bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficacy and Safety of Ginger on Chemotherapy-Induced Nausea and Vomiting
Authors: Lin Ching-Yi , Huang Sih-Huan , Tam Ka-Wai , Huang Tsai-Wei , Gautama Made Satya Nugraha
Published: April 2024

Background

Chemotherapy-induced nausea and vomiting (CINV) is a prevalent and distressing side effect. Historically, ginger has been explored as a potential remedy for various ailments, including its potential efficacy against CINV.

Objective

The aim of this study was to determine whether taking ginger supplements can relieve CINV.

Method

A comprehensive search was conducted across PubMed, EMBASE, Cochrane Library, and the Wanfang database. Randomized controlled trials meeting our inclusion criteria were analyzed. The primary outcomes were the incidence and severity of CINV. The protocol was registered on PROSPERO, and the number is CRD4202232104.

Result

Of the 35 randomized controlled trials analyzed, 22 trials employed ginger capsules as the primary intervention, whereas 13 studies evaluated the prophylactic effects of ginger-partitioned moxibustion. The outcomes indicated that combining ginger capsules with standard antiemetic agents can significantly reduce the incidence of grade 3 acute nausea (Risk Ratio [RR], 0.19; P < .001) and the incidence of high-grade overall vomiting (RR, 0.47; P = .01). Moreover, ginger-partitioned moxibustion can significantly alleviate the incidence of both mild (RR, 0.56; P = .001) and severe (RR, 0.39; P < .00001) vomiting. Only 2.8% of patients experienced dizziness after ginger-partitioned moxibustion.

Conclusions

Our findings indicate that ginger capsules, when used alongside antiemetic drugs, enhance the management of severe CINV, particularly in highly emetogenic chemotherapy regimens.

Implications for Practice

Based on our findings, we recommend initiating ginger supplements before chemotherapy, in conjunction with standard antiemetics, to reduce the severity of CINV. The promising results warrant more rigorous clinical trials to firmly establish the role of ginger in CINV management.
Fear of Cancer and State Anxiety Among Women Undergoing Hysterectomy
Authors: Büyükokudan Şerife , Korukcu Oznur
Published: April 2024

Background

Fear of cancer may develop after surgery in women who underwent surgery for suspected malignancy in preoperative examinations. It is important from a psychosocial point of view that the fear of cancer and the factors affecting anxiety are determined and necessary interventions are made.

Objectives

The aim of this study was to determine the level of state anxiety, fear of cancer, and influencing factors in women who had hysterectomies with a risk of cancer in the waiting period for the pathology result.

Methods

The research data were collected from 109 women who underwent hysterectomy while waiting for the pathology result on the third or fourth postoperative day. Patients completed the Personal Information Form, State-Trait Anxiety Inventory-I, and Cancer Worry Scale.

Results

Women who underwent hysterectomy with the risk of gynecological cancer had high levels of state anxiety and cancer fear after hysterectomy; type of hysterectomy significantly affected cancer fear (P = .022), and social support (P = .015), type of hysterectomy (P = .024), and family history of cancer (P = .022) significantly affected state anxiety.

Conclusion

The management of these women’s concerns can be improved if healthcare professionals know more about the factors affecting their state anxiety and fear.

Implications for Practice

Health professionals witness patients’ most private experiences and play a key role in providing care and support. This study may be foundational in the planning and implementation of nursing interventions to manage causes of anxiety and fear during this waiting period.
Differential susceptibility of cells infected with defective and intact HIV proviruses to killing by obatoclax and other small molecules
Authors: Kadiyala Gayatri Nikhila , Telwatte Sushama , Wedrychowski Adam , Janssens Julie , Kim Sun Jin , Kim Peggy , Deeks Steven , Wong Joseph K. , Yukl Steven A.
Published: April 2024

Objectives:

Some drugs that augment cell-intrinsic defenses or modulate cell death/survival pathways have been reported to selectively kill cells infected with HIV or Simian Immunodeficiency Virus (SIV), but comparative studies are lacking. We hypothesized that these drugs may differ in their ability to kill cells infected with intact and defective proviruses.

Design:

To investigate this hypothesis, drugs were tested ex vivo on peripheral blood mononuclear cells (PBMC) from nine antiretroviral therapy (ART)-suppressed individuals.

Methods:

We tested drugs currently in clinical use or human trials, including auranofin (p53 modulator), interferon alpha2A, interferon gamma, acitretin (RIG-I inducer), GS-9620/vesatolimod (TLR7 agonist), nivolumab (PD-1 blocker), obatoclax (Bcl-2 inhibitor), birinapant [inhibitor of apoptosis proteins (IAP) inhibitor], bortezomib (proteasome inhibitor), and INK128/sapanisertib [mammalian target of rapamycin mTOR] [c]1/2 inhibitor). After 6 days of treatment, we measured cell counts/viabilities and quantified levels of total, intact, and defective HIV DNA by droplet digital PCR (Intact Proviral DNA Assay).

Results:

Obatoclax reduced intact HIV DNA [median = 27–30% of dimethyl sulfoxide control (DMSO)] but not defective or total HIV DNA. Other drugs showed no statistically significant effects.

Conclusion:

Obatoclax and other Bcl-2 inhibitors deserve further study in combination therapies aimed at reducing the intact HIV reservoir in order to achieve a functional cure and/or reduce HIV-associated immune activation.
Small Bowel Gastrointestinal Stromal Tumors: The Value of CT Enterography in Assessing Pathological Aggressiveness
Authors: Tu Huijuan , Chen Qiqi , Tu Jianchun , Dong Bingqing , Zhu Feng , Wang Shiyu , Dai Yanmiao , Chen Xu
Published: April 2024

Objective

This study aimed to characterize the computed tomography (CT) enterography features of the small bowel gastrointestinal stromal tumors (GIST) and to determine the association with pathological aggressiveness.

