bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Library of Electrophysiological Responses in Plants - A Model of Transversal Education and Open Science
Authors: Madariaga Danae , Arro Derek , Irarrázaval Catalina , Soto Alejandro , Guerra Felipe , Romero Angélica , Ovalle Fabián , Fedrigolli Elsa , DesRosiers Tom , Serbe-Kamp Étienne , Marzullo Timothy 
Published: October 2023

AbstractElectrophysiology in plants is understudied, and, moreover, an ideal model for student inclusion at all levels of education. Here we report on an investigation in “open science”, whereby scientists worked with students and faculty from Chile, Germany, Serbia, South Korea, and the USA. The students recorded the electrophysiological signals of >15 plants in response to a flame or tactile stimulus applied to the leaves. We observed that approximately 60% of the plants studied showed an electrophysiological response with a delay of ∼3-6 seconds after stimulus presentation. In preliminary conduction velocity experiments, we verified that observed signals are indeed biological in origin, with information transmission speeds of ∼2-9 mm/s. Such easily replicable experiments can serve to include more investigators and students in contributing to our understanding of plant electrophysiology.
TRANSPOSABLE ELEMENTS ALTER GENE EXPRESSION AND MAY IMPACT RESPONSE TO CISPLATIN THERAPY IN OVARIAN CANCER
Authors: Mombach Daniela Moreira , Vieira Mercuri Rafael Luiz , da Fontoura Gomes Tiago Minuzzi Freire , Galante Pedro A. F. , Silva Loreto Elgion Lucio 
Published: October 2023

ABSTRACTCisplatin is widely employed for cancer treatment; therefore, understanding resistance to this drug is critical for therapeutic practice. While studies have delved into differential gene expression in the context of cisplatin resistance, findings remain somewhat scant. In this study, we employed RNA-seq, ATAC-seq, and in-depth bioinformatics analyses to perform a detailed investigation of the cellular transcriptome, centering on Transposable Elements (TEs) expression in ovarian cancer cell lines both sensitive and resistant to cisplatin treatment. Our results reveal that cisplatin therapy alters the expression of protein-coding genes, but also key TEs, including LINE1,Alu, and endogenous retroviruses, in both cisplatin-sensitive and -resistant cell lines. By co-expressing with downstream genes or by creating chimeric transcripts with host genes at their insertion sites, these TEs seem to control the expression of protein-coding genes, including tumor-related genes. Notably, our model uncovers TEs influencing the expression of cancer genes and cancer pathways. Collectively, our findings indicate that TEs alterations associated with cisplatin treatment occur in critical cancer genes and cellular pathways synergically. In conclusion, this research highlights the importance of considering the entire spectrum of transcribed elements in the genome, especially TE expression, for a complete understanding of complex models like cancer response to treatment.
C4-likeSesuvium sesuvioides(Aizoaceae) exhibits CAM in cotyledons and putative C4+CAM metabolism in adult leaves as revealed by transcriptome analysis
Authors: Siadjeu Christian , Kadereit Gudrun 
Published: October 2023

AbstractThe co-occurrence of C4and CAM photosynthesis in a single species seems to be unusual and rare, probably because of the difficulty to co-regulate both pathways effectively. Nevertheless, it represents a unique chance in gaining new insights into the evolution and regulation of these complex pathways. Comparative transcriptomics using RNA-seq revealed C4-like and CAM photosynthesis inSesuvium sesuvioides(Aizoaceae) leaves and cotyledons, respectively. When compared to cotyledons, phosphoenolpyruvate carboxylase 4 (PEPC4) and some key C4genes were found to be up regulated in leaves. During the day, the expression of NADP-dependent malic enzyme (NADP-ME) was significantly higher in cotyledons than in leaves. The acidity titration confirmed higher acidity in the morning than in the previous evening indicating the induction of weak CAM in cotyledons by environmental conditions. Comparison of the leaves ofS. sesuvioides(C4-like) andS. portulacastrum(C3) revealed that PEPC1 was significantly higher inS. sesuvioides, while PEPC3 and PEPC4 were up-regulated inS. portulacastrum. Finally, potential key regulatory elements involved in the C4and CAM pathways were identified. These findings provide a new species in which C4and CAM co-occur and raises the question if this phenomenon is indeed so rare or just hard to detect and probably more common in succulent C4lineages.HighlightC4and CAM metabolism co-occur in the C4-like speciesSesuvium sesuvioides(Aizoaceae).
Rhythmic lipid and gene expression responses to chilling in panicoid grasses
Authors: Raju Sunil K. Kenchanmane , Zhang Yang , Mahboub Samira , Ngu Daniel W. , Qiu Yumou , Harmon Frank G. , Schnable James C. , Roston Rebecca L. 
Published: October 2023

