bluuebunny/crossref_metadata_2025_split huggingface dataset:
Break-induced replication is the primary recombination pathway in plant somatic hybrid mitochondria: a model for mt-HGT
Authors: Gandini Carolina L. , Garcia Laura E. , Abbona Cinthia C. , Ceriotti Luis F. , Kushnir Sergei , Geelen Danny , Sanchez-Puerta M. Virginia 
Published: January 2023

AbstractSomatic hybrids between distant species offer a remarkable model to study genomic recombination events after mitochondrial fusion. Recently, our lab described highly chimeric mitogenomes in two somatic hybrids between the SolanaceaeNicotiana tabacumandHyoscyamus nigerresulting from interparental homologous recombination. To better examine the recombination map in somatic hybrid mitochondria, we developed a more sensitive bioinformatic strategy to detect recombination activity based on high-throughput sequencing without assembling the hybrid mitogenome. We generated a new intergeneric somatic hybrid and re-analyzed the two Solanaceae somatic hybrids. We inferred 213 homologous recombination events across repeats of 2.1 kb on average. Most of them (∼80%) were asymmetrical, consistent with the break-induced replication (BIR) pathway. Only rare (2.74%) non-homologous events were detected. Interestingly, independent events frequently occurred in the same regions within and across somatic hybrids, suggesting the existence of recombination hotspots in plant mitogenomes. BIR is the main pathway of interparental recombination in somatic hybrid mitochondria. Likewise, under the fusion compatibility model of mitochondrial horizontal transfer, foreign mitochondria fuse with those in the recipient cell and their genomes likely recombine via BIR, resulting in the integration and/or loss of mitochondrial DNA. Findings of this study are also relevant to mitogenome editing assays.HighlightWe show that the chimeric mitochondrial genomes of somatic hybrids result from one of the three described homologous recombination pathways (BIR), mimicking the fusion compatibility model for plant HGT.
Fully automated detection of dendritic spines in 3D live cell imaging data using deep convolutional neural networks
Authors: Vogel Fabian W. , Alipek Sercan , Eppler Jens-Bastian , Triesch Jochen , Bissen Diane , Acker-Palmer Amparo , Rumpel Simon , Kaschube Matthias 
Published: January 2023

AbstractDendritic spines are considered a morphological proxy for excitatory synapses, rendering them a target of many different lines of research. Over recent years, it has become possible to image simultaneously large numbers of dendritic spines in 3D volumes of neural tissue. In contrast, currently no automated method for spine detection exists that comes close to the detection performance reached by human experts. However, exploiting such datasets requires new tools for the fully automated detection and analysis of large numbers of spines. Here, we developed an efficient analysis pipeline to detect large numbers of dendritic spines in volumetric fluorescence imaging data. The core of our pipeline is a deep convolutional neural network, which was pretrained on a general-purpose image library, and then optimized on the spine detection task. This transfer learning approach is data efficient while achieving a high detection precision. To train and validate the model we generated a labelled dataset using five human expert annotators to account for the variability in human spine detection. The pipeline enables fully automated dendritic spine detection and reaches a near human-level detection performance. Our method for spine detection is fast, accurate and robust, and thus well suited for large-scale datasets with thousands of spines. The code is easily applicable to new datasets, achieving high detection performance, even without any retraining or adjustment of model parameters.
Moderating carbohydrate digestion rate promotes metabolic flexibility in mice
Authors: Hayes Anna M.R. , Swackhamer Clay , Quezada-Calvillo Roberto , Butte Nancy F. , Sterchi Erwin E. , Nichols Buford L. , Hamaker Bruce R. 
Published: January 2023

