bluuebunny/crossref_metadata_2025 huggingface dataset:
Starkeya nomas sp. nov., a prosthecate and budding bacterium isolated from an immunocompromized patient
Authors: Sahuquillo-Arce José Miguel , Reyes-Prieto Mariana , Hernández-Cabezas Alicia , Molina-Moreno José Miguel , Saez-Nieto Juan Antonio , Marín María del Pilar , Alcoriza-Balaguer María Isabel , Lahoz Agustín , Sanz Jaime , González-Tarancón Lola , Ferrús María Loreto , Martínez-Priego Llúcia , Magraner-Martínez Adolfo , López-Hontangas José Luis
Published: August 2023

Strain HF14-78462T is an environmental bacterium found in clinical samples from an immunocompromized patient in 2014 at Hospital Universitari i Politècnic La Fe (Valencia, Spain). Phenotypically, strain HF14-78462T cells were Gram-stain-negative, aerobic, non-spore forming and non-motile small rods which formed mucous and whitish-translucent colonies when incubated at 20–36 °C. Phylogenetic analyses based on the 16S rRNA genes and the whole genomes of closest sequenced relatives confirmed that strain HF14-78462T is affiliated with the genus

Starkeya

. The strain was oxidase, catalase and urease positive; but indole, lysine decarboxylase, ornithine decarboxylase and DNase negative, did not produce H2S and was able to utilize a wide variety of carbon sources including acetamide, adonitol, amygdalin, l-arabinose, citric acid, glucose, mannitol and melibiose. Unlike

Starkeya novella

and

Starkeya koreensis

, strain HF14-78462T failed to grow in thiosulphate-oxidizing media and had a narrower temperature growth range. Its genome was characterized by a size of 4.83 Mbp and a C+G content of 67.75 mol%. Major fatty acids were C18:1
ω7c, cyclo C19 : 0 and C16 : 0, its polar acids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an aminophospholipid; while the ubiquinones were Q9 (1.8 %) and Q10 (98.2 %). Digital DNA–DNA hybridization values were 41 and 41.4 against

S. novella

and

S. koreensis

, respectively, while average nucleotide identity values were around 84 %. Phenotypic, average nucleotide identity and phylogenomic comparative studies suggest that strain HF14-78462T is a new representative of the genus

Starkeya

and the name Starkeya nomas sp. nov. is proposed. The type strain is HF14-78462T (=CECT 30124T=LMG 31874T).
Population health impacts from the taxation of salt and sugar in the United Kingdom
Authors: Colombo Patricia Eustachio , Milner James , Pastorino Silvia , Green Rosemary
Published: August 2023

Objective

To estimate the potential health benefits from the reduction in consumption of salt and sugar following the introduction of a proposed tax on salt and sugar in the United Kingdom (UK).

Design

Epidemiological modelling study. Life-table modelling was used to estimate the expected population health benefits from the reduction in consumption of salt and sugar for four scenarios, each reflecting different manufacturer and consumer responses the proposed tax. Relative risks for 24 disease-risk pairs were applied, exploring different pathways between salt and sugar consumption, and mortality and morbidity.

Setting

UK.

Participants

Population of the UK.

Results

The results show that life expectancy in the UK could be increased by 1.7 (0.3-3.6) to 4.9 (1.0-9.4) months, depending on the degree of industry and consumer response to the tax. The tax could also lead to up to nearly 2 (0.4-3.6) million fewer cases of preventable chronic diseases and an increase of as much as 3.5 (0.8-6.4) million years of life gained. The largest health benefits would accrue from reduced mortality and morbidity from cardiovascular diseases.

Conclusions

Significant benefits to population health could be expected from extending the current tax on sugar sweetened beverages to other sugary foods and from adding a tax on foods high in salt. The proposed dietary changes are likely to be insufficient to reach national public health targets; hence, additional measures to reduce the burden of chronic disease in the UK will be equally critical to consider.
Post-COVID rebound of gonorrhoea in England
Authors: Fountain Holly , Migchelsen Stephanie , Charles Hannah , Ram Tika , Fifer Helen , Mohammed Hamish , Sinka Katy
Published: August 2023

With the removal of all COVID-19 restrictions in July 2021, a marked increase in gonorrhoea diagnoses in England was observed. Investigations revealed increases have been widespread, particularly in young people aged 15-to-24 years. Testing numbers have not shown a corresponding increase and have remained below 2019 (pre-pandemic) levels.

Ethical statement

No ethical approval was needed for this study as routine surveillance data was used.

Funding statement

No funding was needed.

Conflict of interest

None
No evidence for a link between childhood (6-10y) cellular aging and brain morphology (12y) in a preregistered longitudinal study
Authors: Brinkman Evie Henrike , Beijers Roseriet , Tyborowska Anna , Roelofs Karin , Kühn Simone , Kievit Rogier , de Weerth Carolina
Published: August 2023

Animal studies show that early life environmental factors, such as stress and trauma, can have a significant impact on a variety of bodily processes, including cellular aging and brain development. However, whether cellular wear-and-tear effects are also associated with individual differences in brain structures in humans, remains unknown. In this pre-registered study in a community sample of children (N=94, Mean age=12.71 years), we prospectively investigated the predictive value of two markers of cellular aging in childhood (at age 6 and 10) for brain morphology in early adolescence (age 12). More specifically, we associated buccal cell telomere length and epigenetic age in childhood to individual differences in adolescent whole-brain grey matter volume (GMV) including volumes of three regions of interest that have been found to be sensitive to effects of early life stress (i.e. amygdala, hippocampus, (pre)frontal cortex -PFC). Multiple regression analyses revealed no significant associations between childhood cellular aging (at 6 and 10 years) and early adolescent brain morphology. Exploratory Bayesian analyses indicated moderate to strong evidence for the null-findings. These results suggest that although our sample is modest, the associations between middle childhood cellular aging and early adolescent brain morphology are, if they do exist, likely not particularly large in community children. Future work should investigate whether these effects are similarly absent in large samples, in samples with a higher risk profile and in samples characterized by different age ranges.

