bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative MODS-Wayne Assay for Rapid Detection of Pyrazinamide Resistance inMycobacterium tuberculosisfrom Sputum Samples
Authors: Toscano-Guerra Emily , Alcántara Roberto , Gilman Robert , Grandjean Louis , Zimic Mirko , Sheen Patria
Published: January 2024

Background

Tuberculosis (TB) remains a significant global health challenge, particularly with the rise of drug-resistant strains, such as Pyrazinamide (PZA)-resistant TB. This resistance hampers treatment effectiveness. Currently, there’s a lack of affordable and precise quantitative tests for detecting PZA resistance, highlighting the need for accessible diagnostic tools. Our study introduces a direct, accurate, and accessible susceptibility test for PZA resistance by quantifying pirazinoic acid (POA).

Methods

We analyzed 264 TB-positive samples (MP and TBN) to assess PZA susceptibility by measuring POA production. This was done using the MODS-Wayne qualitative assay and our developed quantitative approach (MODS-WQ). For MODS-WQ, TBN samples were processed in 7H9 media (MODS-WQ 7H9) and MP samples in citrate buffer (MODS-WQ CB). We measured POA levels using spectrophotometry against a calibration curve, with PZA susceptibility determined by a composite standard. We also investigated the correlation between POA levels and pyrazinamidase mutations. Multidrug-resistant samples were assessed using the MODS test, and statistical analyses were conducted.

Results

Approximately 23.48% of the samples showed PZA resistance, which included 62.8% of the multidrug-resistant (MDR) samples. The MODS-Wayne assay demonstrated an 87.8% sensitivity and 95.9% specificity for MP samples, and 62.5% sensitivity with 93.7% specificity for TBN samples. The MODS-WQ identified specific cut-off points—123.25 μM for MODS-WQ 7H9 and 664.7 μM for MODS-WQ CB—with corresponding sensitivities of 81.25% and 92.31%, and specificities of 77.22% and 95.93%. Significantly lower POA levels were observed in samples with mutations in the metal binding site compared to mutations on the enzyme’s periphery.

Conclusions

The citrate-buffered MODS-WQ demonstrates high sensitivity and specificity in quantifying POA. It offers a significant improvement over qualitative methods, effectively overcoming their subjectivity limitations in PZA resistance detection.
MORPHOMETRIC IMAGE ANALYSIS COMPARISON OF BASAL CELL CARCINOMAS & MELANOMAS OF THE HEAD & NECK VERSUS OTHER SITES
Authors: Hue Jonas , Ekanayake Jinendra , Dehmeshki Jamshid , Dhanda Jagtar
Published: January 2024

Background

Management of skin cancers are heavily dependent on clinical diagnosis via dermoscopy. Dermoscopic morphology of basal cell carcinomas (BCC) and melanomas influence diagnosis and may be influenced by anatomic location.

Objective

In this study, we aimed to investigate the morphologic differences between anatomic sites of the head and neck (H&N) versus other body sites in basal cell carcinomas and melanomas.

Patients and methods

The publicly available HAM10000 dataset was used in this study. Morphometric image analysis of the BCCs (n=422) and melanomas (n=868) in this dataset was performed using an open-source image analysis software. Univariate and multivariate statistical analysis was done to identify differences between H&N and other anatomic sites. The multifactorial data was further interrogated with dimensionality reduction techniques, linear discriminant analysis, principal component analysis and t-distributed stochastic neighbour embedding.

Results

Univariate and multivariate statistical analyses revealed significant differences between H&N and other sites for both BCCs and melanomas (P<0.05). Fifty-three univariate and 11 multivariate features were found to be statistically significant in the BCC group. Thirteen univariate and 8 multivariate features were statistically significant in the melanoma group. Dimensionality reduction via linear discriminant analysis of the BCC groups revealed modest separation of the data by anatomical site. However, melanomas appeared to be more homogenous across H&N and other body sites.

Conclusion

BCCs of the H&N may be morphologically different to BCCs of other body sites. This may influence the accuracy of computer-assisted diagnostic tools and specialist clinicians working predominantly in the H&N region should exercise caution when employing these tools in clinical practice.
Retrospective Analysis of Blood Biomarkers of Neurological Injury in Human Cases of Viral Infection and Bacterial Sepsis
Authors: Bartlett Maggie L. , Goux Heather , Johnson Linwood , Schully Kevin L. , Gregory Melissa , Brandsma Joost , Chenoweth Josh G. , Clark Danielle V. , Rivera Luis Felipe , Lezcano-Coba Carlos , Vittor Amy Y. , Hayes Ronald , Galué Josefrancisco , Carrera Jean-Paul , Smith Darci R.
Published: January 2024

Background

Blood biomarkers of neurological injury could provide a rapid diagnosis of central nervous system (CNS) injury caused by infections. An FDA-approved assay for mild traumatic brain injury (TBI) measures glial fibrillary acidic protein (GFAP) and ubiquitin carboxy-terminal hydrolase L1 (UCH-L1), which signal astrocyte and neuronal injury, respectively. Here, we assessed the applicability of this biomarker assay for determining infection-induced brain injury.

Methods

We measured serum levels of GFAP and UCH-L1 retrospectively in serum samples from three study populations: 1) human cases infected with Venezuelan equine encephalitis virus (VEEV) and Madariaga virus (MADV) (n = 73), 2) human sepsis patients who were severely ill or diagnosed with encephalitis (n = 66), and 3) sepsis cases that were subsequently evaluated for cognitive impairment (n = 64).