AbstractSuperior metabolic flexibility, or the ability to efficiently switch between oxidation of carbohydrate and fat, is inversely associated with obesity and type 2 diabetes. This study examined the impact of dietary carbohydrate digestion rate on metabolic substrate utilization and metabolic flexibility. We employed percent relative cumulative frequency (PRCF) analyses coupled with a new application of modeling using the Mixed Weibull Cumulative Distribution function to examine respiratory exchange ratio (RER) data from wild-type mice and mice lacking the mucosal maltase-glucoamylase enzyme (Mgam, null) under different dietary carbohydrate conditions. We further devised a Metabolic Flexibility Factor (MFF) to quantitate metabolic flexibility, with higher MFF indicating higher metabolic flexibility. The collective results indicated that a diet high in slowly digestible starch exhibited higher metabolic flexibility (MFF) than diets high in resistant starch, sucrose, or fat. These findings show a new-found benefit of consuming slowly digestible carbohydrates for improved metabolic health.
Comparative Transcriptome Profiling Provides Insights into the Growth Promotion Activity ofPseudomonas fluorescensstrain SLU99 in Tomato and Potato Plants
Authors: binti Hanifah Nurul Atilia Shafienaz , Ghadamgahi Farideh , Ghosh Samrat , Ortiz Rodomiro , Whisson Stephen C. , Vetukuri Ramesh R. , Kalyandurg Pruthvi B. 
Published: January 2023

AbstractThe use of biocontrol agents with plant growth-promoting activity has emerged as an approach to support sustainable agriculture. During our field evaluation of potato plants treated with biocontrol rhizobacteria, four bacteria were associated with increased plant height. Using two important solanaceous crop plants, tomato and potato, we carried out a comparative analysis of the growth-promoting activity of the four bacterial strains:Pseudomonas fluorescensSLU99,Serratia plymuthicaS412,S. rubidaeaAV10, andS. rubidaeaEV23. Greenhouse andin vitroexperiments showed thatP. fluorescensSLU99 promoted plant height, biomass accumulation, and yield of potato and tomato plants, while EV23 promoted growth in potato but not in tomato plants. SLU99 induced the expression of plant hormone-related genes in potato and tomato, especially those involved in maintaining homeostasis of auxin, cytokinin, gibberellic acid and ethylene. Our results reveal potential mechanisms underlying the growth promotion and biocontrol effects of these rhizobacteria and suggest which strains may be best deployed for sustainably improving crop yield.
Target complementarity in cnidarians supports a common origin for animal and plant microRNAs
Authors: Admoni Yael , Fridrich Arie , Razin Talya , Salinas-Saavedra Miguel , Rabani Michal , Frank Uri , Moran Yehu 
Published: January 2023

AbstractmicroRNAs (miRNAs) are important post-transcriptional regulators that activate silencing mechanisms by annealing to mRNA transcripts. While plant miRNAs match their targets with nearly-full complementarity leading to mRNA cleavage, miRNAs in most animals require only a short sequence called ‘seed’ to inhibit target translation. Recent findings showed that miRNAs in cnidarians, early-branching metazoans, act similarly to plant miRNAs, by exhibiting full complementarity and target cleavage; however, it remained unknown if seed- based regulation was possible in cnidarians. Here, we investigate the miRNA-target complementarity requirements for miRNA activity in the cnidarianNematostella vectensis. We show that bilaterian-like complementarity of seed-only or seed and supplementary 3’ matches are insufficient for miRNA-mediated knockdown. Furthermore, miRNA-target mismatches in the cleavage site decrease knockdown efficiency. Finally, miRNA silencing of a target with three seed binding sites in the 3’ untranslated region that mimics typical miRNA targeting was repressed in zebrafish but not inNematostellaandHydractinia symbiolongicarpus. Altogether, these results unravel striking similarities between plant and cnidarian miRNAs consolidating the evidence for common evolutionary origin of miRNAs in plants and animals.
Early life experience with natural odors modifies olfactory behavior through an associative process
Authors: Dylla Kristina V. , O’Connell Thomas F. , Hong Elizabeth J. 
Published: January 2023

