bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic stability in the GalápagosScalesiaadaptive radiation: Consistent transposable element accumulation despite hybridization and ecological niche shifts
Authors: Cerca José , Díaz Patricia Jaramillo , Goubert Clément , Yang Heidi , Bieker Vanessa C. , Fernández-Mazuecos Mario , Vargas Pablo , Schley Rowan , Li Siyu , Guevara-Andino Juan Ernesto , Petersen Bent , Petersen Gitte , Sinha Neelima R. , Nielsen Lene R. , Leebens-Mack James H. , Rivas-Torres Gonzalo , Rieseberg Loren H. , Martin Michael D. 
Published: October 2024

AbstractTransposable elements (TEs) have been hypothesized to play a pivotal role in driving diversification by facilitating the emergence of novel phenotypes and the accumulation of divergence between species. Hybridization and adaptation to novel niches are hypothesized to influence TE accumulation in genomes by disrupting genomic regulation, including the suppression of TE replication. The rapid speciation and ecological diversification characteristic of adaptive radiations offer a unique opportunity to examine the link between TE accumulation and speciation, diversification, hybridization and adaptation. Here, focusing on all 15 species of the genusScalesia(Asteraceae), a radiation endemic to the Galápagos Islands, we test whether hybridization or shifts in ecological niche are associated with changes in TE accumulation in genomes. Our analyses reveal little to no variation in TE accumulation amongScalesiaspecies nor its hybrid populations. Shifts in ecological niches, linked to climatic variation, did not result in discernible changes in TE accumulation, a surprising finding given the anticipated selective pressure imposed by aridity, a factor often linked to genome size reduction. We found no distinct patterns in the temporal accumulation of TEs, and no effects at the class or superfamily level. Our findings challenge the assertion that TEs have directly driven diversification, speciation and local adaptation. Instead, we suggest that TEs may simply be ‘along for the ride,’ rather than actively contributing to plant diversification.
Directed Evolution of a Plant Immune Receptor for Broad Spectrum Effector Recognition
Authors: Rim Ellen Y. , Garrett Oscar D. , Howard Alexander J. , Shim Yejin , Li Yuanyuan , Van Dyke Jonathan E. , Packer Ryan C. , Ho Nguyen , Jain Rashmi , Stewart Valley , Dinesh-Kumar Savithramma P. , Notwell James H. , Ronald Pamela C. 
Published: October 2024

AbstractRapid development of immune receptors that protect crops from emerging pathogens is a critical challenge1,2. While novel immune receptors that recognize previously undetected pathogen effectors could provide protection against a wider range of pathogens, engineering such receptors has been constrained by the low throughput and speed ofin plantatesting. We established yeast surface display as a high throughput platform to recapitulate plant immune receptor-ligand interactions and evolve new binding capabilities. Using this directed evolution platform, we engineered the ligand binding domain of the rice immune receptor Pik-1 to recognize diverse effectors from the fast-evolving fungal pathogenMagnaporthe oryzae.Our approach yielded Pik-1 ligand binding domains with affinity for variants of theM. oryzaeeffector Avr-Pik that previously escaped detection by known rice alleles of Pik-1, within plantaassays confirming functional recognition of these effectors. Additional rounds of mutagenesis and selection led to a Pik-1 domain that binds all tested Avr-Pik variants as well as the evolutionarily divergent effector AvrPiz-t. These results demonstrate the potential of directed evolution to engineer immune receptors with new-to-nature recognition of a wide range of pathogen-derived ligands and accelerate development of broad spectrum resistance in crops.
An aneuploidy epistasis map reveals metabolic vulnerabilities associated with supernumerary chromosomes in cancer
Authors: Magesh R. Y. , Kaur A. N. , Keller F. N. , Frederick A. , Tseyang T. , Haley J. A. , Rivera-Nieves A. M. , Liang A. C. , Guertin D. A. , Spinelli J. B. , Elledge S. J. , Watson E. V. 
Published: October 2024

