bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selection shapes plant performance in a grassland biodiversity experiment
Authors: De Giorgi Francesca , Durka Walter , Huang Yuanyuan , Schmid Bernhard , Roscher Christiane 
Published: August 2024

AbstractThe increasing strength of positive biodiversity effects on plant community productivity in long-term biodiversity experiments has been shown to be related to mixed responses at species level. However, it is still not well understood if the varying environments in plant communities with different diversity also exert different selection pressures to which plant species respond adaptively or whether their responses are mainly due to phenotypic plasticity.We conducted a transplant experiment for nine plant species in a 17-year-old grassland biodiversity experiment (Jena Experiment). We used offspring of plantsselectedin communities with different diversity or from plants which did not experience selection in the experiment (naïve). In a Community History Experiment, offspring ofselectedplants were planted in three test environments: their original plant communities with original soil, newly assembled plant communities with original soil, and newly assembled plant communities with new soil. Additionally, in a Selection Experiment we compared the performance ofselectedplants grown in their original environment to the performance ofnaïveplants grown in the same environment.In all test environments, increasing species richness was on average associated with a decrease in plant individual biomass, reproductive output, relative growth rate, plant height, leaf greenness, and leaf nitrogen (N) concentration and an increase in SLA.In the Community History Experiment survival was lower, while plant height, SLA, leaf N and C concentrations were highest in the test environment without plant and soil history. In high-diversity communities, individuals produced more biomass, grew taller and had higher leaf greenness in the original environment than in the other test environments.In the Selection Experimentselectedplants had weaker decline in their biomass, taller stature, and higher leaf C and N concentrations thannaïveplants with increasing species richness.In both experiments, we found evidences of adaptive phenotypic responses. Specifically, in high-diversity communities,selectedplants showed higher performance in their original environment, largely explained by plant community history and positive plant–soil feedbacks established over time.Synthesis:Our study highlights the important role of eco-evolutionary feedbacks of species diversity, which affect plant performance over time.
Pumilio differentially binds to mRNA 3’ UTR isoforms to regulate localization of synaptic proteins
Authors: Grzejda Dominika , Heß Anton , Rezansoff Andrew , Gorey Sakshi , Carrasco Judit , Alfonso-Gonzalez Carlos , Tsagkris Stylianos , Neuhaus Lena , Ozbulut Hasan Can , Vögtle Friederike-Nora , Vlachos Andreas , Hilgers Valérie 
Published: August 2024

AbstractIn neuronal cells, the regulation of RNA is crucial for the spatiotemporal control of gene expression, but how the correct localization, levels, and function of synaptic proteins are achieved is not well understood. In this study, we globally investigate the role of alternative 3’ UTRs in regulating RNA localization in the synaptic regions of the Drosophila brain. We identify direct mRNA targets of the translational repressor Pumilio, finding that mRNAs bound by Pumilio encode proteins enriched in synaptosomes. Pumilio differentially binds to RNA isoforms of the same gene, favoring long, neuronal 3’ UTRs. These longer 3’ UTRs tend to remain in the neuronal soma, whereas shorter UTR isoforms localize to the synapse. In culturedpumiliomutant neurons, severe axon outgrowth defects were accompanied by mRNA isoform mislocalization, and proteins encoded by these Pumilio targets displayed excessive abundance at synaptic boutons. Our study identifies an important and widespread mechanism for the spatiotemporal regulation of protein function in neurons.
A c-opsin functions in a ciliary-marginal zone-like stem cell region of an invertebrate camera-type eye
Authors: Milivojev Nadja , Velastegui Gamboa Camila L. , Andreatta Gabriele , Raible Florian , Tessmar-Raible Kristin 
Published: August 2024

