bluuebunny/crossref_metadata_2025 huggingface dataset:
The Mouse Epididymal Amyloid Matrix: A Mammalian Counterpart of a Bacterial Biofilm
Authors: Myers Caitlyn , Atkins Georgia Rae , Villarreal Johanna , Sutton R. Bryan , Cornwall Gail A.
Published: November 2023

The mouse epididymis is a long tubule connecting the testis to the vas deferens. Its primary functions are to mature spermatozoa into motile and fertile cells and to protect them from pathogens that ascend the male tract. We previously demonstrated that a functional extracellular amyloid matrix surrounds spermatozoa in the epididymal lumen and has host defense functions; properties not unlike that of an extracellular biofilm that surrounds and protects a bacterial community. Here we show the epididymal amyloid matrix also structurally resembles a biofilm by containing eDNA, eRNA, and mucin-like polysaccharides. Further these structural components exhibit comparable behaviors and perform functions like their counterparts in bacterial biofilms. Our studies suggest that nature has used the ancient building blocks of bacterial biofilms to form an analogous structure that nurtures and protects the mammalian male germline.
Using eDNA to elucidate Silver and Bighead Carp range expansion in two Missouri River tributaries in eastern South Dakota
Authors: LaBrie Lindsey A. P. , Wesner Jeff S. , Britten Hugh B.
Published: November 2023

Objective

This study used environmental DNA (eDNA) sampling methods to determine the possibility of Bighead CarpHypophthalmichthys nobilis,and Silver CarpH. molitrix, range expansion above barriers to fish movement in two tributaries of the Missouri River in eastern South Dakota.

Methods

We collected water samples above and below two perceived barriers to fish movement: a natural chain of waterfalls in the Big Sioux River and a spillway at the downstream end of a manmade reservoir in the Vermillion River. We used filtration methods to collect invasive carp eDNA from water samples and implemented qPCR techniques to quantify the amount of eDNA in each sample. A total of 213 samples and 38 field blanks were collected over two years (2021/2022).

Result

We detected carp eDNA below both barriers in both years, and above the barrier in the Vermillion River in 2022. The probability of detecting eDNA below the barrier in the Big Sioux River was 51% (95% Credible Interval (CrI): 2 to 97%) and 77% (95% CrI: 8 to 99%) in the Vermillion River. The probability of detecting eDNA above both barriers was significantly smaller: 1% (95% CrI: 0.02 to 24%) for both rivers.

Conclusion

The detection of positive samples above the spillway barrier in the Vermillion River provides the first evidence that Bighead and Silver Carp may have expanded their range to habitats upstream of their documented range in eastern South Dakota.

Impact Statement

This study demonstrates the utility of using eDNA sampling methods to detect Bighead and Silver Carp in areas of both known and unknown invasive carp presence in smaller tributary streams to the Missouri River.
Comparative and Integrative Single Cell Analysis Reveals New Insights into the Transcriptional Immaturity of Stem Cell-Derived β Cells
Authors: Schmidt Mason D. , Ishahak Matthew , Augsornworawat Punn , Millman Jeffrey R.
Published: November 2023

Diabetes cell replacement therapy has the potential to be transformed by human pluripotent stem cell-derived β cells (SC-β cells). However, the precise identity of SC-β cells in relationship to primary fetal and adult β-cells remains unclear. Here, we used single-cell sequencing datasets to characterize the transcriptional identity of islets from in vitro differentiation, fetal islets, and adult islets. Our analysis revealed that SC-β cells share a core β-cell transcriptional identity with human adult and fetal β-cells, however SC-β cells possess a unique transcriptional profile characterized by the persistent expression and activation of progenitor and neural-biased gene networks. These networks are present in SC-β cells, irrespective of the derivation protocol used. Notably, fetal β-cells also exhibit this neural signature at the transcriptional level. Our findings offer insights into the transcriptional identity of SC-β cells and underscore the need for further investigation of the role of neural transcriptional networks in their development.
Neuronal exosomes transport a miRNA/RISC cargo to preserve germline stem cell integrity during energy stress
Authors: Wong Christopher , Jurczak Elena M. , Roy Richard
Published: November 2023

During periods of nutrient scarcity, many animals undergo germline quiescence to preserve reproductive capacity, and neurons are often necessary for this adaptation. We show here that starvation causes the release of neuronal miRNA/Argonaute-loaded exosomes following AMPK-regulated trafficking changes within serotonergic neurons. This neuron-to-germ line communication is independent of classical serotonergic neurotransmission, but instead relies on endosome-derived vesicles that carry a pro-quiescent miRNA cargo to modify germline gene expression. Using a miRNA activity sensor, we show that neuronally-expressed miRNAs can extinguish the expression of germline-mRNA targets in an exosome-dependent manner. Our findings demonstrate how an adaptive neuronal response can change gene expression at a distance by re-directing intracellular trafficking to release neuronal exosomes with specific miRNA cargos capable of tracking to their appropriate destinations.