Methods

Computed tomography enterography images of 30 patients with the histologically confirmed small bowel GIST were retrospectively enrolled. Tumor size, location, border, growth pattern, enhancement pattern, necrosis, calcification, ulceration, internal air, nodal metastasis, liver metastasis, peritoneal metastasis, and draining vein were evaluated. Relationships between imaging features and pathological aggressiveness were analyzed using χ2 test or Fisher exact test. Correlations among CT features were analyzed using Spearman correlation analysis.

Results

There were significant differences in tumor size between different risk levels (F = 8.388, P < 0.001). There were statistically significant differences in the 5 imaging manifestations of necrosis, ulcer, tumor boundary, drainage vein, and intratumoral gas (P < 0.05). There was a significant negative correlation between tumor size and enhancement type as well as clear tumor boundary. There was a significant positive correlation between tumor size and necrosis, ulcer, drainage vein, intratumoral gas, liver metastasis, and peritoneal metastasis.

Conclusions

Some CT enterography imaging features might be useful in the determination of the pathological aggressiveness in the patients with small bowel GIST.
Comprehensive Assessment of the Intrinsic Pancreatic Microbiome
Authors: Eckhoff Austin M. , Fletcher Ashley A. , Kelly Matthew S. , Dohlman Anders , McIntyre Caitlin A. , Shen Xiling , Iyer Matthew K. , Nussbaum Daniel P. , Allen Peter J.
Published: April 2024

Objective:

We sought to comprehensively profile tissue and cyst fluid in patients with benign, precancerous, and cancerous conditions of the pancreas to characterize the intrinsic pancreatic microbiome.

Summary Background Data:

Small studies in pancreatic ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasm (IPMN) have suggested that intra-pancreatic microbial dysbiosis may drive malignant transformation.

Methods:

Pancreatic samples were collected at the time of resection from 109 patients. Samples included tumor tissue (control, n=20; IPMN, n=20; PDAC, n=19) and pancreatic cyst fluid (IPMN, n=30; SCA, n=10; MCN, n=10). Assessment of bacterial DNA by quantitative PCR and 16S ribosomal RNA gene sequencing was performed. Downstream analyses determined the relative abundances of individual taxa between groups and compared intergroup diversity. Whole-genome sequencing data from 140 patients with PDAC in the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) were analyzed to validate findings.

Results:

Sequencing of pancreatic tissue yielded few microbial reads regardless of diagnosis, and analysis of pancreatic tissue showed no difference in the abundance and composition of bacterial taxa between normal pancreas, IPMN, or PDAC groups. Low-grade dysplasia (LGD) and high-grade dysplasia (HGD) IPMN were characterized by low bacterial abundances with no difference in tissue composition and a slight increase in Pseudomonas and Sediminibacterium in HGD cyst fluid. Decontamination analysis using the CPTAC database confirmed a low-biomass, low-diversity intrinsic pancreatic microbiome that did not differ by pathology.

Conclusions:

Our analysis of the pancreatic microbiome demonstrated very low intrinsic biomass that is relatively conserved across diverse neoplastic conditions and thus unlikely to drive malignant transformation.
Urinary Incontinence in Primary Care—The Gap Between Recommendations and Real World
Authors: Geynisman-Tan Julia , Cherupally Manisha , Alexandria Shaina J. , Brown Tiffany , Collins Sarah , Mathews Ashley , Pedamallu Havisha , Kenton Kimberly S. , Persell Stephen D.
Published: April 2024

Importance

Routine screening for urinary incontinence (UI) by primary care providers (PCPs) is recommended.

Objectives

We aimed to describe the rate of incident UI diagnosed at annual PCP visits, the prevalence of UI in a large primary care population, and estimate the rate of screening for UI during primary care preventive and annual wellness visits. Secondary aims were to describe PCP knowledge and behavior as they relate to UI screening and diagnosis.

Study Design

The electronic health record was used to abstract the number of adult female patients seen by PCPs within a regional health system with a diagnosis of UI before our study period and with a new diagnosis over a 2-year period. Additional new diagnoses and screening practices were found on chart review of an additional 824 representative charts. Primary care providers within the health system were surveyed about their screening practices and knowledge about UI.

Results

There were 192,053 women primary care patients seen over 2 years. A total of 5.7% had a UI diagnosis preceding the study period and 3.4% had a UI diagnosis during the study period. A total of 42% of PCPs reported that they screen for UI at least half the time and none were completely satisfied with their ability to screen for UI. Sixteen percent of annual wellness visits had any documentation of screening for UI.

Conclusion

In a large primary care population, screening for and detection of UI in women was low.
Diet Intake After Diet Modification Intervention in Women With Fecal Incontinence
Authors: Muñoz Jaclyn M. , Groskreutz Molly , Compher Charlene , Andy Uduak U.
Published: April 2024

Importance

Older women with fecal incontinence (FI) who underwent diet modification intervention (DMI) showed significant improvement in FI symptoms. It is unclear whether improvement in symptoms was associated with objective changes in dietary intake quality.

Objectives

The primary aim was to determine if improvement in overall dietary intake quality was associated with improvement in FI symptoms. Our secondary aim was to evaluate whether individual food group consumption changes were associated with changes in FI symptoms.

