bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of smoking on glaucoma
Authors: Mahmoudinezhad Golnoush , Meller Leo , Moghimi Sasan
Published: November 2023

Purpose of review

Assessing whether lifestyle related factors play a role in causing primary open-angle glaucoma (POAG) is of great value to clinicians, public health experts and policy makers. Smoking is a major global public health concern and contributes to ocular diseases such as cataracts, and age-related macular degeneration through ischemic and oxidative mechanisms. Recently, smoking has been investigated as a modifiable risk factor for glaucoma. In the presence of an association with glaucoma, provision of advice and information regarding smoking to patients may help reduce the burden of disease caused by POAG. Therefore, the aim of this review is to summarize the current evidence regarding the effect of smoking in the pathogenesis of glaucoma and its incidence, progression as well as the benefits of smoking cessation.

Recent findings

While the association between glaucoma development and smoking history is controversial, in the last decade, several recent studies have helped to identify possible effects of smoking, especially heavy smoking, in regard to glaucomatous progression. Smoking cessation may possibly be protective against glaucoma progression.

Smoking may play a role in glaucoma progression and long-term smoking cessation may be associated with lower glaucoma progression. The dose-response relationship between smoking and glaucoma as well as therapeutic potential of smoking cessation needs to be further validated with both preclinical and rigorous clinical studies.
Immunoglobulin E–Mediated Food Allergies
Authors: Weston Eva , Myers Esther
Published: November 2023

This second article on food allergies focuses on food allergic reactions involving specific immunoglobulin E (IgE) mechanism within the immune system. An IgE-mediated food allergy diagnosis requires both the sensitization (positive test) and the clinical signs and symptoms consistent with IgE-mediated food allergy response. Having the confirmed diagnosis and management plan is crucial because the signs and symptoms appear rapidly after every ingestion of a food with the potential to progress in severity to a life-threatening situation, anaphylaxis. A clear understanding of what constitutes a food allergy, specifically an IgE-mediated food allergy, will facilitate clear communication among healthcare professionals, patients and caregivers, and those in the public.
Case Series: Mixed Infectious Keratitis by Pythium insidiosum and Fungal Species
Authors: Singh Nimish Kumar , Barik Manas Ranjan , Das Sujata , Sahu Srikant Kumar , Priyadarshini Smruti Rekha , Sharma Savitri , Sahu Soumya Sucharita , Behera Himansu Sekhar
Published: November 2023

SIGNIFICANCE

This case series is the first to illustrate mixed infection from Pythium sp. and fungal species in corneal ulcer.

PURPOSE

This case series aimed to alert all toward the possibility of both Pythium sp. and fungal species infection in case of nonresponding corneal ulcer treated with either antifungals or antipythium drugs alone. Increased suspicion of mixed infection in case of nonresponding fungal/Pythium keratitis may facilitate early and prompt management.

CASE REPORTS

Six patients presented with signs of either fungal or Pythium keratitis. They underwent ophthalmological examinations, smear examinations, cultures, and polymerase chain reaction (PCR). Therapeutic penetrating keratoplasty was performed in cases where symptoms worsened after treatment with either antifungal or antipythium drugs. The half corneal button (HCB) was shared for histopathological and microbiological examinations. In the first case, smear examination from corneal scraping (CS) revealed Pythium-like filaments, which were confirmed with PCR; however, Aspergillus nidulans grew in culture. In the second case, iodine–potassium iodide (IKI) staining was positive for Pythium; however, PCR was positive for both Pythium and fungus, which was further confirmed by DNA sequencing. In the third case, IKI staining and HCB were positive for Pythium; however, PCR was positive for fungus, which was identified as Candida saitoana with DNA sequencing. In the fourth case, Pythium grew in the CS culture; however, Candida sp. grew in the HCB culture. In the fifth case, Cladosporium sp. grew in culture from CS; however, Pythium insidiosum grew from the anterior chamber exudate after therapeutic penetrating keratoplasty. In the sixth case, smear examination revealed septate fungal filaments, and Cladosporium sp. grew in culture; however, HCB on histopathological examination showed features of Pythium keratitis.

CONCLUSIONS

In unresponsive cases of Pythium or fungal keratitis, diagnostic modalities such as IKI and PCR should be implemented as a routine practice, in addition to smears and cultures.
Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes
Authors: Cutts Zachary , Patterson Sarah , Maliskova Lenka , Taylor Kimberly E. , Ye Chun , Dall’Era Maria , Yazdany Jinoos , Criswell Lindsey , Fragiadakis Gabriela K. , Langelier Charles , Capra John A. , Sirota Marina , Lanata Cristina M
Published: November 2023

