bluuebunny/crossref_metadata_2025 huggingface dataset:
ROS-induced translational regulation—through spatiotemporal differences in codon recognition—is a key driver of brown adipogenesis
Authors: Ip Jun Yu , Wijaya Indrik , Lee Li Ting , Lim Yuhua , Teoh Deryn En-Jie , Chan Cheryl Siew Choo , Cui Liang , Begley Thomas J. , Dedon Peter C. , Guo Huili
Published: December 2023

The role of translational regulation in brown adipogenesis is relatively unknown. Localized translation of mRNAs encoding mitochondrial components enables swift mitochondrial responses, but whether this occurs during brown adipogenesis, which involves massive mitochondrial biogenesis, has not been explored. Here, we used ribosome profiling and RNA-Seq, coupled with cellular fractionation, to obtain spatiotemporal insights into translational regulation. During brown adipogenesis, a translation bias towards G/C-ending codons is triggered first in the mitochondrial vicinity by reactive oxygen species (ROS), which later spreads to the rest of the cell. This translation bias is induced through ROS modulating the activity of the tRNA modification enzyme, ELP3. Intriguingly, functionally relevant mRNAs, including those encoding ROS scavengers, benefit from this bias; in so doing, ROS-induced translation bias both fuels differentiation and concurrently minimizes oxidative damage. These ROS-induced changes could enable sustained mitochondrial biogenesis during brown adipogenesis, and explain in part, the molecular basis for ROS hormesis.
Genomic analysis ofStaphylococcus aureusisolates from bacteremia reveals genetic features associated with the COVID-19 pandemic
Authors: Sánchez-Osuna Miquel , Pedrosa Marc , Bierge Paula , Gómez-Sánchez Inmaculada , Alguacil-Guillén Marina , Espasa Mateu , Erill Ivan , Gasch Oriol , Pich Oscar Q.
Published: December 2023

Genomic analyses of bacterial isolates are necessary to monitor the prevalence of antibiotic resistance genes and virulence determinants. Herein, we provide a comprehensive genomic description of a collection of 339Staphylococcus aureusstrains isolated from patients with bacteremia between 2014 and 2022. Nosocomial acquisition accounted for 56.6% of episodes, with vascular catheters being the predominant source of infection (31.8%). Cases of fatality (27.4%), persistent bacteremia (19.5%) and diagnosis of septic emboli (24.2%) were documented. During the COVID-19 pandemic, we observed a 140% increase of the episodes ofS. aureusbacteremia per year, with a concomitant increase of the cases from nosocomial origin. This prompted us to investigate the existence of genetic features associated withS. aureusisolates from the COVID-19 pandemic. While genes conferring resistance to β-lactams (blaI-blaR-blaZ), macrolides (ermA, ermC, ermT, mphC, msrA) and aminoglycosides (ant(4’)-Ia,ant(9)-Ia,aph(3’)-IIIa,aph(2’’)-Ih) were prevalent in our collection, detection of themsrAandmphCgenes increased significantly in pandemicS. aureusisolates. Similarly, we observed a higher prevalence of isolates carrying the genes encoding the Clumping Factors A and B, involved in fibrinogen binding. Of note, macrolides were extensively used as accessory therapy for COVID-19 and fibrinogen levels were usually elevated upon SARS-CoV-2 infection. Therefore, our results reveal a remarkable adaptation of theS. aureusisolates to the COVID-19 pandemic context and demonstrates the potential of whole-genome sequencing to conduct molecular epidemiology studies.
UVB radiation suppresses Dicer expression through β-catenin
Authors: Aktary Zackie , Petit Valérie , Berlin Irina , Charenchaon Nisamanee , Sage Evelyne , Bertrand Juliette , Larue Lionel
Published: December 2023

Ultraviolet (UV) rays prompt a natural response in epidermal cells, particularly within melanocytes. The changes in gene expression and related signaling pathways in melanocytes following exposure to UVR are still not entirely understood. Our findings reveal that UVB irradiation suppresses the expression of Dicer. This repression is intricately linked to the activation of the PI3K, RSK, and WNT/β-catenin signaling pathways and is directly associated with transcriptional repression by β-catenin. Notably, we have identified specific binding sites for the LEF/β-catenin complex in the Dicer promoter. Collectively, these results emphasize the significance of the UV-induced pathway involving LEF/β-catenin, which impacts Dicer expression. This pathway holds potential importance in governing melanocyte physiology.
Activity of oleo-gum resins of myrrha on the growth of Candidiasis
Authors: Alabdalall Amira H.
Published: December 2023

Aims

Medicinal plants have a long and significant history of being used for their healing properties. One famous example is Commiphora, which is mostly found in the southern part of Arabia. The objective of this research was to evaluate the effectiveness of a water-based extract obtained from two different varieties of myrrh in suppressing the proliferation ofCandidaspp. at different concentrations. The objective of this research is to determine the chemical composition ofCommiphoraand its capacity to prevent the development ofCandidaspp.