One Sentence Summary

Neurons release miRNA Argonaute-containing exosomes to establish germline stem cell quiescence in response to energy stress.
Rapid and Highly Sensitive Detection of Fentanyl and its Analogs by a Novel Chemiluminescence Immunoassay
Authors: Zhao Jiang-yang , Uddin Mezbah , Unsihuay Daisy , Butler William , Xia Terrance W. , Xu Jayson Z. , Jannetto Paul J. , Wang Ping , Xia Xiaofeng
Published: November 2023

A highly sensitive immunoassay with sub-picogram limit of detection for fentanyl and a wide range of fentanyl analogs has been developed, using a novel high affinity antibody fused with NanoLuc, a small-size luciferase that can emit strong and stable luminescence. When applied to unaltered clinical human urine samples, the assay has sub-picogram limit of detection for fentanyl, with results fully concordant with gold standard liquid chromatography-mass spectrometry. When applied to environmental samples, the assay can detect as low as 0.25 pg fentanyl per inch2environment surface. Assay turn-around-time is less than 1 hour, with inexpensive equipment needed and potential for high throughput automation or in-field screening. This novel assay has broad potential applications in clinical, environmental, occupational and forensic scenarios by detecting trace amount of fentanyl and its analogs to keep frontline workers safe.
Extended discrete gene regulatory network model for theArabidopsis thalianaroot-hair cell fate
Authors: Castillo-Jiménez Aarón , Garay-Arroyo Adriana , de La Paz Sánchez M. , García-Ponce Berenice , Martínez-García Juan Carlos , Álvarez-Buylla Elena R.
Published: November 2023

The differentiation of the two cell types of the root epidermis, atrichoblasts, which give rise to hair cells, and atrichoblasts, which do not develop as hair cells, is determined by a complex regulatory network of transcriptional factors and hormones that act in concert in space and time to define a characteristic pattern of rows of hair cells and non-hair cells interspersed with each other throughout the root epidermis ofArabidopsis thaliana. Previous models have defined a minimal regulatory network that recovers the Wild Type phenotype and some mutants but fails to recover most of the mutant phenotypes, thus limiting its ability to spread. In this work, we propose a diffusion-coupled regulatory genetic network or meta-Gene Regulatory Network model extended to the model previously published by our research group, to describe the patterns of organization of the epidermis of the root epidermis ofArabidopsis thaliana. This network fully or partially recovers loss-of-function mutants of the identity regulators of the epidermal cell types considered within the model. Not only that, this new extended model is able to describe in quantitative terms the distribution of trichoblasts and atrichoblasts defined at each cellular position with respect to the cortex cells so that it is possible to compare the proportions of each cell type at those positions with that reported in each of the mutants analyzed. In addition, the proposed model allows us to explore the importance of the diffusion processes that are part of the lateral inhibition mechanism underlying the network dynamics and their relative importance in determining the pattern in the Wild Type phenotype and the different mutants.
Melatonin serves as a novel treatment in cystic fibrosis and inhibits cystic fibrosis through TGF-β1/Smad and EMT
Authors: Zhang Yang , Gong Sun , He Weixin , Yuan Jie , Dong Di , Zhang Jialong , Wang Haomin , Chen Binghai
Published: November 2023

Background

Melatonin (MEL) is an indole amine molecule primarily produced in the pineal gland. Melatonin has been shown in numerous studies to have anti-fibrosis characteristics in the kidney, liver, and other organs. However, it is still unclear how melatonin works in bladder fibrosis. We explored how melatonin affected animals with bladder fibrosis and its underlying mechanisms.

Materials and Methods

MEL was used to treat human bladder smooth muscle cells (HBdSMCs) after they were stimulated with TGF-β1 in vitro. Proteomic analysis and then bioinformatic analysis based on the alterations in these proteins were then performed on HBdSMCs from the different processing methods. To construct an in vivo bladder fibrosis model, we injected protamine sulfate (PS) and lipopolysaccharide (LPS) twice a week into the rat bladder for six weeks. After two weeks of PS/LPS treatment, the treatment group was treated with MEL (20mg/kg/d) for 4 weeks. Finally, we detected the expression of fibrosis markers from different perspectives. The TGF-β1/Smad pathway, and EMT in cell and bladder tissues were also identified. Further proteomic analysis was also performed.

Results

In the in vitro experiment, we found that TGF-β1 treatment enhanced the fibrosis markers Collagen III and α-SMA of HBdSMCs. E-cadherin expression decreased while TGF-β1/Smad pathway was activated. Vimentin and N-cadherin expressions were also elevated at the same time. Similar findings were observed in the LPS group. After MEL treatment, the expression of collagen III and α-SMA decreased, and the expression of E-cadherin increased, while the expression of Vimentin and N-cadherin also decreased. CCN1 and SQLE may be the important proteins in the development of bladder fibrosis, according to quantitative proteomics analysis. MEL can decrease their expressions which leadis to relief of bladder fibrosis. Bioinformatics analysis shows that the extracellular space structure related to metabolic pathways, actin filament binding, and stress fibers can serve as a pivotal focus in the management of fibrosis.

