bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractPredation 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

AbstractSoil 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

AbstractPolycomb 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□The confinement of H3K27me3 at PRC2 nucleation sites without its spreading correlates with increased 3D chromatin interactions.□The H3K27M oncohistone concentrates canonical PRC1 that anchors chromatin loop interactions in gliomas, silencing developmental programs.□Stem and progenitor cells require factors promoting H3K27me3 confinement, including H3K36me2, to maintain cPRC1 loop architecture.□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

ABSTRACTIn 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

ABSTRACTMutational 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

AbstractMicrobial 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

AbstractBCL11A/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

AbstractWhen 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

AbstractAerobic 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

SummaryShort-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

ABSTRACTHP1 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

AbstractThe 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.