bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applying Cell Painting in Non-Tumorigenic Breast Cells to Understand Impacts of Common Chemical Exposures
Authors: Tapaswi Anagha , Cemalovic Nicholas , Polemi Katelyn M , Sexton Jonathan Z , Colacino Justin A 
Published: May 2024

ABSTRACTThere are a substantial number of chemicals to which individuals in the general population are exposed which have putative, but still poorly understood, links to breast cancer. Cell Painting is a high-content imaging-basedin vitroassay that allows for rapid and unbiased measurements of the concentration-dependent effects of chemical exposures on cellular morphology. We optimized the Cell Painting assay and measured the effect of exposure to 16 human exposure relevant chemicals, along with 21 small molecules with known mechanisms of action, for 48 hours in non- tumorigenic mammary epithelial cells, the MCF10A cell line. Through unbiased imaging analyses using CellProfiler, we quantified 3042 morphological features across approximately 1.2 millio n cells. We used benchmark concentration modeling to quantify significance and dose-dependent directionality to identify morphological features conserved across chemicals and find features that differentiate the effects of toxicants from one another. Benchmark concentrations were compared to chemical exposure biomarker concentration measurements from the National Health and Nutrition Examination Survey to assess which chemicals induce morphological alterations at human-relevant concentrations. Morphometric fingerprint analysis revealed similar phenotypes between small molecules and prioritized NHANES-toxicants guiding further investigation. A comparison of feature fingerprints via hypergeometric analysis revealed significant feature overlaps between chemicals when stratified by compartment and stain. One such example was the similarities between a metabolite of the organochlorine pesticide DDT (p,p’-DDE) and an activator of canonical Wnt signaling CHIR99201. As CHIR99201 is a known Wnt pathway activator and its role in ꞵ-catenin translocation is well studied, we studied the translocation of ꞵ-catenin following p’-p’ DDE exposure in an orthogonal high-content imaging assay. Consistent with activation of Wnt signaling, low dose p’,p’-DDE (25nM) significantly enhances the nuclear translocation of ꞵ-catenin. Overall, these findings highlight the ability of Cell Painting to enhance mode-of-action studies for toxicants which are common exposures in our environment but have previously been incompletely characterized with respect to breast cancer risk.
Haplotype-resolved genomes and population genetics to analyze glandular secretory trichome formation mechanism in oregano
Authors: Sun Meiyu , Miao Jiahui , Liu Ningning , Zhang Yanan , Zhang Jinzheng , Wang Di , Xia Fei , Bai Hongtong , Li Hui , Shi Lei 
Published: May 2024

AbstractOregano is an important economic plant which has valuable medicinal and aromatic properties. Oregano essential oil, containing carvacrol and thymol, is a preferred material to replace antibiotics in feed additives. Glandular secretory trichome (GST) density has positively correlated with the production of these compounds. Here, two haplotype-resolved genomes were assembled and annotated which contained 15 chromosomes with the total length of 606.75 and 612.74 Mb, respectively. Oregano had experienced two whole-genome duplications corresponding to the divergence ∼5.120/4.564 and ∼66.857/69.923 Mya, respectively. Many transcription factors and genes were found related to GSTs formation mechanism such as R2R3-MYB- and HD-ZIP IV-encoding genes. 2,669,410 SNPs, 569,093 InDels, 14,839 DUPs, 110 INVs, 3,976 TRANSs, and 1,426 CNVs were detected among two haplotype-resolved genomes. Two high density genetic linkage maps consisted of 15 LGs and spanned 2,279.28 and 2,322.83 cM, respectively. GADS, GABS, and GTS of F2segregating populations showed obvious superparental dominance. One/one, one/one, and two/four QTLs for GADS, GABS, and GTS were independently mapped on two genetic maps, respectively. Five candidate genes showed extreme difference in two bulked segregant pools. Our study not only provides significant insight into the GSTs formation mechnism, but also will facilitate molecular breeding in oregano.One Sentence SummaryOregano essential oil is a preferred material to replace antibiotics which will use to study the glandular secretory trichome formation mechanism and analyze the source of essential oil.
WITHDRAWN: Neural Network and Random Forest Algorithms as Catalysts in QSAR/QSAAR Modeling: Targeting Carbonic Anhydrase for Antituberculosis Drug Design
Authors: Bhowmik Ratul , Manaithiya Ajay , Ray Rajarshi , Carta Fabrizio , Supuran Claudiu T , Parkkila Seppo , Aspatwar Ashok 
Published: May 2024