Conclusion

Melatonin attenuates bladder fibrosis by blocking the TGF-β1/Smad pathway and EMT. CCN1 appears to be a possible therapeutic target for bladder fibrosis.
Observations of respiratory syncytial virus (RSV) nucleic-acids in wastewater solids across the United States in the 2022-2023 season: Relationships with RSV infection positivity and hospitalization rates
Authors: Zulli Alessandro , Varkila Meri R.J. , Parsonnet Julie , Wolfe Marlene K. , Boehm Alexandria B.
Published: November 2023

Respiratory syncytial virus (RSV) is a leading cause of respiratory illness and hospitalization but surveillance detects only a minority of cases. Wastewater surveillance could determine onset and extent of RSV circulation in the absence of sensitive case detection, but to date, studies of RSV in wastewater have been few. We measured RSV genomic RNA concentrations in wastewater solids from 176 US sites that provided samples at least three times per week during the 2022-2023 RSV season. Concentrations ranged from undetectable to 107copies per gram dry weight (median = 103cp/g). Wastewater RSV RNA concentration aggregated at state and national levels correlated with case positivity and hospitalization rates. Onset of RSV season was assessed for 14 states that collected data prior to the start of the RSV season. Wastewater and clinical surveillance identified onset of RSV during the same week in 3 states, whereas in 3 states, wastewater onset preceded clinical onset, and in 7 states, wastewater onset occurred after clinical onset. Wastewater concentrations generally peaked in the same week as hospitalization rates, but after case positivity rates peaked. Differences in onset and peaks in the wastewater versus clinical data may reflect inherent differences in the surveillance approaches.
The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients
Authors: Kafkas Şenay , Abdelhakim Marwa , Althagafi Azza , Toonsi Sumyyah , Alghamdi Malak , Schofield Paul N. , Hoehndorf Robert
Published: November 2023

Computational methods for identifying gene–disease associations can use both genomic and phenotypic information to prioritize genes and variants that may be associated with genetic diseases. Phenotype-based methods commonly rely on comparing phenotypes observed in a patient with a database of genotype-to-phenotype associations using a measure of semantic similarity, and are primarily limited by the quality and completeness of this database as well as the quality of phenotypes assigned to a patient. Genotype-to-phenotype associations used by these methods are largely derived from literature and coded using phenotype ontologies. Large Language Models (LLMs) have been trained on large amounts of text and have shown their potential to answer complex questions across multiple domains. Here, we demonstrate that LLMs can prioritize disease-associated genes as well, or better than, dedicated bioinformatics methods relying on calculated phenotype similarity. The LLMs use only natural language information as background knowledge and do not require ontology-based phenotyping or structured genotype-to-phenotype knowledge. We use a cohort of undiagnosed patients with rare diseases and show that LLMs can be used to provide diagnostic support that helps in identifying plausible candidate genes.
Brick kiln pollution and its impact on health: A systematic review and meta-analysis
Authors: Nicolaou Laura , Sylvies Fiona , Veloso Isabel , Lord Katherine , Chandyo Ram K , Sharma Arun K , Shrestha Laxman P , Parker David L , Thygerson Steven M , DeCarlo Peter F , Ramachandran Gurumurthy , Checkley William
Published: November 2023

Background

Brick kiln emissions adversely affect air quality and the health of workers and individuals living near the kilns; however, evidence of the impacts of brick kiln pollution remains limited.

Methods

We conducted a systematic review of brick kiln pollution (emissions, source contributions and personal exposures) and its effects on health. We extracted articles from electronic databases and through manual citation searching. We estimated pooled, sample-size-weighted means and standard deviations for personal exposures by job type; computed mean emission factors and pollutant concentrations by brick kiln design; and meta-analyzed differences in means or proportions for health outcomes between brick kiln workers (BKWs) and controls or for participants living near or far away from kilns.

Results

Our search yielded 1015 articles; 208 (20%) were assessed for eligibility and 101 (10%) were included in our review. We identified three additional studies through manual searching. Of 104 studies, 74 (71%) were conducted in South Asia. The most evaluated pollutants were particulate matter (PM; n=48), sulfur dioxide (SO2; n=24) and carbon monoxide (CO; n=22), and the most evaluated health outcomes were respiratory health (n=34) and musculoskeletal disorders (n=9). PM and CO emissions were higher among traditional than improved brick kilns. Mean respirable silica exposures were only measured in 4 (4%) studies and were as high as 620 μg/m3, exceeding the NIOSH recommended exposure limit by a factor of over 12. BKWs had consistently worse lung function, more respiratory symptoms, more musculoskeletal complaints, and more inflammation when compared to unexposed participants across studies; however, most studies had a small sample size and did not fully describe methods used for sampling or data collection.

Discussion

On average, BKWs had worse health outcomes when compared to unexposed controls but study quality supporting the evidence was low. Few studies reported silica concentrations or personal exposures, but the few that did suggest that exposures are high. Further research is needed to better understand the relationship between brick kiln pollution and health among workers, and to evaluate exposure mitigation strategies.
Skin Pigmentation and Pulse Oximeter Accuracy in the Intensive Care Unit: a Pilot Prospective Study
Authors: Fawzy Ashraf , Ali Harith , Dziedzic Peter H. , Potu Niteesh , Calvillo Eusebia , Golden Sherita H. , Iwashyna Theodore J. , Suarez Jose I. , Hager David N. , Garibaldi Brian T.
Published: November 2023

Rationale

Despite multiple reports of pulse oximeter inaccuracy among hospitalized Black individuals, regulatory testing of pulse oximeters is performed on healthy volunteers.

Objective

Evaluate pulse oximeter accuracy among intensive care unit patients with diverse skin pigmentation.