ABSTRACTChilling stress threatens plant growth and development, particularly affecting membrane fluidity and cellular integrity. Understanding plant membrane responses to chilling stress is important for unraveling the molecular mechanisms of stress tolerance. Whereas core transcriptional responses to chilling stress and stress tolerance are conserved across species, the associated changes in membrane lipids appear to be less conserved, as which lipids are affected by chilling stress varies by species. Here, we investigated changes in gene expression and membrane lipids in response to chilling stress during one diurnal cycle in sorghum (Sorghum bicolor), Urochloa (browntop signal grass,Urochloa fusca) (lipids only), and foxtail millet (Setaria italica), leveraging their evolutionary relatedness and differing levels of chilling-stress tolerance. We show that most chilling-induced lipid changes are conserved across the three species, while we observed distinct, time-specific responses in chilling-tolerant foxtail millet, indicating the presence of a finely orchestrated adaptive mechanism. We detected diurnal rhythmicity in lipid responses to chilling stress in the three grasses, which were also present in Arabidopsis (Arabidopsis thaliana), suggesting the conservation of rhythmic patterns across species and highlighting the importance of accounting for diurnal effects. When integrating lipid datasets with gene expression profiles, we identified potential candidate genes that showed corresponding transcriptional changes in response to chilling stress, providing insights into the differences in regulatory mechanisms between chilling-sensitive sorghum and chilling-tolerant foxtail millet.Significance StatementPlants respond to low-temperature stress in myriad ways. While core transcriptional changes are conserved across species, specific adaptive strategies do exist. However, membrane lipid responses during chilling do not appear to be conserved. Here, we collected samples from control and chilling stress–treated seedlings [PSC4] to assess gene expression and membrane lipids in three panicoid grasses to show that lipid metabolic changes follow a daily rhythm. Lipid changes in chilling-tolerant foxtail millet occurred at specific time points, partly explaining the difficulty in finding conserved chilling-induced lipid changes in previous reports. We identified specific orthologs in sorghum and foxtail millet that showed a correlation between gene expression and lipid metabolic changes; these orthologs may be used as potential target genes for developing chilling-tolerant sorghum varieties.
Mutation Mechanism In DNA: Non-Hermitian Approach
Authors: Sarısaman Mustafa , Tibatan Mehmet Ali , Uzunal Seval 
Published: October 2023

AbstractWe propose a novel mutation mechanism for points and ordinary or palindromic sequences of DNA and RNA. We adopted non-Hermitian approaches based on quantum mechanics. Hermiticity is in the limelight of any physical structure with quantum character, like DNA, or RNA, as it creates quantum stability in that it yields real eigenvalues and orthonormal states. We show that, through the mutation mechanism we constructed based on non-Hermitian physics, the deterioration of the Hermitian character of the original DNA states, nucleotides, does not create a stability problem. We show that Weyl’s perturbation theory helps us determine the stability of mutated DNA or RNA. We prove that mutations made in the laboratory with conventional nucleotides using non-Hermitian physics methods are not different from mutations that occur spontaneously in nature. This result may help to reveal the quantum nature of genetic diseases in the near future and may shape the molecular approaches.
Mitigation of TDP-43-induced toxic phenotype by expression of RGNEF N-terminal fragment in ALS models
Authors: Droppelmann Cristian A. , Campos-Melo Danae , Noches Veronica , McLellan Crystal , Szabla Robert , Lyons Taylor A. , Amzil Hind , Withers Benjamin , Sonkar Kirti S. , Simon Anne , Buratti Emanuele , Junop Murray , Kramer Jamie M. , Strong Michael J. 
Published: October 2023