Withdrawal StatementThe authors have withdrawn their manuscript owing to the inability to complete the revisions or follow up on the manuscript at this time, due to personal circumstances. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Rational Design of Live Biotherapeutic Products for the Prevention ofClostridioides difficileInfection
Authors: Ke Shanlin , Villafuerte Gálvez Javier A , Sun Zheng , Cao Yangchun , Pollock Nira R , Chen Xinhua , Kelly Ciarán P , Liu Yang-Yu 
Published: May 2024

AbstractClostridioides difficileinfection (CDI) is one of the leading causes of healthcare- and antibiotic-associated diarrhea. While fecal microbiota transplantation (FMT) has emerged as a promising therapy for recurrent CDI, its exact mechanisms of action and long-term safety are not fully understood. Defined consortia of clonal bacterial isolates, known as live biotherapeutic products (LBPs), have been proposed as an alternative therapeutic option. However, the rational design of LBPs remains challenging. Here, we employ a computational pipeline and three independent metagenomic datasets to systematically identify microbial strains that have the potential to inhibit CDI. We first constructed the CDI-related microbial genome catalog, comprising 3,741 non-redundant metagenome-assembled genomes (nrMAGs) at the strain level. We then identified multiple potential protective nrMAGs that can be candidates for the design of microbial consortia targeting CDI, including strains fromDorea formicigenerans,Oscillibacter welbionis, andFaecalibacterium prausnitzii. Importantly, some of these potential protective nrMAGs were found to play an important role in the success of FMT, and the majority of the top protective nrMAGs can be validated by various previously reported findings. Our results demonstrate a computational framework for the rational selection of microbial strains targeting CDI, paving the way for the computational design of microbial consortia against other enteric infections.
PhaSeDis: A Manually Curated Database of Phase Separation–Disease Associations and Corresponding Small Molecules
Authors: Chen Taoyu , Tang Guoguo , Li Tianhao , Yanghong Zhining , Hou Chao , Du Zezhou , Ma Liwei , Li Tingting 
Published: May 2024

AbstractBiomacromolecules form membraneless organelles through liquid–liquid phase separation in order to regulate the efficiency of particular biochemical reactions. Dysregulation of phase separation might result in pathological condensation or sequestration of biomolecules, leading to diseases. Thus, phase separation and phase separating factors may serve as drug targets for disease treatment. Nevertheless, such associations have not yet been integrated into phase separation related databases. Therefore, based on MloDisDB, a database for membraneless organelle factor–disease association previously developed by our lab, we constructed PhaSeDis, the phase separation–disease association database. We increased the number of phase separation entries from 52 to 185, and supplemented the evidence provided by the original article verifying the phase separation nature of the factors. Moreover, we included the information of interacting small molecules with low or high-throughput evidence that might serve as potential drugs for phase separation entries. PhaSeDis strives to offer comprehensive descriptions of each entry, elucidating how phase separating factors induce pathological conditions via phase separation and the mechanisms by which small molecules intervene. We believe that PhaSeDis would be very important in the application of phase separation regulation in treating related diseases. PhaSeDis is available athttp://mlodis.phasep.pro.
PAN deadenylase ensures proper mitosis under conditions of microtubule stress by regulating spindle integrity and promoting cell survival
Authors: Verma Jigyasa , He Zhengcheng , Brown Joshua A.R. , Dean Pamela , Young Barry P. , Flibotte Stephane , Howe LeAnn J. , Maxwell Christopher D. , Roskelley Calvin D. , Loewen Christopher J.R. 
Published: May 2024