Results

In the virus infection group, we found elevated GFAP for VEEV (p = 0.014) and MADV (p = 0.011) infections, which correlated with seizures (p = 0.006). In the bacterial sepsis group, GFAP was elevated in cases diagnosed with encephalitis (p = 0.0007) and correlated with headaches (p = 0.0002). In the bacterial sepsis cases with a later cognitive assessment, elevated GFAP (p = 0.0057) at study enrollment was associated with cognitive impairment six months later with a positive prognostic capacity of 79% (CI: 66–95%; p = 0.0068).

Conclusions

GFAP and UCH-L1 levels measured using an FDA-approved assay for TBI may indicate brain injury resulting from viral or bacterial infections and could predict the development of neurological sequelae.
Optimizing the number of models included in outbreak forecasting ensembles
Authors: Fox Spencer J. , Kim Minsu , Meyers Lauren Ancel , Reich Nicholas G. , Ray Evan L.
Published: January 2024

Based on historical influenza and COVID-19 forecasts, we quantify the relationship between the number of models in an ensemble and its accuracy and introduce an ensemble approach that can outperform the current standard. Our results can assist collaborative forecasting efforts by identifying target participation rates and improving ensemble forecast performance.
Relationships of visual impairment and eye conditions with imaging markers, cognition, and diagnoses of dementia: a bi-directional Mendelian randomization study
Authors: Ferguson Erin L , Thoma Mary , Buto Peter , Wang Jingxuan , Glymour M. Maria , Hoffmann Thomas J , Choquet Hélène , Andrews Shea J , Yaffe Kristine , Casaletto Kaitlin , Brenowitz Willa D
Published: January 2024

Objective

To evaluate the causal relationships between visual acuity, eye conditions (focusing on cataracts and myopia), and Alzheimer disease (AD) and related dementias.

Design

Cohort and two sample bi-directional mendelian randomization (MR) study.

Setting

UK Biobank participants and summary statistics from previously published genome-wide association studies on cataract, myopia, and AD.

Participants

UK Biobank participants (n=304,953) aged 55-70 without dementia at baseline, underwent genotyping, reported on eye conditions, and a subset completed visual acuity exams (n=113,756) or brain imaging (n=36,855)

Main outcome measures

All-cause dementia, AD, and vascular dementia (VaD) identified from electronic medical records.

Results

The sample averaged 62.1 years (SD=4.1) of age at baseline, 4.7% had cataracts, and 3.9% had worse than 20/40 vision. History of cataracts (HR=1.18, 95% CI: 1.07 to 1.29) and 20/40 vision (HR=1.35, 95% CI: 1.06 to 1.70) were associated with higher hazard of all-cause dementia. In MR analyses to estimate causal effects, cataracts increased risk of VaD inverse-variance weighted (OR=1.92, 95% CI: 1.26-2.92) borderline increased all-cause dementia (OR =1.21, 95% CI: 0.98 to 1.50) but not AD (OR=1.01, 95% CI: 0.97-1.06). There was no significant association between observed or genetic risk for myopia and dementia. In MR for reverse causality using genetic risk for AD, AD was not significantly associated with cataracts (inverse-variance weighted OR=0.99, 95% CI: 0.96 to 1.01). Genetic risk for cataracts were associated with smaller total brain (β= −597.4 mm3, 95% CI: −1077.9 to −117.0) and grey matter volumes (β= −375.2 mm3, 95% CI: −680.1 to −70.2), but not other brain regions or cognition.

Conclusions

Our findings suggest cataracts increase risk of dementia and may reduce brain volume. This lends further support to the hypothesis that cataract extraction may reduce risk for dementia.
Clinical significance of PD-1-binding soluble PD-L1 and MMPs in the microenvironment of gastric cancer and non-small cell lung cancer treated with PD-1/PD-L1 blockade
Authors: Ando Fumihiko , Kashiwada Takeru , Kuroda Shoko , Fujii Takenori , Takano Ryotaro , Miyabe Yoshishige , Sakatani Takashi , Asatsuma-Okumura Tomoko , Hashiguchi Masaaki , Kanazawa Yoshikazu , Ohashi Ryuji , Yoshida Hiroshi , Seike Masahiro , Gemma Akihiko , Iwai Yoshiko
Published: January 2024

Purpose

The tumor microenvironment (TME) impacts the therapeutic efficacy of immune checkpoint inhibitors (ICIs). No liquid biomarkers are available to evaluate TME heterogeneity. Here, we investigated the clinical significance of PD-1-binding soluble PD-L1 (bsPD-L1) in gastric cancer (GC) patients and non-small cell lung cancer (NSCLC) patients treated with PD-1/PD-L1 blockade.

Experimental Design

We examined bsPD-L1, matrix metalloproteinases (MMPs), and IFN-γ levels in plasma samples from GC patients (n =117) prior to surgery and NSCLC patients (n =72) prior to and two months after ICI treatment and extracellular matrix (ECM) integrity, PD-L1 expression, and T cell infiltration in tumor tissues from 25 GC patients.

Results

bsPD-L1 was detected in 17/117 GC patients and 16/72 NSCLC patients. bsPD-L1 was strongly and moderately correlated with MMP13 and MMP3, respectively. In GC, bsPD-L1 expression was associated with IFN-γ levels and intra-tumoral T cell infiltration; MMP13 levels were associated with loss of ECM integrity, allowing tumor cells to access blood vessels. MMP3 and MMP13 levels were altered during ICI treatment. Combination of bsPD-L1 and MMP levels identified two patient groups; bsPD-L1+MMP13highin GC and bsPD-L1+(MMP3 and MMP13)increasedin NSCLC were associated with poor prognosis, and bsPD-L1+MMP13lowin GC and bsPD-L1+(MMP3 or MMP13)decreasedin NSCLC were associated with favorable prognosis.

