bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a NanoBRET assay for evaluation of 14-3-3σ molecular glues
Authors: Vickery Holly R. , Virta Johanna M. , Konstantinidou Markella , Arkin Michelle R.
Published: January 2024

We report the development of a 384-well formatted NanoBRET assay to characterize molecular glues of 14-3-3/client interactions in living cells. The seven isoforms of 14-3-3 are dimeric hub proteins with diverse roles including transcription factor regulation and signal transduction. 14-3-3 interacts with hundreds of client proteins to regulate their function and is therefore an ideal therapeutic target when client selectivity can be achieved. We have developed the NanoBRET system for three 14-3-3σ client proteins CRAF, TAZ, and estrogen receptor α (ERα), which represent three specific binding modes. We have measured stabilization of 14-3-3σ/client complexes by molecular glues with EC50values between 100 nM and 1 μM in cells, which align with the EC50values calculated by fluorescence anisotropy in vitro. Developing this NanoBRET system for the hub protein 14-3-3σ allows for a streamlined approach, bypassing multiple optimization steps in the assay development process for other 14-3-3σ clients. The NanoBRET system allows for an assessment of PPI stabilization in a more physiologically relevant, cell-based environment using full-length proteins. The method is applicable to diverse protein-protein interactions (PPIs) and offers a robust platform to explore libraries of compounds for both PPI stabilizers and inhibitors.

Abstract Figure
Kinetoplastid kinetochore proteins KKT14-KKT15 are divergent Bub1/BubR1-Bub3 proteins
Authors: Ballmer Daniel , Carter William , van Hooff Jolien J. E. , Tromer Eelco C. , Ishii Midori , Ludzia Patryk , Akiyoshi Bungo
Published: January 2024

Faithful transmission of genetic material is crucial for the survival of all organisms. In many eukaryotes, a feedback control mechanism called the spindle checkpoint ensures chromosome segregation fidelity by delaying cell cycle progression until all chromosomes achieve proper attachment to the mitotic spindle. Kinetochores are the macromolecular complexes that act as the interface between chromosomes and spindle microtubules. While most eukaryotes have canonical kinetochore proteins that are widely conserved, kinetoplastids such asTrypanosoma bruceihave a seemingly unique set of kinetochore proteins including KKT1–25. Available evidence suggests thatT. bruceilacks components of the spindle checkpoint and is unable to delay cell cycle progression in response to spindle defects. It therefore remains poorly understood how kinetoplastids regulate cell cycle progression or ensure chromosome segregation fidelity. Here, we report a crystal structure of the C-terminal domain of KKT14 fromApiculatamorpha spiralisand uncover that it is a pseudokinase. Its structure is most similar to the kinase domain of Bub1, a key component of the spindle checkpoint in other eukaryotes. In addition, KKT14 inT. bruceiand other trypanosomatids has a putative ABBA motif that is present in Bub1 and its paralog BubR1. We also find that the N-terminal part of KKT14 interacts with KKT15, whose WD40 repeat beta-propeller is phylogenetically closely related to a direct interactor of Bub1/BubR1 called Bub3. Our findings indicate that KKT14-KKT15 are divergent orthologs of Bub1/BubR1-Bub3, which promote accurate chromosome segregation in trypanosomes.
Uncovering the Elusive Structures and Mechanisms of Prevalent Antidepressants
Authors: Lin Jieye , Bu Guanhong , Unge Johan , Gonen Tamir
Published: January 2024

Most treatments to alleviate major depression work by either inhibiting human monoamine transporters, vital for the reuptake of monoamine neurotransmitters, or by inhibiting monoamine oxidases, which are vital for their degradation. The analysis of the experimental 3D structures of those antidepressants in their drug formulation state is key to precision drug design and development. In this study, we apply microcrystal electron diffraction (MicroED) to reveal the atomic 3D structures for the first time of five of the most prevalent antidepressants (reboxetine, pipofezine, ansofaxine, phenelzine, bifemelane) directly from the commercially available powder of the active ingredients. Their modes of binding are investigated by molecular docking, revealing the essential contacts and conformational changes into the biologically active state. This study underscores the combined use of MicroED and molecular docking to uncover elusive drug structures and mechanisms to aid in further drug development pipelines.
Epstein–Barr Virus BALF0/1 Subverts the Caveolin and ERAD Pathways to Target B-cell Receptor Complexes for Degradation
Authors: Yiu Stephanie Pei Tung , Weekes Michael , Gewurz Benjamin E.
Published: January 2024