AbstractThe Poly(A) Tail Length (PATL) of mRNAs of certain cell-cycle regulatory genes undergo significant trimming during M-phase, however the functional importance is unknown. The Ccr4-Not and PAN complexes account for the majority of cytoplasmic poly(A) deadenylation, however a role in M phase has not been described. We find that under conditions of microtubule stress in yeast, loss of PAN deadenylase activity leads to arrest in M phase, defective spindles, and increased cell death. PAN consists of the catalytic subunit Pan2 and the RNA binding subunit Pan3. Consistent with a role in mitosis,PAN2interacts genetically with tubulin genes, prefoldin complex genes and the mitotic cyclinCLB1.PAN2knockdown in human cultured cells disrupts mitosis and results in spindle fragmentation leading to abnormal cell division, while expression of humanPAN2in yeast rescuespan2Δ cell-cycle phenotypes. Hence, we reveal an important highly conserved role for PAN in ensuring proper mitosis when cells are under microtubule stress. We propose PAN regulates PATLs of mRNAs of key cell-cycle/mitotic proteins in response to defective spindles.Author SummaryProper cell division is essential for the growth and survival of all living organisms. Our study investigates the role of PAN deadenylase complex in yeast and human cultured cells under microtubule stress, induced by microtubule inhibitors used in cancer treatment. The PAN complex, consisting of Pan2 and Pan3, trims the poly(A) tails of mRNAs. We found that loss of PAN activity leads to cell cycle arrest in M-phase, spindle defects and increased cell death in yeast. Similarly,PAN2knockdown in human cultured cells disrupts mitosis and causes abnormal cell division, indicating a conserved function across species. We propose that PAN regulates mRNA poly(A) tail lengths of key mitotic proteins to ensure proper mitosis under stress. This regulation likely prevents faulty spindle formation by repressing translation of these mRNAs. Interestingly, PAN’s role is specific to stress conditions, as cells without PAN function normally otherwise. Our findings highlight PAN’s critical role in maintaining genomic stability and proper cell division during microtubule stress, providing insights into the post-transcriptional regulation of cell cycle and potential targets for cancer therapy.
Flat-field super-resolution structured illumination microscopy with joint spatial-temporal light modulation
Authors: Liang Yong , Wen Gang , Zhang Jie , Li Simin , Tan Yao , Jin Xin , Wang Linbo , Chen Xiaohu , Gao Jing , Li Hui 
Published: May 2024

AbstractSuper-resolution structured illumination microscope (SR-SIM) has been established as a powerful tool for visualizing subcellular dynamics and studying organelle interactions in live cells. However, the interfering Gaussian beams result in a limited and nonuniform field of view (FOV) which hinders its application for large whole-cell dynamics and pathological sample imaging. Here, we proposed a joint spatial-temporal light modulation (JSTLM) method to reshape the excitation light field into flat-field structured illumination without disturbing the interfering fringes. Our flat-field structured illumination microscopy (flat-field SIM) improves the uniformity across the whole FOV significantly, hence enabling SR image stitching. Skeleton dynamics and vesicle transportation in and between whole cells were visualized by flat-field SIM. With the stitching of multi-FOV flat-field SIM images, millimeter-sized SR images can be obtained which provides the possibility for cell heterogeneity studies and pathological diagnoses. The JSTLM method can be further incorporated with regions of interest to reduce unnecessary photodamage to live cells during multicolor imaging.ContributionsY.L. and X.H.C. conceived and designed the idea. Y.L., S.M.L., X.J., and G.W. built the SIM setup. Y.L. performed the data acquisitions. Y.L. and X.H.C. conducted the optical wave simulation. J.Z. prepared the cell samples. Y.T. and L.B.W. performed the image analyses. Y.L. prepared the illustrations. X.H.C. and J.G. supervised the project. Y.L. and H.L. wrote the manuscript.
Reproductive and ecological adaptations to climate underpin the evolution of sociality in lizards
Authors: Halliwell B , O’Connor E. A , Uller T , Meiri S , Holland B.R , Cornwallis C.K , While G. M 
Published: May 2024

AbstractIdentifying the environmental factors associated with group living is important for understanding how social systems originate, persist and diversify. In endothermic birds and mammals, living in social groups is associated with habitat constraints and harsh climatic conditions. We use phylogenetic comparative analyses to test whether climate and habitat have played similar roles in the evolution of social grouping in a globally distributed clade of ectothermic vertebrates, lizards (Nspecies= 1696). Social grouping was strongly associated with cool, dry climates across the lizard phylogeny. However, this climatic signature arose indirectly, by association with live birth (common in cool climates) and a reliance on rock crevices (common in dry climates), traits which increase parent-offspring associations and reduce offspring dispersal. In contrast, direct effects of cool temperature on the evolution of social grouping were marginal and restricted to live bearing species. Our results demonstrate that relationships between climate and sociality may result from climatic adaptations that go on to promote the emergence of grouping behaviour.
Experimental evolution of evolvability
Authors: Barnett Michael , Zeller Lena , Rainey Paul B. 
Published: May 2024