Methodology and Results

A plant specimen traditionally used in Saudi Arabia for its possible effectiveness againstCandida albicans(ATCC 14053),C. neoformans(ATCC 66031),Candida laurentii(ATCC 18803),Candida guilliermondii(ATCC 6260), andCandida tropicalis(ATCC 66029). The results showed that the aqueous extract of both tested species of Myrrha (Commiphora myrrhaandC. molmol) shown inhibitory effects on all tested isolates. Moreover, it was discovered that the inhibitory impact decreased with increasing concentrations of Myrrha. During the chemical examination of the Myrrha, it was noted that the material included 12 components known for their antimicrobial properties. The components described before are as follows: The specified chemical compounds consist of β-Elemene, β-bisabolene, Dihydro butyl bezodoxepin, Tetradecanol, methyl palmitate, Tribenzo-1,2,3,4,5,6 anthracene, 9-Eicosene, 2-bromo-4-fluoro-N-(thiophen-2-ylmethyl) aniline, Octadecenoic acid methyl ester, dehydroabietic acid, and Docosene.

Conclusion

The antimicrobial activity of five yeasts was assessed using the diffusion technique. The essential oil derived from two varieties of myrrha shown the most significant effects onCandida tropicalis(ATCC 66029),Candida guilliermondii(ATCC 6260),Candida laurentii(ATCC 18803),C. neoformans(ATCC 66031), andCandida albicans(ATCC 14053). Upon conducting a chemical examination of the myrrha, it was shown that it consists of 19 known components, of which 12 compounds have been proven by research to suppress the growth of microorganisms. Further research is needed to fully explore the potential of these water extracts as innovative antifungal medicines, including their effectiveness against various strains ofCandidaand the processes by which they work, as well as the primary components responsible for their action.
Unravelling Silicon’s Transcriptomic Armor in Soybean againstMacrophomina phaseolinacausing Charcoal Rot Disease
Authors: Jadhav P. V. , Magar S. G. , Sharma P. K. , Vaidya E. R. , Moharil M. P. , Jaiswal S. , Nichal S. S. , Ghawade R. S. , Iquebal M. S. , Kawar P. G. , Jadhav P. R. , Sakhare S. B. , Ghorade R. B. , Deshmukh R. , Sonah H. , Kumar D. , Kharche V. K. , Torop E. A. , Dani R. G. , Mane S. S.
Published: December 2023

TheGlycine maxL. has been affected by more than 100 diseases, includingMacrophomina phaseolinaproducing charcoal rot disease, which reduces production by 70%. In this investigation, RNA-Seq analysis is used for the first time to explore role of silicon in preventing soybean charcoal rot. The study explores the molecular mechanism underlying soybeans’ resilience to charcoal rot when treated with potassium silicon. It was meticulously investigated howMacrophomina phaseolinaentered the roots. The SEM, which showed a strong link between potassium silicate accumulation and disease resistance. Further investigation indicates that a potassium silicate concentration of 1.7mM lowers disease incidence. Using Illumina HiSeq NGS data, we present a transcriptome analysis revealing genes associated with charcoal rot resistance, highlighting 3,106 genes with distinct expression patterns. The strong enrichment of pathways including “Biosynthesis of ansamycins” and “Flavone and flavonol biosynthesis,” which contribute to resistance against charcoal rot, is highlighted by KEGG enrichment analysis. The ERF transcription factor and NB leucine-rich repeats stands out among the differentially expressed genes as being particularly connected to resistance. The crucial functions that many other important transcription factors, including as MYB, NAC, and proteins from the FAR1 family, play in enhancing soybeans’ resistance to charcoal rot are also noted. This newly discovered information could help in developing tactics to strengthen soybean’s resistance toMacrophomina phaseolina.
Lethality of West Nile virus strains in a mouse model
Authors: Siniavin A.E. , Dolzhikova I.V. , Pochtovyi A.A. , Reshetnikov D.A. , Gushchin V.A.
Published: December 2023