AbstractCamera-type eyes in vertebrates and invertebrates are striking examples of parallel evolution of a complex structure. Comparisons between such structures can help to deduce their organizational principles. We analyzed the camera-type adult eyes of the bristlewormPlatynereis dumerilii. Employing single-cell RNA sequencing, we identified neurogenic cells in the worms’ adult brains. Among those are distinct neural stem cells in its adult eye, adjacent to the glass body/lens, that produce cells in radial lines, reminiscent of stem cells in the vertebrate eye ciliary marginal zone. A subset of these proliferating cells expresses the photoreceptor genec-opsin1.c-opsin1knock-out reduces eye cell proliferation and influences differentiation. During reproductive maturation, proliferation in eye and brain sharply declines, while cells upregulate molecular characteristics of mammalian adult neural stem cell quiescence. Our data reveal new insights into nervous system functional development and evolution.
Dissecting the oncogenic mechanisms of POT1 cancer mutations through deep scanning mutagenesis
Authors: Martin Annika , Schabort Johannes , Bartke-Croughan Rebecca , Tran Stella , Preetham Atul , Lu Robert , Ho Richard , Gao Jianpu , Jenkins Shirin , Boyle John , Ghanim George E. , Jagota Milind , Song Yun S. , Li Hanqin , Hockemeyer Dirk 
Published: August 2024

AbstractMutations in the shelterin protein POT1 are associated with diverse cancers, but their role in cancer progression remains unclear. To resolve this, we performed deep scanning mutagenesis in POT1 locally haploid human stem cells to assess the impact of POT1 variants on cellular viability and cancer-associated telomeric phenotypes. Though POT1 is essential, frame-shift mutants are rescued by chemical ATR inhibition, indicating that POT1 is not required for telomere replication or lagging strand synthesis. In contrast, a substantial fraction of clinically-validated pathogenic mutations support normal cellular proliferation, but still drive ATR-dependent telomeric DNA damage signaling and ATR-independent telomere elongation. Moreover, this class of cancer-associated POT1 variants elongates telomeres more rapidly than POT1 frame-shifts, indicating they actively drive oncogenesis and are not simple loss-of-function mutations.
Variation in transformation frequency and competence gene expression among serotype 3 Streptococcus pneumoniae
Authors: Shambhu Smitha , Cella Eleonora , Azarian Taj 
Published: August 2024

AbstractBackgroundStreptococcus pneumoniae is a human commensal and the causative agent of pneumococcal disease. Pneumococci are naturally competent – able to uptake exogenous DNA from the environment and incorporate it into their genome through homologous and non- homologous recombination. Recombination has significantly shaped the evolutionary history of S. pneumoniae, as it allows pneumococci to rapidly adapt. Recombination frequencies vary considerably across pneumococcal populations, yet underlying mechanisms for these variations are not well understood. Entry and exit into competence, a state in which the cell can uptake DNA, is tightly regulated through transcriptional changes.MethodsTo elucidate differences in transformation frequency among strains as well as the underlying genetic mechanisms, we carried out in-vitro competence assays and measured gene expression changes during the competent state using RNA sequencing of representative strains belonging to Serotype 3 clonal complex (CC) 180 and a non-CC180 comparison.ResultsWe observed consistent differences in transformation frequencies among groups, which correlated with variation in differentially expressed genes during competence. While all strains exhibited a similar response to competence stimulating peptide (CSP) for early competence genes, we observed variation in expression of late competence genes, which encode the DNA uptake apparatus, DNA repair and recombination proteins. We also observed differences in expression of genes linked to bacteriocin production, which may partially explain observed population-level differences. Further genomic analysis suggests variation in promoter sequences governing late competence genes may be slowing transition from early to late components of the competence pathway.ConclusionsWe show that there is considerable variation in competence even among closely related strains belonging to the same CC and that this variation may be the result of subtle genomic differences. Additional studies are needed to assess the phenotypic impact of genomic variations.
Online movements reflect ongoing deliberation
Authors: Calalo Jan A. , Ngo Truc T. , Sullivan Seth R. , Strand Katy , Buggeln John H. , Lokesh Rakshith , Roth Adam M. , Carter Michael J. , Kurtzer Isaac L. , Cashaback Joshua G.A. 
Published: August 2024