Epstein–Barr virus (EBV) establishes persistent infection, causes infectious mononucleosis, is a major trigger for multiple sclerosis and contributes to multiple cancers. Yet, knowledge remains incomplete about how the virus remodels host B cells to support lytic replication. We previously identified that EBV lytic replication results in selective depletion of plasma membrane B-cell receptor (BCR) complexes, comprised of immunoglobulin and the CD79A and CD79B signaling chains. Here, we used proteomic and biochemical approaches to identify that the EBV early lytic protein BALF0/1 is responsible for EBV lytic cycle BCR degradation. Mechanistically, an immunoglobulin heavy chain cytoplasmic tail KVK motif was required for ubiquitin-mediated BCR degradation, while CD79A and CD79B were dispensable. BALF0/1 subverted caveolin-mediated endocytosis to internalize plasma membrane BCR complexes and to deliver them to the endoplasmic reticulum. BALF0/1 stimulated immunoglobulin heavy chain cytoplasmic tail ubiquitination, which together with the ATPase valosin-containing protein/p97 drove ER-associated degradation of BCR complexes by cytoplasmic proteasomes. BALF0/1 knockout reduced the viral load of secreted EBV particles from B-cells that expressed a monoclonal antibody against EBV glycoprotein 350 and increased viral particle immunoglobulin incorporation. Consistent with downmodulation of plasma membrane BCR, BALF0/1 overexpression reduced viability of a diffuse large B-cell lymphoma cell line dependent upon BCR signaling. Collectively, our results suggest that EBV BALF0/1 downmodulates immunoglobulin upon lytic reactivation to block BCR signaling and support virion release.

SIGNIFICANCE

EBV uses a biphasic lifecycle, in which it switches between a latent state that facilitates immune evasion and a lytic state, where virion are secreted. However, when EBV infects a B-cell that makes antibody against a virion protein, EBV must have a strategy to escape becoming trapped, since maturing virion and antibody each traffic through the secretory pathway. We identified that an EBV-encoded protein expressed, BALF0/1, associates with and targets immunoglobulin complexes for degradation. Intriguingly, BALF0/1 subverts the caveolin-1 and ERAD pathways to route antibody from the plasma membrane to cytoplasmic proteasomes for degradation. We present evidence that this enhances EBV secretion from cells that produce antibody against a viral glycoprotein, which could otherwise trap virus.
The volitional control of individual motor units is constrained within low-dimensional neural manifolds by common inputs
Authors: Rossato Julien , Avrillon Simon , Tucker Kylie , Farina Dario , Hug François
Published: January 2024

Abstract

The implementation of low-dimensional movement control by the central nervous system has been debated for decades. In this study, we investigated the dimensionality of the control signals received by spinal motor neurons when controlling either the ankle or knee joint torque. We first identified the low-dimensional latent factors underlying motor unit activity during torque- matched isometric contractions. Subsequently, we evaluated the extent to which motor units could be independently controlled. To this aim, we used an online control paradigm in which participants received the corresponding motor unit firing rates as visual feedback. We identified two main latent factors, regardless of the muscle group (vastus lateralis-medialis and gastrocnemius lateralis-medialis). The motor units of the gastrocnemius lateralis could be controlled largely independently from those of the gastrocnemius medialis during ankle plantarflexion. This dissociation of motor unit activity imposed similar behavior to the motor units that were not displayed in the feedback. Conversely, it was not possible to dissociate the activity of the motor units between the vastus lateralis and medialis muscles during the knee extension tasks. These results demonstrate that the number of latent factors estimated from linear dimensionality reduction algorithms does not necessarily reflect the dimensionality of volitional control of motor units. Overall, individual motor units were never controlled independently of all others but rather belonged to synergistic groups. Together, these findings provide evidence for a low-dimensional control of motor units constrained by common inputs, with notable differences between muscle groups.

Significance statement

In this study, we initially examined the latent factors underlying motor unit activity in the vastii or gastrocnemii muscles during torque-matched isometric contractions. We then explored the extent to which these motor units could be controlled independently, using an online control paradigm where participants received visual information on motor unit firing rates. Although participants were able to dissociate the activity of a few motor unit pairs (from the gastrocnemius medialis and lateralis muscles), our results provide direct evidence of a low- dimensional control, constrained by common inputs, limiting flexibility in motor unit recruitment. Furthermore, we show that the number of latent factors identified by dimensionality reduction algorithms does not necessarily reflect the dimensionality of volitional control of motor units.
Implication of structural constrains facilitating the functional evolution ofPseudomonas aeruginosaKPR2 into a versatile α-keto acid reductase
Authors: Choudhury Gourab Basu , Datta Saumen
Published: January 2024

Protein structure and function dynamics in molecular evolution are intertwined. Theoretical concepts linking structure, function, and evolution of a protein, while often intuitive, necessitate validation through investigations in real-world systems. Our study empirically explores the implications of multiple panE2 gene copies in an organism, shedding light on the functional roles and evolutionary trajectories ofPseudomonas aeruginosa’ssecond copy of Ketopantoate reductase (PaKPR2) and its inactivity against the natural substrate Ketopantoate. Evolutionary changes in functional traits were examined around the active site through crystal structures and biochemical analysis. Primarily, apoKPR2 structures reveal a transformed active site cleft, forming a two-sided pocket, while substrate entry is regulated by a molecular gate. Despite cleft closure, molecular interaction properties and activity analysis of PaKPR2 suggest that it can be a versatile keto-acid reductase. However, detailed structural insights from the ligand-bound binary complex of PaKPR2-NADPH and PaKPR2-Ketoisoleucine reveal that the ligand-binding interactions at the active site are conserved and restricted to the molecules of appropriate shape and size that can be accommodated in the available space. Finally, a ternary complex structure, PaKPR2-NADP+-KIC, was solved to understand its functional evolution in terms of the residue microenvironment at the catalytic site. Collectively, the results give detailed visual experiences of different structural perspectives of the protein’s functional evolution.
Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment
Authors: Tarau Daniela , Grünberger Felix , Pilsl Michael , Reichelt Robert , Heiß Florian , König Sabine , Urlaub Henning , Hausner Winfried , Engel Christoph , Grohmann Dina
Published: January 2024

Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery ofPyrococcus furiosus(Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly,PfuSpt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activityin vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation.
Identification and validation of ITS2-specific universal primers for DNA barcoding in plants
Authors: Bhat Ajay R , Hegde Subrahmanya , Kammar Supriya S , Muthamma MB , Mudgal Gaurav , R Charukesi , Mohan Thotegowdanapalya C
Published: January 2024

Accurate identification of plant species is fundamental for various purposes, including biodiversity conservation and effective utilization of plants. Molecular-based techniques, particularly DNA barcoding, have emerged as a rapid and accurate alternative to traditional taxonomic methods for plant species identification. DNA barcoding involves analysing specific DNA regions to classify and identify organisms. Among different barcode markers, internal transcribed spacer 2 (ITS2) has gained prominence due to its shorter length and ease of sequencing. In this study we present a comprehensive survey of the literature, identifying a universal set of primers for ITS2 and validating their universality through in silico and in vitro analyses. This manuscript provides valuable insights into establishing a standardized approach for DNA barcoding using ITS2, helping researchers select appropriate primers for accurate plant species identification and classification. Standardized universal primers alleviate the time-consuming primer selection process, promoting efficient and reliable DNA barcoding practices within the plant scientific community.
Timely lagging strand maturation relies on Ubp10-mediated PCNA dissociation from replicating chromatin
Authors: Zamarreño Javier , Muñoz Sofía , Alonso Esmeralda , Alcalá Macarena , Bermejo Rodrigo , Sacristán María P. , Bueno Avelino
Published: January 2024

Synthesis and maturation of Okazaki Fragments is an incessant and highly efficient metabolic process completing the synthesis of the lagging strands at replication forks during S phase. Accurate Okazaki fragment maturation (OFM) is crucial to maintain genome integrity and, therefore, cell survival in all living organisms. In eukaryotes, OFM involves the consecutive action of DNA polymerase Pol ∂, 5’ Flap endonuclease Fen1 and DNA ligase I, and constitutes the best example of a sequential process coordinated by the sliding clamp PCNA. For OFM to occur efficiently, cooperation of these enzymes with PCNA must be highly regulated. Here, we present evidence of a role for the PCNA-deubiquitylase Ubp10 in the maturation of Okazaki fragments in the budding yeastSaccharomyces cerevisiae. We show that Ubp10 associates with lagging-strand DNA synthesis machineries on replicating chromatin to ensure timely ligation of Okazaki fragments by promoting an Elg1ATAD5-independent PCNA unloading mechanism.

This document was written without the use of AI.
The origin, deployment, and evolution of a plant-parasitic nematode effectorome
Authors: Molloy Beth , Shin Dio S. , Long Jonathan , Pellegrin Clement , Senatori Beatrice , Vieira Paulo , Thorpe Peter , Damm Anika , Ahmad Mariam , Vermeulen Kerry , Derevnina Lida , Wei Siyuan , Sperling Alexis , Estévez Estefany Reyes , Bruty Samuel , Moura de Souza Victor Hugo , Kranse Olaf Prosper , Maier Tom , Baum Thomas , Eves-van den Akker Sebastian
Published: January 2024

Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode.

To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematodeHeterodera schachtiiat three key life-stages. We define 659 effector gene loci: 293 “known” high-confidence homologs of plant-parasitic nematode effectors, and 366 “novel” effectors with high gland cell expression. In doing so we define a comprehensive “effectorome” of a plant-parasitic nematode.

Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the comprehensive effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.
MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography
Authors: Lamm Lorenz , Zufferey Simon , Righetto Ricardo D. , Wietrzynski Wojciech , Yamauchi Kevin A. , Burt Alister , Liu Ye , Zhang Hanyi , Martinez-Sanchez Antonio , Ziegler Sebastian , Isensee Fabian , Schnabel Julia A. , Engel Benjamin D. , Peng Tingying
Published: January 2024

Abstract

MemBrain v2 is a deep learning-enabled program aimed at the efficient analysis of membranes in cryo-electron tomography (cryo-ET). The final v2 release of MemBrain will comprise three main modules: 1) MemBrain-seg, which provides automated membrane segmentation, 2) MemBrain-pick, which provides automated picking of particles along segmented membranes, and 3) MemBrain-stats, which provides quantitative statistics of particle distributions and membrane morphometrics.