AbstractAggregation of the RNA-binding protein (RBP) TDP-43 is a hallmark of TDP-proteinopathies including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Since TDP-43 aggregation and dysregulation are causative of neuronal death, there is a special interest in targeting this protein as a therapeutic approach. Previously, we found that TDP-43 extensively co-aggregated with the dual function protein (GEF (guanine exchange factor) and RBP) rho guanine nucleotide exchange factor (RGNEF) in ALS patients. Here, we show that a N-terminal fragment of RGNEF (NF242) interacts directly with the RNA recognition motifs (RRM) of TDP-43 competing with RNA, and that the IPT/TIG domain of NF242 is essential for this interaction. Genetical expression of NF242 in a fruit fly ALS model overexpressing TDP-43 suppressed the neuropathological phenotype increasing lifespan, abolishing motor defects, and preventing neurodegeneration. Intracerebroventricular injections of AAV9/NF242 in a severe TDP-43 murine model (rNLS8) improved lifespan and motor phenotype, and decreased neuroinflammation markers. Our results demonstrate an innovative way to target TDP-43 proteinopathies using a protein fragment with affinity for TDP-43, suggesting a promising therapeutic strategy for TDP-43 proteinopathies such as ALS and FTD.
CellPie: a scalable spatial transcriptomics factor discovery method via joint non-negative matrix factorization
Authors: Georgaka Sokratia , Morgans William Geraint , Zhao Qian , Martinez Diego Sanchez , Ali Amin , Ghafoor Mohamed , Baker Syed-Murtuza , Bristow Robert , Iqbal Mudassar , Rattray Magnus 
Published: October 2023

Spatially resolved transcriptomics has enabled the study of expression of genes within tissues while retaining their spatial identity. Most spatial transcriptomics technologies generate a matched histopathological image as part of the standard pipeline, providing morphological information that can complement the transcriptomics data. Here we presentCellPie, a fast, unsupervised factor discovery method, based on joint non-negative matrix factorisation of spatial RNA transcripts and histological image features.CellPieemploys the accelerated hierarchical least squares method to significantly reduce the computational time, enabling efficient application to high-dimensional spatial transcriptomics datasets. We assessedCellPieon two different human cancer types and spatial resolutions, showing an improved performance against published factorisation methods. Additionally, we appliedCellPieto a highly resolved Visium HD dataset, demonstrating its high computational efficiency compared to standard non-negative matrix factorisation and other existing methods.Availabilityhttps://github.com/ManchesterBioinference/CellPie
C5aR1 signaling promotes region and age dependent synaptic pruning in models of Alzheimer’s Disease
Authors: Gomez-Arboledas Angela , Fonseca Maria I. , Kramar Enikö , Chu Shu-Hui , Schartz Nicole , Selvan Purnika , Wood Marcelo A. , Tenner Andrea J. 
Published: October 2023

AbstractINTRODUCTIONSynaptic loss is a hallmark of Alzheimer’s disease (AD) that correlates with cognitive decline in AD patients. Complement-mediated synaptic pruning has been associated with this excessive loss of synapses in AD. Here, we investigated the effect of C5aR1 inhibition on microglial and astroglial synaptic pruning in two mouse models of AD.METHODSA combination of super-resolution and confocal and tridimensional image reconstruction was used to assess the effect of genetic ablation or pharmacological inhibition of C5aR1 on the Arctic48 and Tg2576 models of AD.RESULTSGenetic ablation or pharmacological inhibition of C5aR1 rescues the excessive pre-synaptic pruning and synaptic loss in an age and region dependent fashion in two mouse models of AD, which correlates with improved long-term potentiation (LTP).DISCUSSIONReduction of excessive synaptic pruning is an additional beneficial outcome of the suppression of C5a-C5aR1 signaling, further supporting its potential as an effective targeted therapy to treat AD.
Sex-Specific DNA Methylation and Gene Expression Changes in Mouse Placentas After Early Preimplantation Alcohol Exposure
Authors: Legault Lisa-Marie , Dupas Thomas , Breton-Larrivée Mélanie , Filion-Bienvenue Fannie , Lemieux Anthony , Langford-Avelar Alexandra , McGraw Serge 
Published: October 2023