AbstractDespite the general detriment of aneuploidy to cellular fitness, >90% of solid tumors carry an imbalanced karyotype. Regardless of this existing paradox, our understanding of the molecular responses to aneuploidy remains limited. Here, we explore these cellular stresses and unique vulnerabilities in aneuploid human mammary epithelial cells (HMECs) enriched for breast cancer-associated copy number alterations (CNAs). To uncover the genetic dependencies specific to aneuploid cells, we conducted a comprehensive, genome-wide CRISPR knockout screen targeting isogenic diploid and aneuploid HMEC lines. Our study reveals that aneuploid HMECs exhibit an increased reliance on pyrimidine biosynthesis and mitochondrial oxidative phosphorylation genes, and demonstrate heightened fitness advantages upon loss of tumor suppressor genes. Using an integrative multi-omic analysis, we confirm nucleotide pool insufficiency as a key contributor to widespread cellular dysfunction in aneuploid HMECs with net copy number gain. While diploid cells can switch seamlessly between pyrimidine synthesis and salvage, cells with increased chromosomal content exhibit p53 activation and S-phase arrest when relying on salvage alone, and exhibit increased sensitivity to DNA-damaging chemotherapeutics. This work advances our understanding of the consequences of aneuploidy and uncovers potential avenues for patient stratification and therapeutic intervention based on tumor ploidy.
AnALPK3truncation variant causing autosomal dominant hypertrophic cardiomyopathy is partially rescued by mavacamten
Authors: Leinhos Lisa , Robinson Paul , Poloni Giulia , Broadway-Stringer Sophie , Beglov Julia , Lokman Adam B. , Douglas Gillian , Nuthay Sajjad , Fonseka Oveena , Schmid Manuel , Singer Evie , Hooper Charlotte , Thomson Kate , Bagnall Richard D. , Ingles Jodie , Semsarian Christopher , Ormondroyd Elizabeth , Toepfer Christopher N. , Davies Benjamin , Redwood Charles , Watkins Hugh , Gehmlich Katja 
Published: October 2024

AbstractTheALPK3gene encodes alpha-protein kinase 3, a cardiac pseudo-kinase of unknown function. Heterozygous truncating variants (ALPK3tv)can cause dominant adult-onset Hypertrophic Cardiomyopathy (HCM). Here we confirm an excess ofALPK3tvin sarcomere-gene negative HCM patients.Moreover, we generated a novel knock-in mouse model carrying anALPK3tv(K201X). Homozygous animals displayed hypertrophy and systolic dysfunction. Heterozygous animals demonstrated no obvious baseline; however, they had an aggravated hypertrophic response upon chronic adrenergic challenge.Isolated cardiomyocytes from heterozygous and homozygous mice showed reduced basal sarcomere length with prolonged relaxation, whilst calcium transients showed increased diastolic calcium levels and prolonged re-uptake. We also observed reduced fractional shortening. Protein kinase A-mediated phosphorylation, including that of cardiac troponin I, was significantly decreased. In agreement with the cellular HCM phenotype, reduced ratios of myosin heads in the super-relaxed state were measured. Contractile and calcium handling defects were partly corrected by treatment with mavacamten, a novel myosin inhibitor.For the first time with a non-sarcomere HCM variant, we have demonstrated hallmark changes in cardiac contractility and calcium handling, some resembling sarcomere-positive HCM, while others are distinct and DCM-like. Mavacamten is able to partially rescue the cellular phenotype, hence could be beneficial to HCM patients withALPK3tv.
Diterpenoid phytoalexins shape rice root microbiomes and their associations with root parasitic nematodes
Authors: Kudjordjie Enoch Narh , Desmedt Willem , Kyndt Tina , Nicolaisen Mogens , Peters Reuben J. , Vestergård Mette 
Published: October 2024

AbstractRice synthesizes diterpenoid phytoalexins (DPs) are known to operate in defense against foliar microbial pathogens and root-knot nematodeMeloidogyne graminicola. Here, we examined the role of DPs in shaping rice⍰associated root microbiomes in nematode-infested rice paddy soils. Further, we assessed how DPs affect interactions between the root microbiomes and nematode communities, particularly rice root-knot nematodes from theMeloidogynegenus. We used 16S and ITS2 rRNA gene amplicon analysis to characterize the rice root-and rhizosphere-associated microbiomes of DP knock-out mutants and their wild-type parental line, at an early (17 days) and late (28 days) stage of plant development in field soil. Disruption of DP synthesis resulted in distinct composition and structure of microbial communities both relative to the parental/wild-type line but also between individual mutants, indicating specificity in DP-microbe interactions. Moreover, nematode-suppressive microbial taxa, includingStreptomyces,Stenotrophomonas,Enterobacter,Massilia, andAcidibacter, negatively correlated withMeloidogyne. Comparative analysis revealed differential enrichment of microbial taxa in the roots of rice diterpenoid phytoalexin (DP) knock-out mutants versus wild-type, suggesting that DPs modulate specific taxa in the rice root microbiome. These findings indicate DPs role in plant-microbiome assembly and nematode interactions, further underscoring the potential of leveraging phytoalexins for sustainable management of crop diseases.
Clostridioides difficilein Equidae necropsied in Normandie, France, in 2019-2021: common carriage of toxigenic strains and virulence of emerging ribotype 017
Authors: Petry Sandrine , Tapprest Jackie , Maillard Karine , Barbut Frédéric , Duquesne Fabien , Kozak Sofia , Foucher Nathalie , Bernez-Romand Maud , Bridoux Ludovic , Poquet Isabelle 
Published: October 2024

