (5.4%,P<0.001), BMI (32.0%,P<0.001), etc.

Conclusions

Contrary to previous findings, our study revealed a positive association between light exposure and BP. Potential mechanisms include inflammation, aging, and behavioral lifestyle changes. Further epidemiological and experimental investigations are warranted to validate these novel findings.
Socio-ecological context modulates significance of territorial contest competition inDrosophila prolongata
Authors: De Nardo Alessio N. , Biswas Broti , Perdigón Ferreira Jhoniel , Meena Abhishek , Lüpold Stefan
Published: April 2024

The intensity and direction of sexual selection is intricately linked to the social and ecological context. Both operational sex ratios (OSRs) and population densities can affect the ability of males to monopolize resources and mates, and thus the form and intensity of sexual selection on them. Here, we studied how the mating system of the promiscuous and strongly sexually dimorphic fruit flyDrosophila prolongataresponds to changes in the OSR and population density. We recorded groups of flies over five days and quantified territory occupancy, mating success, and competitive fertilization success. Although sexual selection was stronger under male-biased than even OSRs but unrelated to density, realized selection on morphological traits was higher under even OSRs and increased with density. Larger and more territorial males achieved both higher mating success and competitive fertilization success, but only under even OSRs. Our combined results also support a shift in the mating system from territorial contest competition to scramble competition under male-biased OSRs and potentially at low density, where there was no clear contribution of the measured traits to reproductive success. Our study emphasizes the limitations of traditional selection metrics and the role of the socio-ecological context in predicting adaptation to a changing environment.

Significance

Mating systems are complex and dynamic, adapting to ongoing ecological change. Studies often assume that changes in the socio-ecological context alter the intensity of sexual selection on traits indicating individual fitness, but our work onDrosophila prolongatachallenges this view. By manipulating operational sex ratio and population density, and jointly investigating territorial behavior and both pre- and post-mating reproductive success over several days, we reveal the plastic mating strategies in this fly. This dynamism underscores the limitations of static classifications and the importance of studying selection across diverse socio-ecological contexts. This broader perspective advances our understanding of the tight connections between environmental change, population demographics, and the evolutionary process.
Syntenic lncRNAs exhibit DNA regulatory functions with sequence evolution
Authors: Ranjan Gyan , Scaria Vinod , Sivasubbu Sridhar
Published: April 2024

Syntenic long non-coding RNAs (lncRNAs) often show limited sequence conservation across species, prompting concern in the field. This study delves into functional signatures of syntenic lncRNAs between humans and zebrafish. Syntenic lncRNAs have high expression in zebrafish and ∼90% near protein-coding genes in sense or antisense orientation. During early zebrafish development and human embryonic stem cells (H1-hESC), are enriched with cis-regulatory repressor signatures, influencing development-associated genes. In later zebrafish developmental stages and specific human cell lines, these lncRNAs serve as enhancers or transcription-start-sites(TSS) for protein-coding. Analysis of Transposable Elements (TEs) in syntenic lncRNA sequence divergence unveils intriguing patterns, human lncRNAs show enrichment in simple repeat elements, while zebrafish counterparts exhibit LTR element enrichment. This sequence evolution, possibly stemming from post-rearrangement mutations, enhances DNA elements or cis-regulatory functions. It may also contribute to vertebrate innovation by creating novel TF binding sites within the locus. This study sheds light on the conserved functionality of syntenic lncRNAs through DNA elements, emphasizing their role across species despite sequence divergence.
An image processing pipeline for electron cryo-tomography in RELION-5
Authors: Burt Alister , Toader Bogdan , Warshamanage Rangana , von Kügelgen Andriko , Pyle Euan , Zivanov Jasenko , Kimanius Dari , Bharat Tanmay A.M. , Scheres Sjors H.W.
Published: April 2024