Methods

Skin pigmentation was measured using a chromameter in 12 patients and individual typology angle (ITA), a measure of constitutive pigmentation, calculated. Arterial blood gas (ABG) arterial oxygen saturation (SaO2) sampling was precisely matched to pulse oximetry (SpO2) using arterial line waveforms analysis. Error (SpO2-SaO2), bias, and average root mean square error (ARMS) were calculated. Multivariable linear mixed effects models evaluated the association of SpO2-SaO2with skin pigmentation.

Measurements and Main Results

Sampling time was determined for 350 ABGs. Five participants (N=96 ABGs) were darkly pigmented (forehead ITA<-30°), and 7 lighter pigmented (N=254 ABGs). Darkly pigmented individuals had 1.05% bias and 4.15% ARMScompared to 0.34% bias and 1.97% ARMSamong lighter pigmented individuals. After adjusting for SaO2, pH, heart rate, and mean arterial pressure, SpO2-SaO2was falsely elevated by 1.00% more among darkly pigmented individuals (95% confidence interval: 0.25-1.76%). SpO2significantly overestimated SaO2for dark, brown, and tan forehead or forearm pigmentation and brown and tan finger pad pigmentation compared to intermediate/light pigmentation.

Conclusions

The pulse oximeter in clinical use at an academic medical center performed worse in darkly pigmented critically ill patients than established criteria for FDA clearance. Pulse oximeter testing in ICU settings is feasible, and could be required by regulators to ensure equivalent device performance by skin pigmentation among patients.
MedEdMENTOR AI: Can artificial intelligence help medical education researchers select theoretical constructs?
Authors: Ow Gregory , Rodman Adam , Stetson Geoffrey V.
Published: November 2023

INTRODUCTION

Medical education scholarship often lacks a strong theoretical underpinning, with this gap most often affecting early-career researchers and researchers in the Global South. Large language models (LLMs) have shown considerable promise to augment human writing and creativity in a variety of settings. In this study, we describe the development of MedEdMENTOR — an online platform for medical education research with a library of over 250 theories — and the development and evaluation of MedEdMENTOR AI, an LLM containing knowledge from MedEdMENTOR and the first AI mentor for medical education research.

METHODS

From a postpositivist paradigm, we evaluated MedEdMENTOR AI by testing it against 6 months of qualitative research published in 24 core medical educational journals. In a blinded fashion, we presented MedEdMENTOR AI with only the phenomenon of the qualitative study, and asked it to recommend 5 theories that could be used to study that phenomenon.

RESULTS

For 55% (29 of 53) of studies, MedEdMENTOR AI recommended the actual theoretical constructs chosen in the respective qualitative studies.

CONCLUSIONS

Our data is preliminary, but it suggests that MedEdMENTOR AI and other LLMs can be highly effective in guiding medical education scholars towards theories that may be applicable in their research. Further research is needed to assess performance on other tasks in medical education research.
Accelerating protein engineering with fitness landscape modeling and reinforcement learning
Authors: Sun Haoran , He Liang , Deng Pan , Liu Guoqing , Liu Haiguang , Cao Chuan , Ju Fusong , Wu Lijun , Qin Tao , Liu Tie-Yan
Published: November 2023

Protein engineering holds significant promise for designing proteins with customized functions, yet the vast landscape of potential mutations versus limited lab capacity constrains the discovery of optimal sequences. To address this, we present theµProtein framework, which accelerates protein engineering by combiningµFormer, a deep learning model for accurate mutational effect prediction, withµSearch, a reinforcement learning algorithm designed to efficiently navigate the protein fitness landscape usingµFormer as an oracle.µProtein uniquely leverages single-point mutation data to predict optimal sequences with complex, multi-point mutations through its modeling of epistatic interactions and a two-step, multi-round search strategy. In benchmark testing,µProtein achieved state-of-the-art results, and in wet-lab experiments, it identified high-gain-of-function multi-point mutants for the enzymeβ-lactamase, including variants that increased bacterial growth rate by up to 2000-fold, surpassing the highest known activity level, all while training solely on single-site mutation data. These results demonstrateµProtein’s capability to discover impactful mutations across vast protein sequence space, offering a robust, efficient approach for protein optimization.
Combining CRISPR/Cas mediated terminal resolution with a novel genetic workflow to achieve high diversity adenoviral libraries
Authors: Fischer Julian , Fedotova Ariana , Jaki Lena , Sallard Erwan , Erhardt Anja , Fuchs Jonas , Ruzsics Zsolt
Published: November 2023

While recombinant Adenoviruses (rAds) are widely used in both laboratory and medical gene transfer, library-based applications using this vector platform are not readily available.

Recently, we developed a new method, the CRISPR/Cas9 mediated in vivo terminal resolution (CTR) aiding high efficiency rescue of rAds from recombinant DNA. Here we report on a genetic workflow that allows construction of BAC-based rAd-libraries employing the efficiency of CTR.

We utilized frequent, pre-existing genomic sequences to allow insertion of a selection marker, complementing two selected target sites into novel endonuclease recognition sites. In a second step, this selection marker is replaced with a transgene or mutation of interest via Gibson assembly. Our approach does not cause unwanted genomic off-target mutations while providing substantial flexibility for the site and nature of the genetic modification.

This new genetic workflow, which we termed half-site directed fragment replacement (HFR) allows introduction of >106unique modifications into rAd encoding BACs using laboratory scale methodology. To demonstrate the power of HFR, we rescued barcoded viral vector libraries yielding a diversity of ∼2.5×104modified rAd per cm2of transfected cell culture.