Study Design

This was an ancillary analysis of a prospective cohort study of women aged 65 years and older with FI who underwent DMI. Seven-day diet-and-bowel diaries at baseline and 6 weeks after DMI were examined for how frequently participants consumed food categories and FI triggers. Adherence to recommended dietary guidelines was assessed between 2 and 4 weeks using a 24-hour diet recall. Baseline and postintervention consumption were compared using the Wilcoxon signed rank test. Spearman correlation was used to compare dietary intake changes with FI symptom changes.

Results

Twenty-four women completed the 24-hour diet recalls, and 17 women completed the 7-day diet-and-bowel diaries at baseline and 6 weeks. More participants who were adherent had clinically significant improvement in symptoms compared with those who were not adherent (70% vs 30%, P=0.57). Decreased consumption of saturated fats (P=0.01) and fried foods (P<0.001) was associated with improvement in FI symptoms.

Conclusions

In this small population, overall dietary intake quality was not associated with change in FI symptom improvement. Decreased intake of saturated fat and fried food was associated with FI symptom improvement.
Telehealth in a Pelvic Floor Physical Therapy Clinic: A Retrospective Cohort Study
Authors: ter Haar Charlotte M. , Class Quetzal A. , Kobak William H. , Pandya Lopa K.
Published: April 2024

Importance

Telehealth offers advantages to patients with pelvic floor disorders because they face unique barriers to care; however, attendance of telehealth appointments is unknown.

Objective

The objective of this study was to examine the attendance of telehealth appointments in urogynecology patients receiving pelvic floor physical therapy as compared with in-person visits before and during the COVID-19 pandemic.

Study Design

We retrospectively collected electronic medical record data from patients engaging in pelvic floor physical therapy from 2019, and pre– and post–COVID-19 in 2020. Information included appointment type, attendance, age, primary diagnoses, insurance status, and zip code. Cohort differences were examined using the χ2 test and analyses of variance.

Results

Our sample included 359 individuals scheduled for in-person visits in 2019, 57 for telehealth visits in 2020, and 283 for in-person visits in 2020. Patients scheduled for telehealth appointments were younger (39 ± 13 years) than patients in 2019 (45 ± 14 years) or 2020 (42 ± 14 years) in-person cohorts (χ2 (2, 696) = 6.8, P < 0.001). Patients attended telehealth appointments at higher rates (73.7%) than in-person visits in 2019 (56.8%) and 2020 (45.6%; χ2 (2, 699) = 26.2, P < 0.001). Attendance did not differ across primary diagnoses. Proximity based on zip code was not associated with attendance.

Conclusions

Pelvic floor physical therapy attendance rates were highest for patients with telehealth visits as compared with in-person visits. Our findings encourage health care providers to continue or begin to offer telehealth visits for pelvic floor physical therapy for the urogynecology patient population.
Detection and significance of anti-Mycobacterium tuberculosis specific IgG antibody response for the diagnosis of pulmonary tuberculosis using enzyme-linked immunosorbent assay
Authors: Chaudhary Pooja , Mohanty Keshar K. , Kumar Santosh , Sikarwar Arun P. , Patil Shripad A
Published: April 2024

Objective: Evaluation of an ELISA test for detection of IgG antibody response using in-house prepared Mycobacterium tuberculosis H37Rv soluble extract (MTSE) as antigen for rapid diagnosis of pulmonary tuberculosis and its clinical usefulness.
Methods: In this study, a total of 758 pulmonary tuberculosis (TB) patients (652 AFB-positive and 106 AFB-negative), 276 healthy controls, and 43 pulmonary infectious disease controls other than TB were recruited. IgG antibody level against MTB soluble extract was measured in sera samples of all study groups using an ELISA test. The level of IgG antibody responses was compared among groups by the Kruskal-Wallis test. The pairwise comparison was made by the Mann-Whitney test, A positive score was represented by optical density above the cut–off value which was calculated from OD values of healthy controls by adding 2SD to the mean OD value. The evaluation of diagnostic value was considered based on sensitivity and specificity.   
Results: Significantly higher levels of IgG antibody response were observed in PTB patients compared to healthy control and non-TB other pulmonary infectious disease control groups (p value<0.0001). The percent positivity for the IgG antibody response was higher in AFB-positive 574/652 (88.04%) and 79/106 (74.53%) AFB-negative PTB patients as compared to healthy control 9/276 (3.26%) and non-TB other pulmonary infectious disease control 3/43 (6.97%). The sensitivity of the test in PTB patients (AFB-positive and AFB-negative) was 86.15% (95% CI; 83.48-88.53), and the specificity was 96.74% (95% CI; 93.90-98.50).
Conclusion: This developed immunological test could be an efficient test in detecting IgG antibody response in PTB patients. Further, this test could be useful for diagnosing AFB-negative presumptive TB cases.
PATHOGENECITY AND ENZYME SCREENING OF SOME SELECTED NON-DERMATOPHYTIC MOLDS
Authors: Nwofor CN , Onyenwe NE , Osuoha CB
Published: April 2024