Highlights (3-5)

- Investigation of cellular aging in relation to brain morphology in a community sample (N=95)

- Epigenetic aging and telomere shortening were not associated with brain structure

- Exploratory Bayesian Analyses reveal moderate to strong evidence for null findings

- No association was found between cellular aging and white matter volume
Multitask Learning of Longitudinal Circulating Biomarkers and Clinical Outcomes: Identification of Optimal Machine-Learning and Deep-Learning Models
Authors: Yuan Min , Su Shixin , Ding Haolun , Yang Yaning , Gupta Manish , Xu Xu Steven
Published: August 2023

Many circulating biomarkers are assessed at different time intervals during clinical studies. Despite of the success of standard joint models in predicting clinical outcomes using low-dimensional longitudinal data (1-2 biomarkers), significant computational challenges are encountered when applying these techniques to high-dimensional biomarker datasets. Modern machine- or deep-learning models show potential for multiple biomarker processes, but systematic evaluations and applications to high-dimensional data in the clinical settings have yet to be reported. We aimed to enhance the scalability of joint modeling and provide guidance on optimal approaches for high-dimensional biomarker data and outcomes. We evaluated multiple deep-learning and machine-learning models using 24 clinical biomarkers and survival data from the SQUIRE trial, a phase 3 randomized clinical trial investigating necitumumab and standard gemcitabine/cisplatin treatment in patients with squamous non-small-cell lung cancer (NSCLC). Overall, we confirmed that longitudinal models enabled more accurate prediction of patients’ survival compared to those solely based on baseline information. Coupling multivariate functional principal component analysis (MFPCA) with Cox regression (MFPCA-Cox) provided the highest predictive discrimination and accuracy for the NSCLC patients with AUC values of 0.7 - >0.8 at various landmark time points and prediction timeframes, outperforming recent advanced Transformer and convolutional neural network deep-learning algorithms (TransformerJM and Match-Net, respectively). In conclusion, we identified that MFPCA-Cox represents a robust and versatile joint modeling algorithm for high-dimensional biomarker longitudinal data with irregular and missing data, capturing complex relationships within the data, yielding accurate predictions for both longitudinal biomarkers and survival outcomes, and gaining insights into the underlying dynamics.
Social complexity affects cognitive abilities but not brain structure in a Poecilid fish
Authors: Triki Zegni , Zhou Tunhe , Argyriou Elli , Sousa de Novais Edson , Servant Oriane , Kolm Niclas
Published: August 2023

Complex cognitive performance is suggested to be the out-turn of complex social life, allowing individuals to achieve higher fitness through sophisticated “Machiavellian” strategies. Although there is ample support for this concept, especially when comparing species, most of the evidence is correlative. Here we provide an experimental investigation of how group size and composition may affect brain and cognitive development in the guppy (Poecilia reticulata). For six months, we reared sexually mature female guppies in one of three different social treatments: (i) three female guppies; (ii) three female guppies mixed with three female splash tetras (Copella arnoldi), a species that co-occurs with the guppy in the wild; and (iii) six female guppies. We then tested the guppies’ performance in inhibitory control, associative learning and reversal learning tasks to evaluate their self-control, operant conditioning and cognitive flexibility capabilities. Afterwards, we estimated their brain size and the size of major brain regions using X-ray imaging technology. We found that individuals in larger groups of six individuals, in both same and mixed species treatments, outperformed individuals from the smaller groups of three guppies in reversal learning, with no apparent differences in the inhibitory control and associative learning tasks. This is rare evidence of how living in larger social groups improves cognitive flexibility, supporting that social pressures play an important role in shaping individual cognitive development. Interestingly, social manipulation had no apparent effect on brain morphology, but relatively larger telencephalons were associated with better individual performance in reversal learning. This suggests alternative mechanisms beyond brain region size enabled greater cognitive flexibility in individuals from larger groups.
Improved Activity and Kinetics of Endoglucanase Biofuel Enzyme with Addition of an AzoTAB Surfactant
Authors: Seidel Zumra Peksaglam , Ted Lee C.
Published: August 2023

