bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intra and interspecific diversity in a tropical plant clade alter herbivory and ecosystem resilience
Authors: Grele Ari J. , Massad Tara J. , Uckele Kathryn A. , Dyer Lee A. , Antonini Yasmine , Braga Laura , Forister Matthew L. , Sulca Lidia , Kato Massuo J. , Lopez Humberto G. , Nascimento Andre R. , Parchman Thomas L. , Simbaña Wilmer R. , Smilanich Angela M. , Stireman John O. , Tepe Eric J. , Walla Thomas R. , Richards Lora A. 
Published: March 2023

AbstractDeclines in biodiversity generated by anthropogenic stressors at both species and population levels can alter emergent processes instrumental to ecosystem function and resilience. As such, understanding the role of biodiversity in ecosystem function and its response to climate perturbation is increasingly important, especially in tropical systems where responses to changes in biodiversity are less predictable and more challenging to assess experimentally. Using large scale transplant experiments conducted at five neotropical sites, we documented the impacts of changes in intraspecific and interspecific plant richness in the genusPiperon insect herbivory, insect richness, and ecosystem resilience to perturbations in water availability. We found that reductions of both intraspecific and interspecificPiperdiversity had measurable and site specific effects on herbivory, herbivorous insect richness, and plant mortality. The responses of these ecosystem-relevant processes to reduced intraspecificPiperrichness were often similar in magnitude to the effects of reduced interspecific richness. Increased water availability reduced herbivory by 4.2% overall, and the response of herbivorous insect richness and herbivory to water availability were altered by both intra and interspecific richness in a site dependent manner. Our results underscore the role of intraspecific and interspecific richness as foundations of ecosystem function and the importance of community and location specific contingencies in controlling function in complex tropical systems.
Unravelling the anticancer and enzyme inhibition potential of different classes of compounds including a new steroid, isolated fromCassia mimosoïdes
Authors: Tchebou Robert Viani Kepdieu , Farooq Umar , Khan Sara , Rasool Azhar , Sarwar Rizwana , Khushal Aneela , Tapondjou Léon Azefack , Bukhari Syed Majid , Teponno Rémy Bertrand 
Published: March 2023

AbstractThe genusCassiais a significant source of secondary metabolites that are physiologically active and come from several chemical classes. The current research deals with the isolation, spectroscopic elucidation (1D and 2D NMR spectroscopy) and enzymatic activity of fifteen known compounds as well as a new unidentified avenasterol derivative namely 21-methylene-24-ethylidene lophenol. The urease andβ-glucosidase inhibitory effects of these compounds were studied for the first time, and molecular docking studies were also performed to verify the structure-activity relationships. All the compounds evaluated towards urease showed higher inhibitory activity (1.224±0.43 < IC50> 6.678±0.11μM) compared to standard thiourea (IC50= 18.61±0.11μM). Molecular docking results revealed that compound7strongly inhibits urease due to the formation of a stable ligand-urease complex via hydrogen bonding, van der Waal and hydrophobic interactions. Formation of a favourable complex of7with the target enzyme gave a more negative docking score (−6.95 kcal/mol) than that of thiourea (−3.13 kcal/mol). Regarding theβ-glucosidase enzyme, all the compounds evaluated did not show activity except compound1which inhibited the latter with a percentage of inhibition of 82.6. These findings imply that this plant may be a contender for developing novel treatments for infectious disorders brought on by urease-producing bacteria.
Diatom adhesive trail proteins acquired by horizontal gene transfer from bacteria serve as primers for marine biofilm formation
Authors: Zackova Suchanova Jirina , Bilcke Gust , Romanowska Beata , Fatlawi Ali , Pippel Martin , Skeffington Alastair , Schroeder Michael , Vyverman Wim , Vandepoele Klaas , Kröger Nils , Poulsen Nicole 
Published: March 2023