A total of 10 non-dermatophytic molds isolated from both symptomatic and asymptomatic cattle skin which includes Penicillum citrinum, Aspergillus welwitschiae, Aspergillus aculeatus, Curvularia kusanol, Cladosporium teniussmum, Pestalotiopsis microspora, Fusarium oxysporum, Fusarium linchenicola, Absidia sp. and Aspergillus fumigatuswere subjected to a pathogenicity test using albino mice. These isolates were also screened for five enzymes using standard plate method. Result from pathogenicity test showed that Absidia sp, C. tenuissimum and Aspergillus welwitschiae were able to elicit discoloration, lesion production and alopecia on the albino mice skin respectively which are evidences of clinical symptoms associated of cutaneous mycoses. The enzyme screening results revealed the highest zone of activity for keratinase (65mm), amylase (86mm), protease (60mm), lipase (60mm) and cellulase (86mm) which were observed on P. microspora, A. welwitschiae, C. tenuissimum, A. welwitschiae and A. welwitschiae respectively.  Pathogenicity test from this study shows that some of these molds may be virulent and that can be attributed to their ability to possess some virulent factors which includes secretion of hydrolytic enzymes.
The recombination landscape of the barn owl, from families to populations
Authors: Topaloudis Alexandros , Lavanchy Eleonore , Cumer Tristan , Ducrest Anne-Lyse , Simon Celine , Machado Ana Paula , Paposhvili Nika , Roulin Alexandre , Goudet Jerome
Published: April 2024

Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of recombination landscapes are lacking due to methodological limitations and a dearth of appropriate data. Linkage mapping based on familial data gives unbiased sex-specific broad-scale estimates of recombination while linkage disequilibrium (LD) based inference based on population data provides finer resolution data albeit depending on the effective population size and acting selective forces. In this study, we use a combination of these two methods, using a dataset of whole genome sequences and elucidate the recombination landscape for the Afro-European barn owl (Tyto alba). Linkage mapping allows us to refine the genome assembly to a chromosome-level quality. We find subtle differences in crossover placement between sexes that leads to differential effective shuffling of alleles. LD based estimates of recombination are concordant with family-based estimates and identify large variation in recombination rates within and among linkage groups. Larger chromosomes show variation in recombination rates while smaller chromosomes have a universally high rate which shapes the diversity landscape. We also identify local recombination hotspots in accordance with other studies in birds lacking thePRDM9gene. However these hotspots show very little evolutionary stability when compared among populations with shallow genetic differentiation. Overall, this comprehensive analysis enhances our understanding of recombination dynamics, genomic architecture, and sex-specific variation in the barn owl, contributing valuable insights to the broader field of avian genomics.

Article summary

To study recombination events we look either in family data or in population data, with each method having advantages over the other. In this study we use both approaches to quantify the barn owl recombination landscape. We find that differences exist between sexes, populations and chromosomes.
Enabling global-scale nucleic acid repositories through versatile, scalable biochemical selection from room-temperature archives
Authors: Berleant Joseph D. , Banal James L. , Rao Dhriti K. , Bathe Mark
Published: April 2024

Conventional collection, preservation, and retrieval of nucleic acid specimens, particularly unstable RNA, require costly cold-chain infrastructure and rely on inefficient robotic sample handling, hindering downstream analyses. These generate critical bottlenecks for global pathogen surveillance and genomic biobanking efforts, prohibiting large-scale nucleic acid sample collection and analyses that are needed to empower pathogen tracing, as well as rare disease diagnostics1. Here, we introduce a scalable nucleic acid storage system that enables rapid and precise retrieval on pooled nucleic acid samples—stored at room-temperature with minimal physical footprint2,3—using versatile database-like queries on barcoded, encapsulated samples. Queries can incorporate numerical ranges, categorical filters, and combinations thereof, which is a significant advancement beyond previous demonstrations limited to single-sample retrieval or Boolean classifiers. We apply our system to a pool of ninety-six mock SARS-CoV-2 genomic samples identified with theoretical patient data including patient age, geographic location, and diagnostic state, allowing rapid, multiplexed nucleic acid sample retrieval in a scalable manner to empower genomic analyses. By avoiding expensive and cumbersome freezer storage and retrieval systems, our approach in principle scales to millions of samples without loss of fidelity or throughput, thereby supporting the development of large-scale pathogen and genomic repositories in under-resourced or isolated regions of the US and worldwide.
Molecular characterization of antimicrobial resistance organisms from drinking water and wastewater in a metropolitan city
Authors: Akhtar Khursheda , Farhana Nasreen , Hossain Alamgir , Khanam Fahmida
Published: April 2024

Background

Antimicrobial resistant (AMR) organisms in environment may harm people. This study assessed the phenotypic and genotypic characteristics of AMR organisms from drinking and wastewater.

Materials and methods

This cross-sectional study conducted randomly on 30 samples (15 drinking water samples from household places; 15 sewage lifts stations) and collected aseptically, filtered, inoculated and isolated from culture plates, identified biochemically of pathogenic bacteria, and disc diffusion tested for antibiotic susceptibility. The primers of the targeted antimicrobial resistance genes were used for molecular amplification.

Results

Twenty-five bacteria were isolated from 30 drinking and wastewater samples.Pseudomonasspp. (36%),Enterobacterspp. (28%),Escherichia coli(20%),Citrobacterspp.(4%), Acinetobacterspp (4%) andKlebsiella oxytoca(4%) were isolated. Most of the isolates exhibited resistance to multiple groups of antibiotics, with meropenem, imipenem, gentamicin, ciprofloxacin, and amikacin showing the highest sensitivity against the isolates. Multiplex PCR confirmed the presence of two ESBL genes (blaSHV andblaCTX-M-15) and five carbapenemase genes (blaIMP,blaVIM,blaKPC,blaOXA1,blaNDM1) in resistant bacteria andblaCTX-M-15 (53.3%) followed byblaKPC (46.7%) genes were the most prevalent from drinking and wastewater samples respectively. According to WHO’s sanitary inspection risk score classification, 60% of drinking water samples scored 4 out of 11, categorizing them as intermediate risk based on hazard score.