Conclusions

Plasma bsPD-L1 and MMP13 levels indicate T cell response and loss of ECM integrity, respectively, in the TME. The combination of bsPD-L1 and MMPs may represent a non-invasive tool to predict recurrence in GC and the efficacy of ICIs in NSCLC.
Large language models for generating medical examinations: systematic review
Authors: Artsi Yaara , Sorin Vera , Konen Eli , Glicksberg Benjamin S. , Nadkarni Girish , Klang Eyal
Published: January 2024

Purpose

Writing multiple choice questions (MCQs) for the purpose of medical exams is challenging. It requires extensive medical knowledge, time and effort from medical educators. This systematic review focuses on the application of large language models (LLMs) in generating medical MCQs.

Methods

The authors searched for studies published up to November 2023. Search terms focused on LLMs generated MCQs for medical examinations. MEDLINE was used as a search database.

Results

Overall, eight studies published between April 2023 and October 2023 were included. Six studies used Chat-GPT 3.5, while two employed GPT 4. Five studies showed that LLMs can produce competent questions valid for medical exams. Three studies used LLMs to write medical questions but did not evaluate the validity of the questions. One study conducted a comparative analysis of different models. One other study compared LLM-generated questions with those written by humans.

All studies presented faulty questions that were deemed inappropriate for medical exams. Some questions required additional modifications in order to qualify.

Conclusions

LLMs can be used to write MCQs for medical examinations. However, their limitations cannot be ignored. Further study in this field is essential and more conclusive evidence is needed. Until then, LLMs may serve as a supplementary tool for writing medical examinations.
Rare splice and missense variants with evidence of pathogenicity in consanguineous families with autosomal recessive intellectual disability from Pakistan
Authors: Waheed Abdul , Eveleigh Robert , Perley Danielle , St-Cyr Janick , Lefebvre François , Khan Abdul Hameed , Majeed Zarqash , Majeed Abrish , Trajanoska Katerina , Cuella-Martin Raquel , Bhérer Claude , Ali Ghazanfar , Mooser Vincent , Taliun Daniel
Published: January 2024

Intellectual disability (ID) is a neurodevelopmental disorder affecting up to 1-3% of people worldwide. Genetic factors, including rarede novoor rare homozygous mutations, explain many cases of autosomal dominant or recessive forms of ID. ID is clinically and genetically heterogeneous, with hundreds of genes associated with it. In this study, we performed high-depth whole-genome sequencing of twenty individuals from five consanguineous families from Pakistan, with nine individuals affected by mild or severe ID. We identified one splice and five missense rare variants (at allele frequencies below 0.001%) in a homozygous state in the affected individuals with supporting and moderate evidence of pathogenicity based on guidance from the American College of Medical Genetics and Genomics. These six variants mapped to different genes (SRD5A3,RDH11,RTF2,PCDHA2,ADAMTS17, andTRPC3), and onlySRD5A3had previously been known to cause ID. The p.Tyr169Cys mutation insideSRD5A3was predicted to be deleterious and affect protein structure by multiplein silicotools. In addition, we found one missense mutation, p.Pro1505Ser, insideUNC13Bwith conflicting evidence of pathogenic and benign effects. Further functional studies are required to confirm the pathogenicity of these variants and understand their role in ID. Our findings provide additional needed information for interpreting rare variants in the genetic testing of ID.
De novovariants inPLCG1are associated with hearing impairment, ocular pathology, and cardiac defects
Authors: Ma Mengqi , Zheng Yiming , Lu Shenzhao , Pan Xueyang , Worley Kim C. , Burrage Lindsay C. , Blieden Lauren S. , Allworth Aimee , Chen Wei-Liang , Merla Giuseppe , Mandriani Barbara , Rosenfeld Jill A. , Li-Kroeger David , Dutta Debdeep , Yamamoto Shinya , Wangler Michael F. ,   Undiagnosed Diseases Network, Glass Ian A. , Strohbehn Sam , Blue Elizabeth , Prontera Paolo , Lalani Seema R. , Bellen Hugo J.
Published: January 2024

Phospholipase C isozymes (PLCs) hydrolyze phosphatidylinositol 4,5-bisphosphate into inositol 1,4,5-trisphosphate and diacylglycerol, important signaling molecules involved in many cellular processes.PLCG1encodes the PLCγ1 isozyme that is broadly expressed. Hyperactive somatic mutations ofPLCG1are observed in multiple cancers, but only one germline variant has been reported. Here we describe three unrelated individuals withde novoheterozygous missense variants inPLCG1(p.Asp1019Gly, p.His380Arg, and p.Asp1165Gly) who exhibit variable phenotypes including hearing loss, ocular pathology and cardiac septal defects. To model these variantsin vivo, we generated the analogous variants in theDrosophilaortholog,small wing(sl). We created a null alleleslT2Aand assessed the expression pattern.slis broadly expressed, including in wing discs, eye discs, and a subset of neurons and glia. Loss ofslcauses wing size reductions, ectopic wing veins and supernumerary photoreceptors. We document that mutant flies exhibit a reduced lifespan and age-dependent locomotor defects. Expressing wild-typeslinslT2Amutant rescues the loss-of-function phenotypes whereas expressing the variants causes lethality. Ubiquitous overexpression of the variants also reduces viability, suggesting that the variants are toxic. Ectopic expression of an established hyperactivePLCG1variant (p.Asp1165His) in the wing pouch causes severe wing phenotypes, resembling those observed with overexpression of the p.Asp1019Gly or p.Asp1165Gly variants, further arguing that these two are gain-of-function variants. However, the wing phenotypes associated with p.His380Arg overexpression are mild. Our data suggest that thePLCG1 de novoheterozygous missense variants are pathogenic and contribute to the features observed in the probands.
Insulin-like Growth Factor 1 Receptor Expression Correlates with Programmed Death Ligand 1 Expression and Poor Survival in Non-small Cell Lung Cancer
Authors: Nagamine Hiroaki , Yashiro Masakazu , Mizutani Megumi , Sugimoto Akira , Matsumoto Yoshiya , Tani Yoko , Sawa Kenji , Kaneda Hiroyasu , Yamada Kazuhiro , Watanabe Tetsuya , Asai Kazuhisa , Suzuki Satoshi , Kawaguchi Tomoya
Published: January 2024