AbstractBackgroundClostridioides difficileis an anaerobic, spore-forming entero-pathogen, causing diarrhea in humans and animals. We aimed to evaluateC. difficileoccurrence, diversity, virulence and putative circulation among French Equidae.MethodsWe took advantage of necropsies of Equidae in Normandie, France, from 2019 to 2021 (n=100), to systematically recover the caecal content and, if watery and possibly diarrheal, any intestinal content. We searched forC. difficileand characterized isolates for their toxin gene profile and PCR-ribotype according to the WEBRIBO database. We performed free toxin detection to reach a high-standard diagnosis of infection.ResultsTwenty-seven Equidae were positive forC. difficileand twenty had a toxigenic strain, including one animal also colonized by a non-toxigenic strain. Toxigenic isolates belonged to eight ribotypes: 078, 126 (three-toxin profile), 005, 012, 020, 181, AI-53 (two-toxin profile), 017 (one-toxin profile), and non-toxigenic isolates to ribotypes 009, 035 and 439. 017 and 009 were the predominant ribotypes (n=5). In two premises, few Equidae shared the same ribotype, either 020 or 009, suggesting two potential transmission clusters. Free toxin detection demonstratedC. difficileinfection in four animals displayingpost-mortemsigns of diarrhea and toxigenic isolates of ribotype 126 (n=1) or 017 (n=3), which were the least susceptible to vancomycin. The infection by ribotype 017 caused animal death in two cases.ConclusionsFrench Equidae represented an underestimated reservoir ofC. difficileand ribotype 017 was highly virulent in these animals, both preoccupying findings in a One Health perspective.
A Metagenomic Study of Antibiotic Resistance Across Diverse Soil Types and Geographical Locations
Authors: Pillay Stephanie , Tepeli Yasin , van Lent Paul , Abeel Thomas 
Published: October 2024

AbstractBackgroundSoil naturally harbours antibiotic resistant bacteria and is considered to be a reservoir for antibiotic resistance. The overuse of antibiotics across human, animal, and environmental sectors has intensified this issue leading to an increased acquisition of antibiotic resistant genes by bacteria in soil. Various biogeographical factors, such as soil pH, temperature, and pollutants, play a role in the spread and emergence of antibiotic resistance in soil. In this study, we utilised publicly available metagenomic datasets from four different soil types (rhizosphere, urban, natural, and rural areas) sampled from nine distinct geographic locations to explore the patterns of antibiotic resistance in soils from different regions.ResultsBradyrhizobiumwas predominant in vegetation soil types regardless of soil pH and temperature. ESKAPE pathogenPseudomonas aeruginosawas prevalent in rural soil samples. Antibiotic resistance gene families such as 16s rRNA with mutations conferring resistance to aminoglycoside antibiotics, OXA β-lactamase, ANT(3’’), and the RND and MFS efflux pump gene were identified in all soil types, with their abundances influenced by anthropogenic activities, vegetation, and climate in different geographical locations. Plasmids were more abundant in rural soils and were linked to aminoglycoside resistance. Integrons and integrative elements identified were associated with commonly used and naturally occurring antibiotics, showing similar abundances across different soil types and geographical locations.ConclusionAntimicrobial resistance in soil may be driven by anthropogenic activities and biogeographical factors, increasing the risk of bacteria developing resistance and leading to higher morbidity and mortality rates in humans and animals.
Ribozyme-based biosensor for imaging gene expression in plants
Authors: Liu Yang , Rajput Ruchika , Islam Torikul , Del Valle Ilenne , Yao Tao , Agarwal Rekha , Boone Brandon A. , Eckert Carrie , Abraham Paul E. , Chen Jin-Gui , Tuskan Gerald A. , Yang Xiaohan 
Published: October 2024