Endoglucanases degradeβ-1,4-glycosidic bonds of crystalline cellulose into insoluble or soluble cellooligosaccharides at the solid-liquid interface. The enhanced activity and kinetics of endoglucanase fromAspergillus nigerwith addition of a light responsive azobenzene trimethyl ammonium bromide (azoTAB) surfactant is studied. AzoTAB is a photoresponsive surfactant that exists as a relatively-hydrophobictransisomer under visible light (434 nm) and a relatively-hydrophiliccisisomer under UV light (350 nm). Endoglucanase catalytic activity can be controlled with light illumination slightly for microcrystalline cellulose natural substate (∼15%) and significantly for p-nitrophenol-based model substrate (∼2-fold) by switching between thetrans(higher enzyme binding affinity, resulting higher enzyme unfolding) andcisform of azoTAB. Endoglucanase activity increases 45% towards avicel crystalline substate and 4-fold towards 4-nitrophenyl β-D-cellobioside substrate in the presence of 0.4 mM azoTAB under UV light (90%cisand 10%transisomers). In comparison, endoglucanase catalytic activity increases 5-10% towards crystalline cellulose substrate with the addition of sodium dodecyl benzene sulfonate (SDBS), sodium dodecyl sulfate (SDS) and dodecyl trimethyl ammonium (DTAB). 0.4 mM AzoTAB-UV addition leads to an increase of maximum endoglucanase adsorption (Emax) from 7.89 mg enzyme/g avicel to 12.92 mg enzyme/g avicel and catalytic enzyme efficiency (kcat/KM) from 0.031 L/(mg.s) to 0.061 L/(mg.s). It is found that adsorbed enzyme concentration on substrate correlates to enzyme specific activity for azoTAB containing reaction. Additionally, 40-50% activity enhancement and increased bound enzyme to substrate are detected with azoTAB addition at different enzyme, substrate, and inhibitor concentrations. Improvement of substrate properties of azoTAB addition is associated with lower reciprocal terms of Michaelis constant (KM), the adsorption coefficient (Kad) and fractal parameter (h) values similar to the presence of other surfactants in this study and the literature. Furthermore, 45-50% activity enhancement via azoTAB surfactant preserved for all three cellulase enzyme mixture of endoglucanase, cellohydrolase andβ-glucosidase. Consequently, azoTAB can be applied as profitable additive for the heterogenous enzymatic cellulose hydrolysis, resulting in a 30% decrease in the enzyme load based on the specific activity, adsorption, and fractal kinetics results.
Transcobalamin Receptor Autoantibodies in Central Vitamin B12 Deficiency
Authors: Pluvinage John V. , Ngo Thomas , Bartley Christopher M. , Bodansky Aaron , Alvarenga Bonny D. , Zorn Kelsey C. , Fouassier Camille , Zamecnik Colin , McCann Adrian , Huynh Trung , Browne Weston , Tubati Asritha , Kondapavulur Sravani , Anderson Mark S. , Green Ari J. , Green Ralph , Douglas Vanja , Louine Martineau , Cree Bruce , Hauser Stephen , Seeley William , Holmes Brandon B. , Wells James A. , Spudich Serena , Farhadian Shelli , Ramachandran Prashanth , Gillum Leslie , Hales Chadwick M. , Smith Bryan , Nath Avindra , Suh Gina , Flanagan Eoin P. , Gelfand Jeffrey M. , DeRisi Joseph L. , Pleasure Samuel J. , Wilson Michael R.
Published: August 2023

Vitamin B12 is critical for hematopoiesis and myelination.1Deficiency can cause neurologic deficits including loss of coordination, spasticity, and cognitive decline.2,3,4However, diagnosis relies on vitamin B12 measurement in the blood which may not accurately reflect levels in the brain. Here, we discovered an autoimmune cause of vitamin B12 deficiency restricted to the central nervous system (CNS), termed autoimmune B12 central deficiency (ABCD). Using programmable phage display, we identified an autoantibody targeting the transcobalamin receptor (CD320) in a patient with progressive tremor, ataxia, and scanning speech. Patient immunoglobulins impaired cellular uptake of vitamin B12in vitro. Despite normal serum levels, vitamin B12 was nearly undetectable in her cerebrospinal fluid (CSF). Immunosuppressive treatment and high-dose systemic vitamin B12 supplementation were associated with increased CSF B12 levels and clinical improvement. Autoantibodies targeting the same epitope of CD320 were identified in 7 other patients with neurologic deficits of unknown etiology and in 6 percent of healthy controls. In 132 paired serum and CSF samples, detection of anti-CD320 in the blood predicted B12 deficiency in the brain. These findings elucidate a new autoimmune cause of metabolic neurologic disease that may be amenable to immunomodulatory treatment and/or nutritional supplementation.
Knowledge, Attitude and Practices (KAP) towards ketogenic Diet and its risk among Bangladeshi Population: A Cross Sectional Study
Authors: Tanha Arifa Farzana , Chandra Pradip , Haque Tasnima , Rahman Mohammad Mahmudur
Published: August 2023

In recent years, the ketogenic diet has become more popular in Bangladesh. Despite the potential negative effects, people are increasingly embracing and adjusting to this diet. Accounting for this manner, the current study addresses a gap that has existed as no research has been done on grown-up adults’ knowledge, attitudes, and practices about the ketogenic diet and its possible risks. To assess their Knowledge, Attitude, and Practice of the Ketogenic Diet and its risks, a descriptive cross-sectional study of the adult Bangladeshi population was carried out. A number of questions were asked to participants regarding their demographics, sources of dietary knowledge, attitudes toward the diet, understanding of the Ketogenic Diet, and views on it. Descriptive statistics were used to analyze the data. Out of 383 participants, women (63.20%) and people under the age of 30 (68.15%) dominated the study. 359 (93.70%) of the participants reported having inadequate knowledge about the ketogenic diet. Around 43.42% of Participants who ever followed KD were assessed to have a healthy BMI. The results revealed a significant association between respondents’ perceptions of KD as a typical weight loss treatment and their knowledge score. Social media was the main source of information for followers (60.53%), while peers were the source of information for 30.26% of respondents. Participants who ever followed the ketogenic diet were less aware of its risks and often considered it safe to follow for a long period believing its benefits outweighed any possible drawbacks. The findings of the current study suggest that Bangladeshis are not well-informed about the therapeutic applications of the ketogenic diet. It appears that pre-diet counselling is essential for everyone to understand every component and proper approach for following this diet.
Predicting the onset of internalizing disorders in early adolescence using deep learning optimized with AI
Authors: de Lacy Nina , Ramshaw Michael J.
Published: August 2023