Electron tomography of frozen, hydrated samples allows structure determination of macromolecular complexes that are embedded in complex environments. Provided that the target complexes may be localised in noisy, three-dimensional tomographic reconstructions, averaging images of multiple instances of these molecules can lead to structures with sufficient resolution forde novoatomic modelling. Although many research groups have contributed image processing tools for these tasks, a lack of standardisation and inter-operability represents a barrier for newcomers to the field. Here, we present an image processing pipeline for electron tomography data in RELION-5, with functionality ranging from the import of unprocessed movies to the automated building of atomic models in the final maps. Our explicit definition of metadata items that describe the steps of our pipeline has been designed for inter-operability with other software tools and provides a framework for further standardisation.
PARP14 is pro- and anti-viral host factor that promotes IFN production and affects the replication of multiple viruses
Authors: Parthasarathy Srivatsan , Saenjamsai Pradtahna , Hao Hongping , Ferkul Anna , Pfannenstiel Jessica J. , Suder Ellen L. , Bejan Daniel S. , Chen Yating , Schwarting Nancy , Aikawa Masanori , Muhlberger Elke , Orozco Robin C. , Sullivan Christopher S. , Cohen Michael S. , Davido David J. , Hume Adam J. , Fehr Anthony R.
Published: April 2024

PARP14 is a 203 kDa multi-domain protein that is primarily known as an ADP-ribosyltransferase, and is involved in a variety of cellular functions including DNA damage, microglial activation, inflammation, and cancer progression. In addition, PARP14 is upregulated by interferon (IFN), indicating a role in the antiviral response. Furthermore, PARP14 has evolved under positive selection, again indicating that it is involved in host-pathogen conflict. We found that PARP14 is required for increased IFN-I production in response to coronavirus infection lacking ADP-ribosylhydrolase (ARH) activity and poly(I:C), however, whether it has direct antiviral function remains unclear. Here we demonstrate that the catalytic activity of PARP14 enhances IFN-I and IFN-III responses and restricts ARH-deficient murine hepatitis virus (MHV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. To determine if PARP14’s antiviral functions extended beyond CoVs, we tested the ability of herpes simplex virus 1 (HSV-1) and several negative-sense RNA viruses, including vesicular stomatitis virus (VSV), Ebola virus (EBOV), and Nipah virus (NiV), to infect A549 PARP14 knockout (KO) cells. HSV-1 had increased replication in PARP14 KO cells, indicating that PARP14 restricts HSV-1 replication. In contrast, PARP14 was critical for the efficient infection of VSV, EBOV, and NiV, with EBOV infectivity at less than 1% of WT cells. A PARP14 active site inhibitor had no impact on HSV-1 or EBOV infection, indicating that its effect on these viruses was independent of its catalytic activity. These data demonstrate that PARP14 promotes IFN production and has both pro– and anti-viral functions targeting multiple viruses.

IMPORTANCE

The antiviral response is largely regulated by post-translation modifications (PTM), including ADP-ribosylation. PARP14 is an ADP-ribosyltransferase that is upregulated by interferon and is under positive selection, indicating that it is involved in host-pathogen conflict. However, no anti-viral function has been described for PARP14. Here, we found that PARP14 represses both coronavirus and HSV-1 replication, demonstrating that PARP14 has anti-viral functions. Surprisingly, we also found that PARP14 also has pro-viral functions, as it was critical for the efficient infection of several RNA viruses, including Ebola and Nipah viruses, which have high mortality and are viruses with pandemic potential. These data indicate that PARP14 has both pro– and anti-viral functions and is a potential therapeutic target for highly pathogenic RNA viruses.
Loss of RNF2 delays tumour development in BAP1-deficient mesothelioma
Authors: Landman Nick , Hulsman Danielle , Badhai Jitendra , van Lohuizen Maarten
Published: April 2024

The tumour suppressor geneBAP1is mutated in more than half of the malignant mesothelioma patients. This catalytic subunit of Polycomb repressive deubiquitinating (PR-DUB) complex, plays an important role in maintaining gene expression levels by deubiquitinating the PRC1-mediated histone H2A lysine 119 mono-ubiquitination (H2AK119ub1). Published studies report varying degrees of importance of H2AK119ub1 in Polycomb-regulated gene expression in different cell types. Recently published data by our own lab suggests a global redistribution of the H2AK119ub1 mark from promoter to intergenic regions upon loss of BAP1. PRC1-mediated mono-ubiquitination is dependent on the E3 ubiquitin ligase function of RNF2 (RING1B). Here, by knocking-outRnf2, we show that loss of H2AK119ub1 levels leads to a decrease in clonogenic potential ofBap1-deficient mesothelioma cellsin vitroand a delay in tumour onsetin vivo.
Ultra-deep proteomics by Thin-diaPASEF with a 60-cm long column system
Authors: Konno Ryo , Ishikawa Masaki , Nakajima Daisuke , Hagiwara Sho , Inukai Kaori , Ohara Osamu , Kawashima Yusuke
Published: April 2024