There is an established yet unexplained link between interferon (IFN) and systemic lupus erythematosus (SLE). The expression of sequences derived from transposable elements (TEs) may contribute to production of type I IFNs and generation of autoantibodies. We profiled cell-sorted RNA-seq data (CD4+ T cells, CD14+ monocytes, CD19+ B cells, and NK cells) from PBMCs of 120 SLE patients and quantified TE expression identifying 27,135 TEs. We tested for differential TE expression across 10 SLE phenotypes including autoantibody production and disease activity and discovered 731 differentially expressed (DE) TEs whose effects were mostly cell-specific and phenotype-specific. DE TEs were enriched for specific families and viral genes encoded in TE sequences. Increased expression of DE TEs was associated with genes involved in antiviral activity such as LY6E, ISG15, TRIM22 and pathways such as interferon signaling. These findings suggest that expression of TEs contributes to activation of SLE-related mechanisms in a cell-specific manner, which can impact disease diagnostics and therapeutics.
Sex matters: the MouseX DW-ALLEN Atlas for mice diffusion-weighted MR imaging
Authors: Martínez-Tazo Patricia , Santos Alexandra , Kotb Selim Mohamed , Espinós-Soler Elena , De Santis Silvia
Published: November 2023

Overcoming sex bias in preclinical research requires not only including animals of both sexes in the experiments, but also developing proper tools to handle such data. Recent work revealed sensitivity of diffusion-weighted MRI to glia morphological changes in response to inflammatory stimuli, opening up exciting possibilities to characterize inflammation in a variety of preclinical models of pathologies, the great majority of them available in mice. However, there are limited resources dedicated to mouse imaging, like those required for the data processing and analysis. To fill this gap, we build a mouse MRI template of both structural and diffusion contrasts, with anatomical annotation according to the Allen Mouse Brain Atlas, the most detailed public resource for mouse brain investigation. To achieve a standardized resource, we use a large cohort of animalsin vivo, and include animals of both sexes. To prove the utility of this resource to integrate imaging and molecular data, we demonstrate significant association between the mean diffusivity from MRI and gene expression-based glial counting. To demonstrate the need of equitable sex representation, we compared across sexes the warp fields needed to match a male-based template, and our template built with both sexes. Then, we use both templates for analysing mice imaging data obtained in animals of different ages, demonstrating that using a male-based template creates spurious significant sex effects, not present otherwise. All in all, our MouseX DW-ALLEN Atlas will be a widely useful resource getting us one step closer to equitable healthcare.

Graphical abstract
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants and isogenic strain populations
Authors: Sintsova Anna , Ruscheweyh Hans-Joachim , Field Christopher M. , Feer Lilith , Nguyen Bidong D. , Daniel Benjamin , Hardt Wolf-Dietrich , Vorholt Julia A. , Sunagawa Shinichi
Published: November 2023

DNA barcoding has become a powerful tool for assessing the fitness of strains in a variety of studies, including random transposon mutagenesis screens, attenuation of site-directed mutants, and population dynamics of isogenic strain pools. However, the statistical analysis, visualization and contextualization of the data resulting from such experiments can be complex and require bioinformatic skills. Here, we developed mBARq, a user-friendly tool designed to simplify these steps for diverse experimental setups. The tool is seamlessly integrated with an intuitive web app for interactive data exploration via the STRING and KEGG databases to accelerate scientific discovery.
HUNGER DRIVES SWITCHING AND SEARCHING RESPONSE IN A SOCIAL PREDATOR
Authors: Prokopenko CM , Zabihi-Seissan S , Dupont DLJ , Kingdon KA , Turner JW , Vander Wal E
Published: November 2023

Abstract

Hunger is a frequent state for many predators and increasing hunger is likely to motivate costly behaviour to acquire necessary resources. Generalist predators must balance the costs and gains of hunting different prey, including increasing encounter rates and improving success rates by seeking areas with greater prey catchability. Large carnivores face threats when they interact with humans or conspecifics. We use integrated step selection analysis to describe spatiotemporal factors that influence wolf (Canis lupus) hunting behavior in Riding Mountain National Park, a natural area that wolves share with moose (Alces alces) and elk (Cervus canadensis). If hunger generates more risky behavior by wolves, as time-from-kill increases we expect wolves will: (1) search for and kill a prey that poses higher risk of injury, (2) use the periphery of their range, (3) use areas closer to the park boundary. Hunger alters wolf space use and drives a fine scale change in prey tracking. Movement patterns of hungry wolves are indicative of search behavior, i.e., shorter steps and more turning. Contrary to our predictions, hungry wolves moved further into the park. As wolves become hungrier, they switch their response from a weak selection to avoidance of elk. In contrast, the response to the primary and emergent prey, moose varied between individuals with some pack level similarities. Therefore, the state-based response to a pervasive risk and a historical resource was conserved in a population residing in a prey rich ‘island’ interfacing with human disturbance.
Translation elongation as a rate limiting step of protein production
Authors: Lyons Elijah F , Devanneaux Lou C , Muller Ryan Y , Freitas Anna V , Meacham Zuriah A , McSharry Maria V , Trinh Van N , Rogers Anna J , Ingolia Nicholas T , Lareau Liana F
Published: November 2023