Internalizing disorders (depression, anxiety, somatic symptom disorder) are among the most common mental health conditions that can substantially reduce daily life function. Early adolescence is an important developmental stage for the increase in prevalence of internalizing disorders and understanding specific factors that predict their onset may be germane to intervention and prevention strategies. We analyzed ∼6,000 candidate predictors from multiple knowledge domains (cognitive, psychosocial, neural, biological) contributed by children of late elementary school age (9-10 yrs) and their parents in the ABCD cohort to construct individual-level models predicting the later (11-12 yrs) onset of depression, anxiety and somatic symptom disorder using deep learning with artificial neural networks. Deep learning was guided by an evolutionary algorithm that jointly performed optimization across hyperparameters and automated feature selection, allowing more candidate predictors and a wider variety of predictor types to be analyzed than the largest previous comparable machine learning studies. We found that the future onset of internalizing disorders could be robustly predicted in early adolescence with AUROCs ≥∼0.90 and ≥∼80% accuracy. Each disorder had a specific set of predictors, though parent problem behavioral traits and sleep disturbances represented cross-cutting themes. Additional computational experiments revealed that psychosocial predictors were more important to predicting early adolescent internalizing disorders than cognitive, neural or biological factors and generated models with better performance. We also observed that the accuracy of individual-level models was highly correlated to the relative importance of their constituent predictors, suggesting that principled searches for predictors with higher importance or effect sizes could support the construction of more accurate individual-level models of internalizing disorders. Future work, including replication in additional datasets, will help test the generalizability of our findings and explore their application to other stages in human development and mental health conditions.
Comparisons of new-onset peripheral arterial disease in Type 2 diabetes mellitus patients exposed to SGLT2I, DPP4I or GLP1a: a population-based cohort study
Authors: Chou Oscar Hou-In , Luo Zhiyao , Chung Cheuk To Skylar , Chan Jeffrey , Li Huixian , Lakhani Ishan , Lee Sharen , Zhang Qingpeng , Liu Tong , Wong Wing Tak , Cheung Bernard Man Yung , Lip Gregory Y. H. , Tse Gary , Leung Fung Ping , Zhou Jiandong
Published: August 2023

Background

Sodium-glucose cotransporter-2 inhibitors (SGLT2I) have been suggested to have beneficial effects against atherosclerotic cardiovascular disease. The comparative risks of new onset peripheral arterial disease (PAD) between SGLT2Is, dipeptidyl peptidase-4 inhibitors (DPP4Is) and glucagon-like peptide-1 receptor agonist (GLP1a) remain unknown.

Objective

This real-world study aims to compare the risks of PAD upon exposure to SGLT2I and dipeptidyl peptidase-4 inhibitors (DPP4I).

Methods

This was a retrospective population-based cohort study of patients with type-2 diabetes mellitus (T2DM) on either SGLT2I or DPP4I between 1st January 2015 and 31st December 2020 using a territory-wide registry in Hong Kong. The primary outcome was new-onset PAD. The secondary outcome was all-cause mortality. Propensity score matching (1:1 ratio) using the nearest neighbour search was performed. Multivariable Cox regression was applied to identify significant associations. A three-arm sensitivity analysis including the GLP1a cohort was conducted.

Results

This cohort included 75470 T2DM patients (median age: 62.3 years old [SD: 12.8]; 55.79 % males). The SGLT2I and DPP4I groups consisted of 28753 patients and 46717 patients, respectively. After matching, 186 and 256 patients suffered from PAD in the SGLT2I and DPP4I groups respectively, over a median follow-up of 5.6 years. SGLT2I use was associated with lower risks of PAD (Hazard ratio [HR]: 0.85; 95% Confidence Interval [CI]: 0.67-0.98) compared to DPP4I use after adjustments for demographics, comorbidities, medications, renal function, and diabetic laboratory tests. Similar associations were observed in subgroup analyses in male patients above 65 years old, with hypertension, and low HbA1c levels. In the sensitivity analysis, SGLT2I was not associated with lower risks of PAD compared to GLP1a (HR: 0.88; 95% CI: 0.65-1.18). The results remained consistent in the competing risk and the sensitivity analyses.

Conclusions

SGLT2I use amongst T2DM patients was associated with lower risks of new-onset PAD and PAD-related outcomes when compared to DPP4I after adjustments.