GRAPHICAL ABSTRACT
Aperiodic activity as a central neural feature of hypnotic susceptibility outside of hypnosis
Authors: Landry Mathieu , da Silva Castanheira Jason , Boisvert Catherine , Rousseaux Floriane , Sackur Jérôme , Raz Amir , Richebé Philippe , Ogez David , Rainville Pierre , Jerbi Karim
Published: November 2023

How well a person responds to hypnosis is a stable trait, which exhibits considerable inter-individual diversity across the general population. Yet, its neural underpinning remains elusive. Here, we address this gap by combining EEG data, multivariate statistics, and machine learning in order to identify brain patterns that differentiate between individuals high and low in susceptibility to hypnosis. In particular, we computed the periodic and aperiodic components of the EEG power spectrum, as well as graph theoretical measures derived from functional connectivity, from data acquired at rest (pre-induction) and under hypnosis (post-induction). We found that the 1/f slope of the EEG spectrum at rest was the best predictor of hypnotic susceptibility. Our findings support the idea that hypnotic susceptibility is a trait linked to the balance of cortical excitation and inhibition at baseline and offers novel perspectives on the neural foundations of hypnotic susceptibility. Future work can explore the contribution of background 1/f activity as a novel target to distinguish the responsiveness of individuals to hypnosis at baseline in the clinic.

Significance Statement

Hypnotic phenomena reflect the ability to alter one’s subjective experiences based on targeted verbal suggestions. This ability varies greatly in the population. The brain correlates to explain this variability remain elusive. Addressing this gap, our study employs machine learning to predict hypnotic susceptibility. By recording electroencephalography (EEG) before and after a hypnotic induction and analyzing diverse neurophysiological features, we were able to determine that several features differentiate between high and low hypnotic susceptible individuals both at baseline and during hypnosis. Our analysis revealed that the paramount discriminative feature is non-oscillatory EEG activity before the induction—a new finding in the field. This outcome aligns with the idea that hypnotic susceptibility represents a latent trait observable through a plain five-minutes resting-state EEG.
Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO)
Authors: Saha Enakshi , Fanfani Viola , Mandros Panagiotis , Ben-Guebila Marouen , Fischer Jonas , Hoff-Shutta Katherine , Glass Kimberly , DeMeo Dawn Lisa , Lopes-Ramos Camila , Quackenbush John
Published: November 2023

Gene regulatory networks (GRNs) are effective tools for inferring complex interactions between molecules that regulate biological processes and hence can provide insights into drivers of biological systems. Inferring co-expression networks is a critical element of GRN inference as the correlation between expression patterns may indicate that genes are coregulated by common factors. However, methods that estimate co-expression networks generally derive an aggregate network representing the mean regulatory properties of the population and so fail to fully capture population heterogeneity. To address these concerns, we introduce BONOBO (Bayesian Optimized Networks Obtained By assimilating Omics data), a scalable Bayesian model for deriving individual sample-specific co-expression networks by recognizing variations in molecular interactions across individuals. For every sample, BONOBO assumes a Gaussian distribution on the log-transformed centered gene expression and a conjugate prior distribution on the sample-specific co-expression matrix constructed from all other samples in the data. Combining the sample-specific gene expression with the prior distribution, BONOBO yields a closed-form solution for the posterior distribution of the sample-specific co-expression matrices, thus making the method extremely scalable. We demonstrate the utility of BONOBO in several contexts, including analyzing gene regulation in yeast transcription factor knockout studies, prognostic significance of miRNA-mRNA interaction in human breast cancer subtypes, and sex differences in gene regulation within human thyroid tissue. We find that BONOBO outperforms other sample-specific co-expression network inference methods and provides insight into individual differences in the drivers of biological processes.

Graphical Abstract
Analyzing ER stress response in ALS patient derived motor neurons identifies druggable neuroprotective targets
Authors: Watts Michelle E. , Giadone Richard M. , Ordureau Alban , Holton Kristina M. , Harper J. Wade , Rubin Lee L.
Published: November 2023

Amyotrophic lateral sclerosis (ALS) is a degenerative motor neuron (MN) disease with severely limited treatment options. Identification of effective treatments has been limited in part by the lack of predictive animal models for complex age-related human disorders. Here, we utilized pharmacologic ER stressors to exacerbate underlying sensitivities conferred by ALS patient genetics in induced pluripotent stem cell (iPSC)-derived motor neurons (MNs). In doing so, we found that thapsigargin and tunicamycin exposure recapitulated ALS-associated degeneration, and that we could rescue this degeneration via MAP4K4 inhibition (MAP4K4i). We subsequently identified mechanisms underlying MAP4K4i-mediated protection by performing phosphoproteomics on iPSC-derived MNs treated with ER stressors -/+ MAP4K4i. Through these analyses, we found JNK, PKC, and BRAF to be differentially modulated in MAP4K4i-protected MNs, and that inhibitors to these proteins could also rescue MN toxicity. Collectively, this study highlights the value of utilizing ER stressors in ALS patient MNs to identify novel druggable targets.
A metagenomics approach to identification of eukaryotes in metazoan-associated microbiomes
Authors: Crouch Audra L. , Monsey Laine , Ramos Cameron , Anderson Matthew Z.
Published: November 2023

Background

Microbial eukaryotes are integral components of the microbiome where they shape community composition and ecological interactions. However, the abundance and diversity of eukaryotic species within the microbiome, the ‘eukaryome’, remains poorly defined. These deficiencies arise from unresolved technical limitations in recovering DNA from microbial eukaryotes due to their relatively low abundance in most samples and resilience to extraction. To overcome these limitations, we developed an extraction protocol that specifically targets recovery of eukaryotic microbes from microbiome samples and allows for metagenomics sequencing of eukaryotic species.