ABSTRACTFrom navigating a crowded hallway to skiing down a treacherous hill, humans are constantly making decisions while moving. Insightful past work has provided a glimpse of decision deliberation at the moment of movement onset. Yet it is unknown whether ongoing deliberation can be expressed during movement, following movement onset and prior to any decision. Here we tested the idea that an ongoing deliberation continually influences motor processes—prior to a decision—directing online movements. Over three experiments, we manipulated evidence to influence deliberation during movement. The deliberation process was manipulated by having participants observe evidence in the form of tokens that moved into a left or right target. Supporting our hypothesis we found that lateral hand movements reflected deliberation, prior to a decision. We also found that a deliberation urgency signal, which more heavily weighs later evidence, was fundamental to predicting decisions and explains past movement behaviour in a new light. Our paradigm promotes the expression of ongoing deliberation through movement, providing a powerful new window into understanding the interplay between decision and action.
Removal of developmentally regulated microexons has a minimal impact on larval zebrafish brain morphology and function
Authors: Calhoun Caleb C.S. , Capps Mary E.S. , Muya Kristie , Gannaway William C. , Martina Verdion , Conklin Claire L. , Klein Morgan C. , Webster Jhodi M. , Torija-Olson Emma G. , Thyme Summer B. 
Published: August 2024

AbstractMicroexon splicing is a vertebrate-conserved process through which small, often in-frame, exons are differentially included during brain development and across neuron types. Although the protein sequences encoded by these exons are highly conserved and can mediate interactions, the neurobiological functions of only a small number have been characterized. To establish a more generalized understanding of their roles in brain development, we used CRISPR/Cas9 to remove 45 microexons in zebrafish and assessed larval brain activity, morphology, and behavior. Most mutants had minimal or no phenotypes at this developmental stage. Among previously studied microexons, we uncovered baseline and stimulus-driven phenotypes for two microexons (meA and meB) inptprdand reduced activity in the telencephalon in thetenm3B0isoform. Although mild, neural phenotypes were discovered for several microexons that have not been previously characterized, including inppp6r3, sptan1, dop1a, rapgef2, dctn4, vti1a, andmeaf6. This study establishes a general approach for investigating conserved alternative splicing events and prioritizes microexons for downstream analysis.
Bacterial cross-feeding can promote gene retention by lowering gene expression costs
Authors: Chuang Ying-Chih , Behringer Megan G. , Patton Gillian , Bird Jordan T. , Love Crystal E. , Dalia Ankur , McKinlay James B. 
Published: August 2024

ABSTRACTGene loss is expected in microbial communities when the benefit of obtaining a biosynthetic precursor from a neighbor via cross-feeding outweighs the cost of retaining a biosynthetic gene. However, gene cost primarily comes from expression, and many biosynthetic genes are only expressed when needed. Thus, one can conversely expect cross-feeding to repress biosynthetic gene expression and promote gene retention by lowering gene cost. Here we examined long-term bacterial cocultures pairingEscherichia coliandRhodopseudomonas palustrisfor evidence of gene loss or retention in response to cross-feeding of non-essential adenine. AlthoughR. palustriscontinued to externalize adenine in long-term cultures,E. colidid not accumulate mutations in purine synthesis genes, even after 700 generations.E. colipurine synthesis gene expression was low in coculture, suggesting that gene repression removed selective pressure for gene loss. In support of this explanation,R. palustrisalso had low transcript levels for iron-scavenging siderophore genes in coculture, likely becauseE. colifacilitated iron acquisition byR. palustris. R. palustrissiderophore gene mutations were correspondingly rare in long-term cocultures but were prevalent in monocultures where transcript levels were high. Our data suggests that cross-feeding does not always drive gene loss, but can instead promote gene retention by repressing costly expression.Graphical abstract
Feeding a rich diet supplemented with the translation inhibitor cycloheximide decreases lifespan and ovary size in Drosophila
Authors: Hwang Hye Jin , Cox Rachel T. 
Published: August 2024