The insulin-like growth factor 1 receptor (IGF1R) has been associated with growth and metastasis in various cancers. However, its role in postoperative recurrence and prognosis in lung cancer lacks clear consensus. Therefore, this study aimed to investigate the potential relationship between IGF1R and postoperative recurrence as well as long-term survival in a large cohort. Additionally, we assessed the relationship between IGF1R and programmed death ligand 1 (PD-L1) expression. Our study encompassed 782 patients with non-small cell lung cancer (NSCLC). Immunostaining of surgical specimens was performed to evaluate IGF1R and PD-L1 expression. Among the patients, 279 (35.8%) showed positive IGF1R expression, with significantly worse relapse-free survival (RFS) and overall survival (OS). Notably, no significant differences in RFS and OS were observed between IGF1R-positive and -negative groups in stages 2 and 3. However, in the early stages (0-1), the positive group displayed significantly worse RFS and OS. In addition, PD-L1 expression was detected in 100 (12.8%) patients, with a significant predominance in the IGF1R-positive. IGF1R may serve as a prognostic indicator and a guide for perioperative treatment strategies in early-stage lung cancer. In conclusion, our findings underscore an association between IGF1R expression and poor survival and PD-L1 expression in NSCLC.
Demographic characteristics and prevalence of asymptomaticLeishmania donovaniinfection in migrant workers working in an endemic area in Northwest Ethiopia
Authors: Yimer Mulat , Takele Yegnasew , Yizengaw Endalew , Nibret Endalkachew , Sumova Petra , Volf Petr , Yismaw Gizachew , Alehegn Michael , Rowan Aileen , Müller Ingrid , Cotton James A. , Chapman Lloyd A. C. , Kropf Pascale
Published: January 2024

Visceral leishmaniasis (VL), a neglected tropical disease that causes substantial morbidity and mortality, is a serious health problem in Ethiopia. Infections are caused byLeishmania(L.)donovaniparasites. Most individuals remain asymptomatic, but some develop VL, which is fatal if not treated.

We identified the area of Metema-Humera in Northwest Ethiopia as a setting in which we could follow migrant workers when they arrived in an endemic area. The demographic characteristics of this population and factors associated with their risk of asymptomatic infection are poorly characterised. We divided our cohort into individuals who visited this area for the first time (first comers, FC) and those who had already been in this area (repeat comers, RC). We followed them from the beginning (Time 1, T1) to the end of the agricultural season (Time 2, T2), performing tests for sand fly bite exposure (anti-sand fly saliva antibody ELISA) and serology forLeishmaniainfection (rK39 rapid diagnostic test and the direct agglutination test) at each time point and collecting information on risk factors for infection.

Our results show that most migrant workers come from non-endemic areas, are male, young (median age of 20 years) and are farmers or students.

At T1, >80% of them had been already exposed to sand fly bites, as shown by the presence of anti-saliva antibodies. However, due to seasonality of sand flies there was no difference in exposure between FC and RC, or between T1 and T2. The serology data showed that at T1, but not at T2, a significantly higher proportion of RC were asymptomatic. Furthermore, 28.6% of FC became asymptomatic between T1 and T2. Over the duration of this study, one FC and one RC developed VL.

In multivariable logistic regression of asymptomatic infection at T1, only age and the number of visits to Metema/Humera were significantly associated with asymptomatic infection.

A better understanding of the dynamics of parasite transmission and the risk factors associated with the development of asymptomatic infections and potentially VL will be essential for the development of new strategies to prevent leishmaniasis.
Remote and unsupervised digital memory assessments can reliably detect cognitive impairment in Alzheimer’s disease
Authors: Berron David , Olsson Emil , Andersson Felix , Janelidze Shorena , Tideman Pontus , Düzel Emrah , Palmqvist Sebastian , Stomrud Erik , Hansson Oskar
Published: January 2024

INTRODUCTION

Remote unsupervised cognitive assessments have the potential to complement and facilitate cognitive assessment in clinical and research settings.

METHODS

Here we evaluate the usability, validity and reliability of unsupervised remote memory assessments via mobile devices in individuals without dementia from the Swedish BioFINDER-2 study and explore their prognostic utility regarding future cognitive decline.

RESULTS

Usability was rated positively; remote memory assessments showed good construct validity with traditional neuropsychological assessments and were significantly associated with tau-PET and downstream MRI measures. Memory performance at baseline was associated with future cognitive decline and prediction of future cognitive decline was further improved by combining remote digital memory assessments with plasma p-tau217. Finally, retest reliability was moderate for a single assessment and good for an aggregate of two sessions.