This initial version of the manuscript is focused on the beta release of MemBrain-seg, which combines iterative training with diverse data and specialized Fourier-based data augmentations. These augmentations are specifically designed to enhance the tool’s adaptability to a variety of tomographic data and address common challenges in cryo-ET analysis. A key feature of MemBrain-seg is the implementation of the Surface-Dice loss function, which improves the network’s focus on membrane connectivity and allows for the effective incorporation of manual annotations from different sources. This function is beneficial in handling the variability inherent in membrane structures and annotations. Our ongoing collaboration with the cryo-ET community plays an important role in continually improving MemBrain v2 with a wide array of training data. This collaborative approach ensures that MemBrain v2 remains attuned to the field’s needs, enhancing its robustness and generalizability across different types of tomographic data.

The current version of MemBrain-seg is available athttps://github.com/teamtomo/membrain-seg, and the predecessor of MemBrain-pick (also called MemBrain v1) is deposited athttps://github.com/CellArchLab/MemBrain. This preprint will be updated concomitantly with the code until the three integrated modules of MemBrain v2 are complete.
Pathogen infection induces sickness behaviors by recruiting neuromodulatory systems linked to stress and satiety inC. elegans
Authors: Pradhan Sreeparna , Madan Gurrein K. , Kang Di , Bueno Eric , Atanas Adam A. , Kramer Talya S. , Dag Ugur , Lage Jessica D. , Gomes Matthew A. , Lu Alicia Kun-Yang , Park Jungyeon , Flavell Steven W.
Published: January 2024

When animals are infected by a pathogen, peripheral sensors of infection signal to the brain to coordinate a set of adaptive behavioral changes known as sickness behaviors. While the pathways that signal from the periphery to the brain have been intensively studied in recent years, how central circuits are reconfigured to elicit sickness behaviors is not well understood. Here we find that neuromodulatory systems linked to stress and satiety are recruited upon infection to drive sickness behaviors inC. elegans. Upon chronic infection by the bacteriumPseudomonas aeruginosaPA14,C. elegansdecrease their feeding behavior, then display reversible bouts of quiescence, and eventually die. The ALA neuron and its neuropeptides FLP-7, FLP-24, and NLP-8, which control stress-induced sleep in uninfected animals, promote the PA14-induced feeding reduction. However, the ALA neuropeptide FLP-13 instead acts to delay quiescence and death in infected animals. Cell-specific genetic perturbations show that the neurons that release FLP-13 to delay quiescence in infected animals are distinct from ALA. A brain-wide imaging screen reveals that infection-induced quiescence involves ASI and DAF-7/TGF-beta, which control satiety-induced quiescence in uninfected animals. Our results suggest that a common set of neuromodulators are recruited across different physiological states, acting from distinct neural sources and in distinct combinations to drive state-dependent behaviors.
A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models
Authors: Puray-Chavez Maritza , Eschbach Jenna E. , Xia Ming , LaPak Kyle M. , Zhou Qianzi , Jasuja Ria , Pan Jiehong , Xu Jian , Zhou Zixiang , Mohammed Shawn , Wang Qibo , Lawson Dana Q. , Djokic Sanja , Hou Gaopeng , Ding Siyuan , Brody Steven L. , Major Michael B. , Goldfarb Dennis , Kutluay Sebla B.
Published: January 2024

Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. Here we report that SARS-CoV-2 replication is restricted at a post-entry step in a number of ACE2-positive airway-derived cell lines due to tonic activation of the cGAS-STING pathway mediated by mitochondrial DNA leakage and naturally occurring cGAS and STING variants. Genetic and pharmacological inhibition of the cGAS-STING and type I/III IFN pathways as well as ACE2 overexpression overcome these blocks. SARS-CoV-2 replication in STING knockout cell lines and primary airway cultures induces ISG expression but only in uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway in productively infected cells. Pharmacological inhibition of STING in primary airway cells enhances SARS-CoV-2 replication and reduces virus-induced innate immune activation. Together, our study highlights that tonic activation of the cGAS-STING and IFN pathways can impact SARS-CoV-2 cellular tropism in a manner dependent on ACE2 expression levels.
A Functional Analysis of a Resorbable Citrate-based Composite Tendon Anchor
Authors: Thirumaran Arun , Poudel Anup , Sankar Magesh , Doulgkeroglou Meletios , Easley Jeremiah , Gadomski Ben , Biggs Manus
Published: January 2024

Orthopaedic fixation seeks solutions to the challenges of non-union, reconstructive surgery, and soft tissue injuries by providing stability and tissue alignment during the healing process. Risks associated with fixation devices such as peri-implant resorption, implant loosening and sub-optimal device resorption remain a significant challenge in the development of transient fixation devices. Osteomimetic biomaterials, and in particular, bio-resorbable polymer composites designed to match the mineral phase content of native bone have been shown to exhibit osteoinductive and osteoconductive propertiesin vivoand have been used in bone fixation for the past 2 decades. However, the specific signalling pathways driving the osteogenic response to these biomaterials remain largely unknown.