Conclusions

This study addresses antimicrobial resistance in the environment, emphasizing public health implications; advocating for improved environmental regulations to mitigate AMR organism discharge through wastewater and drinking water.

The significance of the study

The study attempted to determine the pattern of antimicrobial resistance of microorganisms using phenotypic and genotypic methods by polymerase chain reaction (PCR), targeting particular genes with specific sequence of primers. As in Bangladesh very few studies for antimicrobial resistance organisms from drinking water and wastewater around household and hospital environments in Dhaka city, yet finished to change public health perspectives, and inform respective authorities for making decision. Thus the research contributes to generating some evidence-based information about the reservoir of antimicrobial resistance in environment.
In situinvestigation of extracellular vesicles in viscous formulations: interplay of nanoparticle transport and nano rheology through interferometric light microscopy analysis
Authors: Alexandre Lucile , Dubrova Anastasiia , Kunduru Aruna , Berger Marie , Boucenna Imane , Gazeau Florence , Silva Amanda K. A. , Mangenot Stéphanie , Aubertin Kelly
Published: April 2024

While extracellular vesicles (EVs) demonstrate growing potential as innovative therapeutics in diverse medical context (cancer, regenerative medicine, etc.) or as naturally circulant diagnostic / prognostic probes, their physical properties (size, transport, etc.) remains a critical concern. Here, we introduce a pipeline that relies on interferometric light microscopy (ILM) for measuring not only nanoparticle concentration and size distribution but also for analyzing the interactions of these nanoparticles with their environment. The analysis of interference patterns allows for the physical characterization of (bio)nanoparticles not only in aqueous solutions but also in challenging media with relatively high viscosity, particularly pertinent for characterizing gel-based EV-delivery systems. Through exploration of the instrument’s functionality and the use of calibrated NPs of various known sizes, we successfully obtained information about the local viscosity characteristics of a complex fluid embedding EVs. We present a proof-of-concept for characterizing EVs suspended in unconventional media and their interactions with their surroundings. Leveraging the outcomes of this investigation, we not only highlight the advantages of using ILM for characterizing EVs in complex fluid, particularly pertinent for the development of optimized biological carriers for targeted drug delivery and therapeutic applications, but we also validate a new method for measuring viscosity at the nanoscale.
p53 mediated regulation of LINE1 retrotransposition derived R-loops
Authors: Paul Pratyashaa , Kumar Arun , De Astik Kumar , Parida Ankita Subhadarsani , Bhadke Gauri , Khatua Satyajeet , Pattanayak Fizalin , Tiwari Bhavana
Published: April 2024

Long Interspersed Nuclear Element 1 (LINE1/L1) retrotransposons, comprising around 17% of the human genome, typically remain quiescent in healthy somatic cells but become activated in various cancer types. Our recent investigation reveals that p53 silences L1 transposons in human somatic cells, potentially constituting a tumor suppressive pathway. In this study, we demonstrate that p53 silences both L1mRNA-gDNA (cis L1 R-loops) and L1mRNA-cDNA hybrids (trans L1 R-loops) formed during retrotransposition. The activation of L1 transposons by HDAC inhibitors (HDACi) led to accumulation of these cis and trans L1 R-loops in p53-/-cells, which were mitigated by treatment with a reverse transcriptase inhibitor. Furthermore, p53 established re-silencing of hyperactivated L1 transposons induced by HDACi. The p53-mediated restoration of silencing was accompanied by recruiting histone repressive marks specifically H3K9me3 and H3K27me3 and inhibiting the deposition of H3K4me3 and H3K9ac marks at the L1 promoter. This study elucidates a novel role of p53 in regulating the formation of RNA-DNA hybrids, a pivotal intermediate component of retrotransposition, and initiating the suppression of hyperactivated L1 elements. These findings underscore the significance of p53 in preserving genome stability through the regulation of L1-derived R-loops.

In Brief

The role of L1 transposon derived L1mRNA-cDNA hybrids; an intermediate product formed during retrotransposition, in DNA damage and inflammation is not clear. Paul et al. reveals that p53 prevents L1cDNA derived RNA-DNA hybrids to control DNA damage and activation of inflammatory genes. The findings also elucidate the role of p53 in initiating the repression of hyperactivated transposons by facilitating the recruitment of epigenetic repressive marks and preventing the deposition of activating marks at L1-5’UTR.

Highlights

p53 loss facilitates accumulation of both cis (L1mRNA-gDNA) and trans (L1mRNA-cDNA) forms of L1 R-loops.

The youngest, actively retrotransposing full-length L1s contribute to the formation of trans (L1mRNA-cDNA) R-loops.

p53 aids immediate L1 re-silencing by restoring deposition of epigenetic repressive and inhibition of activating marks.

Reverse transcriptase inhibitor prevents L1 mediated DNA damage.