Methods

Microbes were seeded in synthetic stool prior to DNA extraction to mimic microbiome samples from the gastrointestinal tract. Assessment of cell disruption was performed using intracellular staining with the azo dye trypan blue or quantification of DNA recovery. A mock microbial community of five bacteria and five eukaryotes was built to test the effectiveness of the full protocol by seeding stool with defined numbers of cells from each species.

Results

Mechanical disruption efficiently released DNA from bacterial, fungal, and protozoan species where standard microbiome DNA extraction kits did not. Optimization of the bead beating parameters lysed >95% of fungal cells within synthetic stool samples. In a mixed bacteria- eukaryote sample, eukaryotic DNA could be further enriched by targeting methylated DNA for destruction with methyl-specific restriction endonucleases. Application of this approach to a defined community of 10 different microbes, five eukaryotes and five bacteria, seeded in synthetic stool demonstrated the success of this strategy by enriching for eukaryotes approximately 72-fold and producing a eukaryote-dominated DNA pool.

Conclusions

Overall, development of a microbiome sample protocol that includes DNA extraction and enrichment from eukaryotic species will facilitate exploration of the eukaryome and its impact on human health.
Single-Molecule Direct RNA Sequencing Reveals the Shaping of Epitranscriptome Across Multiple Species
Authors: Xie Ying-Yuan , Zhong Zhen-Dong , Chen Hong-Xuan , Qiu Yuan-Tao , Ren Ze-Hui , Lan Ye-Lin , Wu Fu , Kong Jin-Wen , Luo Ru-Jia , Zhang Delong , Liu Biao-Di , Shu Yang , Yin Feng , Wu Jian , Li Zigang , Zhang Zhang , Luo Guan-Zheng
Published: November 2023

N6-methyladenosine (m6A) is an essential RNA modification that regulates gene expression and influences diverse cellular processes. Yet, fully characterizing its transcriptome-wide landscape and biogenesis mechanisms remains challenging. Traditional next-generation sequencing (NGS) methods rely on short-reads aggregation, overlooking the inherent heterogeneity of RNA transcripts. Third-generation sequencing (TGS) platforms offer direct RNA sequencing (DRS) at the resolution of individual RNA molecules, enabling simultaneous detection of RNA modifications and RNA processing events. In this study, we introduce SingleMod, a deep learning model tailored for precise m6A modification mapping on individual RNA molecules from DRS data. Applying SingleMod to human cell lines, we systematically dissect the transcriptome-wide m6A landscape at single-molecule and single-base resolution, characterizing m6A heterogeneity in RNA molecules from the same transcript and revealing that multiple m6A sites on an RNA molecule can cumulatively influence its splicing and stability. Through comparative analyses across eight diverse species, we quantitatively elucidate three distinct m6A distribution patterns that suggest divergent regulatory mechanisms. This study provides a novel framework for understanding the shaping of epitranscriptome in a single-molecule perspective.
Do aposematic species have larger range sizes? A case study with Neotropical poison frogs
Authors: Silveira Priscila , Sousa Fernanda Gonçalves de , Böning Philipp , Maciel Natan M. , Stropp Juliana , Lötters Stefan
Published: November 2023

Aim

Aposematic animals, i.e. those that are defended and warn potential predators through signals, are suggested to have resource-gathering advantages against non-aposematic ones. We here explore this in a biogeographic frame expecting that aposematic species are better dispersers, which translates into larger geographic range size.

Location

South America.

Taxon

Poison frogs (Amphibia; Aromobatidae and Dendrobatidae).

Methods

We use 43 toxic and 26 non-toxic poison frog species from the lowlands only as representatives of aposematic and non-aposematic study organisms, respectively. Realized and potential geographic ranges are calculated using minimum convex polygon and species distribution modelling methods, respectively. Accounting for species body size and phylogeny, we test if both range and aposematism are correlated using linear mixed models.

Results

Aposematic and non-aposematic species do neither differ in realized nor in potential geographic range size. There was no effect of body size.

Main conclusions

The role of aposematism yet is not as clear as suggested and determinants of poison frog range sizes are multifaceted. A more integrative approach is needed using information of behaviour, predation risk, and reproductive biology to assess the role of aposematism on observed species distributions. Such data are not yet available for most species, neither poison frogs nor other aposematic animals.
Genetic causes and genomic consequences of breakdown of distyly inLinum trigynum
Authors: Gutiérrez-Valencia Juanita , Zervakis Panagiotis-Ioannis , Postel Zoé , Fracassetti Marco , Losvik Aleksandra , Mehrabi Sara , Bunikis Ignas , Soler Lucile , Hughes P. William , Désamoré Aurélie , Laenen Benjamin , Abdelaziz Mohamed , Pettersson Olga Vinnere , Arroyo Juan , Slotte Tanja
Published: November 2023