In this study a resorbable, bioactive, and mechanically robust citrate-based composite, formulated from poly(octamethylene citrate) (POC) and hydroxyapatite (HA) (POC-HA) was investigated as a potential orthopedic biomaterial.In vitroanalysis with human Mesenchymal Stem Cells (hMSCs) indicated that POC-HA composite materials supported cell adhesion, growth, and proliferation and increased calcium deposition, alkaline phosphatase production, the expression of osteogenic specific genes and activation of canonical pathways leading to osteoinduction and osteoconduction. Furtherin vivoevaluation of a POC-HA tendon fixation device in a sheep metaphyseal model indicated the regenerative and remodelling potential of this citrate-based composite material in orthopedic applications.
Deuteration of proteins boosted by cell lysates: high-resolution amide and Hα MAS NMR without re-protonation bottleneck
Authors: Napoli Federico , Guan Jia-Ying , Arnaud Charles-Adrien , Macek Pavel , Fraga Hugo , Breyton Cécile , Schanda Paul
Published: January 2024

Amide-proton detected magic-angle spinning NMR of deuterated proteins has become a main technique in NMR-based structural biology. In standard deuteration protocols that rely on D2O-based culture media, non-exchangeable amide sites remain deuterated, making these sites unobservable. Here we demonstrate that proteins produced with H2O-based culture medium doped with deuterated cell lysate allow to overcome this “reprotonation bottleneck”, while retaining a high level of deuteration (ca. 80 %) and narrow line widths. We quantified coherence life times of several proteins prepared with this labelling pattern over a range of MAS frequencies (40-100 kHz). We demonstrate that under commonly used conditions (50-60 kHz MAS), amide1H line widths with our labelling approach are comparable to those of perdeuterated proteins and better than those of protonated samples at 100 kHz. For three proteins in the 33-50 kDa size range many previously unobserved amides become visible. We report how to prepare the deuterated cell lysate for our approach from fractions of perdeuterated cultures which are usually discarded, and show that such media can be used identically to commercial media. The residual protonation of Hα sites allows for well-resolved Hα-detected spectra and Hα resonance assignment, exemplified by thede novoassignment of 168 Hα sites in a 39 kDa protein. The approach based on this H2O/cell-lysate deuteration and MAS frequencies compatible with 1.3 or 1.9 mm rotors presents a strong sensitivity benefit over 0.7 mm/100 kHz MAS experiments.
Phago-mixotrophy of small eukaryotic phytoplankton might alleviate iron limitation in HNLC Southern Ocean
Authors: Ong Denise Rui Ying , Gutiérrez-Rodríguez Andrés , Safi Karl A. , Marie Dominique , Selph Karen E. , Stukel Michael R. , Décima Moira , Lopes dos Santos Adriana
Published: January 2024

Small phytoplankton, consisting of pico and nano size fractions, are diverse in size and taxonomy. Yet, the differences in their productivity and taxonomic diversity are poorly described. Here, we measured the cell-specific carbon fixation rates of picocyanobacteriaSynechococcus, picoeukaryote and nanoeukaryote populations while unveiling their taxonomic composition in oligotrophic subtropical (ST) and high-nutrient low-chlorophyll subantarctic (SA) waters. We coupled 24 h in-situ radiolabelled14C incubations to flow cytometry sorting (FCM-sorting) and DNA metabarcoding from the same incubated samples, offering a direct account of the community associated with the carbon fixation rates measured. In both water masses, nanoeukaryotes had the highest cell-specific carbon fixation rate, followed by picoeukaryotes andSynechococcus(2.24±29.99, 2.18±2.08 and 0.78±0.55 fgC cell-1h-1, respectively). The cell-specific carbon fixation rates and growth rates ofSynechococcuswere 3-fold higher in ST compared to SA waters, while the rates of picoeukaryotes and nanoeukaryotes had no significant difference between the biogeochemically-contrasting water masses. Despite significant differences in their taxonomic composition, the FCM-sorted picoeukaryote and nanoeukaryote populations in SA waters were dominated by taxa with reported phago-mixotrophic strategies (Chrysophyceae, Dinophyceae and Prymnesiophyceae), suggesting phago-mixotrophy might alleviate nutrient stress in iron-limited conditions for discrete small photosynthetic eukaryote populations.
Early survival in Atlantic salmon is associated with parental genotypes at loci linked to timing of maturation
Authors: Aykanat Tutku , McLennan Darryl , Metcalfe Neil B. , Prokkola Jenni M.
Published: January 2024