Recent advances have allowed for the detection of 10,000 proteins from cultured human cell samples, such as HeLa and HEK293T cells in a single-shot proteome analysis. However, deeper analysis remains challenging. Therefore, in this study, we aimed to perform a deep proteomic single-shot analysis using timsTOF HT. To achieve deep proteomics, we developed Thin-diaPASEF, a parallel accumulation-serial fragmentation (PASEF) technology featuring a thinly dividedm/zaxis only in regions of high ion density. Furthermore, using a 60-cm long C18 column with a particle size of 1.7 µm, an average of 11,698, 11,615 and 11,019 unique proteins were successfully detected from 500 ng of HEK293T, HeLa and K562 cell digests, respectively, with a 100 min active gradient. The same system was used to analyzeLycopersicon esculentumlectin (LEL) enriched plasma and serum. The LEL method identified an average of 8,613 and 4,078 unique proteins, in plasma and serum, respectively. Our ultra-deep proteomic analysis system will be helpful for the in-depth comparison of proteins in medical and biological research because it enables the analysis of highly proteome coverage in a single-shot.
In vitrotranscription-based biosensing of glycolate for prototyping of a complex enzyme cascade
Authors: Barthel Sebastian , Brenker Luca , Diehl Christoph , Bohra Nitin , Giaveri Simone , Paczia Nicole , Erb Tobias J
Published: April 2024

In vitrometabolic systems allow the reconstitution of natural and new-to-nature pathways outside of their cellular context and are of increasing interest in bottom-up synthetic biology, cell-free manufacturing and metabolic engineering. Yet, the prototyping of suchin vitronetworks is very often restricted by time- and cost-intensive analytical methods. To overcome these limitations, we sought to develop anin vitrotranscription (IVT)-based biosensing workflow that offers fast results at low-cost, minimal volumes and high-throughput. As a proof-of-concept, we present an IVT biosensor for the so-called CETCH cycle, a complexin vitrometabolic system that converts CO2into glycolate. To quantify glycolate production, we constructed a sensor module that is based on the glycolate repressor GlcR fromParacoccus denitrificans, and established an IVT biosensing off-line workflow that allows to measure glycolate from CETCH samples from the µM to mM range. We characterized the influence of different cofactors on IVT output and further optimized our IVT biosensor against varying sample conditions. We show that availability of free Mg2+is a critical factor in IVT biosensing and that IVT output is heavily influenced by ATP, NADPH and other phosphorylated metabolites frequently used inin vitrosystems. Our final biosensor is highly robust and shows an excellent correlation between IVT output and classical LC-MS quantification, but notably at ∼10-fold lowered cost and ∼10 times faster turnover time. Our results demonstrate the potential of IVT-based biosensor systems to break current limitations in biological design-build-test cycles for the prototyping of individual enzymes, complex reaction cascades andin vitrometabolic networks.
Rescue of lysosomal acid lipase deficiency in mice by rAAV8 liver gene transfer
Authors: Laurent Marine , Harb Rim , Jenny Christine , Oustelandt Julie , Jimenez Simon , Cosette Jeremie , Landini Francesca , Ferrante Aristide , Corre Guillaume , Vujic Nemanja , Piccoli Claudia , Brassier Anais , Van Wittenberghe Laetitia , Ronzitti Giuseppe , Kratky Dagmar , Pacelli Consiglia , Amendola Mario
Published: April 2024

Lysosomal acid lipase deficiency (LAL-D) is an autosomal recessive disorder caused by mutations in theLIPAgene, which results in lipid accumulation leading to multi-organ failure. If left untreated, the severe form of LAL-D results in premature death within the first year of life due to failure to thrive and hepatic insufficiency. Enzyme replacement therapy is the only available supportive treatment consisting in weekly systemic injections of recombinant LAL protein. Here, we characterized a novelLipa-/-mouse model and developed a curative gene therapy treatment based on thein vivoadministration of recombinant (r)AAV8 vector encoding the humanLIPAtransgene under the control of a hepatocyte-specific promoter. We defined the minimal rAAV8 dose required to rescue disease lethality and to correct cholesterol and triglyceride accumulation in multiple organs and blood. Finally, using liver transcriptomic and biochemical analysis, we showed mitochondrial impairment inLipa-/-mice and its recovery by gene therapy. Overall, ourin vivogene therapy strategy achieves a stable long-term LAL expression sufficient to correct the disease phenotype in theLipa-/-mouse model and offers a new therapeutic option for LAL-D patients.