Distyly is an iconic floral polymorphism governed by a supergene, which promotes efficient pollen transfer and outcrossing through reciprocal differences in the position of sexual organs in flowers, often coupled with heteromorphic self-incompatibility (SI). Distyly has evolved convergently in multiple flowering plant lineages, but has also broken down repeatedly, often resulting in homostylous, self-compatible populations with elevated rates of self-fertilization. Here, we aimed to study the genetic causes and genomic consequences of the shift to homostyly inLinum trigynum, which is closely related to distylousLinum tenue.Building on a high-quality genome assembly, we show thatL. trigynumharbors a genomic region homologous to the dominant haplotype of the distyly supergene conferring long stamens and short styles inL. tenue, suggesting that loss of distyly first occurred in a short-styled individual. In contrast to homostylousPrimulaandFagopyrum,L. trigynumharbors no fixed loss-of-function mutations in coding sequences ofS-linked distyly candidate genes. Instead, floral gene expression analyses and controlled crosses suggest that mutations downregulating theS-linkedLtWDR-44candidate gene for male SI and/or anther height could underlie homostyly and self-compatibility (SC) inL. trigynum. Population genomic analyses of 224 whole-genome sequences further demonstrate thatL. trigynumis highly self-fertilizing, exhibits significantly lower genetic diversity genome-wide, and is experiencing relaxed purifying selection and less frequent positive selection on nonsynonymous mutations relative toL. tenue. Our analyses shed light on the loss of distyly inL. trigynum, and advance our understanding of a common evolutionary transition in flowering plants.
Mode III tear resistance ofBombyx morisilk cocoons
Authors: Rehman Ateeq Ur , Koutsos Vasileios , Alam Parvez
Published: November 2023

This paper concerns the tear properties and behaviour ofBombyx morisilk cocoons. The tear resistance of cocoon layers is found to increase progressively from the innermost layer to the outermost layer. Importantly, the increase in tear strength correlates with increased porosity, which itself affects fibre mobility. We propose a microstructural mechanism for tear failure, which begins with fibre stretching and sliding, leading to fibre piling, and eventuating in fibre fracture. The direction of fracture is then deemed to be a function of the orientation of piled fibres, which is influenced by the presence of junctions where fibres cross at different angles and which may then acts as nucleating sites for fibre piling. The interfaces between cocoon wall layers inBombyx moricocoon walls account for 38% of the total wall tear strength. When comparing the tear energies and densities ofBombyx moricocoon walls against other materials, we find that theBombyx moricocoon walls exhibit a balanced trade-off between tear resistance and lightweightness.
Whole-body positive synchronization pattern of metabolic transcriptomes
Authors: Sussman Ehud Z. , Mor Dana , Somekh Judith
Published: November 2023

Understanding the relationship between transcriptomes in the entire body is crucial for comprehending health and disease. To achieve this, we have developed a framework that allows us to measure the general coordination pattern of functionally similar transcriptomes at a whole-body scale. Our approach employs meta-network level analysis to determine the interconnectivity level of metabolic co-expression modules throughout the body as opposed to randomly selected modules. We utilize dimensionality reduction of co-expression modules, inter-tissue connectivity, and clique community analysis. We applied our methodology to 19 distinct human tissues obtained from the GTEx project and detected 40/52 metabolic co-expression modules out of 609/652 cross-tissue generated modules in Cohort 1 and 2 respectively. We detected that the ratio of positive to negative inter-tissue co-expression of metabolic modules was significantly higher than control. We further validated these results for an additional cohort. Moreover, to detect a global concurrent synchronization pattern we performed graph theoretical analysis, specifically a clique community analysis of metabolic transcriptomes showing a significantly larger inter-tissue metabolic transcriptome community that control with a significantly higher connectivity for each metabolic module within the community. Additionally, we performed gene-level validation of our results. In summary, our findings reveal a significant global synchronization pattern of metabolic modules throughout the body. Our framework can be further used for other type of transcriptomes and serve as a measure detecting change in this global coordination pattern across conditions.
Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy
Authors: Semenova Lesia , Wang Yingfan , Falcinelli Shane , Archin Nancie , Cooper-Volkheimer Alicia D , Margolis David M , Goonetilleke Nilu , Murdoch David M , Rudin Cynthia D , Browne Edward P
Published: November 2023

Understanding the interplay between the HIV reservoir and the host immune system may yield insights into HIV persistence during antiretroviral therapy (ART) and inform strategies for a cure. Here, we applied machine learning approaches to cross-sectional high-parameter HIV reservoir and immunology data in order to characterize host-reservoir associations and generate new hypotheses about HIV reservoir biology. High-dimensional immunophenotyping, quantification of HIV-specific T cell responses, and measurement of genetically intact and total HIV proviral DNA frequencies were performed on peripheral blood samples from 115 people with HIV (PWH) on long-term ART. Analysis demonstrated that both intact and total proviral DNA frequencies were positively correlated with T cell activation and exhaustion. Years of ART and select bifunctional HIV-specific CD4 T cell responses were negatively correlated with the percentage of intact proviruses. A Leave-One-Covariate-Out (LOCO) inference approach identified specific HIV reservoir and clinical-demographic parameters, such as age and biological sex, that were particularly important in predicting immunophenotypes. Overall, immune parameters were more strongly associated with total HIV proviral frequencies than intact proviral frequencies. Uniquely, however, expression of the IL-7 receptor alpha chain (CD127) on CD4 T cells was more strongly correlated with the intact reservoir. Unsupervised dimension reduction analysis identified two main clusters of PWH with distinct immune and reservoir characteristics. Using reservoir correlates identified in these initial analyses, decision tree methods were employed to visualize relationships among multiple immune and clinical-demographic parameters and the HIV reservoir. Finally, using random splits of our data as training-test sets, machine learning algorithms predicted with approximately 70% accuracy whether a given participant had qualitatively high or low levels of total or intact HIV DNA. The techniques described here may be useful for assessing global patterns within the increasingly high-dimensional data used in HIV reservoir and other studies of complex biology.
Deep learning assisted single particle tracking for automated correlation between diffusion and function
Authors: Kæstel-Hansen Jacob , de Sautu Marilina , Saminathan Anand , Scanavachi Gustavo , Da Cunha Correia Ricardo F. Bango , Nielsen Annette Juma , Bleshøy Sara Vogt , Boomsma Wouter , Kirchhausen Tom , Hatzakis Nikos S.
Published: November 2023