The impact of synonymous codon choice on protein output has important implications for understanding endogenous gene expression and design of synthetic mRNAs. Synonymous codons are decoded at different speeds, but simple models predict that this should not drive protein output. Instead, translation initiation should be the rate limiting step for production of protein per mRNA, with little impact of codon choice. Previously, we used a neural network model to design a series of synonymous fluorescent reporters and showed that their protein output in yeast spanned a seven-fold range corresponding to their predicted translation elongation speed. Here, we show that this effect is not due primarily to the established impact of slow elongation on mRNA stability, but rather, that slow elongation further decreases the number of proteins made per mRNA. We combine simulations and careful experiments on fluorescent reporters to show that translation is limited on non-optimally encoded transcripts. Using a genome-wide CRISPRi screen, we find that impairing translation initiation attenuates the impact of slow elongation, showing a dynamic balance between rate limiting steps of protein production. Our results show that codon choice can directly limit protein production across the full range of endogenous variability in codon usage.
Streamlining Computational Fragment-Based Drug Discovery through Evolutionary Optimization Informed by Ligand-Based Virtual Prescreening
Authors: Chandraghatgi Rohan , Ji Hai-Feng , Rosen Gail L. , Sokhansanj Bahrad A.
Published: November 2023

Recent advances in computational methods provide the promise of dramatically accelerating drug discovery. While math-ematical modeling and machine learning have become vital in predicting drug-target interactions and properties, there is untapped potential in computational drug discovery due to the vast and complex chemical space. This paper advances a novel computational fragment-based drug discovery (FBDD) method called Fragment Databases from Screened Ligands Drug Discovery (FDSL-DD), which aims to streamline drug design by applying a two-stage optimization process. In this ap-proach,in silicoscreening identifies ligands from a vast library, which are then fragmentized while attaching specific at-tributes based on predicted binding affinity and interaction with the target sub-domain. This process both shrinks the search space and focuses on promising regions within it. The first optimization stage assembles these fragments into larger com-pounds using evolutionary strategies, and the second stage iteratively refines resulting compounds for enhanced bioac-tivity. The methodology is validated across three diverse protein targets involved in human solid cancers, bacterial antimi-crobial resistance, and SARS-CoV-2 viral entry, demonstrating the approach’s broad applicability. Using the proposed FDSL-DD and two-stage optimization approach yields high-affinity ligand candidates more efficiently than other state-of-the-art computational methods. Furthermore, a multiobjective optimization method is presented that accounts for druglikeness while still producing potential candidate ligands with high binding affinity. Overall, the results demonstrate that integrat-ing detailed chemical information with a constrained search framework can markedly optimize the initial drug discovery process, offering a more precise and efficient route to developing new therapeutics.
Invasive European green crab (Carcinus maenas) predation revealed with quantitative DNA metabarcoding
Authors: Fisher Mary C , Grason Emily W. , Stote Alex , Kelly Ryan P. , Litle Kate , Sean McDonald P.
Published: November 2023

Predation by invasive species can threaten local ecosystems and economies. The European green crab (Carcinus maenas), one of the most widespread marine invasive species, is an effective predator associated with clam and crab population declines outside of its native range. In the U.S. Pacific Northwest, green crab have recently experienced increases in abundance and expanding distributions, generating concern for estuarine ecosystems and associated aquaculture production. However, regionally-specific information on the trophic impacts of invasive green crab is highly limited. We compared the stomach contents of green crabs collected on aquaculture beds versus natural intertidal sloughs in Willapa Bay, Washington, to provide the first in-depth description of European green crab diet at a particularly crucial time for regional management. We first identified putative prey items using DNA metabarcoding. For key prey species, we also applied a quantitative model to calculate the true abundance of each species in stomach content DNA samples. From the stomach contents of 62 green crabs, we identified 56 unique taxa belonging to nine phyla. The stomach contents of crabs collected from aquaculture beds were significantly different from the stomach contents of crabs collected at natural intertidal sloughs. Across all sites, arthropods were the most frequently detected prey, with the native hairy shore crab (Hemigrapsus oregonensis) the single most common prey item. Of the eight species included in the quantitative model, two ecologically-important native species – the sand shrimp (Crangon franciscorum)and the Pacific staghorn sculpin (Leptocottus armatus) – were the most abundant in crab stomach contents, when present. In addition to providing timely information on green crab diet, our research demonstrates the novel application of a recently developed model for quantitative DNA metabarcoding. This represents another step in the ongoing evolution of DNA-based diet analysis towards producing the quantitative data necessary for modeling invasive species impacts.
A new conceptual framework explaining spatial variation in soil nitrous oxide emissions
Authors: Zhang Ziliang , Eddy William C. , Stuchiner Emily R. , DeLucia Evan H. , Yang Wendy H.
Published: November 2023