Large effects loci often contain genes with critical developmental functions with potentially broad effects across life-stages. However, the life-stage-specific fitness consequences are rarely explored. In Atlantic salmon, variation in two large-effect loci,six6andvgll3, is linked to age at maturity, and several physiological and behavioural traits in early life. By genotyping the progeny of wild Atlantic salmon that were planted into natural streams with nutrient manipulations, we tested if genetic variation in these loci is associated with survival in early life. We found that higher early life survival was linked to the genotype associated with late maturation in thevgll3, but with early maturation in thesix6locus. These effects were significant in high-nutrient, but not in in low-nutrient streams. The differences in early survival were not explained by additive genetic effects in the offspring generation, but by maternal genotypes in thesix6locus, and by both parents’ genotypes in thevgll3locus. Our results suggest that indirect genetic effects by large-effect loci can be significant determinants of offspring fitness. This study demonstrates an intriguing case of how large-effect loci can exhibit complex fitness associations across life stages in the wild and indicates that predicting evolutionary dynamics is difficult.
BLADE-ON-PETIOLE interacts with CYCLOIDEA to fine-tuneCYCLOIDEA-mediated flower symmetry in Monkeyflowers (Mimulus)
Authors: Gao Yuan , Li Jingjian , He Jiayue , Yu Yaqi , Qian Zexin , Geng Zhiqiang , Yang Liuhui , Zhang Yumin , Ke Yujie , Lin Qiaoshan , Wang Jing , Chen Sumei , Chen Fadi , Yuan Yao-Wu , Ding Baoqing
Published: January 2024

Abstract

Morphological novelties, or key innovations, are instrumental to the diversification of the organisms. In plants, one such innovation is the evolution of zygomorphic flowers, which is thought to promote outcrossing and increases flower morphological diversity. We isolated three allelic mutants from twoMimulusspecies displaying altered floral symmetry and identified the causal gene as the orthologue ofArabidopsis BLADE-ON-PETIOLE. We found that MlBOP and MlCYC2a physically interact and this BOP-CYC interaction module is highly conserved across the angiosperms. Furthermore, MlBOP self-ubiquitinates and suppressesMlCYC2aself- activation. MlCYC2a, in turn, impedes MlBOP ubiquitination. Thus, this molecular tug-of-war between MlBOP and MlCYC2a fine-tunes the expression ofMlCYC2a, contributing to the formation of bilateral symmetry flowers, a key trait in angiosperm evolution.

One Sentence Summary

Molecular tug-of-war between MlBOP and MlCYC2a fine-tunes the expression ofMlCYC2a, contributing to the bilateral flower symmetry formation.
Effect of finite volume on thermodynamics of quark-hadron matter
Authors: Pal Somenath , Motornenko Anton , Vovchenko Volodymyr , Bhattacharyya Abhijit , Steinheimer Jan , Stoecker Horst
Published: January 2024

The effects of a finite system volume on thermodynamic quantities, such as the pressure, energy density, specific heat, speed of sound, conserved charge susceptibilities, and correlations, in hot and dense strongly interacting matter are studied within the parity-doublet chiral mean field model. Such an investigation is motivated by relativistic heavy-ion collisions, which create a blob of hot QCD matter of a finite volume, consisting of strongly interacting hadrons and potentially deconfined quarks and gluons. The effect of the finite volume of the system is incorporated by introducing lower momentum cutoffs in the momentum integrals appearing in the model, the numerical value of the momentum cutoff being related to the de Broglie wavelength of the given particle species. It is found that some of these quantities show a significant volume dependence, in particular, those sensitive to pion degrees of freedom, and the crossover transition is generally observed to become smoother in finite volume. These findings are relevant for the effective equation of state used in fluid dynamical simulations of heavy-ion collisions and efforts to extract the freeze-out properties of heavy-ion collisions with susceptibilities involving electric charge and strangeness.

Published by the American Physical Society
2024
Adiabatic axion-photon mixing near neutron stars
Authors: Tjemsland Jonas , McDonald Jamie , Witte Samuel J.
Published: January 2024

One of the promising new proposals to search for axions in astrophysical environments is to look for narrow radio lines produced from the resonant conversion of axion dark matter falling through the magnetospheres of neutron stars. For sufficiently strong magnetic fields, axion masses in the O(10  μeV) range, and axion-photon couplings gaγ≳10−12  GeV−1, the conversion can become hyperefficient, allowing axion-photon and photon-axion transitions to occur with O(1) probabilities. Despite the strong mixing between these particles, the observable radio flux emanating from the magnetosphere is expected to be heavily suppressed—this is a consequence of the fact that photons sourced by infalling axions have a high probability of converting back into axions before escaping the magnetosphere. In this work, we study the evolution of the axion and photon phase space near the surface of highly magnetized neutron stars in the adiabatic regime, quantifying for the first time the properties of the radio flux that arise at high axion-photon couplings. We show that previous attempts to mimic the scaling in this regime have been overly conservative in their treatment, and that the suppression can be largely circumvented for radio observations targeting neutron star populations.