ABSTRACTPast work has shown that chronic exposure ofDrosophilato intense monomolecular odors in early life leads to homeostatic adaptation of olfactory neural responses and behavioral habituation to the familiar odor. Here, we found that, in contrast, persistent exposure to natural odors in early life increases behavioral attraction selectively to familiar odors. Odor experience increases the attractiveness of natural odors that are innately attractive and decreases the aversiveness of natural odors that are innately aversive. These changes in olfactory behavior are unlikely to arise from changes in the sensitivity of olfactory neurons at the first stages of olfactory processing: odor-evoked output from antennal lobe projection neurons was unchanged by chronic exposure to natural odors in terms of olfactory sensitivity, relational distances between odors, or response dynamics. We reveal a requirement for additional features of the environment beyond the odor in establishing odor experience-dependent behavioral plasticity. Passive odor exposure in a featureless environment lacking strong reinforcing cues was insufficient to elicit changes in olfactory preference; however, the same odor exposure resulted in behavioral plasticity when food was present in the environment. Together, these results indicate that behavioral plasticity elicited by persistent exposure to natural odors in early life is mediated by an associative process. In addition, they highlight the importance of using naturalistic odor stimuli for investigating olfactory function.
Astrocytic L-lactate signaling in the anterior cingulate cortex is essential for schema memory and neuronal mitochondrial biogenesis
Authors: Akter Mastura , Hasan Mahadi , Ramkrishnan Aruna Surendran , Zheng Xianlin , Iqbal Zafar , Fu Zhongqi , Lei Zhuogui , Karim Anwarul , Li Ying 
Published: January 2023

AbstractAstrocyte-derived L-lactate was shown to confer beneficial effects on synaptic plasticity and cognitive functions. However, how astrocytic Gisignaling in the anterior cingulate cortex (ACC) modulates L-lactate levels and schema memory is not clear. Here, using chemogenetic approach and well-established behavioral paradigm, we demonstrate that astrocytic Gipathway activation in ACC causes significant impairment in flavor-place paired associates (PA) learning, schema formation, and PA memory retrieval in rats. It also impairs new PA learning even if a prior associative schema exists. These impairments were mediated by decreased L-lactate in ACC due to astrocytic Giactivation. Concurrent exogenous L-lactate administration bilaterally into the ACC rescues these impairments. Furthermore, we show that the impaired schema memory formation was associated with a decreased neuronal mitochondrial biogenesis caused by decreased L-lactate level in ACC upon Giactivation. Our study also reveals that L-lactate mediated mitochondrial biogenesis is dependent on monocarboxylate transporter 2 and NMDA receptor activity – discovering a previously unrecognized signaling role of L-lactate. These findings expand our understanding of the role of astrocytes and L-lactate in brain functions.
Electron transport chain RNAi in glutamate neurons extends life span, increases sleep, and decreases locomotor activity inDrosophila melanogaster
Authors: Landis Jessie E. , Sungu Kevin , Sipe Hannah , Copeland Jeffrey M. 
Published: January 2023

AbstractRNAi targeting the electron transport chain has been proven to prolong life span in many different species, and experiments specifically withDrosophila melanogasterandCaenorhabditis eleganshave shown a distinct role for neurons. To determine which subset of neurons is implicated in this life span extension, we used the GAL4/UAS system to activate RNAi against genes of Complex I and Complex V. We found life span extension of 18 – 24% with two glutamate neuron (D42andVGlut) GAL4 lines. We used the GAL80 system to determine if the overlapping set of glutamate neurons in these two GAL4 lines imparts the life span extension. Limiting GAL4 activity to non-VGlutglutamate neurons in theD42background failed to extend life span, suggesting that glutamate neurons have a unique role in aging. Interestingly, RNAi of the electron transport chain inD42glutamate neurons also caused an increase in daytime and nighttime sleep and a decrease in nighttime locomotor activity. Changes to sleep patterns and prolonged life span were not accompanied by any changes in female fertility or response to starvation. Our findings demonstrate that a small subset of neurons can control life span, and further studies exploring the role of the electron transport chain in aging can be focused on the activity of glutamate neurons.
A pilot study of stable isotope fractionation inBombyx morirearing
Authors: Hao Li , He Yujie , Lu Jinzhong , Jia Liling , Liu Yong , Yang Dan , Shao Shuai , Lv Gang , Yang Hailiang , Zheng Hailing , Cui Xuhong , Zhou Yang , Peng Zhiqin 
Published: January 2023