DISCUSSION

Our results demonstrate that unsupervised digital memory assessments might be used for diagnosis and prognosis in Alzheimer’s disease, potentially in combination with plasma biomarkers.
Pontine Infarction: A Prospective Cohort Study on Its Clinical Features, Prognosis, and Association with Branch Atheromatous Disease
Authors: Motoie Ryota , Ono Kotaro , Oketani Hiroshi , Kawano Yosuke , Nagaoka Shintaro , Maeda Kazushi , Suyama Yoshio , Gi Hidefuku , Kanemoto Yukihide
Published: January 2024

Introduction

This study aimed to analyse disease characteristics and prognostic factors among a cohort of 407 patients with pontine infarction, focusing on the effect of branch atheromatous disease (BAD).

Patients and Methods

A retrospective analysis of patients diagnosed with brainstem stroke at Baba Memorial Hospital from 2012 to 2022 was conducted. The study included patients with pontine stroke, excluding those with missing data, chronic or multiple cerebral infarctions, non-brainstem stroke, or without timely MRI. Patient analysis involved age, sex, Japan Coma Scale (JCS) score, medical history, symptoms at admission, and MRI findings. Prognostic groups were classified based on the modified Rankin Scale (mRS) and Functional Independence Measure (FIM) scores at admission and discharge.

Results

Of the 407 patients, 66.1% belonged to the good prognosis group (mRS 0–2) and 33.9% to the poor prognosis group (mRS 35). Younger patients tended to have a better prognosis. JCS scores correlated with prognosis severity. Significant differences in dysarthria, paralysis, and admission FIM scores were observed between patients with and without BAD. Logistic regression analysis identified the FIM score at admission as an independent predictor of prognosis.

Discussion

BAD was not directly related to prognosis. The absence of differences in discharge FIM scores and similar prognoses to other stroke types suggested effective rehabilitation. However, due to the lack of pre-stroke FIM measurements and specific treatment details, further research is needed.

Conclusion

Age and JCS scores were significant prognostic factors, with BAD not directly affecting prognosis. There is need for investigation into treatment methods and detailed prognostic factors.
Triterpene RDF: Developing a database of plant enzymes and transcription factors involved in triterpene biosynthesis using the Resource Description Framework
Authors: Tamura Keita , Chiba Hirokazu , Bono Hidemasa
Published: January 2024

Plants produce structurally diverse triterpenes (triterpenoids and steroids). Their biosynthesis occurs from a common precursor, namely 2,3-oxidosqualene, followed by cyclization catalyzed by oxidosqualene cyclases (OSCs) to yield various triterpene skeletons. Steroids, which are biosynthesized from cycloartenol or lanosterol, are essential primary metabolites in most plant species, along with lineage-specific steroids, such as steroidal glycoalkaloids found in theSolanumspecies. Other diverse triterpene skeletons are converted into triterpenoids, often classified as specialized compounds that are biosynthesized only in a limited number of plant species with tissue-or cell-type-specific accumulation in plants. Recent studies have identified various tailoring enzymes involved in the structural diversification of triterpenes as well as transcription factors that regulate the expression of these enzymes. However, the coverage of these proteins is scarce in publicly available databases for curated proteins or enzymes, which complicates the functional annotation of newly assembled genomes or transcriptome sequences. Here, we created the Triterpene RDF, a manually curated database of enzymes and transcription factors involved in plant triterpene biosynthesis. The database (https://github.com/ktamura2021/triterpene_rdf/) contains 526 proteins, with links to the UniProt Knowledgebase or NCBI protein database, and it enables direct download of a set of protein sequences filtered by protein type or taxonomy. Triterpene RDF will enhance the functional annotation of enzymes and regulatory elements for triterpene biosynthesis, in a current expansion of availability of genomic information on various plant species.
Deep rhizospheres extend the nitrogen cycle meters below the base of soil into weathered bedrock
Authors: Crutchfield-Peters Kelsey , Rempe Daniella M. , Tune Alison K. , Dawson Todd E.
Published: January 2024

Nitrogen is the most limiting nutrient to forest productivity worldwide. Recently, it has been established that diverse ecosystems source a substantial fraction of their water from weathered bedrock, leading to questions about whether root-driven nitrogen cycling extends into weathered bedrock as well. In this study, we specifically examined nitrogen dynamics using specialized instrumentation distributed across a 16 m weathered bedrock vadose zone (WBVZ) underlying an old growth forest in northern California where the rhizosphere—composed of plant roots and their associated microbiome—extends meters into rock. We documented total dissolved nitrogen (TDN), dissolved organic carbon (DOC), inorganic N (ammonium and nitrate) and CO2and O2gasses every 1.5 m to 16 m depth for two years. We found that biologically available nitrogen in the weathered bedrock rhizosphere was comparable in concentration to temperate forest soils and primarily organic. TDN concentrations in the WBVZ exhibited distinct patterns with depth and were correlated with periods of increased whole-ecosystem metabolic activity as well as stream discharge, suggesting competing rhizosphere and leaching processes in the fate of TDN in the WBVZ. Carbon isotope composition of the DOC suggests that dissolved organic matter in the WBVZ is primarily derived from fresh plant sources. We conclude that N cycling in the WBVZ is driven by an active rhizosphere meters below the base of soil and represents an important and overlooked component of deeply rooted ecosystems that must be incorporated into future models and theory of ecosystem function.
Hippocampal trauma memory processing conveying susceptibility to traumatic stress
Authors: Dirven Bart C.J. , Melis Lennart van , Daneva Teya , Dillen Lieke , Homberg Judith R. , Kozicz Tamas , Henckens Marloes J.A.G.
Published: January 2024