Illustrated Abstract
Functional characterization of ATP13A2 variants associated with distinct neurodegenerative disorders
Authors: Vrijsen Stephanie , El Asrar Rania Abou , Houdou Marine , Van Den Haute Chris , Baekelandt Veerle , Lyons Joseph A. , Eggermont Jan , Vangheluwe Peter
Published: August 2023

ATP13A2 is a late endolysosomal transporter that exports the polyamines spermine and spermidine from the organellar lumen to the cytosol. Loss-of-function variants inATP13A2are causative for Kufor-Rakeb syndrome (KRS, a recessive juvenile-onset parkinsonism with dementia) and have also been identified in early-onset PD (EOPD) and hereditary spastic paraplegia (HSP). Furthermore, candidate pathogenic ATP13A2 variants have been identified in neuronal ceroid lipofuscinosis (NCL; M854R), multiple system atrophy (MSA; Y1020C) and amyotrophic lateral sclerosis (ALS; I411M) suggesting that ATP13A2 may be implicated in a broader range of neurodegenerative disorders. Since the functional consequences of the NCL, MSA, and ALS variants have not yet been examined, we here characterized these ATP13A2 variants in terms of subcellular localization, cellular polyamine uptake, and transport activity. We found that the homozygous NCL-associated M854R variant results in an instable protein with low expression levels, leading to complete loss of ATPase and cellular polyamine uptake activity. The heterozygous MSA-linked Y1020C variant is properly localized and presents only partially decreased ATPase activity without affecting cellular polyamine uptake. The ALS-associated I411M variant is also correctly localized and exhibits a minor effect on cellular polyamine uptake, however, without a significant impact on ATPase activity. Taken together, only the homozygous NCL variant of ATP13A2 causes a complete loss-of-function, validating that ATP13A2 dysfunction is implicated in NCL. The ALS and MSA variants only presented a subtle functional defect, questioning whether these heterozygous variants are pathogenic and whether ATP13A2 dysfunction may cause MSA or ALS.
Enhancing In Vitro SMN Protein Expression and Cell Viability through Xeno-Nucleic Acid-Based ASOs in Spinal Muscular Atrophy
Authors: Kilic Ozum , Babar Hale Ahsen , Inci Cemre Can , Odabas Sibel Pinar , Yelgen Gamze , Oltan Sevgi , Kulac Sila , Tastan Cihan
Published: August 2023

Spinal Muscular Atrophy (SMA) stands as a devastating ailment arising from the dearth of functional SMN (Survival Motor Neuron) protein due to genetic anomalies within the SMN1 gene. This condition is marked by the consequential attrition of motor neurons, precipitating a progressive decline in muscular strength and culminating in the disruption of neuromuscular junctions. Existing therapeutic approaches encompassing Zolgensma, Nursinersen, and Evrysdi employ innovative genetic therapeutic strategies involving transgene delivery, Antisense Oligonucleotide (ASO) technology, and modulation of pre-mRNA processing to enhance functional SMN protein expression. However, the ASO therapeutics remain suboptimal in establishing a sustained panacea for SMA, as they inadequately maintain consistent levels of functional SMN protein expression. In this study, we present a discerning inquiry into focusing on XNA-DNA-ASO products that exhibit enhanced safety and stability compared to conventional DNA/RNA-ASO sequences. Through precise targeting of the ISSN-1 region within SMN2 gene’s intron 7, our approach seeks to amplify SMN protein expression. Employing Xeno Nucleic Acid (XNA) bases, known for their augmented hydrophobicity and stability, our strategy surmounts previous limitations associated with chemical modifications, showcasing heightened endonuclease resistance. Comparative analyses with conventional DNA/RNA-ASO products substantiate the superiority of XNA-DNA-ASO sequences, underscoring elevated SMN protein expression and reduced toxicity. In a comprehensive evaluation, our gene therapy paradigm is scrutinized within a type 1 SMA fibroblast cell line. Utilizing diverse analytical methodologies, encompassing Annexin V-PI analysis for cytotoxicity, MTT assays for mitochondrial activity, and flow cytometry for SMN protein expression profile, we gauge therapeutic impact and potential toxicity. In conclusion, our investigation not only spotlights the promise of XNA-DNA-ASO sequences but also holds implications for refining SMA treatment strategies, converging on minimized dosages, lowered toxicity, and heightened therapeutic efficacy, thus shaping the landscape of gene therapy for SMA.
NYUS.2: an Automated Machine Learning Prediction Model for the Large-scale Real-time Simulation of Grapevine Freezing Tolerance in North America
Authors: Wang Hongrui , Moghe Gaurav D. , Kovaleski Al P. , Keller Markus , Martinson Timothy E. , Wright A. Harrison , Franklin Jeffrey L. , Hébert-Haché Andréanne , Provost Caroline , Reinke Michael , Atucha Amaya , North Michael G. , Helwi Pierre , Centinari Michela , Londo Jason P.
Published: August 2023

Accurate and real-time monitoring of grapevine freezing tolerance is crucial for the sustainability of the grape industry in cool climate viticultural regions. However, on-site data is limited. Current prediction models underperform under diverse climate conditions, which limits the large-scale deployment of these methods.

We combined grapevine freezing tolerance data from multiple regions in North America and generated a predictive model based on hourly temperature-derived features and cultivar features using AutoGluon, an automatic machine learning engine. Feature importance was quantified by AutoGluon and SHAP value. The final model was evaluated and compared with previous models for its performance under different climate conditions.

The final model achieved an overall 1.36 °C root-mean-square error during model testing and outperformed two previous models using three test cultivars at all testing regions. Two feature importance quantification methods identified five shared essential features. Detailed analysis of the features indicates that the model might have adequately extracted some biological mechanisms during training.