AbstractHydrogen, oxygen, carbon, and nitrogen isotopes derived from three different strains of silkworms at different life stages involved in silkworm rearing, were measured to understand the fractionation characteristics of stable isotopes at different stages of silkworm development, and to trace the movement of these isotopes from food to larva to excrement and finally to silk. We found that silkworm strain had little effect on δ2H, δ18O and δ13C values. However, a large difference was found in the δ15N levels of newly-hatched silkworms between Jingsong Haoyue and Hua Kang No.3 orthogonal strains, suggesting that the mating and egg laying differences may result in an inconsistent kinetic nitrogen isotope fractionation. The δ13C values of silkworm pupae and silkworm cocoon also displayed significant differences, suggesting that heavy carbon isotopes are greatly fractionated from the larva to the silk during cocoon formation. Overall, these results may be used to clarify the relationship between isotope fractionation and the ecological process of theBombyx moriand expand our ability to resolve stable isotope anomalies at a small regional-scale level.
Simultaneous Determination of the Size and Shape of Single α-Synuclein Oligomers in Solution
Authors: Awasthi Saurabh , Ying Cuifeng , Li Jiali , Mayer Michael 
Published: January 2023

AbstractSoluble oligomers of amyloid-forming proteins are implicated as toxic species in the context of several neurodegenerative diseases. Since the size and shape of these oligomers influences their toxicity, their biophysical characterization is essential for a better understanding of the structure-toxicity relationship. Amyloid oligomers are difficult to characterize by conventional approaches due to their heterogeneity in size and shape, their dynamic aggregation process, and their low abundance. This paper demonstrates that resistive-pulse measurements using polymer-coated solid-state nanopores enable single-particle level characterization of the size and shape of individual αSyn oligomers in solution within minutes. A comparison of the resulting size distribution with single-particle analysis by transmission electron microscopy and mass photometry reveals that nanopore-based characterization agrees well with both methods, while providing better size resolution and elucidating that αSyn samples are composed of stable oligomer sub-populations that contain multiples of approximately 12 monomers (i.e., 12-, 24-, 48-, 60-, 84-mers). Applying the unique capability of nanopores to approximate particle size and shape to picomolar concentrations of αSyn oligomers in the putatively toxic size range, revealed shapes that agree well with previous estimates by cryo-EM with the added advantage that nanopore-based analysis occurs rapidly, in solution, and has the potential to become a widely accessible technique.
Glial-dependent clustering of voltage-gated ion channels in Drosophila precedes myelin formation
Authors: Rey Simone , Ohm Henrike , Moschref Frederieke , Zeuschner Dagmar , Klämbt Christian 
Published: January 2023

AbstractNeuronal information conductance depends on transmission of action potentials. The conductance of action potentials is based on three physical parameters: The axial resistance of the axon, the axonal insulation by glial membranes, and the positioning of voltage-gated ion channels. In vertebrates, myelin and channel clustering allow fast saltatory conductance. Here we show that inDrosophila melanogastervoltage-gated sodium and potassium channels, Para and Shal, co-localize and cluster in an area of motor axons resembling the axon initial segment. Para but not Shal localization depends on peripheral glia. In larvae, relatively low levels of Para channels are needed to allow proper signal transduction and nerves are simply wrapped by glial cells. In adults, the concentration of Para at the axon initial segment increases. Concomitantly, these axon domains are covered by a mesh of glial processes forming a lacunar structure that serves as an ion reservoir. Directly flanking the voltage-gated ion channel rich axon segment, the lacunar structures collapse forming a myelin-like insulation. Thus, Drosophila development may reflect the evolution of myelin which forms in response to increased levels of clustered voltage-gated ion channels.One-Sentence SummaryEvolution of saltatory conductance is mirrored in fly development where glia dependent clustering of voltage-gated ion channels precedes myelination.
A Multiscale Protein Abundance Structured Population Kinetic Model Systematically Explores the Design Space of Constitutive and Inducible CAR-T cells
Authors: Rajakaruna Harshana , Desai Milie , Das Jayajit 
Published: January 2023