While the majority of the population is ever exposed to a traumatic event during their lifetime, only a fraction develops posttraumatic stress disorder (PTSD). Disrupted trauma memory processing has been proposed as a core factor underlying PTSD symptomatology. We used transgenic Targeted- Recombination-in-Active-Populations (TRAP) mice to investigate potential alterations in trauma- related hippocampal memory engrams associated with the development of PTSD-like symptomatology. Mice were exposed to a stress-enhanced fear learning paradigm, in which prior exposure to a stressor affects the learning of a subsequent fearful event (contextual fear conditioning using foot shocks), during which neuronal activity was labeled. One week later, mice were behaviorally phenotyped to identify mice resilient and susceptible to developing PTSD-like symptomatology. Three weeks post-learning, mice were re-exposed to the conditioning context to induce remote fear memory recall, and associated hippocampal neuronal activity was assessed. While no differences in the size of the hippocampal neuronal ensemble activated during fear learning were observed between groups, susceptible mice displayed a smaller ensemble activated upon remote fear memory recall in the ventral CA1, higher regional hippocampal PV+neuronal density and a relatively lower activity of PV+interneurons upon recall. Investigation of potential epigenetic regulators of the engram revealed rather generic (rather than engram-specific) differences between groups, with susceptible mice displaying lower hippocampal histone deacetylase 2 expression, and higher methylation and hydroxymethylation levels. These finding implicate variation in epigenetic regulation within the hippocampus, as well as reduced regional hippocampal activity during remote fear memory recall in interindividual differences in susceptibility to traumatic stress.
Unraveling the seasonal dynamics of ixodid ticks: A flexible matrix population model with delayed life history effects
Authors: Vindenes Yngvild , Mysterud Atle
Published: January 2024

Many vector-borne diseases are sensitive to changes in land use and climate, making it crucial to understand the factors that govern the vector populations. Ixodid ticks, which serve as vectors for multiple diseases, have a slow life cycle compared to many of their hosts. The duration of each active life stage (larvae, nymph, adult) varies greatly and depends on factors such as timing of questing and development, host availability throughout the seasons, and photoperiod-related behavioral and developmental diapause. Importantly, the observable questing population only represents a fraction of the total tick population and may include overlapping generations in each stage. Mathematical models are therefore essential to understand how complex life cycle transitions and host interactions impact the dynamics of the tick population. In this study, we present a flexible seasonal matrix model for ixodid ticks that feed on small and large hosts varying in seasonal availability. This model incorporates the delayed life history effects of overwintering and seasonal timing of feeding, density regulation through limited host capacity, and scramble competition among larvae and nymphs for small hosts. We extract the equilibrium seasonal numbers of questing, feeding, and emerging ticks for each life stage, as well as the seasonal patterns of host use. We also calculate key life history characteristics including the mean generation time, stable stage structure, and reproductive values. The baseline model represents a northern life history of the sheep tick (Ixodes ricinus) feeding on a seasonal small host and constant large host, which is compared to a scenario without host seasonality and a scenario representing a southern ecosystem. Our findings support the importance of small hosts in regulating tick populations, and highlight that feeding of larvae is a critical transition. Our analyses shed light on the complex mechanisms underlying the seasonal composition of the questing population, with its important implications for disease risk. The model can be applied to other ixodid tick species and provides a framework for future investigations into population dynamics under various tick and host scenarios.
Absolute quantitative and base-resolution sequencing reveals comprehensive landscape of pseudouridine across the human transcriptome
Authors: Xu Haiqi , Kong Linzhen , Cheng Jingfei , Moussawi Khatoun Al , Chen Xiufei , Iqbal Aleema , Wing Peter A. C. , Harris James M. , Tsukuda Senko , Embarc-Buh Azman , Wei Guifeng , Castello Alfredo , Kriaucionis Skirmantas , McKeating Jane A. , Lu Xin , Song Chun-Xiao
Published: January 2024

Pseudouridine (Ψ) is one of the most abundant modifications in cellular RNA. However, its function remains elusive, mainly due to the lack of highly sensitive and accurate detection methods. To address this challenge, we introduced 2-bromoacrylamide-assisted cyclization sequencing (BACS) for quantitative profiling of Ψ at single-base resolution. Based on novel bromoacrylamide cyclization chemistry, BACS enables a Ψ-to-C transition. Compared to previous methods, BACS allowed the precise identification of Ψ positions, especially in densely modified Ψ regions and consecutive uridine sequences. BACS successfully detected all known Ψ sites in human rRNA and spliceosomal snRNAs and generated the first quantitative Ψ map of human snoRNA and tRNA. Furthermore, BACS simultaneously detected adenosine-to-inosine (A-to-I) editing sites andN1-methyladenosine (m1A). Depletion of three key pseudouridine synthases (PUS) enabled us to elucidate the targets and sequence motifs of TRUB1, PUS7, and PUS1 in HeLa cells. We further applied BACS to Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) and identified a highly abundant Ψ114site in EBER2. Surprisingly, applying BACS to a panel of RNA viruses demonstrated the absence of Ψ in their viral transcripts or genomes, shedding light on differences in pseudouridylation between virus families. We anticipate BACS to serve as a powerful tool to uncover the biological importance of Ψ in future studies.
The predictive outfielder: a critical test across gravities
Authors: Aguado Borja , López-Moliner Joan
Published: January 2024