West Nile fever (WNF) is a viral infection caused by West Nile virus (WNV), a flavivirus of theFlaviviridaefamily. Virus circulates between mosquitoes and wild birds, but can infect other species, including humans. The first cases of West Nile fever were reported in Africa in the 1930s. Currently, WNV has a wide geographic range, which includes countries in Europe, Asia, Africa, Australia, and North and South America, where it periodically causes WNF outbreaks. The disease in human occurs with the development of fever, and in some cases ending up severe neurological complications. Studies of the virus in animal models demonstrate that virulence varies depending on the host species, the genotype of the virus, and the presence of substitutions in key viral proteins, even within the same genotype. These studies highlight the need for comparative studies of different WNV strains to evaluate the impact of amino acid substitutions on WNV pathogenesis. Analysis of key mutations and substitutions will allow the development of a safe and effective vaccine for the prevention of WNF.
Adaptive responding to stimulus-outcome associations requires noradrenergic transmission in the medial prefrontal cortex
Authors: Piccin Alessandro , Plat Hadrien , Wolff Mathieu , Coutureau Etienne
Published: December 2023

A dynamic environment, such as the one we inhabit, requires organisms to continuously update their knowledge of the setting. While the prefrontal cortex is recognized for its pivotal role in regulating such adaptive behavior, the specific contributions of each prefrontal area remain elusive. In the current work, we investigated the direct involvement of two major prefrontal subregions, the medial prefrontal cortex (mPFC) and the ventrolateral orbitofrontal cortex (vlOFC), in updating Pavlovian stimulus-outcome (S-O) associations following contingency degradation. Specifically, animals had to learn that a specific cue, previously fully predicting the delivery of a specific reward, was no longer a reliable predictor. First, we found that chemogenetic inhibition of mPFC, but not of vlOFC, neurons altered the rats’ ability to adaptively respond to degraded and non-degraded cues. Next, given the growing evidence pointing at noradrenaline (NA) as a main neuromodulator of adaptive behavior, we decided to investigate the possible involvement of NA projections to the two subregions in this higher-order cognitive process. Employing a pair of novel retrograde vectors, we traced NA projections from the locus coeruleus (LC) to both structures and observed an equivalent yet relatively segregated amount of inputs. Then, we showed that chemogenetic inhibition of NA projections to the mPFC, but not to the vlOFC, also impaired the rats’ ability to adaptively respond to the degradation procedure. Altogether, our findings provide important evidence of functional parcellation within the prefrontal cortex and point at mPFC-NA as key for updating Pavlovian S-O associations.

Significant statement

The ability to update stimulus-outcome (S-O) associations is a key adaptive behavior, essential for surviving in an ever-changing environment. The prefrontal cortex is well-known for playing a key role in this process. The discrete contribution of each prefrontal subregion and of different neurotransmitters, however, remains unclear. In the current study, we show that inhibiting medial prefrontal (mPFC), but not ventrolateral orbitofrontal cortex (vlOFC), neurons impairs the rats’ ability to update S-O associations following contingency degradation. Moreover, we demonstrate that discrete noradrenergic projections to the two subregions exist and that inhibiting the ones projecting to the mPFC, but not to the vlOFC, once again impairs the rats’ behavior, thereby implying a substantial contribution of noradrenaline in orchestrating this higher-order cognitive process.
Concurrent representations of reinstated and transformed memories and their modulation by reward
Authors: Schultz Heidrun , Stoffregen Hanna , Dabas Aroma , Alcobendas María , Benoit Roland G.
Published: December 2023