SummaryBiofilm-forming benthic diatoms are key primary producers in coastal habitats, where they frequently dominate sunlit submerged and intertidal substrata. The development of a unique form of gliding motility in raphid diatoms was a key molecular adaptation that contributed to their evolutionary success. Gliding motility is hypothesized to be driven by an intracellular actin-myosin motor and requires the secretion of polysaccharide- and protein-based adhesive materials. To date, the structure-function correlation between diatom adhesives utilized for gliding and their relationship to the extracellular matrix that constitutes the diatom biofilm is unknown.Proteomics analysis of the adhesive material fromCraspedostauros australisrevealed eight novel, diatom-specific proteins. Four of them constitute a new family of proteins, named Trailins, which contain an enigmatic domain termed Choice-of-Anchor-A (CAA). Immunostaining demonstrated that Trailins are only present in the adhesive trails required to generate traction on native substrata, but are absent from the extracellular matrix of biofilms. Phylogenetic analysis and Protein 3D structure prediction suggests that the CAA-domains in Trailins were obtained from bacteria by horizontal gene transfer, and exhibit a striking structural similarity to ice-binding proteins.Our work advances the understanding of the molecular basis for diatom underwater adhesion and biofilm formation providing evidence that there is a molecular switch between proteins required for initial surface colonization and those required for 3D biofilm matrix formation.
GenoDrawing: An autoencoder framework for image prediction from SNP markers
Authors: Jurado-Ruiz Federico , Rousseau David , Botía Juan A. , Aranzana Maria José 
Published: March 2023

AbstractAdvancements in genome sequencing have facilitated whole genome characterization of numerous plant species, providing an abundance of genotypic data for genomic analysis. Genomic selection and neural networks, particularly deep learning, have been developed to predict complex traits from dense genotypic data. Autoencoders, a neural network model to extract features from images in an unsupervised manner, has proven to be useful for plant phenotyping. This study introduces an autoencoder framework, GenoDrawing, for predicting and retrieving apple images from a low-depth single nucleotide polymorphism (SNP) array, potentially useful in predicting traits that are difficult to define. GenoDrawing demonstrated proficiency in its task while using a small dataset of shape-related SNPs, and multiple experiments were conducted to evaluate the impact of SNP selection and shape relation. Results indicated that the correct relationship of SNPs with visual traits had a significant impact on the generated images, consistent with biological interpretation. While using significant SNPs is crucial, incorporating additional, unrelated SNPs results in performance degradation for simple NN architectures that cannot easily identify the most important inputs. The proposed GenoDrawing method is a practical framework for exploring genomic prediction in fruit tree phenotyping, particularly beneficial for small to medium breeding companies to predict economically significant heritable traits. Although GenoDrawing has limitations, it sets the groundwork for future research in image prediction from genomic markers. Future studies should focus on using stronger models for image reproduction, SNP information extraction, and improved dataset balance in terms of shape for more precise outcomes.
Re-engineering a lost trait:IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss
Authors: Hornstein Eli D. , Charles Melodi , Franklin Megan , Edwards Brianne , Vintila Simina , Kleiner Manuel , Sederoff Heike 
Published: March 2023

AbstractArbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the modelArabidopsis thaliana. To explore why an apparently beneficial trait would be repeatedly lost, we generatedArabidopsisplants expressing a constitutively active form ofInteracting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost fromArabidopsisalong with the AM host trait. We characterize the transcriptomic effect of expressingIPD3inArabidopsiswith and without exposure to the AM fungus (AMF)Rhizophagus irregularis, and compare these results to the AM modelLotus japonicusand itsipd3knockout mutantcyclops-4. Despite its long history as a non-AM species, restoringIPD3in the form of its constitutively active DNA-binding domain toArabidopsisaltered expression of specific gene networks. Surprisingly, the effect of expressingIPD3inArabidopsisand knocking it out inLotuswas strongest in plants not exposed to AMF, which is revealed to be due to changes inIPD3genotype causing a transcriptional state which partially mimics AMF exposure in non-inoculated plants. Our results indicate that despite the long interval since loss of AM andIPD3inArabidopsis, molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.
Fagalean phylogeny in a nutshell: Chronicling the diversification history of Fagales
Authors: Siniscalchi Carolina M. , Correa-Narvaez Julian , Kates Heather R. , Soltis Douglas E. , Soltis Pamela S. , Guralnick Robert P. , Manchester Steven R. , Folk Ryan A. 
Published: March 2023