Subject Categories: L1/LINE1, p53, Retrotransposons, RNA-DNA hybrids, Cis R loops, Trans R-loop, L1/LINE1

Graphical
The ER Thioredoxin-Related Transmembrane Protein TMX2 Controls Redox-Mediated Tethering of ER-Mitochondria Contacts (ERMCS)
Authors: Chen Junsheng , Yap Megan C. , Bassot Arthur , Pascual Danielle M. , Makio Tadashi , Zimmermann Jannik , Mast Heather , Bhat Rakesh , Fleury Samuel G. , Fan Yuxiang , Buzatto Adriana Zardini , Moore Jack , Ballanyi Klaus , Li Liang , Overduin Michael , Lemieux M. Joanne , Lemieux Hélène , Tan Wen-Hann , Mancini Grazia M.S. , Morgan Bruce , Marcogliese Paul C. , Simmen Thomas
Published: April 2024

Thioredoxin-related transmembrane proteins (TMX) of the endoplasmic reticulum (ER) have emerged as key regulators of ER membrane properties. Within the ER lumen, TMX proteins and other ER redox enzymes determine oxidative conditions, which control the formation of ER-mitochondria membrane contacts (ERMCS) and determine their function. ERMCS exhibit cytoplasmic redox nanodomains, derived from ER and mitochondrial reactive oxygen species (ROS), whose mechanistic regulation is uncharacterized. Our research has identified the ER protein TMX2, which uses its unique cytosolic thioredoxin domain to prevent cytosolic sulfenylation of mitochondrial outer membrane proteins such as TOM70 through a functional interaction with peroxiredoxin-1 (PRDX1). By doing so, TMX2 interferes with the TOM70 ERMCS tethering function and reduces mitochondrial Ca2+flux and metabolism. Recently, TMX2 mutations have been identified to cause a neurodevelopmental disorder with microcephaly, cortical malformations, and spasticity (NEDMCMS). Using TMX2-mutated NEDMCMS patient cells, we demonstrate that compromising TMX2 through mutation reproduces mitochondrial defects. In a flyin vivomodel, TMX2 knockdown manifests predominantly in glial cells. Our results therefore provide important mechanistic insight into NEDMCMS and mechanistically link TMX2-mediated control of ERMCS to brain development and function.

Graphical Abstract

The transmembrane thioredoxin-related TMX2 prevents TOM70 sulfenylation at ERMCS, thus maintaining normal mitochondria metabolism in wild-type cells. TMX2 knockout leads to TOM70 sulfenylation and tight ERMCS formation. This then increases ROS production, unbalances mitochondrial lipids, and relatively shifts OXPHOS electron supply to complex II.
Hyperacetylation mimetics within the tau filament core inhibits prion-like propagation of misfolded tau
Authors: Smith Ethan D , McKenna Robert , Mietzsch Mario , Borchelt David R , Prokop Stefan , Chakrabarty Paramita
Published: April 2024

Acetylation of key Lysine residues characterizes aggregates of the microtubule-associated protein tau constituting the neuropathological hallmark of many neurodegenerative diseases, such as Alzheimer’s disease (AD) and Progressive Supranuclear Palsy (PSP). This has led to the idea that acetylation influences tau aggregation. Using a HEK293 cell-based aggregation assay, we tested whether acetylation-mimicking substitutions (K→Q) on five AD-associated acetyl-modified sites (AcK-311, 353, 369, 370, 375) influenced its propensity to aggregate when exposed to tau seeds derived from two clinically distinctive diseases – AD and PSP. In combination, the presence of 5K→Q sites ablated tau aggregation induced by seeds from both AD and PSP patients, indicating that acetylation within the filament core domain of tau could have an inhibitory effect on seed-mediated aggregation. We had previously identified that a phosphorylation-mimetic on Ser305 (S→E) abrogated tau aggregation by seeds from AD patients, without affecting seeding by PSP patients. Combining the S305→E to the 5K→Q acetyl-modified sites, we found that this tau could now be seeded only by PSP patients, but not by AD patients, confirming Ser305 as a critical determinant of strain-specific tau seeding. On the other hand, acetylation-nullifying substitutions (K→R or K→A) on these same Lys sites did not alter tau seeding abilities compared to the parental tau construct. Notably, the combined acetylation-nullifying Alanine substitutions on these 5 Lys sites resulted in spontaneous self-aggregation, with the filaments resembling amorphous deposits. All together, we demonstrate that cooperative acetyl-occupancy in the tau filament core influences seeded propagation of misfolded tau as well as drives self-aggregation.
A novel method to guide biomarker combinations to optimize the sensitivity
Authors: Ghasem Seyyed Mahmood , Fahrmann Johannes F. , Hanash Samir , Do Kim-Anh , Long James P. , Irajizad Ehsan
Published: April 2024

Logistic regression has demonstrated its utility in classifying binary labeled datasets through the maximum likelihood approach. However, in numerous biological and clinical contexts, the aim is often to determine coefficients that yield the highest sensitivity at the pre-specified specificity or vice versa. Therefore, the application of logistic regression is limited in such settings. To this end, we have developed an improved regression framework, SMAGS, for binary classification that, for a given specificity, finds the linear decision rule that yields the maximum sensitivity. Furthermore, we employed the method for feature selection to find the features that are satisfying the sensitivity maximization goal. We compared our method with normal logistic regression by applying it to real clinical data as well as synthetic data. In the real application data (colorectal cancer dataset), we found 14% improvement of sensitivity at 98.5% specificity.

Availability and implementation

Software is made available in Python (https://github.com/smahmoodghasemi/SMAGS)
CD4-mediated immunity shapes neutrophil-driven tuberculous pathology
Authors: Gern Benjamin H , Klas Josepha M , Foster Kimberly A , Cohen Sara B , Plumlee Courtney R , Duffy Fergal J , Neal Maxwell L , Halima Mehnaz , Gustin Andrew T , Diercks Alan H , Aderem Alan , Gale Michael , Aitchison John D , Gerner Michael Y , Urdahl Kevin B
Published: April 2024