An integral part of episodic retrieval is the reinstatement of neural activity that was present in the medial temporal lobe during encoding. However, neural memory representations do not remain static. Consolidation promotes the transformation of representations that are specific to individual episodes towards more generalized representations that reflect commonalities across episodes. Moreover, reward has been shown to augment episodic memory by enhancing consolidation, and it may accelerate the transformation of neural memory representations. We investigated this account with n=40 human participants using fMRI and an associative memory task. They encoded pictures of objects, each with one of four recurring scenes. Two scenes led to high reward, two led to low reward. The next day, participants encountered the objects again and retrieved the scenes from memory. Using representational similarity analysis, we demonstrate that retrieval is concurrently accompanied by the reinstatement of original neural representations and the activation of transformed, more generalized memories. Specifically, the parahippocampal cortex reinstates scene-specific patterns from the encoding phase during successful retrieval. In contrast, activity patterns in the medial prefrontal cortex and anterior hippocampus reflect transformed memories: They become more similar to each other for memories sharing the same scene, independent of memory success. Importantly, high reward enhances memory transformation in the anterior hippocampus. The brain thus maintains complementary memory representations: An episodic representation that resembles the original encoding pattern, and a generalized representation that summarizes commonalities across memories - in part for particularly valuable information.
In vivosingle-molecule imaging of RecB reveals efficient repair of DNA damage in Escherichia coli
Authors: Lepore Alessia , Thédié Daniel , McLaren Lorna , Azeroglu Benura , Pambos Oliver J. , Kapanidis Achillefs N. , Karoui Meriem El
Published: December 2023

Efficient DNA repair is crucial for maintaining genome integrity and ensuring cell survival. InEscherichia coli, RecBCD plays a crucial role in processing DNA ends following a DNA double-strand break (DSB) to initiate repair by homologous recombination. While RecBCD has been extensively studiedin vitro, less is known about how it contributes to rapid and efficient repair in living bacteria. Here, we perform single-molecule microscopy to investigate DNA repair in real-time inE. coli. We quantify RecB single-molecule mobility and monitor the induction of the DNA damage response (SOS response) in individual cells. We show that RecB binding to broken DNA ends leads to efficient repair without SOS induction. In contrast, in a RecB mutant with modified activities leading to the activation of an alternative repair pathway, repair is less efficient and leads to high SOS induction. Our findings reveal how subtle alterations in RecB activity profoundly impact the efficiency of DNA repair inE. coli.
Calcium binding site in AA10 LPMO fromVibrio choleraesuggests modulating effects during environment survival and infection
Authors: Montserrat-Canals Mateu , Bjerregard-Andersen Kaare , Sørensen Henrik Vinter , Cordara Gabriele , Vaaje-Kolstad Gustav , Krengel Ute
Published: December 2023

Despite major efforts towards its eradication, cholera remains a major health and economic burden in many developing countries. Between outbreaks, the bacterium responsible for the disease,Vibrio cholerae, survives in aquatic environmental reservoirs, where it commonly forms biofilms,e.g., on zooplankton.N-acetyl glucosamine binding protein A (GbpA) is an adhesin that binds to the chitinaceous surface of zooplankton and breaks its dense crystalline packing thanks to its lytic polysaccharide monooxygenase (LPMO) activity, which providesV. choleraewith nutrients. In addition, GbpA is an important colonization factor associated with bacterial pathogenicity, allowing the binding to mucins in the host intestine. Here, we report the discovery of a cation-binding site in proximity of the GbpA active site, which allows Ca2+, Mg2+or K+to bind close to its carbohydrate-binding surface. In addition to the X-ray crystal structures, we explored how the presence of ions affects the stability of the protein, compared the new GbpA LPMO structures to those of other LPMOs, and discussed the relevance of our discovery for bacterial survival. Calcium ions, abundant in natural sources of chitin, have been found to have the strongest effect on GbpA stability. Our findings suggest aV. cholerae-specific cation-binding site in GbpA that may fine-tune activity and binding to the different substrates during environmental survival and host infection.
RNA-sequencing reveals strong predominance ofTHRAsplicing isoform 2 in the developing and adult human brain
Authors: Graceffo Eugenio , Opitz Robert , Megges Matthias , Krude Heiko , Schuelke Markus
Published: December 2023