Intercepting moving targets, like fly balls, is a common challenge faced by several species. Historically, models attempting to explain this behavior in humans have relied on optical variables alone. Such models, while insightful, fall short in several respects, particularly in their lack of predictive capabilities. This absence of prediction limits the ability to plan movements or compensate for inherent sensorimotor delays. Moreover, these traditional models often imply that an outfielder must maintain a constant gaze on the target throughout to achieve successful interception. In this study, we present a new model that continuously updates its predictions, not just on the immediate trajectory of the ball, but also on its eventual landing position in the 3D scene and remaining flight time based on the outfielder’s real time movements. A distinct feature is the model’s adaptability to different gravitational scenarios, making its predictions inherently tailored to specific environmental conditions. By actively integrating gravity, our model produces trajectory predictions that can be validated against actual paths, providing a significant departure from previous models. To compare our model to the traditional ones, we conducted experiments within a virtual reality setting, strategically varying simulated gravity among other parameters. This gravity variation yielded qualitatively distinct predictions between error-nulling optical-based heuristics and our model. The trajectories, kinematic patterns and timing responses produced by participants were in good agreement with the predictions of our proposed model, suggesting a paradigm shift in our understanding of interceptive actions.

Significance statement

Catching a moving target, a challenge consistently faced across various species, exemplifies the complex interplay between perception, prediction, and motor action in dynamic environments. Prevailing models have been largely rooted in optical cues, often overlooking the predictive capacities essential for understanding real-world human behaviors and sidestepping crucial physical variables such as gravity. Our research introduces a novel model that emphasizes both the predictive component and the broader gravitational dynamics allowing for a more holistic understanding of interception tasks. This innovative approach not only holds implications for refining existing models of interception but also carries broader significance for training platforms, ensuring relevance across diverse settings, from Earth to altered gravity environments.
Methane and ethane production rates by methyl-coenzyme M reductase in cell extracts from different methanogens
Authors: Nguyen V. P. Thinh , Keller Sebastian , Scheller Silvan
Published: January 2024

The enzyme methyl-coenzyme M reductase (Mcr) is responsible for most of the biologically produced methane. Mcr catalyzes the reversible conversion of methyl-coenzyme M and coenzyme B to methane and the corresponding heterodisulfide CoM-S-S-CoB as the last step in all methanogens. In anaerobic methanotrophs, it catalyzes the same reaction to proceed in the reverse direction.

While Mcr has been historically considered as an enzyme exclusive to the one-carbon metabolism, recent studies have demonstrated that homologs of Mcr have evolved to catalyze the first step of the archaeal anaerobic oxidation of medium and long-chain alkanes to their corresponding alkyl-coenzyme M thioethers.

While ample metagenomic studies and data related to Mcr is available, in vitro experiments are limited, because purifying Mcr in its active nickel-I form is challenging. Fully active enzyme has only been reported forMethanothermobacter marburgensisisoenzyme I, from which most of the enzyme studies have been performed.

To get an overview of the substrate scope of different Mcr variants, we tested cell-free lysates from the methanogensMethanosarcina mazei, Methanosarcina acetivorans, Methanococcus maripaludis, Methanothermococcus okinawensis, andM. marburgensisfor their rates to convert methyl- and ethyl-coenzyme M to methane and to ethane, respectively.

Cell extracts fromM. mazeishowed an ethane production rate of ca. 8% relative to methane production at 37 °C, and about 14% at 49 °C in an assay relying on titanium (III) citrate and cobalamin to regenerate coenzyme B from the CoM-S-S-CoB heterodisulfide.

For cell extracts ofM. marburgensis, we found an ethane-to-methane production rate of 8%, which is substantially higher than the reported value of ca. 0.3% for the ratio of their maximal catalytic rate for purified isoenzyme I. SinceM. marburgensisis known to express two isoenzymes depending on the growth conditions, we hypothesize that isoenzyme II is substantially more promiscuous towards ethane formation than the well-described isoenzyme I.

Which it is still challenging to obtain accurate kinetic parameters of the Mcr-catalyzed reaction, our experiments demonstrate that Mcr activity can be quickly and conveniently studiedviacell-free lysates, and that substrate promiscuity towards ethane formation is generally larger than anticipated.
Electrostatic Trade-Off between Mesophilic Stability and Adaptation in Halophilic Proteins
Authors: Herrero Pablo , Pejenaute Alba , Millet Oscar , Ortega Gabriel
Published: January 2024

Extremophile organisms have adapted to extreme physicochemical conditions. Halophilic organisms, in particular, survive at very high salt concentrations. To achieve this, they have engineered the surface of their proteins to increase the number of short, polar and acidic amino acids, while decreasing large, hydrophobic and basic residues. While these adaptations initially decrease the thermodynamic stability in the absence of salt, they grant halophilic proteins remarkable stability in environments with extremely high salt concentrations, where non-adapted proteins unfold and aggregate. The molecular mechanisms by which halophilic proteins achieve this, however, are not yet clear. Here, we test the hypothesis that the halophilic amino acid composition destabilizes the surface of the protein, but in exchange improves the stability in the presence of salts. To do that, we have measured the folding thermodynamics of various protein variants with different degrees of halophilicity in the absence and presence of different salts, and at different pH values to tune the ionization state of the acidic amino acids. Our results show that, although electrostatic interactions decrease the stability of halophilic proteins, in exchange they induce a significant salt-induced stabilization and improve solubility. Besides electrostatic interactions, we also show that other general contributions, such as hydrophobic effect and preferential exclusion, are important. Overall, our findings suggest a trade-off between folding thermodynamics and halophilic adaptation to optimize the stability of halophilic proteins in hypersaline environments.