Published by the American Physical Society
2024
N-Methyl-2-{3-methyl-2-[(2Z)-pent-2-en-1-yl]cyclopent-2-en-1-ylidene}hydrazinecarbothioamide
Authors: Oliveira Adriano Bof de , Bresolin Leandro , Beck Johannes , Daniels Jörg
Published: January 2024

The equimolar and hydrochloric acid-catalysed reaction between cis-jasmone and 4-methylthiosemicarbazide in ethanolic solution yields the title compound, C13H21N3S (common name: cis-jasmone 4-methylthiosemicarbazone). Two molecules with all atoms in general positions are present in the asymmetric unit. In one of them, the carbon chain is disordered [site occupancy ratio = 0.821 (3):0.179 (3)]. The thiosemicarbazone entities [N—N—C(=S)—N] are approximately planar, with the maximum deviation from the mean plane through the selected atoms being −0.0115 (16) Å (r.m.s.d. = 0.0078 Å) for the non-disordered molecule and 0.0052 (14) Å (r.m.s.d. = 0.0031 Å) for the disordered one. The molecules are not planar, since the jasmone groups have a chain with sp
3-hybridized carbon atoms and, in addition, the thiosemicarbazone fragments are attached to the respective carbon five-membered rings and the dihedral angles between them for each molecule amount to 8.9 (1) and 6.3 (1)°. In the crystal, the molecules are connected through pairs of N—H...S and C—H...S interactions into crystallographically independent centrosymmetric dimers, in which rings of graph-set motifs R
2
2(8) and R
2
1(7) are observed. A Hirshfeld surface analysis indicates that the major contributions for the crystal cohesion are from H...H (70.6%), H...S/S...H (16.7%), H...C/C...H (7.5%) and H...N/N...H (4.9%) interactions [considering the two crystallographically independent molecules and only the disordered atoms with the highest s.o.f. for the evaluation].
Illuminating the dark corners: a qualitative examination of cryptocurrency’s risk
Authors: Mehta Kriti , Chawla Sonia
Published: January 2024

Purpose

The study provides a comprehensive understanding of the issues and illegal activities related to cryptocurrencies and their negative repercussions. This study aims to identify and classify cryptocurrency downsides using grounded theory and in-depth interviews. The study also analysed investors’ reluctance to invest in cryptocurrency. This pioneering qualitative study illuminates a deep and multifaceted criminal aspect of cryptocurrency.

Design/methodology/approach

The study conducted in-depth interviews with respondents who have experience and knowledge of cryptocurrency investments. The interviews were recorded and transcribed. The analysis was performed using the NVivo 14 software in the study.

Findings

The study specified two major types of cryptocurrency’s negative aspects: barriers and illegal usage. Barriers to cryptocurrency investment include technological, security, trust, market-related and regulatory reasons. Terrorist funding, money laundering, fraud and ransom payments are all examples of illegal usage. The results of the word cloud analysis are consistent with the overall findings of the survey, which highlighted illegal usage as a prominent negative element of cryptocurrencies. It is a key reason why cryptocurrency is not included in investing portfolios by investors.

Originality/value

The study’s findings provide useful insights for policymakers to develop better methods for successfully mitigating risks and ensuring responsible and sustainable usage of cryptocurrencies. In addition, the study could serve as a stepping stone for more cryptocurrency-related studies, contributing to the development of a more complete and nuanced comprehension of this emergent technology and its societal effects.
Reactions to gender-(counter)normative behavior online in the United States: attraction and hiring implications
Authors: Badawy Rebecca , Brouer Robyn , Stefanone Michael
Published: January 2024

Purpose

Research indicates that inconsistent gender norm presentations are met with backlash, which is particularly damaging to women. With social media use in selection rising, it is important to understand if this remains consistent for job applicants on social media.

Design/methodology/approach

In two experiments, this study investigates hiring managers' reactions to job applicant (in)consistent gender norm-based communication on Facebook (n = 197) and YouTube (n = 203). Participants located in the United States were asked to review social media materials, reported perceptions of task and social attraction, and make hiring recommendations.

Findings

Inconsistent with work on backlash in face-to-face settings, results demonstrated that masculine communication styles on social media may be detrimental to job seekers, and this was more pronounced for male job seekers. Feminine presentation styles had more favorable results.

Practical implications

The findings challenge the long-held understanding that men have more leeway to behave in agentic ways in job seeking contexts. While this may remain true in face-to-face settings, these findings suggest that social media, lacking media richness, may be a context in which males experience backlash for agentic behavior.

Originality/value

The research offers a novel perspective investigating traditional gender expectations in the digital realm, paving the way for a more comprehensive understanding of gender in employment contexts. This study contributes to the growing body of research on online behavior and expands understanding of how hiring managers react to gender norms in the era of social media.
Examining the boundary conditions of tokenism: within-occupation gender wage gaps and female representation in the Canadian labor market
Authors: Stephenson Amber L. , Yerger David B.
Published: January 2024

Purpose

The purpose of this study was to examine the boundary conditions of Kanter's (1977) tokenism theory as applied to the gender wage gap. The authors aimed to discover if there was a point where the relationship between the percentage of women in a job category and the gender wage gap changed, and, if so, where the threshold was located and what was the nature of the shift in relationship.

Design/methodology/approach

The authors used the Andrews’ (1993) threshold effects technique. Using 22 separate years of publicly available Canadian wage data, they examined the relationship between the percentage of females in 40 unique occupational categories and the female-to-male earnings ratio (for a total of 880 observations).

Findings

The results showed the existence of a threshold point, and that early gains in percent female within an occupation, up to approximately 14% female in the occupation, associate with strong gains in the female-to-male wage ratio. However, beyond that point, further gains in percent female associate with smaller improvements in the female-to-male wage ratio.