Thyroid hormone receptor alpha (THRα) is a nuclear hormone receptor that binds triiodothyronine (T3) and acts as an important transcription factor in development, metabolism and reproduction. THRαhas in mammals two major splicing isoforms, THRα1 and THRα2. The better characterized isoform, THRα1, is a transcriptional stimulator of genes involved in cell metabolism and growth. The less well characterized isoform, THRα2, lacks the Ligand Binding Domain (LBD) and is thought to act as an inhibitor of THRα1 action. The ratio of THRα1 to THRα2 splicing isoforms is therefore critical for transcriptional regulation in different tissues and during development. However, the expression patterns of both isoforms have not been studied in healthy human tissues or in the developing brain. Given the lack of commercially available isoform-specific antibodies, we addressed this question by analyzing four bulk RNA-sequencing datasets and two scRNA-sequencing datasets to determine the RNA expression levels of humanTHRA1andTHRA2transcripts in healthy adult tissues and in the developing brain. We demonstrate how 10X Chromium scRNA-seq datasets can be used to perform splicing-sensitive analyses of isoforms that differ at the 3’-end. In all datasets, we discovered a strong predominance ofTHRA2transcripts at all investigated stages of human brain development and in the central nervous system from healthy human adults.
A cell-free system for functional studies of small membrane proteins
Authors: Jiang Shan , Çelen Gülce , Glatter Timo , Niederholtmeyer Henrike , Yuan Jing
Published: December 2023

Numerous small proteins have been discovered across all domains of life, among which many are hydrophobic and predicted to localize to the cell membrane. Based on a few that are well-studied, small membrane proteins are regulators involved in various biological processes, such as cell signaling, nutrient transport, drug resistance, and stress response. However, the function of most identified small membrane proteins remains elusive. Their small size and hydrophobicity make protein production challenging, hindering function discovery. Here, we combined a cell-free system with lipid sponge droplets and synthesized small membrane proteinsin vitro. Lipid sponge droplets contain a dense network of lipid bilayers, which accommodates and extracts newly synthesized small membrane proteins from the aqueous surroundings. Using small bacterial membrane proteins MgrB, SafA, and AcrZ as proof of principle, we showed that thein vitroproduced membrane proteins were functionally active, for example, modulating the activity of their target kinase as expected. The cell-free system produced small membrane proteins, including one from human, up to micromolar concentrations, indicating its high level of versatility and productivity. Furthermore, AcrZ produced in this system was used successfully forin vitroco-immunoprecipitations to identify interaction partners. This work presents a robust alternative approach for producing small membrane proteins, which opens a door to their function discovery in different domains of life.

Importance

Small membrane proteins are shown to be involved in various biological processes in all domains of life and “can no longer be ignored”. Due to their small size and hydrophobicity, functional investigation of small membrane proteins is challenging. In this work, we present a simple, versatile, cell-free approach for synthesizing small membrane proteinsin vitro. We show that the small membrane proteins produced with our system are functional and in sufficient amounts for downstream target discoveries. Furthermore, our approach may uncover additional regulatory functions of small membrane proteins studied with conventional methods. Our work provides a robust alternative workflow for functional studies, which opens up new possibilities to advance our understanding of small membrane protein biology.
DNA nicks in both leading and lagging strand templates can trigger break-induced replication
Authors: Xu Yuanlin , Laksir Yassine , Morrow Carl A. , Taylor Kezia , Tsiappourdhi Costas , Collins Patrick , Jia Su , Andreadis Christos , Whitby Matthew C.
Published: December 2023

Encounters between replication forks and unrepaired single-strand DNA breaks (SSBs) generate single-ended double-strand breaks (seDSBs) that can later become double-ended (deDSBs) through fork convergence. seDSBs can be repaired by break-induced replication (BIR), which is a highly mutagenic pathway that is thought to be repsonsible for many of the mutations and genome rearrangements that drive cancer development. However, the frequency of BIR’s deployment and its ability to be triggered by both leading and lagging template strand SSBs was unclear. Using site- and strand-specific SSBs generated by nicking enzymes, including CRISPR-Cas9n, we demonstrate that leading and lagging template strand SSBs in fission yeast are typically converted into deDSBs that are repaired primarily by error-free homologous recombination. However, both types of SSB can also trigger BIR, and the frequency of these events increases when the converging fork is delayed and the non-homologous end joining protein Ku70 is deleted.
Probability of stealth multiplets in sample-multiplexing for droplet-based single-cell analysis
Authors: Nakaki Fumio , Sharpe James
Published: December 2023

Background

Recent advances in sample-multiplexing droplet-based single-cell RNA sequencing (mx-scRNA-seq) enable us to evaluate large numbers of different samples or experiments simultaneously by reducing the occurrence of undetectable multiplets, that is, the droplets that capture multiple cells. However, the probability of potential multiplets in mx-scRNA-seq is yet to be quantitatively examined.