Soil emissions of nitrous oxide (N2O), a potent greenhouse gas, contribute substantially to global warming from agriculture. Spatial variation in N2O emissions within agricultural fields leads to high uncertainty in the benefits of climate-smart agricultural practices. Here, we present a new conceptual framework explaining spatial variation in soil N2O emissions developed from high spatial resolution automated measurements of soil N2O emissions together with measurements of gross N2O fluxes and soil physicochemical properties in two separately managed maize fields in central Illinois, USA. We found that sub-field locations with consistently low N2O emissions had distinct biogeochemical properties compared to locations where high emissions occurred episodically, leading to spatial variation in which factors control N2O production rates. In the consistent N2O cold spots, soil nitrate (NO3-) and dissolved organic carbon (DOC) constrained N2O production irrespective of changes in soil moisture. In contrast, in the episodic N2O hot spots which had higher soil NO3-and DOC availability, N2O production was stimulated by increases in soil moisture. These findings form the ‘cannon model’ which conceptualizes how sub-field scale variation in soil NO3-and DOC determines where increases in soil moisture can trigger high soil N2O emissions within agricultural fields.
H3K27me3 spreading organizes canonical PRC1 chromatin architecture to regulate developmental programs
Authors: Krug Brian , Hu Bo , Chen Haifen , Ptack Adam , Chen Xiao , Gretarsson Kristjan H. , Deshmukh Shriya , Kabir Nisha , Andrade Augusto Faria , Jabbour Elias , Harutyunyan Ashot S. , Lee John J. Y. , Hulswit Maud , Faury Damien , Russo Caterina , Xu Xinjing , Johnston Michael J. , Baguette Audrey , Dahl Nathan A. , Weil Alexander G. , Ellezam Benjamin , Dali Rola , Blanchette Mathieu , Wilson Khadija , Garcia Benjamin A. , Soni Rajesh Kumar , Gallo Marco , Taylor Michael D. , Kleinman Claudia L. , Majewski Jacek , Jabado Nada , Lu Chao
Published: November 2023

Polycomb Repressive Complex 2 (PRC2)-mediated histone H3K27 tri-methylation (H3K27me3) recruits canonical PRC1 (cPRC1) to maintain heterochromatin. In early development, polycomb-regulated genes are connected through long-range 3D interactions which resolve upon differentiation. Here, we report that polycomb looping is controlled by H3K27me3 spreading and regulates target gene silencing and cell fate specification. Using glioma-derived H3 Lys-27-Met (H3K27M) mutations as tools to restrict H3K27me3 deposition, we show that H3K27me3 confinement concentrates the chromatin pool of cPRC1, resulting in heightened 3D interactions mirroring chromatin architecture of pluripotency, and stringent gene repression that maintains cells in progenitor states to facilitate tumor development. Conversely, H3K27me3 spread in pluripotent stem cells, following neural differentiation or loss of the H3K36 methyltransferase NSD1, dilutes cPRC1 concentration and dissolves polycomb loops. These results identify the regulatory principles and disease implications of polycomb looping and nominate histone modification-guided distribution of reader complexes as an important mechanism for nuclear compartment organization.

Highlights

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The confinement of H3K27me3 at PRC2 nucleation sites without its spreading correlates with increased 3D chromatin interactions.

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The H3K27M oncohistone concentrates canonical PRC1 that anchors chromatin loop interactions in gliomas, silencing developmental programs.

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Stem and progenitor cells require factors promoting H3K27me3 confinement, including H3K36me2, to maintain cPRC1 loop architecture.

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The cPRC1-H3K27me3 interaction is a targetable driver of aberrant self-renewal in tumor cells.
Mycelium-bound lipases of psychrophilic and mesophilic fungi as biocatalysts for biodiesel synthesis
Authors: Kutyła Mateusz , Jaszek Natalia , Jędrys Wiktoria , Graba Sandra , Pluta Ewelina , Gdula Katarzyna , Batyra Aleksandra , Szczepańska Amelia , Śliwa Alicja , Cieślak Laura , Marzec-Grządziel Anna , Trytek Mariusz
Published: November 2023

In this study, biocatalysts in the form of mycelium-bound lipases of psychrotrophic and mesophilic fungi were screened for their ability to synthesize fatty acid methyl (FAME) and ethyl esters (FAEE). It has been shown that the hydrolytic activity of biocatalysts is not accompanied by their biodiesel synthetic activity. Preliminary studies showed for the first time, that the FTIR technique can be used to predict synthetic activity. The highest correlation between the intensity of the bands and synthetic activity, negative and positive, respectively, was observed for two neighboring bands at 1745 cm-1(R= −0.73) and 1699 cm-1(R= 0.68). The psychrotrophic strainPenicilliumsp. 59, isolated from the soil of the Arctic tundra (Spitsbergen), has been shown for the first time as an efficient whole-cell biocatalyst for fatty acid ethyl ester synthesis and is stable in organic solvents. Mathematical optimization of biosynthesis was also performed using RSM. A molar canola oil conversion value of 83.3% into FAEE was obtained at 24.2 °C in n-hexane using 12.5% of used canola oil and 5.3% of the fungal biocatalyst within 6 h. Dry mycelium ofPenicilliumsp. 59 is a promising new biocatalyst for large-scale biosynthesis of biodiesel, given its low-cost production, high activity at room temperature, no need to mix reactions, and reusability in a minimum of six cycles.
The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress
Authors: O’Leary David R. , Hansen Ava R. , Fingerman Dylan F. , Tran Thi , Harris Brooke R. , Hayer Katharina E. , Fan Jiayi , Chen Emily , Tennakoon Mithila , DeWeerd Rachel A. , Meroni Alice , Szeto Julia H. , Weitzman Matthew D. , Shalem Ophir , Bednarski Jeffrey , Vindigni Alessandro , Zhao Xiaolan , Green Abby M.
Published: November 2023

Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.
Combinatorial optimization of pathway, process and media for the production of p-coumaric acid bySaccharomyces cerevisiae
Authors: Moreno-Paz Sara , van der Hoek Rianne , Eliana Elif , Martins dos Santos Vitor A.P. , Schmitz Joep , Suarez-Diez Maria
Published: November 2023

Microbial cell factories are instrumental in transitioning towards a sustainable bio-based economy, offering alternatives to conventional chemical processes. However, fulfilling their potential requires simultaneous screening for optimal media composition, process and genetic factors, acknowledging the complex interplay between the organism’s genotype and its environment. This study employs statistical Design of Experiments (DoE) to systematically explore these relationships and optimize the production of p-coumaric acid (pCA) inSaccharomyces cerevisiae. Two rounds of fractional factorial designs were used to identify factors with a significant effect on pCA production, which resulted on a 168-fold improvement on pCA titer. Moreover, a significant interaction between the culture temperature and expression of ARO4 highlighted the importance of simultaneous process and strain optimization. The presented approach leverages the strengths of experimental design and statistical analysis and could be systematically applied during strain and bio-process design efforts to unlock the full potential of microbial cell factories.
Prioritization of The Zinc finger domain withinBCL11A by theAmelioration capability of hemoglobinopathies using CRISPR-Cas9 technology
Authors: Mumtaz Kainaat , Hussain Irfan , Iftikhar Fizza , Rehman Fawad U , Jameel Muhammad , Farooq Safana , Hassan Hammad , Fatima Ambrin , Ottmann Oliver Gerhard , Mian Afsar Ali
Published: November 2023

BCL11A/EVI9, a zinc-finger protein primarily expressed in brain and hematopoietic cells, plays a central role in lymphocyte development, gamma-globin suppression, spinal neuron development, sensory innervation, neuronal polarity, migration, and is associated with microcephaly and dysregulated brain-related genes, offering therapeutic potential for sickle cell disease. The function of the transcriptional regulator is intricately linked to its structural organization, which determines its ability to interact with specific DNA sequences and modulate gene expression. BCL11A boasts multiple domains, including six C2H2 zinc fingers, a C2HC zinc finger, a NuRD-interacting domain, an acidic domain, and a proline-rich domain. In the present study, we delve into the intricate structure and function of the zinc finger domains located in the BCL11A gene, which plays a crucial role in regulating the expression of gamma-globin gene. Specifically, three C2H2-type zinc finger domains, Znf4, Znf5, and Znf6, within BCL11A, are known to bind to DNA. Znf4 and Znf5 demonstrate a significant interaction with the TGACCA motif in the gamma-globin −115 HPFH region sequence, contributing substantially to DNA binding specificity. Although Znf3 and Znf6 also interact with DNA, their contributions are comparatively minor. Employing CRISPR-Cas9 technology, targeted genomic deletions of Znf4 exhibit high efficiency, opening doors for further research. Edited CD34+ cells successfully differentiate into erythrocytes without impairments, underscoring CRISPR-Cas9’s suitability for studying gene functions in erythropoiesis. Furthermore, BCL11A knockdown via sgRNAs results in elevated gamma-globin expression, offering a promising therapeutic avenue for beta-hemoglobinopathies. HPLC analysis reveals a substantial increase in HbF levels, particularly upon Znf4 deletion, emphasizing BCL11A gene potential as a therapeutic target. These findings also highlight the connection between the function of BCL11A and its structural organization, which can be modulated, and this insight can potentially be extended to uncover its roles in various other domains.
Stability of Oral and Fecal Microbiome at Room Temperature: Impact on Diversity
Authors: Rius-Sansalvador Blanca , Bars-Cortina David , Khannous-Lleiffe Olfat , Serrano Ainhoa Garcia- , Guinó Elisabet , Saus Ester , Gabaldón Toni , Moreno Victor , Obón-Santacana Mireia
Published: November 2023

When collecting oral and fecal samples for large epidemiological microbiome studies, optimal storage conditions such as immediate freezing, are not always feasible. It is fundamental to study the impact of temporary room temperature (RT) storage and shipping on the microbiome diversity obtained in different types of samples. We performed a pilot study aimed at validating the sampling protocol based on the viability of the 16S rRNA gene sequencing in microbiome samples.

Fecal and oral samples from five participants were collected and preserved in different conditions: a) 70% ethanol; b) in a FIT tube for stool samples; and c) in a chlorhexidine solution for oral wash samples. Four aliquots were prepared per sample, which were stored at RT, and frozen at days 0, 5, 10 and 15, respectively. In terms of alpha diversity, the maximum average decrease in 5 days was 0.3%, 1.6% and 1.7% for oral, stool in ethanol and stool in FIT, respectively. Furthermore, the relative abundances of the most important phyla and orders remained stable over the two weeks.