AbstractDetection of gene expression in plants is critical for understanding the molecular basis of complex plant biosystems and plant responses to environmental stresses. Here, we report the development of a split ribozyme-based biosensor that enablesin vivovisualization of gene expression in plants. We demonstrated the utility of this biosensor in transient expression experiments (i.e., leaf infiltration inNicotiana benthamiana) to detect RNAs derived from transgenes and tobacco rattle virus, respectively. Furthermore, we successfully engineered a split ribozyme-based biosensor inArabidopsis thalianaforin vivovisualization of endogenous gene expression at the cellular level. In addition, we developed a platform for easy incorporation of different reporters into the RNA biosensor.
Identification and determination of the urinary metabolite of iodotyrosinein vivo
Authors: Ji Cindy Xinyu , Zonias Danae , Djumaeva Nafisa , Cheng Ranchu , Salim Kawther , Alikhani Pouya , Oyelade Tope , Moore Kevin P. , Moreno José C. , Mani Ali R. 
Published: October 2024

AbstractBackgroundCongenital hypothyroidism screening traditionally relies on detecting elevated thyroid-stimulating hormone levels, yet this approach may not detect a specific type of congenital hypothyroidism caused by iodotyrosine dehalogenase-1 (Dehal1) deficiency. The deficiency of this enzyme prevents the deiodination of mono-iodotyrosine (MIT) and di-iodotyrosine (DIT) in the process of iodine recycling. This underscores the potential use of iodotyrosine or its metabolites as non-invasive urinary biomarkers for early diagnosis of congenital hypothyroidism. However, the urinary metabolites of MIT/DIT have not yet been discovered. Thus, this study aimed to identify the urinary metabolites of iodotyrosine in experimental models.MethodGas chromatography mass spectrometry was used to identify the urinary metabolites of iodotyrosine following intraperitoneal injection of MIT in rats. An isotope dilution mass spectrometric assay was developed for assessment of identified metabolites. Urine samples fromDehal1knockout mice were used to confirm the results.ResultsWe identified novel iodotyrosine metabolites, 3-iodo-4-hydroxyphenylacetic acid (IHPA), and 3,5-diiodo-4-hydroxyphenylacetic acid (Di-IHPA) as the primary urinary metabolites of MIT and DIT respectively. The concentrations of urinary IHPA and Di-IHPA were significantly higher inDehal1knockout mice.ConclusionOur findings suggest that IHPA is detected in larger quantities and may hold more clinical significance than previously identified biomarkers like MIT and DIT, making it a promising candidate for diagnosing congenital hypothyroidism or other conditions associated with iodine recycling inhibition.
Two transmembrane transcriptional regulators coordinate to activate chitin-induced natural transformation inVibrio cholerae
Authors: Hullinger Allison C. , Green Virginia E. , Klancher Catherine A. , Dalia Triana N. , Dalia Ankur B. 
Published: October 2024

ABSTRACTTranscriptional regulators are a broad class of proteins that alter gene expression in response to environmental stimuli. Transmembrane transcriptional regulators (TTRs) are a subset of transcriptional regulators in bacteria that can directly regulate gene expression while remaining anchored in the membrane. Whether this constraint impacts the ability of TTRs to bind their DNA targets remains unclear.Vibrio choleraeuses two TTRs, ChiS and TfoS, to activate horizontal gene transfer by natural transformation in response to chitin by inducing thetfoRpromoter (PtfoR). While TfoS was previously shown to bind and regulate PtfoRdirectly, the role of ChiS in PtfoRactivation remains unclear. Here, we show that ChiS directly binds PtfoRupstream of TfoS, and that ChiS directly interacts with TfoS. By independently disrupting ChiS-PtfoRand ChiS-TfoS interactions, we show that ChiS-PtfoRinteractions play the dominant role in PtfoRactivation. Correspondingly, we show that in the absence of ChiS, recruitment of the PtfoRlocus to the membrane is sufficient for PtfoRactivation when TfoS is expressed at native levels. Finally, we show that the overexpression of TfoS can bypass the need for ChiS for PtfoRactivation. All together, these data suggest a model whereby ChiS both (1) recruits the PtfoRDNA locus to the membrane for TfoS and (2) directly interacts with TfoS, thereby recruiting it to the membrane-proximal promoter. This work furthers our understanding of the molecular mechanisms that drive chitin-induced responses inV. choleraeand more broadly highlights how the membrane-embedded localization of TTRs can impact their activity.AUTHOR SUMMARYLiving organisms inhabit diverse environments where they encounter a wide range of stressors. To survive, they must rapidly sense and respond to their surroundings. One universally conserved mechanism to respond to stimuli is via the action of DNA-binding transcriptional regulators. In bacterial species, these regulators are canonically cytoplasmic proteins that freely diffuse within the cytoplasm. In contrast, an emerging class of transmembrane transcriptional regulators (TTRs) directly regulate gene expression from the cell membrane. Prior work shows that two TTRs, TfoS and ChiS, cooperate to activate horizontal gene transfer by natural transformation in response to chitin in the facultative pathogenVibrio cholerae. However, how these TTRs coordinate to activate this response has remained unclear. Here, we show that ChiS likely promotes TfoS-dependent activation of natural transformation by (1) relocalizing its target promoter to the membrane and (2) recruiting TfoS to the membrane proximal promoter through a direct interaction. Together, these results inform our understanding of both theV. choleraechitin response and how TTR function can be impacted by their membrane localization.
Sunfuel Electric: charting a differentiated go-to-market-strategy in the EV charging space
Authors: Pereira Mundkur Jacqueline , Desai Riva 
Published: October 2024