Results

We developed a simple theoretical model to predict four classes of possible multiplets in mx-scRNA-seq: Homogeneous stealth, partial stealth, multilabelled, and unlabelled. We estimated the probability of each class and have found that the partial tsealth multiplet, which has been overlooked, may sub-stantially affect the whole data when the labelling process is suboptimal. Next, we illustrated their presence in actual mx-scRNA-seq datasets when the sample labelling was suboptimal. In addition, we found that choosing a suitable sample-demultiplexing algorithm was critical to circumvent the partial stealth multiplets.

Conclusion

Our results show the necessity of optimising the labelling procedure and offer a theoretical basis to estimate the probability of each type of multiplets to ensure the integrity of mx-scRNA-seq.
EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues
Authors: Clarke D. Nathaniel , Martin Adam C.
Published: December 2023

The movements that give rise to the body’s structure are powered by cell shape changes and rearrangements that are coordinated at supracellular scales. How such cellular coordination arises and integrates different morphogenetic programs is unclear. Using quantitative imaging, we found a complex pattern of adherens junction (AJ) levels in the ectoderm prior to gastrulation onset inDrosophila. AJ intensity exhibited a double- sided gradient, with peaks at the dorsal midline and ventral neuroectoderm. We show that this dorsal-ventral AJ pattern is regulated by epidermal growth factor (EGF) signaling and that this signal is required for ectoderm cell movement during mesoderm invagination and axis extension. We identify AJ levels and junctional actomyosin as downstream effectors of EGFR signaling. Overall, our study demonstrates a mechanism of coordination between tissue folding and convergent extension that facilitates embryo-wide gastrulation movements.
Increased HIF-2α Activity in the Nucleus Pulposus Causes Intervertebral Disc Degeneration in the Aging Mouse Spine
Authors: Johnston Shira N. , Tsingas Maria , Ain Rahatul , Barve Ruteja A. , Risbud Makarand V.
Published: December 2023

Hypoxia-inducible factors (HIFs) are essential to the homeostasis of hypoxic tissues. Although HIF-2α, is expressed in nucleus pulposus (NP) cells, consequences of elevated HIF-2 activity on disc health remains unknown. We expressed HIF-2α with proline to alanine substitutions (P405A;P531A) in the Oxygen-dependent degradation domain (HIF-2αdPA) in the NP tissue using an inducible, nucleus pulposus-specific K19CreERTallele to study HIF-2α function in the adult intervertebral disc. Expression of HIF-2α in NP impacted disc morphology, as evident from small but significantly higher scores of degeneration in NP of 24-month-old K19CreERT; HIF-2αdPA(K19-dPA) mice. Noteworthy, comparisons of grades within each genotype between 14 months and 24 months indicated that HIF-2α overexpression contributed to more pronounced changes than aging alone. The annulus fibrosus (AF) compartment in the 14-month-old K19-dPA mice exhibited lower collagen turnover and Fourier transform-infrared (FTIR) spectroscopic imaging analyses showed changes in the biochemical composition of the 14-and 24-month-old K19-dPA mice. Moreover, there were changes in aggrecan, chondroitin sulfate, and COMP abundance without alterations in NP phenotypic marker CA3, suggesting the overexpression of HIF-2α had some impact on matrix composition but not the cell phenotype. Mechanistically, the global transcriptomic analysis showed enrichment of differentially expressed genes in themes closely related to NP cell function such as cilia, SLIT/ROBO pathway, and HIF/Hypoxia signaling at both 14- and 24-months. Together, these findings underscore the role of HIF-2α in the pathogenesis of disc degeneration in the aged spine.
Emergence of synchronised growth oscillations in filamentous fungi
Authors: Prakash Praneet , Jiang Xue , Richards Luke , Schofield Zoe , Schafer Patrick , Polin Marco , Soyer Orkun S. , Asally Munehiro
Published: December 2023