AbstractDrosophilaoogenesis has long been an important model for understanding myriad cellular processes controlling development, RNA biology, and patterning. Flies are easily fed drugs to disrupt various molecular pathways. However, this is often done under poor nutrient conditions that adversely affect oogenesis, thus making analysis challenging. Cycloheximide is a widely used compound that binds to and stalls the ribosome, therefore reducing protein synthesis. Since egg production is a highly nutrient-dependent process, we developed a method to feed femaleDrosophilaa rich diet of yeast paste supplemented with cycloheximide to better determine the effect of cycloheximide treatment on oogenesis. We find flies readily consume cycloheximide-supplemented yeast paste. Males and females have reduced lifespans when maintained on cycloheximide, with males exhibiting a dose-dependent decrease. While females did not exhibit decreased egg-laying, their ovaries were smaller and the number of progeny reduced, indicating substandard egg quality. Finally, females fed cycloheximide have disrupted oogenesis, with smaller ovaries, missing ovariole stages, and an increase in apoptotic follicles. Together, these data support that reduced protein synthesis adversely affects oogenesis with a rich diet that provides optimal nutrient conditions. In addition, this method could be used more broadly to test the effect of other drugs onDrosophilaoogenesis without the confounding effects caused by poor nutrition.
A single-molecule nanopore sequencing platform
Authors: Zhang Jia-Yuan , Zhang Yuning , Wang Lele , Guo Fei , Yun Quanxin , Zeng Tao , Yan Xu , Yu Lei , Cheng Lei , Wu Wei , Shi Xiao , Chen Junyi , Sun Yuhui , Yang Jingnan , Guo Rongrong , Zhang Xianda , Kong Liu’er , Wang Zong’an , Yao Junlei , Tan Yangsheng , Shi Liuxin , Zhao Zhentao , Feng Zhongwang , Yu Xiaopeng , Li Chuang , Zhan Wu , Ren Yulin , Yang Fan , Liu Zhenjun , Fan Guangnan , Zhong Weilian , Li Dachang , He Lei , Qi Yanwei , Zhang Meng , Zhu Yening , Chi Heng , Zhao Ziyu , Wei Zhuofang , Song Ziqi , Ju Yanmei , Guo Ruijin , Xiao Liang , Lin Xiumei , Chen Liang , Yang Chentao , Li Qiye , Wang Ou , Jin Xin , Ni Ming , Zhang Wenwei , Liu Longqi , Gu Ying , Wang Jian , Li Yuxiang , Xu Xun , Dong Yuliang 
Published: August 2024

ABSTRACTNanopore sequencing, a third-generation sequencing technology, has revolutionized the gene sequencing industry with its advantages of long reads, fast speed, real-time sequencing and analysis, and potential in detecting base modifications. This technology allows researchers to sequence longer DNA fragments in a single read, providing more comprehensive genomic information compared to previous methods. Nanopore sequencing operates on electrical signals generated by a nanopore embedded in a membrane separating two electrolyte-filled chambers. When single-stranded DNA (ssDNA) passes through the nanopore, it creates variations in the current that correspond to different DNA bases. By analyzing these current fluctuations with machine learning algorithms, the DNA sequence can be determined. In this study, we introduced several improvements to nanopore sequencing, including nanopore local chemistry sequencing, novel motor and pore proteins, chip design, and basecalling algorithms. Our new nanopore sequencing platform, CycloneSEQ, demonstrated long-duration sequencing (107 hours) on a single chip with high yield (>50 Gb). In human genomic DNA sequencing, CycloneSEQ was able to produce long reads with N50 33.6 kb and modal identity 97.0%. Preliminary findings on human whole-genomede novoassembly, variant calling, metagenomics sequencing, and single-cell RNA sequencing have further highlighted CycloneSEQ’s potential across different areas of genomics.
Dynamins combine mechano-constriction and membrane remodeling to enable two-step mitochondrial fission via a ‘snap-through’ instability
Authors: Alimohamadi Haleh , Luo Elizabeth Wei-Chia , Yang Rena , Gupta Shivam , Nolden Kelsey A , Mandal Taraknath , Hill R. Blake , Wong Gerard C. L. 
Published: August 2024

AbstractMitochondrial fission is controlled by dynamin proteins, the dysregulation of which is correlated with diverse diseases. Fission dynamins are GTP hydrolysis-driven mechanoenzymes that self-oligomerize into helical structures that constrict membrane to achieve fission, but details are not well understood. However, dynamins can also remodel membranes by inducing negative Gaussian curvature, the type of curvature required for completion of fission. Here, we examine how these drastically different mechanisms synergistically exert their influences on a membrane, via a mechanical model calibrated with small-angle X-ray scattering structural data. We find that free dynamin can trigger a “snap-through instability” that enforces a shape transition from an oligomer-confined cylindrical membrane to a drastically narrower catenoid-shaped neck within the spontaneous hemi-fission regime, in a manner that depends critically on the length of the confined tube. These results indicate how the combination of dynamin assembly, and paradoxically disassembly, can lead to diverse pathways to scission.TeaserDynamin mechano-constriction by assembly and curvature-driven instability by free monomers synergistically drive mitochondrial fission.
Genetic heterogeneity induces nonadditive behavioural changes inDrosophila
Authors: Okuyama Takahira , Sato Daiki X. , Takahashi Yuma 
Published: August 2024