ABSTRACTDuring pregnancy, exposure to alcohol represents an environmental insult capable of negatively impacting embryonic development. This influence can stem from disruption of molecular profiles, ultimately leading to manifestation of fetal alcohol spectrum disorder. Despite the central role of the placenta in proper embryonic development and successful pregnancy, studies on the placenta in a prenatal alcohol exposure and fetal alcohol spectrum disorder context are markedly lacking. Here, we employed a well-established model for preimplantation alcohol exposure, specifically targeting embryonic day 2.5, corresponding to the 8-cell stage. The exposure was administered to pregnant C57BL/6 female mice through subcutaneous injection, involving two doses of either 2.5 g/kg 50% ethanol or an equivalent volume of saline at 2-hour intervals. Morphology, DNA methylation and gene expression patterns were assessed in male and female late-gestation (E18.5) placentas. While overall placental morphology was not altered, we found a significant decrease in male ethanol-exposed embryo weights. When looking at molecular profiles, we uncovered numerous differentially methylated regions (DMRs; 991 in males; 1309 in females) and differentially expressed genes (DEGs; 1046 in males; 340 in females) in the placentas. Remarkably, only 21 DMRs and 54 DEGs were common to both sexes, which were enriched for genes involved in growth factor response pathways. Preimplantation alcohol exposure had a greater impact on imprinted genes expression in male placentas (imprinted DEGs: 18 in males; 1 in females). Finally, by using machine learning model (L1 regularization), we were able to precisely discriminate control and ethanol-exposed placentas based on their specific DNA methylation patterns. This is the first study demonstrating that preimplantation alcohol exposure alters the DNA methylation and transcriptomic profiles of late-gestation placentas in a sex-specific manner. Our findings highlight that the DNA methylation profiles of the placenta could serve as a potent predictive molecular signature for early preimplantation alcohol exposure.GRAPHICAL ABSTRACT
Relative importance of bacterivorous mixotrophs in an estuary-coast environment
Authors: Li Qian , Dong Kaiyi , Wang Ying , Edwards Kyle F. 
Published: October 2023

AbstractMixotrophic eukaryotes are important bacterivores in oligotrophic open oceans, but their significance as grazers in more nutrient-rich waters is less clear. Here we investigated the bacterivory partition between mixotrophs and heterotrophs in a productive, estuary-influenced coastal region in East China Sea. We found ubiquitous, actively feeding phytoplankton populations and taxa with mixotrophic potential, by identifying ingestion of fluorescent prey surrogate and analyzing community 18S rRNA gene amplicons. Potential and active mixotrophs accounted for 10-63% of total eukaryotic community and 17-69% of bacterivores observed, respectively, contributing 6-48% of estimated in situ bacterivory. The much higher mixotroph fitness outside of the turbid plume were potentially driven by increased light and decreased nutrients availability. Our results suggest that, although heterotrophs dominated overall in situ bacterivory, mixotrophs were abundant and important bacterivores in this low-latitude mesotrophic coastal region.Scientific Significance StatementMixotrophy, the combing of photosynthetic and phagotrophic nutrition, can dramatically increase primary production and alter material movements in aquatic food webs. Understanding the distribution and fitness of phagotrophic mixotrophs in a range of habitats are therefore critical to properly understand the biogeochemical cycles of the ocean. We developed a robust method to estimate active mixotrophs in situ and demonstrate rapid shifts of bacterivory partition between mixotrophs and heterotrophs across an estuary-coast environment in East China Sea. Our results help fill the knowledge gap of mixotroph niches in mesotrophic coastal environments that are impacted by riverine discharge, shedding light on relationships among mixotrophy, light and nutrient conditions.
HIV Infection impairs the Host Response toMycobacterium tuberculosisInfection by altering Surfactant Protein D function in the Human Lung Alveolar Mucosa
Authors: Akhter Anwari , Moliva Juan I. , Azad Abul K. , Olmo-Fontánez Angélica , Garcia-Vilanova Andreu , Scordo Julia M. , Gavrilin Mikhail A. , Diaz Phillip T. , Endsley Janice J. , Weintraub Susan T. , Schlesinger Larry S. , Wewers Mark D. , Torrelles Jordi B. 
Published: October 2023

ABSTRACTTuberculosis is the leading cause of death for people living with HIV (PLWH). We hypothesized that altered functions of innate immune components in the human alveolar lining fluid of PLWH (HIV-ALF), drive susceptibility toMycobacterium tuberculosis(M.tb) infection. Our results indicate a significant increase in oxidation of innate proteins and chemokine levels, and significantly lower levels and function of complement components and Th1/Th2/Th17 cytokines in HIV-ALFvs.control-ALF (non-HIV infected people). We further found a deficiency of surfactant protein-D (SP-D) and reduced binding of SP-D toM.tbthat had been exposed to HIV-ALF. Primary human macrophages infected withM.tbexposed to HIV-ALF were significantly less capable of controlling the infection, which was reversed by SP-D replenishment in HIV-ALF. Thus, our data suggest that PLWH without antiretroviral therapy (ART) have declining host innate defense function in their lung mucosa, thereby favoringM.tband potentially other pulmonary infections.
Molecular de-extinction of antibiotics enabled by deep learning
Authors: Wan Fangping , Torres Marcelo D. T. , Peng Jacqueline , de la Fuente-Nunez Cesar 
Published: October 2023