The final model, named NYUS.2, was deployed along with two previous models as an R shiny-based application in the 2022-2023 dormancy season, enabling large-scale and real-time simulation of grapevine freezing tolerance in North America for the first time.
PfAgo-based dual signal amplification biosensor for rapid and highly sensitive detection of alkaline phosphatase activity
Authors: Ke Weikang , Qin Yuqing , Zhou Bosheng , Hu Yonggang
Published: August 2023

Developing rapid and highly sensitive methods for alkaline phosphatase (ALP) activity analysis is significant for the clinical diagnosis and treatment of diseases. Here, aPyrococcus furiosusArgonaute (PfAgo)-based biosensor is presented for ALP activity detection in which the ALP-catalyzed hydrolysis of 3’-phosphate-modified functional DNA activates the strand displacement amplification, and the amplicon -mediates the fluorescent reporter cleavage as a guide sequence ofPfAgo. Under the dual amplification mode ofPfAgo-catalyzed multiple-turnover cleavage activity and pre-amplification technology, the developed method was successfully applied in ALP activity analysis with a detection limit (LOD) of 0.0013 U L−1(3σ) and a detection range of 0.0025 U L−1to 1 U L−1within 90 min. ThePfAgo-based method exhibits satisfactory analytic performance in the presence of the potential interferents and in complex human serum samples. The proposed method shows several advantages, such as rapid, highly sensitive, low-cost, and easy operation, and has great potential in disease evolution fundamental studies and clinical diagnosis applications.
ediTONSIL: Activation-Neutral Gene Editing of CD4 T cells in Human ex Vivo Tonsil Cultures
Authors: Morath K. , Sadhu L. , Dyckhoff G. , Gapp Madeleine , Keppler Oliver T. , Fackler O.T.
Published: August 2023

Motivation

CD4 T cells are central players of adaptive immunity that rapidly change activation states in response to exogenous T cell receptor (TCR) stimulation. While molecular processes in activated human CD4 T cells from peripheral blood are well studied, resting CD4 T cells are refractory to gene-editing transduction and transfection methods without prior activation. Knowledge on the molecular biology of truly resting CD4 T cells is therefore lacking. We present here the culture and editing workflow ediTONSIL that allows for gene editing of tissue-resident CD4 T cells without compromising their activation state or immunological function. This will enable molecular mechanistic analyses of this cell type in their native/physiological tissue context.

The molecular and immunological properties of resting CD4 T cell biology are understudied due to the lack of suitable gene editing methods. Here we describe theex vivoculture and gene editing methodology ediTONSIL for tissue-resident CD4 T cells from human tonsil tissue. CRISPR/Cas9 RNP nucleofection under optimized culture conditions and cytokine concentrations results in knock out efficacies of over 90%, which are e.g. sufficient to prevent HIV-1 infection when targeting the viral entry co-receptor CXCR4. EdiTONSIL does not impair tonsil CD4 T cell viability, activation state or immunocompetence and does not require exogenous activation. Editing can be performed on multiple cell types in bulk cultures or of CD4 T cells previously isolated from tonsils that can be added back to the non-CD4 T cell fraction post gene editing to reassemble into immunocompetent organotypic lymphoid aggregate structures. This highly efficient and versatile workflow for gene editing of tonsillar CD4 T cells enables the dissection of molecular mechanisms inex vivocultures of human lymphoid tissue and can be adapted to other tonsil-resident cell types.

Graphical Abstract
Unraveling Vulnerabilities in Endocrine Therapy-Resistant HER2+/ER+ Breast Cancer
Authors: Bahnassy Shaymaa , Stires Hillary , Jin Lu , Tam Stanley , Mobin Dua , Balachandran Manasi , Podar Mircea , McCoy Matthew D. , Beckman Robert A. , Riggins Rebecca B.
Published: August 2023

Background

Breast tumors overexpressing human epidermal growth factor receptor (HER2) confer intrinsic resistance to endocrine therapy (ET), and patients with HER2/ estrogen receptor-positive (HER2+/HR+) breast cancer (BCa) are less responsive to ET than HER2−/ER+. However, real-world evidence reveals that a large subset of HER2+/ER+ patients receive ET as monotherapy, positioning this treatment pattern as a clinical challenge. In the present study, we developed and characterized two distinctin vitromodels of ET-resistant (ETR) HER2+/ER+ BCa to identify possible therapeutic vulnerabilities.

Methods

To mimic ETR to aromatase inhibitors (AI), we developed two long-term estrogen-deprived (LTED) cell lines from BT-474 (BT474) and MDA-MB-361 (MM361). Growth assays, PAM50 molecular subtyping, genomic and transcriptomic analyses, followed by validation and functional studies, were used to identify targetable differences between ET-responsive parental and ETR-LTED HER2+/ER+ cells.

Results

Compared to their parental cells, MM361 LTEDs grew faster, lost ER, and increased HER2 expression, whereas BT474 LTEDs grew slower and maintained ER and HER2 expression. Both LTED variants had reduced responsiveness to fulvestrant. Whole-genome sequencing of the more aggressive MM361 LTED model system identified exonic mutations in genes encoding transcription factors and chromatin modifiers. Single-cell RNA sequencing demonstrated a shift towards non-luminal phenotypes, and revealed metabolic remodeling of MM361 LTEDs, with upregulated lipid metabolism and antioxidant genes associated with ferroptosis, includingGPX4. Combining the GPX4 inhibitor RSL3 with anti-HER2 agents induced significant cell death in both the MM361 and BT474 LTEDs.