AbstractCapacity to generate adaptive variation can evolve by natural selection. However, the idea that mutation becomes biased toward specific adaptive outcomes is controversial. Here, using experimental bacterial populations, we report the evolution of enhanced evolvability via localised hyper-mutation. Key to realisation was a lineage-level birth-death dynamic, where lineage success depended upon capacity to mutate between two phenotypic states, each optima in a cycling environment. The evolved mechanism is analogous to “contingency loci” in pathogenic bacteria, whose origin was previously unclear. Subsequent evolution showed lineages with localised hyper-mutability were more likely to acquire additional adaptive mutations. Our results provide a detailed mechanistic account of the adaptive evolution of evolvability.
Monovalent Ion Effect on Liquid–Liquid Phase Separation of Aqueous Polyphosphate–Salt Mixtures
Authors: Furuki Tomohiro , Togo Azusa , Usuda Hatsuho , Nobeyama Tomohiro , Hirano Atsushi , Shiraki Kentaro 
Published: May 2024

ABSTRACTPolyphosphate (polyP) is one of the most conserved biomacromolecules and can form aggregates, such as polyP granules in bacteria, which are generated through liquid–liquid phase separation (LLPS). Studies have examined the mechanism of polyP aggregation using LLPS systems containing artificial polyP molecules as aggregation system models, where LLPS is typically induced by multivalent salts and polyelectrolytes. Although the typical concentrations of monovalent ions in living cells are approximately 100 times higher than those of divalent ions, the effects of monovalent ions on the LLPS of polyP solutions are little known. This study demonstrated that submolar NaCl induces LLPS of polyP solutions, whereas other monovalent salts did not at the same concentrations. Small-angle X-ray scattering measurements revealed that NaCl significantly stabilizes the intermolecular association of polyP, inducing LLPS. These findings suggest that the modulation of monovalent ion concentrations is an underlying mechanism of polyP aggregate formation/deformation within living cells.TOC GRAPHIC
Virome responses to heating of a forest soil suggest that most dsDNA viral particles do not persist at 90°C
Authors: Geonczy Sara E. , Hillary Luke S. , Santos-Medellín Christian , Fudyma Jane D. , Sorensen Jess W. , Emerson Joanne B. 
Published: May 2024

ABSTRACTMany fundamental characteristics of soil viruses remain underexplored, including the effects of high temperatures on viruses and their hosts, as would be encountered under disturbances like wildland fire, prescribed burning, and soil solarization. In this study, we leveraged three data types (DNase-treated viromes, non-DNase-treated viromes, and 16S rRNA gene amplicon sequencing) to measure the responses of soil viral and prokaryotic communities to heating to 30°C, 60°C, or 90°C, in comparison to field and control conditions. We investigated (1) the response of dsDNA viral communities to heating of soils from two horizons (O and A) from the same forest soil profile, (2) the extent to which specific viral taxa could be identified as heat-sensitive or heat-tolerant across replicates and soil horizons, and (3) prokaryotic and virus-host dynamics in response to heating. We found that both viral and prokaryotic communities responded similarly to the treatment variables. Community composition differed most significantly by soil source (O or A horizon). Within both soil horizons, viral and prokaryotic communities clustered into three groups, based on beta-diversity patterns: the ambient community (field, control, and 30°C samples) and the 60°C and 90°C communities. As DNase-treated viromic DNA yields were below detection limits at 90°C, we infer that most viral capsids were compromised after the 90°C treatment, indicating a maximum temperature threshold between 60°C and 90°C for most viral particles in these soils. We also identified groups of heat-tolerant and heat-sensitive vOTUs across both soil sources. Overall, we found that over 70% of viral populations, like their prokaryotic counterparts, could withstand temperatures as high as 60°C, with shifts in relative abundance explaining most community compositional differences across heating treatments.
An Open-Source Membrane Stretcher for Simultaneous Mechanical and Structural Characterizations of Soft Materials and Biological Tissues
Authors: Li Shannon , Gee Alyssa , Cai Nathan , Bermudez Alexandra , Lin Neil Y.C. 
Published: May 2024