Soil fungi are important decomposers of organic matter and play crucial roles in the biogeochemical cycles in the soil. Many species of fungi grow in the form of branched networks. While there have been investigations on the growth and architecture of the fungal networks, their growth dynamics in space and time is still not fully understood. In this study, we monitor the growth dynamics of the plant-promoting filamentous fungusSerendipita indicafor several days in a controlled environment within a microfluidic channel. We find that this species displays synchronized growth oscillations with the onset of sporulation and at a period of 3 hours. Quantifying this experimental synchronisation of oscillatory dynamics, we show that the synchronisation can be captured by the nearest neighbour Kuramoto model. Our analysis suggested the existence of millimetre-scale cell-cell communication across the fungi network. The microfluidic setup presented in this work may aid the future characterization of the molecular mechanisms of the cell-cell communication, which could in turn be exploited in order to control fungi growth and reproductive sporulation in soil and plant health management.
De novodesign of drug-binding proteins with predictable binding energy and specificity
Authors: Lu Lei , Gou Xuxu , Tan Sophia K , Mann Samuel I. , Yang Hyunjun , Zhong Xiaofang , Gazgalis Dimitrios , Valdiviezo Jesús , Jo Hyunil , Wu Yibing , Diolaiti Morgan E. , Ashworth Alan , Polizzi Nicholas F. , DeGrado William F.
Published: December 2023

The de novo design of small-molecule-binding proteins has seen exciting recent progress; however, the ability to achieve exquisite affinity for binding small molecules while tuning specificity has not yet been demonstrated directly from computation. Here, we develop a computational procedure that results in the highest affinity binders to date with predetermined relative affinities, targeting a series of PARP1 inhibitors. Two of four designed proteins bound with affinities ranging from < 5 nM to low μM, in a predictable manner. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free-energy calculations performed directly on the designed models are in excellent agreement with the experimentally measured affinities, suggesting that the de novo design of small-molecule-binding proteins with tuned interaction energies is now feasible entirely from computation. We expect these methods to open many opportunities in biomedicine, including rapid sensor development, antidote design, and drug delivery vehicles.

One Sentence Summary

We use informatic sampling to design low nM drug-binding proteins, and physics-based calculations to accurately predict affinities.
Creating Aesthetically Pleasing SBGN Visualisations for Presentation and Exploration
Authors: Czauderna Tobias , Schreiber Falk
Published: December 2023

Visualisations are widely used to present, assess, and convey data and understanding in systems biology and other fields, and graphical representations of data and information should be precise, visually engaging, informative, and aesthetically pleasing. The Systems Biology Graphical Notation (SBGN) is a standard for visual representations of processes and networks in systems biology in the form of SBGN maps. It defines graphical elements and connection rules for knowledge representation in the form of maps. Whereas the form of the map elements is defined, those map elements have to be placed in a proper way in order to obtain useful and aesthetically pleasing visualisations. Here, we present layout considerations and guidelines for SBGN maps, as well as workflows for SBGN-ED as a tool for crafting visually pleasing SBGN visualisations for presentation and exploration.
COVID-19-induced changes to food consumption and perceived well-being among low-income consumers in Trinidad and Tobago
Authors: Pacheco Barney G. , Pacheco Marvin H.
Published: December 2023

Purpose

The global impact of the COVID-19 pandemic has been well documented, but there is still limited insight into the complex interaction of factors that determine its longer-term effects on the most vulnerable sectors of society. The current study therefore develops an integrated conceptual framework to investigate how consumers' fear of mortality and the perceived risk of severe illness associated with COVID-19 act as critical determinants of consumer food choices and perceived well-being.

Design/methodology/approach

An online survey was utilized to collect data from a sample of 407 adult, low-income consumers across Trinidad and Tobago. The PROCESS macro was used to empirically test the hypothesized relationships in a moderated mediation model.

Findings

The results confirm that an increase in the perceived risk of severe illness has a significant negative effect on the consumption of healthy foods and perceived well-being. Moreover, consumers' choice of healthy foods mediates the negative relationship between consumers' perceived risk of severe COVID-19 illness and subjective well-being. Finally, the negative relationship between perceived risk of illness and healthy food choice weakens as an individual's fear of pandemic-related mortality increases.

Originality/value

This research integrates multiple related theoretical constructs to provide a more nuanced understanding of the lingering impact that risk perceptions and fear have on consumer food choices and associated well-being among a vulnerable Caribbean population. The changes identified have important implications for researchers interested in consumer food preferences as well as policymakers seeking to promote a healthy lifestyle among individuals coping with psychologically stressful circumstances.
The rationale for affirmative action (AA) being overturned by SCOTUS: an informational perspective of its pros and cons for the American dream
Authors: Mujtaba Bahaudin Ghulam
Published: December 2023

Purpose

This paper aims to provide a historical overview of AA, its purpose and benefits, the legal rationale for the SCOTUS ruling and what it means for colleges and the workplace regarding equitable opportunities for minority groups (which include women, Blacks, Hispanics, Asians and other low-income populations), as they aim for the “American dream”.