AbstractReconstructing the biogeographical history and timing of the diversification of temperate forests is essential for understanding their history and resolving uncertainties about how flowering plants emerged from their deep tropical origins to dominate in today’s freezing terrestrial environments. The angiosperm order Fagales, comprising iconic components of temperate forests worldwide with an extensive fossil record, are an excellent plant system in which to apply a fossil-aware paradigm, such as the fossilized birth-death (FBD) process, for investigating the macroevolution of temperate forest biomes. Here, we improve upon previous efforts to resolve phylogeny and incorporate fossils in Fagales using low-copy nuclear loci and an expanded morphological matrix to reevaluate the Fagales fossil record and: (1) infer the phylogenetic relationships and the time of origin of the clade using the FBD model as implemented in RevBayes, (2) provide a framework for evaluating the climatic and biogeographic history of Fagales, and (3) investigate how the inclusion of fossils via the FBD method influences ancestral reconstruction and diversification estimation. The phylogenetic relationships we recovered are conventional except for the position of Nothofagaceae, while our inferred ages support older timelines than previously proposed, with a mid-Cretaceous date for the most recent common ancestor (MRCA) of the order. Biogeographical analysis shows an origin of Fagales consistent with an ancestral circumboreal temperate distribution corroborated by ancestral niche reconstructions. While distributions today largely reflect the general conservatism of temperate forests, we identified two episodes of high diversification, one at the mid-Cretaceous origin of the clade and the other continuing from the Miocene to the present. Removing fossil taxa from the tree reveals a different story, shifting the origin of extant families from North America to East Asia, reflecting refugial distributions in this biodiversity “museum” and implying a general bias towards low extinction areas in biogeographic reconstruction. Likewise, without fossil data, diversification estimates were higher and unable to detect an early diversification burst. Based on our analyses, we close with recommendations regarding the interpretation of estimates of diversification and ancestral state reconstruction using phylogenetic trees with only extant species as tips.
Functional Ambidexterity of an Ancient Nucleic Acid-Binding Domain
Authors: Weil-Ktorza Orit , Despotović Dragana , Fridmann-Sirkis Yael , Naveh-Tassa Segev , Levy Yaacov , Metanis Norman , Longo Liam M. 
Published: March 2023

AbstractHomochirality of biopolymers emerged early in the history of life on Earth, nearly 4 billion years ago. Whether the establishment of homochirality was the result of abiotic physical and chemical processes, or biological selection, remains unknown. However, given that significant events in protein evolution predate the last universal common ancestor, the history of homochirality may have been written into some of the oldest protein folds. To test this hypothesis, the evolutionary trajectory of the ancient and ubiquitous helix-hairpin-helix (HhH) protein family was analyzed for functional robustness to total chiral inversion of just one binding partner. Against expectations, functional ‘ambidexterity’ was observed across the entire trajectory, from phase separation of HhH peptides with RNA to dsDNA binding of the duplicated (HhH)2-Fold. Moreover, dissociation kinetics, mutational analysis, and molecular dynamics simulations revealed significant overlap between the binding modes of a natural and a mirror-image protein to natural dsDNA. These data suggest that the veil between worlds with alternative chiral preferences may not be as impenetrable as is often assumed, and that the HhH protein family is an intriguing exception to the dogma of reciprocal chiral substrate specificity proposed by Milton and Kent (Miltonet al. Science 1992).
The ComRS-SigX pathway regulates natural transformation inStreptococcus ferus
Authors: Rued Britta E. , Federle Michael J. 
Published: March 2023