AbstractMolecular de-extinction is an emerging field that aims to resurrect molecules to solve present-day problems such as antibiotic resistance. Here, we introduce a deep learning approach called Antibiotic Peptide de-Extinction (APEX) to mine the proteomes of all available extinct organisms (the “extinctome”) searching for encrypted peptide (EP) antibiotics. APEX mined a total of 10,311,899 EPs and identified 37,176 sequences predicted to have broad-spectrum antimicrobial activity, 11,035 of which were not found in extant organisms. Chemical synthesis and experimental validation yielded archaic EPs (AEPs) with activity against dangerous bacterial pathogens. Most peptides killed bacteria by depolarizing their cytoplasmic membrane, contrary to known antimicrobial peptides, which target the outer membrane. Notably, lead peptides, including those derived from the woolly mammoth, ancient sea cow, giant sloth, and extinct giant elk, exhibited anti-infective activity in preclinical mouse models. We propose molecular de-extinction, accelerated by deep learning, as a framework for discovering therapeutic molecules.
Reciprocal interactions between the sorghum root microbiome and the parasitic weedStriga hermonthica
Authors: Etalo Desalegn W. , Rybka Dominika , Lombard Lorenzo , Leite Marcio F.A. , Ossowicki Adam , Dini-Andreote Francisco , Arias-Giraldo Luisa , Kuramae Eiko E. , Crous Pedro W. , Tessema Taye , Raaijmakers Jos M. 
Published: October 2023

SummaryThe soil microbiome plays a crucial role in protecting plants against various pests and pathogens. However, its impact on interactions between plants and parasitic weeds, such asStriga hermonthica, is poorly understood. In this study, sorghum plants susceptible toStrigawere grown in 22 different field soils infested with parasite seeds. Significant variations inStrigainfections were observed among the soils. When the mostStriga-suppressive soil was gamma-irradiated, there was a significant increase inStrigaattachments, highlighting the importance of the soil microbiome in disrupting parasite infection. In the presence of the soil microbiome, theStriga-susceptible sorghum plants performed similarly to threeStriga-resistant genotypes. This effect was lost when the soil microbiome was eliminated by gamma-irradiation. Subsequent analysis revealed thatStrigasubstantially affected the sorghum rhizosphere microbiome and that both the sorghum rhizosphere mycobiome and bacteriome composition significantly correlated withStrigaattachment. Interestingly, certain fungal species in the sorghum rhizosphere mycobiome were only detected whenStrigaseeds were present. Further investigation showed that these fungal taxa originated from theStrigaseeds and are known sorghum pathogens, suggesting a potential partnership betweenStrigaand fungal pathogens to invade their shared host. Overall, our study demonstrated that the soil microbiome influencesStrigainfection and sorghum performance in a genotype-dependent manner, and the microbiome ofStrigaseeds affects the composition of the sorghum rhizosphere microbiome.
Neutralisation of SARS-CoV-2 Omicron subvariants BA.2.86 and EG.5.1 by antibodies induced by earlier infection or vaccination
Authors: Lassaunière Ria , Polacek Charlotta , Baig Sharmin , Ellegaard Kirsten , Escobar-Herrera Leandro André , Fomsgaard Anders , Spiess Katja , Schwartz Olivier , Planas Delphine , Simon-Lorière Etienne , Schneider Uffe Vest , Sieber Raphael Niklaus , Stegger Marc , Krause Tyra Grove , Ullum Henrik , Jokelainen Pikka , Rasmussen Morten 
Published: October 2023

AbstractHighly mutated SARS-CoV-2 Omicron subvariant BA.2.86 emerged in July 2023. We investigated the neutralisation of isolated virus by antibodies induced by earlier infection or vaccination. The neutralisation titres for BA.2.86 were comparable to those for XBB.1 and EG.5.1, by antibodies induced by XBB.1.5 or BA.4/5 breakthrough infection or BA.4/5 vaccination.