Practical implications

The findings are useful in understanding the dynamics of occupational group gender composition, potential theoretical reasons for the nuances in relationship, as well as opportunities that may facilitate more equitable outcomes.

Originality/value

The results show that, though improvements were made above and below the threshold point, enhancements in the wage gap are actually larger when there are less women in the job category (e.g. tokens).
Academic motivation and academic satisfaction: a moderated mediation model of academic engagement and academic self-efficacy
Authors: Pham Thi Thuy Hang , Ho Thi Truc Quynh , Nguyen Be Thi Ngoc , Nguyen Hung Thanh , Nguyen Thi Ha
Published: January 2024

Purpose

This study aims to investigate the conditional indirect effect of academic self-efficacy in the interplay between academic motivation and academic satisfaction through academic engagement among university students.

Design/methodology/approach

A cross-sectional study was performed on 1,638 Vietnamese university students (31.9% males and 68.1% females) aged 16 to 36 (Mean = 20.06, SD = 1.428). The participants filled out a questionnaire with the Vietnam versions of the General Self-Efficacy Scale, Academic Motivation Scale, Academic Life Satisfaction Scale and Academic Engagement Scale. Model 4 and Model 7 in the PROCESS macro were used for the mediation analysis and the moderated mediation analysis.

Findings

Results showed that the indirect effect of academic engagement on the academic motivation-academic satisfaction link was significant. Furthermore, academic self-efficacy moderated this indirect effect. The indirect effect was stronger among students with high academic self-efficacy and weaker among students with low academic self-efficacy.

Originality/value

This study’s findings contribute to educational research on academic satisfaction and can be used by institutions of higher education and educators to enhance academic satisfaction among university students.
Dancing with the devil: the use and perceptions of academic journal ranking lists in the management field
Authors: Serenko Alexander , Bontis Nick
Published: January 2024

Purpose

This study explores the use and perceptions of scholarly journal ranking lists in the management field based on stakeholders’ lived experience.

Design/methodology/approach

The results are based on a survey of 463 active knowledge management and intellectual capital researchers.

Findings

Journal ranking lists have become an integral part of contemporary management academia: 33% and 37% of institutions and individual scholars employ journal ranking lists, respectively. The Australian Business Deans Council (ABDC) Journal Quality List and the UK Academic Journal Guide (AJG) by the Chartered Association of Business Schools (CABS) are the most frequently used national lists, and their influence has spread far beyond the national borders. Some institutions and individuals create their own journal rankings.

Practical implications

Management researchers employ journal ranking lists under two conditions: mandatory and voluntary. The forced mode of use is necessary to comply with institutional pressure that restrains the choice of target outlets. At the same time, researchers willingly consult ranking lists to advance their personal career, maximize their research exposure, learn about the relative standing of unfamiliar journals, and direct their students. Scholars, academic administrators, and policymakers should realize that journal ranking lists may serve as a useful tool when used appropriately, in particular when individuals themselves decide how and for what purpose to employ them to inform their research practices.

Originality/value

The findings reveal a journal ranking lists paradox: management researchers are aware of the limitations of ranking lists and their deleterious impact on scientific progress; however, they generally find journal ranking lists to be useful and employ them.
Propagating a permanent war economy? U.S. FDI in warring host countries
Authors: Dai Li , Paik Yongsun
Published: January 2024

Purpose

Conventional wisdom suggests that war in the host country makes it unattractive for foreign firms to invest. To see if this is true for US firms on the aggregate, this paper aims to examine the veracity of a “permanent war economy” hypothesis, that foreign direct investment (FDI) may, in fact, increase in the host country not despite, but because of, war, i.e. one that lends credence to the idea that, in the USA, “defense [has] become one of constant preparation for future wars and foreign interventions rather than an exercise in response to one-off threats.”

Design/methodology/approach

The authors test the hypotheses using Generalized Method of Moments estimation, with Heckman Selection, on US FDI data from the Bureau of Economic Analysis and war data from the Correlates of War2 Project, the Uppsala Conflict Data Program/International Peace Research Institute data set, the International Crisis Behavior Project and the Center for Systemic Peace Major Episodes of Political Violence data set. The final sample consists of 351 country-year observations in 55 host countries from 1982 to 2006.

Findings

The findings indicate that overall US FDI in a host country in a given year decreases if the host country is engaged in wars with multiple countries and if the US Government is involved in the war. Most notably, the results show that US involvement in multiple host country wars is actually correlated with increased US FDI into the host country, providing empirical support for the “permanent war economy” hypothesis.

Originality/value

While other studies have focused on war and FDI, the authors have sought to show the impact of the involvement of arguably the most influential country, i.e. the USA, in the sovereign matters of a focal host country. By studying FDI from the USA as a function of US involvement in wars overseas, over the years with the greatest use of private military companies by the USA and the largest portion of global FDI accounted for by the USA, this work motivates a research agenda on home-host-"other” relations in the context of war and FDI, with the “other” being the supranational “elephant in the room.”