The stability of fecal and oral samples for microbiome studies preserved at RT with 70% ethanol, chlorhexidine and in FIT tubes was verified for a 15-day window, with no substantial changes in terms of alpha diversity and relative abundances.
Vertical distribution and light energy capture by AAP bacteria along contrasted areas of productivity in the Atlantic Ocean
Authors: Gazulla Carlota R. , Koblížek Michal , Mercado Jesús M. , Gasol Josep M. , Sánchez Olga , Ferrera Isabel
Published: November 2023

Aerobic anoxygenic phototrophic (AAP) bacteria are a common part of microbial communities in the sunlit ocean. They contain bacteriochlorophylla-based photosystems that harvest solar energy for their metabolism. Across different oceanic areas and regimes, AAP bacteria seem to be more abundant in eutrophic areas, associated to high chlorophyll concentrations. While most of these studies are based on surface samples, little information is available on their vertical distribution in euphotic zones of the major ocean basins. We hypothesize that AAPs will follow a similar structure to the chlorophyll depth profile across areas with different degrees of stratification. To test this hypothesis, we enumerated AAP cells and determined bacteriochlorophyllaconcentrations along the photic zone of a latitudinal transect in the South and Mid Atlantic Ocean. We show that the distribution of AAP bacteria is highly correlated to the chlorophyllaconcentration and the abundance of picophytoplankton across vertical and horizontal gradients. Furthermore, we estimate the light energy captured by AAP bacteria across the water column and find that, while they share a common latitudinal pattern of light capture with the picophytoplankton, they display a unique vertical arrangement with highest photoheterotrophic activity is in the surface ocean.
Differential proteome diversification in yeast populations: modes of short-term adaptation and fitness outcomes
Authors: Knafo Maor , Rezenmen Shahar , Nevo Reinat , Tsigalnitski Igal , Reich Ziv , Kapon Ruti
Published: November 2023

Short-term proteomic adaptations serve as an initial line of defence, allowing populations to cope with environmental changes before long-term genetic alterations occur. Using a representative set of genes, we examined how stress affects gene expression variability for different types and levels of abiotic stresses and how this influences population-level adaptation. Our data reveal that, depending on the nature of the stress, two distinct modes of response can be employed. In one, the levels of most proteins vary between individuals, leading to varied fitness levels in the population. In the other, a more limited range of expression is seen, and fitness is more even. This suggests different levels of complexity and plasticity in adaptation to different types of stress.
Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein 1
Authors: Ames Amanda , Seman Melissa , Larkin Ajay , Raiymbek Gulzhan , Chen Ziyuan , Levashkevich Alex , Kim Bo , Biteen Julie Suzanne , Ragunathan Kaushik
Published: November 2023

HP1 proteins are essential for establishing and maintaining transcriptionally silent heterochromatin. They dimerize, forming a binding interface to recruit diverse chromatin-associated factors. HP1 proteins are specialized and rapidly evolve, but the extent of variation required to achieve functional specialization is unknown. To investigate how changes in amino acid sequence impacts epigenetic inheritance, we performed a targeted mutagenesis screen of the S. pombe HP1 homolog, Swi6. Substitutions within an auxiliary surface adjacent to the HP1 dimerization interface produced Swi6 variants with divergent maintenance properties. Remarkably, substitutions at a single amino acid position led to the persistent gain or loss of epigenetic inheritance. These substitutions increased Swi6 chromatin occupancyin vivoand altered Swi6-protein interactions that reprogram H3K9me maintenance. We show that relatively minor changes in Swi6 amino acid composition can lead to profound changes in epigenetic inheritance which provides a redundant mechanism to evolve novel effector specificity.
A deep lung cell atlas reveals cytokine-mediated lineage switching of a rare cell progenitor of the human airway epithelium
Authors: Waghray Avinash , Monga Isha , Lin Brian , Shah Viral , Slyper Michal , Giotti Bruno , Xu Jiajie , Waldman Julia , Dionne Danielle , Nguyen Lan T. , Lou Wendy , Cai Peiwen , Park Eric , Muus Christoph , Sun Jiawei , Surve Manalee V , Yang Lujia Cha Cha , Rozenblatt-Rosen Orit , Dolerey Toni M , Saladi Srinivas Vinod , Tsankov Alexander M , Regev Aviv , Rajagopal Jayaraj
Published: November 2023