AbstractThe ability to simultaneously measure material mechanics and structure is central for understanding their nonlinear relationship that underlies the mechanical properties of materials, such as hysteresis, strain-stiffening and -softening, and plasticity. This experimental capability is also critical in biomechanics and mechanobiology research, as it enables direct characterizations of the intricate interplay between cellular responses and tissue mechanics. Stretching devices developed over the past few decades, however, do not often allow simultaneous measurements of the structural and mechanical responses of the sample. In this work, we introduce an open-source stretching system that can apply uniaxial strain at a submicron resolution, report the tensile force response of the sample, and be mounted on an inverted microscope for real-time imaging. Our system consists of a pair of stepper-based linear motors that stretch the sample symmetrically, a force transducer that records the sample tensile force, and an optically clear sample holder that allows for high-magnification microscopy. Using polymer samples and cellular specimens, we characterized the motion control accuracy, force measurement robustness, and microscopy compatibility of our stretching system. We envision that this uniaxial stretching system will be a valuable tool for characterizing soft and living materials.
Multiple inositol phosphate species enhance stability of active mTOR
Authors: Rameh Lucia E. , York John D. , Blind Raymond D. 
Published: May 2024

SummaryMechanistic Target of Rapamycin (mTOR) binds the small metabolite inositol hexakisphosphate (IP6) as shown in structures of mTOR, however it remains unclear if IP6, or any other inositol phosphate species, can activate mTOR kinase activity. Here, we show that multiple, exogenously added inositol phosphate species (IP6, IP5, IP4and IP3) can all enhance the ability of mTOR and mTORC1 to auto-phosphorylate and incorporate radiolabeled phosphate into peptide substrates inin vitrokinase reactions. Although IP6did not affect the apparent KMof mTORC1 for ATP, monitoring kinase activity over longer reaction times showed increased product formation, suggesting inositol phosphates stabilize an active form of mTORC1in vitro. The effects of IP6on mTOR were reversible, suggesting IP6bound to mTOR can be exchanged dynamically with the free solvent. Interestingly, we also observed that IP6could alter mTOR solubility and electrophoretic mobility in SDS-PAGE in the presence of manganese, suggesting divalent cations may play a role in inositol phosphate regulation of mTOR. Together, these data suggest for the first time that multiple inositol phosphate species (IP4, IP5and IP6) can dynamically regulate mTOR and mTORC1 by promoting a stable, active state of the kinase. Our data suggest that studies of the dynamics of inositol phosphate regulation of mTOR are well justified.
Impact of exogenous aminoacyl-tRNA synthetase and tRNA on temperature sensitivity inEscherichia coli
Authors: Choi Jongdoo , Ahn Jiyeun , Bae Jieun , Yoon Moonsang , Yun Hwayoung , Koh Minseob 
Published: May 2024

AbstractGenetic code expansion (GCE) is a powerful strategy that expands the genetic code of an organism for incorporating non-canonical amino acids (ncAAs) into proteins using engineered tRNAs and aminoacyl-tRNA synthetases (aaRSs). While GCE has opened up new possibilities for synthetic biology, little is known about the potential side effects of exogenous aaRS/tRNA pairs. In this study, we investigated the impact of exogenous aaRS and amber suppressor tRNA on gene expression inEscherichia coli. We discovered that in DH10β ΔcyaA, transformed with the F1RP/F2P two-hybrid system, high consumption rate of cellular ATP by exogenous aaRS/tRNA at elevated temperatures induces temperature sensitivity in the expression of genes regulated by the catabolite activator protein. We harnessed this temperature sensitivity to create a novel biological AND gate inE. coli, responsive to bothp-benzoylphenylalanine (BzF) and low temperature, using a BzF-dependent variant ofE. colichorismate mutase and split subunits ofBordetella pertussisadenylate cyclase. Our study provides new insights into the unexpected effects of exogenous aaRS/tRNA pairs and offers a new approach for constructing a biological logic gate.