AbstractEngineered chimeric antigen receptor (CAR)-T cells are designed to bind to antigens overexpressed on the surface of tumor cells and induce tumor cell lysis. However, healthy cells can express these antigens at lower abundances and can get lysed by CAR-T cells. A wide variety of CAR-T cells have been designed that increase tumor cell elimination while decreasing destruction of healthy cells. However, given the cost and labor-intensive nature of such efforts, a systematic exploration of potential hypotheses becomes limited. To this end, we develop a framework (PASCAR) by combining multiscale population dynamic models and multi-objective optimization approaches with data obtained from published cytometry and cytotoxicity assays to systematically explore design space of constitutive and tunable CAR-T cells. We demonstrate PASCAR can quantitatively describe in vitro and in vivo results for constitutive and inducible CAR-T cells and can successfully predict experiments outside the training data. Our exploration of the CAR design space reveals that CAR affinities in an intermediate range of dissociation constants (KD) in constitutive and tunable CAR-T cells can dramatically decrease healthy cell lysis but sustain a high rate of tumor cell killing. In addition, our modeling provides guidance towards optimal tuning of CAR expressions in synNotch CAR T cells. The proposed framework can be extended for other CAR immune cells.
Linking workplace incivility and frontline employees' subjective well-being: the role of work-home enrichment and coping strategies
Authors: Tam Do Uyen , Trang Nguyen Thi Mai 
Published: January 2023

PurposeWorkplace incivility (WI) has been extensively studied. However, less is known about how WI spills over into employees' lives. Building on the work-home resources model, the authors develop a conceptual model investigating work-family enrichment (WFE) as the mediator between WI and subjective well-being (SWB) and coping strategies as the moderator of this indirect relationship.Design/methodology/approachSurvey data were gathered from 266 frontline employees (FLEs) working in different banks in Vietnam, using a convenience sampling technique. The partial least squares structural equation modeling (PLS-SEM) technique was employed.FindingsThe results show that coworker incivility (COWI) predicts a lower level of WFE, which in turn is associated with SWB, while supervisor incivility is not. The authors also found that coping strategies moderate the adverse influence of COWI on employees' WFE.Originality/valueAlthough much research has been conducted on the predictors of SWB, little is known about how WI and WFE together impact SWB, and insight into how to buffer the effects of WI are also lacking. This study thus fills a gap in the literature. Implications for theory, practice and future research are discussed.
The effect of formal financial accessibility on love money investment
Authors: Pinto-Gutierrez Cristian , Romaní Gianni , Atienza Miguel 
Published: January 2023

Purpose
This paper aims to analyse whether the degree of formal financial access in a country affects love money investment, defined as capital provided to entrepreneurs from family and friends to finance their businesses, in early-stage entrepreneurial activities.

Design/methodology/approach
The authors use multilevel mixed-effect regression models and an extensive database of over 700 thousand individuals from 53 countries between 2007 and 2017 taken from the Global Entrepreneurship Monitor adult population survey.

Findings
This paper finds that a country’s level of accessibility to bank debt and venture capital is positively associated with the likelihood of an individual becoming a love money investor. It also finds that the amount of capital invested by love money investors is positively correlated to the level of access to bank debt and venture capital. The results of this paper confirm the hypothesis of complementarity between the financial system and friends and family financing in the capital market for early-stage entrepreneurs.

Originality/value
This paper contributes to the entrepreneurial finance literature, particularly to a better understanding of the love money investors, an important source of funding and segment of the informal investment that is sparsely studied.