Significance statement

This work explores how extreme halophiles adapt their proteins for survival in hypersaline environments. By engineering the protein surface, evolution has selected proteins adapted to high salt concentrations. Our findings suggest a delicate balance between protein stability and haloadaptation modulated in part by electrostatic interactions, furthering our understanding of life adaptation to extreme environments.
Signaling events at TMEM doorways provide potential targets for inhibiting breast cancer dissemination
Authors: Surve Chinmay R. , Duran Camille L. , Ye Xianjun , Chen Xiaoming , Lin Yu , Harney Allison S. , Wang Yarong , Sharma Ved P. , Stanley E. Richard , Cox Dianne , McAuliffe John C. , Entenberg David , Oktay Maja H. , Condeelis John S.
Published: January 2024

Tumor cell intravasation is essential for metastatic dissemination, but its exact mechanism is incompletely understood. We have previously shown that in breast cancer, the direct and stable association of a tumor cell expressing Mena, a Tie2hi/VEGFhimacrophage, and a vascular endothelial cell, creates an intravasation portal, called a “tumor microenvironment of metastasis” (TMEM) doorway, for tumor cell intravasation, leading to dissemination to distant sites. The density of TMEM doorways, also called TMEM doorway score, is a clinically validated prognostic marker of distant metastasis in breast cancer patients. Although we know that tumor cells utilize TMEM doorway-associated transient vascular openings to intravasate, the precise signaling mechanisms involved in TMEM doorway function are only partially understood. Using two mouse models of breast cancer and anin vitroassay of intravasation, we report that CSF-1 secreted by the TMEM doorway tumor cell stimulates local secretion of VEGF-A from the Tie2hiTMEM doorway macrophage, leading to the dissociation of endothelial junctions between TMEM doorway associated endothelial cells, supporting tumor cell intravasation. Acute blockade of CSF-1R signaling decreases macrophage VEGF-A secretion as well as TMEM doorway-associated vascular opening, tumor cell trans-endothelial migration, and dissemination. These new insights into signaling events regulating TMEM doorway function should be explored further as treatment strategies for metastatic disease.
Evaluation of the effects of ripening-related genes on fruit metabolites and the associated regulatory mechanisms in tomato
Authors: Jia Huimin , Xu Yaping , Deng Yuanwen , Xie Yinhuan , Gao Zhongshan , Lang Zhaobo , Niu Qingfeng
Published: January 2024

Fruit ripening, which is a complex process involving dynamic changes to metabolites, is controlled by multiple factors, including transcription factors (TFs). Several TFs are reportedly essential regulators of tomato fruit ripening. To evaluate the effects of specific TFs on metabolite accumulation during fruit ripening, CRISPR/Cas9-mediated mutagenesis was combined with metabolome and transcriptome analyses to explore regulatory mechanisms. Specifically, we generated various genetically engineered tomato lines that differed regarding metabolite contents and fruit colors. The metabolite and transcript profiles indicated that the selected TFs have distinct functions that control fruit metabolite contents, especially carotenoids and sugars. Our findings may provide new insights into the regulatory mechanisms governing tomato fruit ripening. Moreover, a mutation toELONGATED HYPOCOTYL5(HY5) increased the tomato fruit fructose and glucose contents by approximately 20% (relative to the wild-type levels). Ourin vitroassay showed that HY5 can bind directly to the G-boxcis-element in theSWEET12cpromoter to activate expression, thereby modulating sugar transport. Our findings have clarified the mechanism regulating fruit metabolic networks, while also providing the theoretical basis for breeding horticultural crops that produce fruit with diverse flavors and colors.g
Ultrasound-Driven Programmable Artificial Muscles
Authors: Shi Zhan , Zhang Zhiyuan , Ahmed Daniel
Published: January 2024

Despite their promise for technological and medical innovations, the advancement of artificial muscles faces challenges in dynamic programmability, wireless control, scalability, and responsiveness. Ultrasound offers a promising yet underutilized solution, providing effective and robust actuation. We introduce an innovative design paradigm for soft artificial muscles, utilizing tens of thousands of resonant microbubbles for targeted activation, enabling a wide range of programmable motions. We developed a comprehensive theoretical model and conducted various applications: from actuating soft grippers and powering centimeter-scale biomimetic stingraybots for propulsion to demonstrating the multimodal shape transformation of a functional surface and equipping static objects with transformative robotic skins for mobility. Our approach is marked by its compactness, high force intensity, rapid responsiveness, and lightweightness. The customizable, scalable design of our artificial muscles offers both immediate and long-term impact on robotics, wearable technology, haptics, prosthetic development, and the development of avant-garde biomedical devices like soft surgical tools.

One-Sentence Summary

We introduced a first-of-its-kind, programmable artificial muscle using ultrasound-activated microbubbles, providing a compact, responsive, and scalable solution.
Hierarchical Ordination, A unifying framework for drivers of community processes
Authors: O’Hara R.B. , van der Veen B.
Published: January 2024

Ordination methods have been used by community ecologists to describe and explore the communities they sample by reducing this variation down to a small number of dimensions. More recently, Joint Species Distribution Models have been developed to model and predict the distributions of several species simultaneously. Contemporary models for the data for both of these problems are essentially the same, called Generalised Linear Latent Variable Models (GLLVMs). Based on this we suggest some avenues of cross-fertilisation between the two areas of research. We also describe some of the extensions to GLLVMs, and from this suggest the development of Hierarchical Ordination, as a way of efficiently modelling communities of species in space.