Conclusions

The BT474 and MM361 AI-resistant models capture distinct phenotypes of HER2+/ER+ BCa and identify altered lipid metabolism and ferroptosis remodeling as vulnerabilities of this type of ETR BCa.
The “Duckweed Dip”: AquaticSpirodela polyrhizaPlants Can Efficiently Uptake Dissolved, DNA-Wrapped Carbon Nanotubes from Their Environment for Transient Gene Expression
Authors: Islam Tasmia , Kalkar Swapna , Tinker-Kulberg Rachel , Ignatova Tetyana , Josephs Eric A.
Published: August 2023

Duckweeds (Lemnaceae) are aquatic non-grass monocots that are the smallest and fastest-growing flowering plants in the world. While having simplified morphologies, relatively small genomes, and many other ideal traits for emerging applications in plant biotechnology, duckweeds have been largely overlooked in this era of synthetic biology. Here, we report that Greater Duckweed (Spirodela polyrhiza), when simply incubated in a solution containing plasmid-wrapped carbon nanotubes (DNA-CNTs), can directly up-take the DNA-CNTs from their growth media with high efficiency and that transgenes encoded within the plasmids are expressed by the plants—without the usual need for large doses of nanomaterials or agrobacterium to be directly infiltrated into plant tissue. This process, called the “duckweed dip”, represents a streamlined, ‘hands-off’ tool for transgene delivery to a higher plant that we expect will enhance the throughput of duckweed engineering and help to realize duckweed’s potential as a powerhouse for plant synthetic biology. (148 words)
Joint representation learning for retrieval and annotation of genomic interval sets
Authors: Gharavi Erfaneh , LeRoy Nathan J. , Zheng Guangtao , Zhang Aidong , Brown Donald E. , Sheffield Nathan C.
Published: August 2023

Motivation

As available genomic interval data increases in scale, we require fast systems to search it. A common approach is simple string matching to compare a search term to metadata, but this is limited by incomplete or inaccurate annotations. An alternative is to compare data directly through genomic region overlap analysis, but these approaches lead to challenges like sparsity, high dimensionality, and computational expense. We require novel methods to quickly and flexibly query large, messy genomic interval databases.

Results

Here, we develop a genomic interval search system using representation learning. We train numerical embeddings for a collection of region sets simultaneously with their metadata labels, capturing similarity between region sets and their metadata in a low-dimensional space. Using these learned co-embeddings, we develop a system that solves three related information retrieval tasks using embedding distance computations: retrieving region sets related to a user query string; suggesting new labels for database region sets; and retrieving database region sets similar to a query region set. We evaluate these use cases and show that jointly learned representations of region sets and metadata are a promising approach for fast, flexible, and accurate genomic region information retrieval.
Active learning of enhancer and silencer regulatory grammar in photoreceptors
Authors: Friedman Ryan Z. , Ramu Avinash , Lichtarge Sara , Myers Connie A. , Granas David M. , Gause Maria , Corbo Joseph C. , Cohen Barak A. , White Michael A.
Published: August 2023

Cis-regulatory elements (CREs) direct gene expression in health and disease, and models that can accurately predict their activities from DNA sequences are crucial for biomedicine. Deep learning represents one emerging strategy to model the regulatory grammar that relates CRE sequence to function. However, these models require training data on a scale that exceeds the number of CREs in the genome. We address this problem using active machine learning to iteratively train models on multiple rounds of synthetic DNA sequences assayed in live mammalian retinas. During each round of training the model actively selects sequence perturbations to assay, thereby efficiently generating informative training data. We iteratively trained a model that predicts the activities of sequences containing binding motifs for the photoreceptor transcription factor Cone-rod homeobox (CRX) using an order of magnitude less training data than current approaches. The model’s internal confidence estimates of its predictions are reliable guides for designing sequences with high activity. The model correctly identified critical sequence differences between active and inactive sequences with nearly identical transcription factor binding sites, and revealed order and spacing preferences for combinations of motifs. Our results establish active learning as an effective method to train accurate deep learning models ofcis-regulatory function after exhausting naturally occurring training examples in the genome.
Olfaction regulates peripheral mitophagy and mitochondrial function
Authors: Dishart Julian G. , Pender Corinne , Shen Koning , Zhang Hanlin , Ly Megan , Webb Madison , Dillin Andrew
Published: August 2023