The human airway contains specialized rare epithelial cells whose roles in respiratory disease are not well understood. Ionocytes express the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), while chemosensory tuft cells express asthma-associated alarmins. However, surprisingly, exceedingly few mature tuft cells have been identified in human lung cell atlases despite the ready identification of rare ionocytes and neuroendocrine cells. To identify human rare cell progenitors and define their lineage relationship to mature tuft cells, we generated a deep lung cell atlas containing 311,748 single cell RNA-Seq (scRNA-seq) profiles from discrete anatomic sites along the large and small airways and lung lobes of explanted donor lungs that could not be used for organ transplantation. Of 154,222 airway epithelial cells, we identified 687 ionocytes (0.45%) that are present in similar proportions in both large and small airways, suggesting that they may contribute to both large and small airways pathologies in CF. In stark contrast, we recovered only 3 mature tuft cells (0.002%). Instead, we identified rare bipotent progenitor cells that can give rise to both ionocytes and tuft cells, which we termed tuft-ionocyte progenitor cells (TIP cells). Remarkably, the cycling fraction of these TIP cells was comparable to that of basal stem cells. We used scRNA-seq and scATAC-seq to predict transcription factors that mark this novel rare cell progenitor population and define intermediate states during TIP cell lineage transitions en route to the differentiation of mature ionocytes and tuft cells. The default lineage of TIP cell descendants is skewed towards ionocytes, explaining the paucity of mature tuft cells in the human airway. However, Type 2 and Type 17 cytokines, associated with asthma and CF, diverted the lineage of TIP cell descendantsin vitro, resulting in the differentiation of mature tuft cells at the expense of ionocytes. Consistent with this model of mature tuft cell differentiation, we identify mature tuft cells in a patient who died from an asthma flare. Overall, our findings suggest that the immune signaling pathways active in asthma and CF may skew the composition of disease-relevant rare cells and illustrate how deep atlases are required for identifying physiologically-relevant scarce cell populations.
Comparing the predictors of mutability among healthy human tissues inferred from mutations in single cell genome data
Authors: Oman Madeleine , Ness Rob W.
Published: November 2023

Studying mutation in healthy somatic tissues is key for understanding the genesis of cancer and other genetic diseases. Mutation rate varies from site to site in the human genome by up to 100-fold and is influenced by numerous epigenetic and genetic factors including GC content, trinucleotide sequence context, and DNAse accessibility. These factors influence mutation at both local and regional scales and are often interrelated with one another, meaning that predicting mutability or uncovering its drivers requires modelling multiple factors and scales simultaneously. Historically, most investigations have focused either on analyzing the local sequence scale through triplet signatures or on examining the impact of epigenetic processes at larger scales, but not both concurrently. Additionally, sequencing technology limitations have restricted analyses of healthy mutations to coding regions (RNA-seq) or to those that have been influenced by selection (e.g. bulk samples from cancer tissue). Here we leverage single cell mutations and present a comprehensive analysis of epigenetic and genetic factors at multiple scales in the germline and three healthy somatic tissues. We create models that predict mutability with on average 2% error, and find up to 63-fold variation among sites within the same tissue. We observe varying degrees of similarity between tissues: the mutability of genomic positions was 93.4% similar between liver and germline tissues, but sites in germline and skin were only 85.9% similar. We observe both universal and tissue-specific mutagenic processes in healthy tissues, with implications for understanding the maintenance of germline versus soma and the mechanisms underlying early tumorigenesis.

Mutations in healthy tissues can reveal how genetic diseases originate. In this study, we explore how mutation rates vary across the human genome and what influences these variations. We leverage advanced single-cell analysis to analyze genetic and epigenetic factors in germline and three healthy tissues. We trained models that exhibit high accuracy and discover large variation within the same tissue. We also identified differences in mutability between tissues, suggesting both universal and tissue-specific mutation patterns with implications for understanding oncogenesis.
The Small Tumor Antigen of Merkel Cell Polyomavirus Accomplishes Cellular Transformation by Uniquely Localizing to the Nucleus Despite the Absence of a Known Nuclear Localization Signal
Authors: Thevenin Kaira R. , Tieche Isabella S. , Di Benedetto Cody E. , Schrager Matt , Dye Kristine N.
Published: November 2023

Background

Merkel Cell Carcinoma (MCC) is an aggressive skin cancer that is three times deadlier than melanoma. In 2008, it was found that 80% of MCC cases are caused by the genomic integration of a novel polyomavirus, Merkel Cell Polyomavirus (MCPyV), and the expression of its small and truncated large tumor antigens (ST and LT-t, respectively). MCPyV belongs to a family of human polyomaviruses; however, it is the only one with a clear association to cancer.

Methods

To investigate the role and mechanisms of various polyomavirus tumor antigens in cellular transformation, Rat-2, 293A, and human foreskin fibroblasts were transduced with pLENTI MCPyV LT-t, MCPyV ST, TSPyV ST, HPyV7 ST, or empty pLENTI and assessed through multiple transformation assays, and subcellular fractionations. One-way ANOVA tests were used to assess statistical significance.