Sub-cellular diffusion in living systems reflects cellular processes and interactions. Recent advances in optical microscopy allow the tracking of this nanoscale diffusion of individual objects with an unprecedented level of precision. However, the agnostic and automated extraction of functional information from the diffusion of molecules and organelles within the sub-cellular environment, is labor-intensive and poses a significant challenge. Here we introduce DeepSPT, a deep learning framework to interpret the diffusional 2D or 3D temporal behavior of objects in a rapid and efficient manner, agnostically. Demonstrating its versatility, we have applied DeepSPT to automated mapping of the early events of viral infections, identifying distinct types of endosomal organelles, and clathrin-coated pits and vesicles with up to 95% accuracy and within seconds instead of weeks. The fact that DeepSPT effectively extracts biological information from diffusion alone indicates that besides structure, motion encodes function at the molecular and subcellular level.
Building a barrier: investigating the defensive role of induced trichome production in herbicide exposed plants
Authors: Johnson Nia M , Baucom Regina S
Published: November 2023

Induced plant defense is commonly hypothesized to be an adaptive response to environmental heterogeneity reflecting phenotypic costs and benefits. While various studies have explored the adaptability of induced trichomes in response to biotic factors, we have limited understanding of whether induced trichomes can be an adaptive defense strategy in the presence of novel anthropogenic environmental stressors, such as herbicide exposure.

Using annual invasive weed velvetleaf (Abutilon theophrasti), we explore whether induced trichome production contributes to herbicide resistance and determine its impact on growth and fitness in the presence and absence of glyphosate (active ingredient in “Roundup”).

We observed trichome traits (proportion of polymorphs and density) and found a significant tradeoff between constitutive and inducible strategies for total trichome density. We identified positive correlations between induced total trichome density and herbicide resistance as well as induced branched trichomes and herbicide resistance. Additionally, our selection analysis revealed positive linear selection acting upon induced increase of total trichome production and correlative selection favoring high induced trichome production and intermediate growth.

Overall, our study indicates that induced trichome production may evolve as an adaptive defense strategy in agroecosystems and identifies significant constraints impacting the evolution of induced trichome defense.
Microbiota of laboratory channel catfish skin mucosa and aquaria water exposed to chloramine-T trihydrate
Authors: Kittel Elliott , Crosby Tina , Kocurek Brandon , Ottesen Andrea , Gieseker Charles
Published: November 2023

Here, we describe the skin mucosa microbiome of channel catfish (Ictalurus punctatus) before and after exposure to chloramine-T. We also describe the aquaria water microbiome after the post-treatment period. These data provide a unique baseline description of skin mucosa and aquaria water microbiome from catfish reared in research aquaria.

Disclaimer

The views expressed in this announcement are those of the authors and do not necessarily reflect the official policy of the Department of Health and Human Services, the U.S. Food and Drug Administration, or the U.S. Government. Reference to any commercial materials, equipment, or process does not in any way constitute approval, endorsement, or recommendation by the Food and Drug Administration
Outbreak of Highly Pathogenic Avian Influenza Virus H5N1 in Seals in the St. Lawrence Estuary, Quebec, Canada
Authors: Lair Stéphane , Quesnel Louise , Berhane Yohannes , Delnatte Pauline , Embury-Hyatt Carissa , Nadeau Marie-Soleil , Lung Oliver , Ferrell Shannon T. , Michaud Robert
Published: November 2023

We describe an unusual mortality event caused by a highly pathogenic avian influenza virus (HPAI) H5N1 clade 2.3.4.4b involving harbor (Phoca vitulina) and grey (Halichoerus grypus) seals in the St. Lawrence Estuary, Quebec, Canada. Fifteen (56%) of the seals submitted for necropsy were considered to be fatally infected by H5N1 containing fully Eurasian (EA) or Eurasian/North American genome constellation.

Concurrently, presence of large numbers of bird carcasses infected with H5N1 at haul-out sites most likely contributed to the spill-over of infection to the seals. Histologic changes included meningoencephalitis (100%), fibrinosuppurative alveolitis, and multi-organ acute necrotizing inflammation. This is the first report of fatal H5N1 infection in pinnipeds in Canada, raising concerns about the expanding host of this virus, potential for establishment of a marine mammal reservoir, and the public health risks associated with spillover to mammals.