ABSTRACTThe ability to take up and incorporate foreign DNA via natural transformation is a well-known characteristic of some species ofStreptococcus,and is a mechanism that rapidly allows for the acquisition of antibacterial resistance. Here, we describe that the understudied speciesStreptococcus ferusis also capable of natural transformation and uses a system analogous to that identified inStreptococcus mutans.S. mutansnatural transformation is under the control of the alternative sigma factorsigX(also known ascomX), whose expression is induced by two types of peptide signals: CSP (competencestimulatingpeptide, encoded bycomC) and XIP (sigX-inducingpeptide, encoded bycomS). These systems induce competence via either the two-component signal-transduction system ComDE or the RRNPP transcriptional regulator ComR, respectively. Protein and nucleotide homology searches identified putative orthologs ofcomRSandsigXinS. ferus, but not homologs ofS. mutans blpRH(also known ascomDE). We demonstrate that natural transformation inS. ferusis induced by a small, double-tryptophan containing competence-inducing peptide (XIP), akin to that ofS. mutans, and requires the presence of thecomRandsigXorthologs for efficient transformation. Additionally, we find that natural transformation is induced inS. ferusby both the native XIP and the XIP variant ofS. mutans, implying that crosstalk between the two species is possible. This process has been harnessed to construct gene deletions inS. ferusand provides a method to genetically manipulate this understudied species.IMPORTANCENatural transformation is the process by which bacteria take up DNA and allows for acquisition of new genetic traits, including those involved in antibiotic resistance. This study demonstrates that the understudied speciesStreptococcus ferusis capable of natural transformation using a peptide-pheromone system like that previously identified inStreptococcus mutansand provides a framework for future studies concerning this organism.
Mechanical transmission of Dengue Virus byAedes aegyptimay influence disease transmission dynamics during outbreaks
Authors: Li Hsing-Han , Su Matthew P. , Wu Shih-Cheng , Tsou Hsiao-Hui , Chang Meng-Chun , Cheng Yu-Chieh , Tsai Kuen-Nan , Wang Hsin-Wei , Chen Guan-Hua , Tang Cheng-Kang , Chung Pei-Jung , Tsai Wan-Tin , Huang Li-Rung , Yueh Yueh Andrew , Chen Hsin-Wei , Pan Chao-Ying , Akbari Omar S. , Chang Hsiao-Han , Yu Guann-Yi , Marshall John M. , Chen Chun-Hong 
Published: March 2023

AbstractThe escalating number of dengue virus (DENV) outbreaks and their worldwide spread pose a major threat to global public health. DENV transmission dynamics significantly influence outbreak duration and magnitude. Conventional DENV transmission requires an incubation period between mosquitoes biting infected humans and the mosquitoes becoming infectious. However, the possibility of immediate, mechanical transmission of DENV without viral replication in the mosquito has received little attention despite its potential importance.Here, we show thatAedes aegyptimosquitoes can mechanically transmit DENV to susceptible mice immediately after biting infected mice without the need for an incubation period. By incorporating parameters from our experiments into a newly developed mathematical model, we found a significant impact on DENV outbreak characteristics.Mechanical transmission may amplify existing disease transmission routes and influence outbreak dynamics. Our findings have implications for vector control strategies that target mosquito lifespan and suggest the possibility of similar mechanical transmission routes in other disease-carrying mosquitoes.
Brassinosteroid receptor BRL3 triggers systemic plant adaptation to elevated temperature from the phloem cells
Authors: Gupta Aditi , Rico-Medina Andrés , Lozano-Elena Fidel , Marqués-Bueno Mar , Fontanet Juan B. , Fàbregas Norma , Alseekh Saleh , Fernie Alisdair R. , Caño-Delgado Ana I. 
Published: March 2023