One Sentence Summary

We’ve developed a liver-targeted gene therapy using recombinant AAV8 to effectively cure Lysosomal acid lipase deficiency by correcting lipid accumulation and by normalizing gene expression pattern and mitochondrial function inLipa-/-mouse model.
Metabolic engineering of narrow-leafed lupin for the production of enantiomerically pure (‒)-sparteine
Authors: Mancinotti Davide , Yang Ting , Geu-Flores Fernando
Published: April 2024

Sparteine is a plant-derived alkaloid widely known for its utility as chiral ligand in asymmetric synthesis1-3. However, its variable market price and availability have failed to meet the demand for a cheap and reliable product4-6. Sparteine is naturally synthesized by a sub-group of legume plants, which typically accumulate complex mixtures of closely related alkaloids. Here, we identified two enzymes from narrow-leafed lupin (NLL,L. angustifolius) that can sequentially oxidize (−)-sparteine to (+)-lupanine. The first enzyme is a cytochrome P450 monooxygenase belonging to family 71 (CYP71D189) and the second one is a short-chain dehydrogenase/reductase (SDR1). We also screened a non-GMO NLL mutant library and isolated a knockout in CYP71D189. The knockout displayed an altered metabolic profile where (−)-sparteine accounted for 96% of the alkaloid content in the seeds (GC-MS basis). The (−)-sparteine isolated from the mutant seeds was enantiomerically pure (99%ee). Apart from the altered alkaloid profile, the mutant did not have any noticeable phenotype. Our work demonstrates that (−)-sparteine is the precursor of most QAs in NLL and provides a convenient source of this valuable compound for academia and industry.
Targeting the sphingolipid rheostat in IDH1mutglioma alters cholesterol homeostasis and triggers apoptosis via membrane degradation
Authors: Dowdy Tyrone , Vilamu Helena Muley , Lita Adrian , Li Aiguo , Yamasaki Tomohiro , Zhang Lumin , Chari Raj , Song Hua , Zhang Meili , Zhang Wei , Briceno Nicole , Davis Dionne , Gilbert Mark R. , Larion Mioara
Published: April 2024

The cross-regulation of metabolism and trafficking is not well understood for the vital sphingolipids and cholesterol constituents of cellular compartments. While reports are starting to surface on how sphingolipids like sphingomyelin (SM) dysregulate cholesterol levels in different cellular compartments (Jiang et al., 2022), limited research is available on the mechanisms driving the relationship between sphingolipids and cholesterol homeostasis, or its biological implications. Previously, we have identified sphingolipid metabolism as a unique vulnerability for IDH1mutgliomas via a rational drug design. Herein, we show how modulating sphingolipid levels affects cholesterol homeostasis in brain tumors. However, we unexpectedly discovered for the first time that C17 sphingosine and NDMS addition to cancer cells alters cholesterol homeostasis by impacting its cellular synthesis, uptake, and efflux leading to a net decrease in cholesterol levels and inducing apoptosis. Our results reflect a reverse correlation between the levels of sphingosines, NDMS, and unesterified, free cholesterol in the cells. We show that increasing sphingosine and NDMS (a sphingosine analog) levels alter not only the trafficking of cholesterol between membranes but also the efflux and synthesis of cholesterol. We also demonstrate that despite the effort to remove free cholesterol by ABCA1-mediated efflux or by suppressing machinery for the influx (LDLR) and biosynthetic pathway (HMGCR), apoptosis is inevitable for IDH1mutglioma cells. This is the first study that shows how altering sphingosine levels directly affects cholesterol homeostasis in cancer cells and can be used to manipulate this relationship to induce apoptosis in IDH1mutgliomas.