PulmonaryMycobacterium tuberculosis(Mtb) infection results in highly heterogeneous lesions ranging from granulomas with central necrosis to those primarily comprised of alveolitis. While alveolitis has been associated with prior immunity in human post-mortem studies, the drivers of these distinct pathologic outcomes are poorly understood. Here, we show that these divergent lesion structures can be modeled in C3HeB/FeJ mice and are regulated by prior immunity. Using quantitative imaging, scRNAseq, and flow cytometry, we demonstrate that Mtb infection in the absence of prior immunity elicits dysregulated neutrophil recruitment and necrotic granulomas. In contrast, prior immunity induces rapid recruitment and activation of T cells, local macrophage activation, and diminished late neutrophil responses. Depletion studies at distinct infection stages demonstrated that neutrophils are required for early necrosis initiation and necrosis propagation at chronic stages, whereas early CD4 T cell responses prevent neutrophil feedforward circuits and necrosis. Together, these studies reveal fundamental determinants of tuberculosis lesion structure and pathogenesis, which have important implications for new strategies to prevent or treat tuberculosis.
Unlocking TAS2R14 activation through intricate multi-ligand binding networks
Authors: Hu Xiaolong , Ao Weizhen , Gao Mingxin , Wu Lijie , Pei Yuan , Liu Shenhui , Sun Qianqian , Liu Junlin , Jiang Longquan , Wu Yiran , Wang Xin , Li Yan , Tan Qiwen , Cheng Jie , Yang Fan , Yang Chi , Sun Jinpeng , Hua Tian , Liu Zhi-Jie
Published: April 2024

Bitter taste receptors, particularly TAS2R14, play central roles in discerning a wide array of bitter substances, ranging from dietary components to pharmaceutical agents1–3. In addition, TAS2R14 has broad expression in non-gustatory tissues, suggesting its important roles in selective physiological processes and therapeutic potential4. Here, we present cryo-electron microcopy structures of TAS2R14 in complex with flufenamic acid and aristolochic acid, coupling with G protein subtypes gustducin and Gi. Distinct from most known GPCRs, agonists of TAS2R14 bind to multiple intracellular pockets. We highlight the cholesterol molecules occupying an upper transmembrane site, typically the orthosteric pocket in other GPCRs, also binding in the entrance to an intracellular agonist binding pocket, suggesting an endogenous modulatory function5. The structural and mutagenesis analysis illuminate the receptor’s broad-spectrum ligand recognition and activation via intricate multiple ligand-binding sites. Furthermore, we unveil the structural configuration of gustducin and its interaction with TAS2R14, as well as the coupling mode of Gi1. This investigation should be instrumental in advancing our knowledge of the mechanisms underlying bitter taste recognition and response, with broader relevance to sensory biology and pharmacology.
Rbpjdeletion in hepatic progenitor cells attenuates endothelial responses in a mouse model of cholestatic liver disease
Authors: Lee Sanghoon , Ren Lu , Paranjpe Aditi , Zhou Ping , Potter Andrew , Huppert Stacey S. , Shin Soona
Published: April 2024

Background and Aims

Since the role of hepatic progenitor cells (HPCs) constituting ductular reactions in pathogenesis remains ambiguous, we aimed to establish the in vivo cause-and-effect relationship between HPCs and angiogenesis, a process associated with chronic liver disease progression. We previously demonstrated that peritumoral ductules are associated with angiogenesis in liver tumors and forkhead box L1 (Foxl1)- expressing murine HPCs secrete angiogenic factors in vitro. Therefore, we hypothesized that HPCs are capable of remodeling the vascular microenvironment and this function of HPCs is dependent on recombination signal binding protein for immunoglobulin kappa J region (RBPJ), a key effector of the Notch signaling pathway.

Approach and Results

We generated HPC-specificRbpjconditional knockout mice usingFoxl1-Creand treated them with the 3,5-diethoxycarbonyl-1,4-dihydrocollidine-supplemented diet to induce cholestatic liver disease. Knockout mice displayed significant reduction of HPC proliferation and ductular reactions as well as attenuated vascular and fibrotic areas compared to control mice. Assessment of vascular endothelial growth factor A-positive areas in vivo and the effects ofRbpjshRNAs in vitro indicated thatRbpjknockout in HPCs reduces the total number of angiogenic factor-expressing cells rather than affecting angiogenic factor expression within HPCs. Single-nucleus RNA sequencing analysis indicated that conditionalRbpjknockout in HPCs induces transcriptional changes in endothelial cells and alters expression of genes involved in various functions of the endothelium.

Conclusion

Our findings indicate that HPCs regulate endothelial responses to cholestatic liver disease andRbpjdeletion in HPCs attenuates these responses, identifying novel targets for modulating angiogenesis during disease progression.
Parameter quantification for oxygen transport in the human brain
Authors: Bing Yun , Józsa Tamás I. , Payne Stephen J.
Published: April 2024

Oxygen is carried to the brain by blood flow through generations of vessels across a wide range of length scales. This multi-scale nature of blood flow and oxygen transport poses challenges on investigating the mechanisms underlying both healthy and pathological states through imaging techniques alone. Recently, multi-scale models describing whole brain perfusion and oxygen transport have been developed. Such models rely on effective parameters that represent the microscopic properties. While parameters of the perfusion models have been characterised, those for oxygen transport are still lacking. In this study, we set to quantify the parameters associated with oxygen transport and their uncertainties. We first present a multi-scale, multi-compartment oxygen transport model based on a porous continuum approach. We then determine the effective values of the model parameters. By using statistically accurate capillary networks, geometric parameters (vessel volume fraction and surface area to volume ratio) that capture the microvascular topologies are found to be 1.42% and 627 [mm2/mm3], respectively. These values compare well with those obtained from human and monkey vascular samples. In addition, maximum consumption rates of oxygen are optimised to uniquely define the oxygen distribution over depth. Simulation results from a one-dimensional tissue column show qualitative agreement with experimental measurements of tissue oxygen partial pressure in rats. We highlight the importance of anatomical accuracy through simulation performed within a patient-specific brain mesh. Finally, one-at-a-time sensitivity analysis reveals that the oxygen model is not sensitive to most of its parameters; however, perturbations in oxygen solubilities and plasma to whole blood oxygen concentration ratio have a considerable impact on the tissue oxygenation. These findings demonstrate the validity of using a porous continuum approach to model organ-scale oxygen transport and draw attention to the significance of anatomy and certain parameter values.
Mol-AE: Auto-Encoder Based Molecular Representation Learning With 3D Cloze Test Objective
Authors: Yang Junwei , Zheng Kangjie , Long Siyu , Nie Zaiqing , Zhang Ming , Dai Xinyu , Ma Wei-Ying , Zhou Hao
Published: April 2024