Results

Soft agar, proliferation, doubling time, glucose uptake, and serum dependence assays confirmed ST to be the dominant transforming protein of MCPyV. Furthermore, it was found that MCPyV ST is uniquely transforming, as the ST antigens of other non-oncogenic human polyomaviruses such as Trichodysplasia Spinulosa Polyomavirus (TSPyV) and Human Polyomavirus 7 (HPyV7) were not transforming when similarly assessed. Identification of structural dissimilarities between transforming and non-transforming tumor antigens revealed that the uniquely transforming domain(s) of MCPyV ST are likely located within the structurally dissimilar loops of the MCPyV ST unique region. Of all known MCPyV ST cellular interactors, 62% are exclusively or transiently nuclear, suggesting that MCPyV ST localizes to the nucleus despite the absence of a canonical nuclear localization signal. Indeed, subcellular fractionations confirmed that MCPyV ST could achieve nuclear localization through a currently unknown, regulated mechanism independent of its small size, as HPyV7 and TSPyV ST proteins were incapable of nuclear translocation. Although nuclear localization was found to be important for several transforming properties of MCPyV ST, some properties were also performed by a cytoplasmic sequestered MCPyV ST, suggesting that MCPyV ST may perform different transforming functions in individual subcellular compartments.

Conclusions

Together, these data further elucidate the unique differences between MCPyV ST and other polyomavirus ST proteins necessary to understand MCPyV as the only known human oncogenic polyomavirus.
Spartin-mediated lipid transfer facilitates lipid droplet turnover
Authors: Wan Neng , Hong Zhouping , Parson Matthew A. H. , Korfhage Justin , Burke John E. , Melia Thomas J. , Reinisch Karin M.
Published: November 2023

Lipid droplets (LDs) are organelles critical for energy storage and membrane lipid homeostasis, whose number and size are carefully regulated in response to cellular conditions. The molecular mechanisms underlying lipid droplet biogenesis and degradation, however, are not well understood. The Troyer syndrome protein spartin (SPG20) supports LD delivery to autophagosomes for turnover via lipophagy. Here, we characterize spartin as a lipid transfer protein whose transfer ability is required for LD degradation. Spartin co-purifies with phospholipids and neutral lipids from cells and transfers phospholipids in vitro via its senescence domain. A senescence domain truncation that impairs lipid transfer in vitro also impairs LD turnover in cells while not affecting spartin association with either LDs or autophagosomes, supporting that spartin’s lipid transfer ability is physiologically relevant. Our data indicate a role for spartin-mediated lipid transfer in LD turnover.

Significance

The Troyer syndrome protein spartin was proposed to function as a lipophagy receptor that delivers lipid droplets, organelles key for energy storage and membrane lipid homeostasis, to autophagosomes for degradation. We identify an additional function for spartin as a lipid transfer protein and show its transfer ability is required for lipid droplet degradation, including by lipophagy. Our data support that protein-mediated lipid transfer plays a role in lipid droplet turnover. Moreover, in spartin’s senescence domain we have discovered a new lipid transport module that likely also features in still undiscovered aspects of lipid droplet biology and membrane homeostasis.
Genomic transfers help to decipher the ancient evolution of filoviruses and interactions with vertebrate hosts
Authors: Taylor Derek J. , Barnhart Max H.
Published: November 2023

Although several filoviruses are dangerous human pathogens, there is conflicting evidence regarding their origins and interactions with animal hosts. Here we attempt to improve this understanding using the paleoviral record over a geological time scale, protein structure predictions, tests for evolutionary maintenance, and phylogenetic methods that alleviate sources of bias and error. We found evidence for long branch attraction bias in the L gene tree for filoviruses, and that using codon-specific models and protein structural comparisons of paleoviruses ameliorated conflict and bias. We found evidence for four ancient filoviral groups, each with extant viruses and paleoviruses with open reading frames. Furthermore, we found evidence of repeated transfers of filovirus-like elements to mouse-like rodents. A filovirus-like nucleoprotein ortholog with an open reading frame was detected in three subfamilies of spalacid rodents (present since the Miocene). These elements were unique among the detected filovirus-like paleoviruses in possessing open reading frames, expression products, and evidence for purifying selection. Our finding of structural conservation over geological time for paleoviruses informs virus and paleovirus discovery methods. Our results resolve a deep conflict in the evolutionary framework for filoviruses and reveal that genomic transfers to vertebrate hosts with potentially functional co-options have been more widespread than previously appreciated.

Author Summary

Filoviruses are a family of RNA viruses discovered in 1967 and notorious for spillover of the dangerous pathogens, Ebola virus and Marburg virus. However, their origins, deeper relations, diversity, and interactions with animal hosts remain controversial. Part of the confusion may be that differing rates of evolution among divergent viral lineages can create a bias termed long branch attraction (LBA). We tested for this scenario in the L protein gene sequence of filoviruses and found evidence that LBA is occurring leading to a false pairing of filovirus lineages associated with a fish and a snake. We found that using nucleotides instead of amino acids when inferring trees, paleoviral sequences with open reading frames, additional conserved genes, and comparisons of predicted protein structures can resolve the LBA. We found four major groups of filoviruses, with the paleoviral record and trees being consistent with a fish origin for the family. Moreover, we found evidence of a filovirus-like element in spalacid rodents that has been evolutionarily maintained at the open-reading frame, amino acid sequence and structural level for over 20 million years. This element was also expressed in the liver, a target of filoviral infections. We conclude that genomic interactions of filoviruses with vertebrates, including the co-option of viral genes, are more important than previously appreciated.