AbstractThe formation and dynamics of group behaviours are important topics in ecology and evolution. Although several theoretical studies assume homogeneity among individuals, real-world organisms often display remarkable behavioural diversity within groups. This study investigated the synergistic impact of genetic heterogeneity on group behaviour and reveals the behavioural underpinnings of diversity effects using 83 genetically distinct strains ofDrosophila melanogaster. Various indices of foraging behaviour, including movement speed, search comprehensiveness, spatial preference and stopping time, were measured using homogeneous (single strain) and heterogeneous (mixing two distinct strains) groups of flies. The heterogeneous groups exhibited significant increases in spatial preference and stopping time compared with the homogeneous groups, suggesting that genetic heterogeneity induces nonadditive changes in group behaviour. Furthermore, the magnitude and direction of the behavioural change varied among different combinations. Multiple regression analysis showed that the phenotypic distance in some traits between mixed strains could explain the emergence of diversity effects on group behaviour. Specifically, interindividual heterogeneity in the locomotor activity level showed a positive correlation with diversity effects. These results emphasise the importance of intraspecific diversity in group dynamics and suggest that genetic heterogeneity can improve group performance through the acquisition of novel behavioural traits.
Rational homotopy type of projectivization of the tangent bundle of certain spaces
Authors: Gastinzi Jean Baptiste , Ndlovu Meshach 
Published: August 2024

PurposeThe paper aims to determine the rational homotopy type of the total space of projectivized bundles over complex projective spaces using Sullivan minimal models, providing insights into the algebraic structure of these spaces.Design/methodology/approachThe paper utilises techniques from Sullivan’s theory of minimal models to analyse the differential graded algebraic structure of projectivized bundles. It employs algebraic methods to compute the Sullivan minimal model of P(E) and establish relationships with the base space.FindingsThe paper determines the rational homotopy type of projectivized bundles over complex projective spaces. Of great interest is how the Chern classes of the fibre space and base space, play a critical role in determining the Sullivan model of P(E). We also provide the homogeneous space of P(E) when n = 2. Finally, we prove the formality of P(E) over a homogeneous space of equal rank.Research limitations/implicationsLimitations may include the complexity of computing minimal models for higher-dimensional bundles.Practical implicationsUnderstanding the rational homotopy type of projectivized bundles facilitates computations in algebraic topology and differential geometry, potentially aiding in applications such as topological data analysis and geometric modelling.Social implicationsWhile the direct social impact may be indirect, advancements in algebraic topology contribute to broader mathematical knowledge, which can underpin developments in science, engineering, and technology with societal benefits.Originality/valueThe paper’s originality lies in its application of Sullivan minimal models to determine the rational homotopy type of projectivized bundles over complex projective spaces, offering valuable insights into the algebraic structure of these spaces and their associated complex vector bundles.
Trade and energy efficiency: theory and evidence
Authors: Huang Geng , Lin Xi , He Ling-Yun 
Published: August 2024

PurposeSome existing studies have begun to discuss how trade will change the environment from a country or province perspective. However, so far, only a limited number of studies have provided evidence at the product level. This study aims to investigate the environmental impacts of trade at the product level.Design/methodology/approachThe effects of importing intermediates and capital inputs on energy performance are examined using theoretical analysis. Empirical analyses are conducted using data on product trade, and the effects of importing intermediate inputs and capital inputs on energy efficiency are identified using a Propensity Score Matching-Difference in Difference (PSM-DID) estimation.FindingsThe results demonstrate that importing intermediates and capital inputs effectively enhance energy efficiency. Importing these inputs from foreign markets leads to increased productivity and ultimately improves energy performance.Originality/valueThis research provides new evidence on the relationship between importing and energy use at the product trade level. It offers insights into enterprise behaviors regarding importing intermediates and capital inputs, contributing to a deeper understanding of the environmental effects of trade. Additionally, a micro-theoretical model is developed to examine the impacts of imports on energy efficiency, complementing existing literature with theoretical insights.