AbstractUnderstanding plant receptor signaling is crucial to mitigate climate change impact on agriculture. BRs bind to membrane receptor-kinase BR-INSENSITIVE 1 (BRI1) in most plant cells that is essential to promote growth and stress responses, while the roles of vascular BRI1-LIKE1 and 3 (BRL3) receptors were considered redundant. While going unnoticed for twenty years, our study unveils thatbrl3mutants show conditional phenotypes to climate stress factors such as elevated temperatures, water deprivation and rising CO2levels. In response to adverse climate conditions such as elevated temperature, BRL3 signaling at the phloem-companion cells can promote growth by activating BRI1-EMS-SUPPRESSOR1 (BES1) effector, hormonal homeostasis, and central carbon metabolism. This study shifts the paradigm for our present understanding of BR signaling and opens innovative strategies to develop climate-smart crops.One sentence summaryPhloem-specific BRL3 receptor pathway controls plant adaption to elevated temperature.
MeC3HDZ1/MeCNA is a strong candidate for cassava storage root productivity improvement
Authors: Solé-Gil Anna , López Anselmo , Ombrosi Damiano , Urbez Cristina , Brumós Javier , Agustí Javier 
Published: March 2023

ABSTRACTThe storage root (SR) of cassava is the main staple food in sub-Saharan Africa, where it feeds over 500 million people. However, little is known about the genetic and molecular regulation underlying its development. Unraveling such regulation would pave the way for biotechnology approaches aimed at enhancing cassava productivity. Anatomical studies indicate that SR development relies on the massive accumulation of xylem parenchyma, a cell-type derived from the vascular cambium. The C3HDZ family of transcription factors regulate cambial cells proliferation and xylem differentiation in Arabidopsis and other species. We thus aimed at identifying C3HDZ proteins in cassava and determining whether any of them shows preferential activity in the SR cambium and/or xylem. Using phylogeny and synteny studies, we identified eight C3HDZ proteins in cassava, namely MeCH3DZ1-8. We observed that the expression ofMeC3HDZ1in SR cambium and xylem is higher than that of any otherMeC3HDZgene in any of the SR vascular tissues or any of the other vegetative organs. We established anin-silicopipeline which revealed the existence of a number of theoretical C3HDZ targets displaying significant preferential expression in the SR. Subsequent Y1H analyses proved that MeC3HDZ1 can bind canonical C3HDZ binding sites in the promoters of these targets. Transactivation assays demonstrated that MeC3HDZ1 can regulate the expression of genes downstream of promoters harboring such binding sites, thereby demonstrating that MeC3HDZ1 is a C3HDZ transcription factor which constitutes a strong candidate for future biotechnology strategies directed at increasing cassava productivity.
Sexuality and gender within Afghanistan'sbacha bereeshpopulation
Authors: Racine Elise E. 
Published: March 2023

PurposeLimited evidence exists onbacha bazi, Afghanistan's steadily revived practice involving transgenerational same-sex relationships, despite its frequent association with violence towards young males, known asbacha bereesh. This paper aims to fill this critical gap.Design/methodology/approachThe author conducted an integrative literature review using qualitative and quantitative secondary data. An ecological framework for violence was applied to the findings.FindingsThe findings offer a comprehensive overview ofbacha baziin its modern form, including the unique health needs, sexual practices, and gender identities and orientations ofbacha bereesh. The author reveals how Afghan masculine identities and male-male sexual activity occur in relation to power structures and notions of honor. Numerous risk factors increasingbacha bereeshvulnerability for violence and socio-legal barriers constraining access to crucial services are also discussed.Research limitations/implicationsAfghanistan's shame-based culture limits accurate data collection by obscuring the practice and stigmatizingbacha bereeshwho serve in feminized roles.Practical implicationsThe research highlights the inadequacies of applying Western gender-binary frameworks to bacha bazi. It contributes to our understanding of sexuality, gender, masculinity, and male-directed sexual violence within Afghan culture. These insights will help us better address the health needs of this underserved population.Originality/valueThe lack of evidence addressing these topics highlights our paper's originality, while the literature firmly linking violence to poor physical and psychological health outcomes emphasizes the importance of its contribution.