The central nervous system is a master regulator of peripheral homeostasis and cellular-stress responses; however, the contexts for which this regulatory capability evolved remain unknown. The olfactory sensory nervous system has access to privileged information about environmental conditions and can signal to the periphery to prepare for potential metabolic perturbations. The unfolded protein response of the mitochondria (UPRMT) is upregulated upon infection by many pathogens and in metabolic flux, and pathogenic infection and metabolic byproducts are a present hazard in consuming nutrients. Therefore, we asked whether the olfactory nervous system inC. elegansregulates the UPRMTcell nonautonomously. We found that loss of a single olfactory neuron pair, AWC, led to robust induction of the UPRMTdownstream of enhanced, serotonin-dependent mitophagy. Further, AWC ablation confers resistance to the pathogenic bacteriaPseudomonas aeruginosapartially dependent on the UPRMTtranscription factoratfs-1, and fully dependent on mitophagy machinerypdr-1/Parkin. These data demonstrate a novel role for the olfactory nervous system in regulating whole-organism mitochondrial dynamics, perhaps in preparation for postprandial metabolic stress or pathogenic infection.
UBAP2L drives scaffold assembly of nuclear pore complexes at the intact nuclear envelope
Authors: Liao Yongrong , Andronov Leonid , Liu Xiaotian , Lin Junyan , Guerber Lucile , Lu Linjie , Agote-Arán Arantxa , Pangou Evanthia , Ran Li , Kleiss Charlotte , Qu Mengdi , Schmucker Stephane , Cirillo Luca , Zhang Zhirong , Riveline Daniel , Gotta Monica , Klaholz Bruno P. , Sumara Izabela
Published: August 2023

Assembly of macromolecular complexes at correct cellular sites is crucial for cell function. Nuclear pore complexes (NPCs) are large cylindrical assemblies with eightfold rotational symmetry, built through hierarchical binding of nucleoporins (Nups) forming distinct subcomplexes. Here, we uncover a direct role of ubiquitin-associated protein 2-like (UBAP2L) in the biogenesis of properly organized and functional NPCs at the intact nuclear envelope (NE) in human cells. UBAP2L localizes to the nuclear pores and drives the formation of the Y-complex, an essential scaffold component of the NPC, and its localization to the NE. UBAP2L facilitates the interaction of the Y-complex with POM121 and Nup153, the critical upstream factors in a well-defined sequential order of Nups assembly onto NE during interphase. Timely localization of the cytoplasmic Nup transport factor fragile X-related protein 1 (FXR1) to the NE and its interaction with the Y-complex are likewise dependent on UBAP2L. Thus, this NPC biogenesis mechanism integrates the cytoplasmic and the nuclear NPC assembly signals and ensures efficient nuclear transport, adaptation to nutrient stress and cellular proliferative capacity, highlighting the importance of NPC homeostasis at the intact nuclear envelope.

Teaser

Liao et al. show how UBAP2L drives the assembly of the scaffold elements into symmetrical and functional NPCs at the nuclear envelope in human cells.
Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species
Authors: Omondi Victor VictorO , Bosire Geoffrey O , Onyari John M , Kibet Caleb , Mwasya Samuel , Onyonyi Vanessa N , Getahun Merid N.
Published: August 2023

Ruminant livestock like cattle, sheep, goat, and camel, have a unique digestive system with complex microbiota communities that facilitate feed conversion and production of various secondary metabolites including greenhouse gases, which are significant in livestock-vector and livestock environment interactions. However, there is limited understanding of the diversity of rumen microbes and secondary metabolites that have advantageous traits to livestock physiology, productivity, climate, and defense across different ruminant species. In this study using metagenomics and metabolomics data from four evolutionary distinct livestock species, we show that there are signature microbes and secondary metabolites for each species. For instance, camels host a unique anaerobic fungus(F) called Oontomyces, cattle harbor more unique microbes like Psychrobacter (F) and three unique bacteria genera Anaeromyces, Cyllamyces, and Orpinomyces. Goats have Cleistothelebolus (F), while sheep host Liebetanzomyces (F). This phenomenon may indicate that there are species-specific microbes that requires host rumen-microbes’ environment balance. Additionally, there are conserved core bacterial microbes present and in equal abundance regardless of the host genetics, indicating their essential role in maintaining crucial functions. The studied livestock fed on diverse plant materials, including grass, shrubs to acacia trees. Regarding secondary metabolites camel rumen is rich in organic acids, goat with alcohols, and hydrocarbons, sheep with indoles and cattle with sesquiterpenes. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.
Mutual homeostasis of charged proteins
Authors: Faraway Rupert , Heaven Neve Costello , Digby Holly , Wilkins Oscar G. , Chakrabarti Anob M. , Iosub Ira A. , Knez Lea , Ameres Stefan L. , Plaschka Clemens , Ule Jernej
Published: August 2023

Protein dosage is regulated to maintain cellular homeostasis and health. The dosage of proteins containing disordered low complexity domains (LCDs) must be particularly well-controlled to prevent aberrant disease, yet no mechanism to maintain homeostasis has been identified1, 2. Here we report a mutual homeostatic mechanism that controls the concentration of such proteins, termed ’interstasis’, in which proteins with similar LCDs co-regulate their combined dosage through collective negative feedback. We focused on the mechanism that exploits the fundamental multivalency of GA-rich RNA regions that encode charged LCDs, including those with arginine-enriched mixed charge domains (R-MCDs). Modest variations in the abundance of an R-MCD protein change the properties of nuclear speckles, a protein-RNA condensate, selectively trapping multivalent GA-rich mRNAs to promote their nuclear retention. This interstasis depends on conserved codon biases, shared by amniotes, which enhance the multivalency of GA-rich regions encoding charged LCDs. The threshold of interstasis is modulated by CLK kinases, which affect the nuclear speckle localisation of proteins such as TRA2B, key binder of GA-rich RNAs. Notably, many classes of LCDs are encoded by RNA regions containing multivalency-enhancing codon biases, each preferentially bound by specific proteins, suggesting that interstasis might co-regulate many classes of functionally related LCD-containing proteins through dose-sensitivity of various types of protein-RNA condensates.