Learning outcomes
After completion of the case study, students will be able to understand the service offerings within the nascent electric vehicle (EV) sector and end-consumer needs of EV charging services, understand the reasoning behind Sunfuel Electrics (SFEs) prioritisation of destination charging for their first go-to-market (GTM) strategy and appreciate SFE’s use of community marketing and alliance partners to execute its various strategies. Connect game-theory with the proposed strategies.

Case overview/synopsis
SFE was an early start-up in EV charging space. The co-founders believed that any success would hinge on their ability to play a differentiated game and carve a distinct yet profitable niche in the EV charging arena. SFE deliberately focussed on “destination charging” and identified a segment that they were confident of making a difference: the discerning high-end consumer. Soon, SFE’s success caught the eye of its deep-pocketed competitors who also entered the same space. As a single service company, the co-founders set in motion a back-up plan and identified three new strategic thrust areas to maintain SFE’s competitive edge. The first involved entering the city charging segment, and the second was a pioneering concept branded “E-Trails” targeted at a community of EV owners who were motor enthusiasts. Thirdly, SFE conceptualised an EV-Roadhouse concept, promising a full-bouquet of select premium services at a pit-stops along the highway. The co-founders needed to test which and to what extent would these initiatives would translate into real gains and if returns were commensurate with investments and SFE’s ability to deliver a scalable consistent experience. Specifically, if these proposed asset-light avenues added the required heft to their GTM strategy.

Complexity academic level
This case study is suitable for post-graduate students in marketing, strategy, entrepreneurship and sustainability courses.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS 8: Marketing.
Three–dimensional matrices for enhanced coral settlement through design for additive manufacturing
Authors: Vieira Miguel Ângelo , M.O. Tavares Sérgio , Félix Silvina L. 
Published: October 2024

Purpose
The effects of climate change have been contributing to coral reef degradation. Artificial reefs are one method being used to counteract this destruction. However, the most common artificial approaches, such as sunken vehicles and prefabricated cement reefs, do not allow adequate coral development. This paper aims to demonstrate how designers, using additive manufacturing and computational design techniques, can create artificial reefs that better mimic natural reef structures.

Design/methodology/approach
This research focuses on developing three-dimensional matrices through computational design using additive manufacturing to achieve better coral settlement. A “Nature Centered Design” approach was followed, with the corals at the center of the design project. Samples with different geometries and roughness, produced using paste-based extrusion with porcelain and porcelain with oyster shell, were tested in a controlled environment to investigate the settlement preference of soft corals.

Findings
The rapid prototyping of samples confirmed the preference of corals to settle to complex surfaces compared to smooth surfaces. Porcelain showed comparable results to Portland cement, suggesting further testing potential. A closer resemblance to the natural and intricate forms found in coral reefs was achieved through computational design.

Originality/value
This paper proposes a new approach combining rapid prototyping with coral’s biological responses to enhance the understanding of their surface settlement preference. The Nature Centered Design approach, with additive manufacturing and computational design, made it possible to create an innovative working model that could be customized depending on the implementation area or intended coral species, validating the design approach as a method to support environmental conservation.