3D molecular representation learning has gained tremendous interest and achieved promising performance in various downstream tasks. A series of recent approaches follow a prevalent framework: an encoder-only model coupled with a coordinate denoising objective. However, through a series of analytical experiments, we prove that the encoderonly model with coordinate denoising objective exhibits inconsistency between pre-training and downstream objectives, as well as issues with disrupted atomic identifiers. To address these two issues, we propose Mol-AE for molecular representation learning, an auto-encoder model using positional encoding as atomic identifiers. We also propose a new training objective named 3D Cloze Test to make the model learn better atom spatial relationships from real molecular substructures. Empirical results demonstrate that Mol-AE achieves a large margin performance gain compared to the current state-of-the-art 3D molecular modeling approach. The source codes of Mol-AE are publicly available athttps://github.com/yjwtheonly/MolAE.
Multi-scale Simulations of MUT-16 Scaffold Protein Phase Separation and Client Recognition
Authors: Gaurav Kumar , Busetto Virginia , Páez-Moscoso Diego Javier , Changiarath Arya , Hanson Sonya M. , Falk Sebastian , Ketting René F. , Stelzl Lukas S.
Published: April 2024

Phase separation of proteins plays a critical role in cellular organisation. How phase separated protein condensates underpin biological function and how condensates achieve specificity remain elusive. We investigated the phase separation of MUT-16, a scaffold protein inMutator foci, and its role in recruiting the client protein MUT-8, a key component in RNA silencing inC. elegans. We employed a multiscale approach that combined coarse-grained (residue-level CALVADOS2 and near-atomistic Martini3) and atomistic simulations. Simulations across different resolutions provide a consistent perspective on how MUT-16 condensates recruit MUT-8, enabling the fine-tuning of chemical details while balancing the computational cost. Both coarse-grained models (CALVADOS2 and Martini3) predicted the relative phase separation propensities of MUT-16’s disordered regions, which we confirmed throughin vitroexperiments. Simulations also identified key sequence features and residues driving phase separation while revealing differences in residue interaction propensities between CALVADOS2 and Martini3. Furthermore, Martini3 and 350 µs atomistic simulations on Folding@Home of MUT-8’s N-terminal prion-like domain with MUT-16 M8BR cluster highlighted the importance of cation-πinteractions between Tyr residues of MUT-8 and Arg residues of MUT-16 M8BR. Lys residues were observed to be more prone to interact in Martini3. Atomistic simulations revealed that the guanidinium group of Arg also engages in sp2-πinteractions and hydrogen bonds with the backbone of Tyr, making Arg-Tyr interactions stronger than Lys-Tyr, where these additional favourable contacts are absent. In agreement with our simulations,in vitroco-expression pulldown experiments demonstrated a progressive loss of MUT-8 recruitment following the mutation of Arg in MUT-16 M8BR to Lys or Ala, confirming the critical role of Arg in this interaction. These findings advance our understanding of MUT-16 phase separation and subsequent MUT-8 recruitment, key processes in assemblingMutator focithat drive RNA silencing inC. elegans.

Statement of Significance

In cells proteins phase separate and form condensates. These protein condensates can play important role in bringing molecules together and facilitate biochemical processes. In this work, we used molecular dynamics simulations to understand how MUT-16 phase separates and forms the scaffold of the so-calledMutator focus.Mutator fociproduce small RNA which help to regulates genes. As the scaffold of theMutator focus, MUT-16 recruit multiple proteins which are important for the production of such small RNAs.
Latent-based Directed Evolution accelerated by Gradient Ascent for Protein Sequence Design
Authors: Ngo Nhat Khang , Tran Thanh V. T. , Duy Nguyen Viet Thanh , Hy Truong Son
Published: April 2024

Directed evolution has been the most effective method for protein engineering that optimizes biological functionalities through a resource-intensive process of screening or selecting among a vast range of mutations. To mitigate this extensive procedure, recent advancements in machine learning-guided methodologies center around the establishment of a surrogate sequence-function model. In this paper, we propose Latent-based Directed Evolution (LDE), an evolutionary algorithm designed to prioritize the exploration of high-fitness mutants in the latent space. At its core, LDE is a regularized variational autoencoder (VAE), harnessing the capabilities of the state-of-the-art Protein Language Model (pLM), ESM-2, to construct a meaningful latent space of sequences. From this encoded representation, we present a novel approach for efficient traversal on the fitness landscape, employing a combination of gradient-based methods and directed evolution. Experimental evaluations conducted on eight protein sequence design tasks demonstrate the superior performance of our proposed LDE over previous baseline algorithms. Our implementation is publicly available athttps://github.com/HySonLab/LatentDE.