Design/methodology/approach

SCOTUS decision and rationale, along with literature.

Findings

The race-based affirmative action (AA) precedent was recently overturned by the Supreme Court of the United States (SCOTUS) in the case of Students for Fair Admission (SFFA), Inc. vs President and Fellows of Harvard College/University of North Carolina. SCOTUS ruled that race cannot be a specific basis for college admission. In other words, public and private colleges and universities will no longer be able to consider “race” as a factor in deciding which qualified applicants should be admitted to enhance the diversity of their student body.

Originality/value

This is an original analysis.
Factors influencing public engagement in government TikTok during the COVID-19 crisis
Authors: Zhang Wei , Yuan Hui , Zhu Chengyan , Chen Qiang , Evans Richard David , Min Chen
Published: December 2023

Purpose

Although governments have used social media platforms to interact with the public in an attempt to minimize anxiety and provide a forum for public discussion during the pandemic, governments require sufficient crisis communication skills to engage citizens in taking appropriate action effectively. This study aims to examine how the National Health Commission of China (NHCC) has used TikTok, the leading short video–based platform, to facilitate public engagement during COVID-19.

Design/methodology/approach

Building upon dual process theories, this study integrates the activation of information exposure, prosocial interaction theory and social sharing of emotion theory to explore how public engagement is related to message sensation value (MSV), media character, content theme and emotional valence. A total of 354 TikTok videos posted by NHCC were collected during the pandemic to explore the determinants of public engagement in crises.

Findings

The findings demonstrate that MSV negatively predicts public engagement with government TikTok, but that instructional information increases engagement. The presence of celebrities and health-care professionals negatively affects public engagement with government TikTok accounts. In addition, emotional valence serves a moderating role between MSV, media characters and public engagement.

Originality/value

Government agencies must be fully aware of the different combinations of MSV and emotion use in the video title when releasing crisis-related videos. Government agencies can also leverage media characters – health professionals in particular – to enhance public engagement. Government agencies are encouraged to solicit public demand for the specific content of instructing information through data mining techniques.
Mitigating the lack of prior entrepreneurial experience and exposure through entrepreneurship education programs
Authors: Aadland Torgeir , Hägg Gustav , Lundqvist Mats A. , Stockhaus Martin , Williams Middleton Karen
Published: December 2023

Purpose

To increase the understanding of how entrepreneurship education impacts entrepreneurial careers, the purpose of the paper is to investigate the role that a venture creation program (VCP) might have in mitigating or surpassing a lack of other antecedents of entrepreneurial careers. In particular, the authors focus on entrepreneurial pedigree and prior entrepreneurial experience.

Design/methodology/approach

Data from graduates of VCPs at three universities in Northern Europe were collected through an online survey. Questions addressed graduate background prior to education, yearly occupational employment subsequent to graduation and graduates' own perceptions of entrepreneurial activity in employment positions. The survey was sent to 1,326 graduates and received 692 responses (52.2% response rate).

Findings

The type of VCP, either independent (Ind-VCP) or corporate venture creation (Corp-VCP), influenced the mitigation of prior entrepreneurial experience. Prior entrepreneurial experience, together with Ind-VCP, made a career as self-employed more likely. However, this was not the case for Corp-VCP in subsequently choosing intrapreneurial careers. Entrepreneurial pedigree had no significant effect on career choice other than for hybrid careers.

Research limitations/implications

Entrepreneurial experience gained from VCPs seems to influence graduates toward future entrepreneurial careers. Evidence supports the conclusion that many VCP graduates who lack prior entrepreneurial experience or entrepreneurial pedigree can develop sufficient entrepreneurial competencies through the program.

Originality/value

This study offers novel evidence that entrepreneurship education can compensate for a lack of prior entrepreneurial experience and exposure for students preparing for entrepreneurial careers.
Factors influencing purchase intention towards energy efficient air conditioners: a study of Indian households
Authors: Kaur Nirmal , Bedi Sarbjit Singh , Singh Jagwinder
Published: December 2023

Purpose

This study aims to examine the antecedents of purchase intention toward energy efficient air conditioners by incorporating the theory of planned behavior (TPB) with two additional constructs, i.e. environmental concern and personal norms. TPB is one of the most widely used theoretical framework to study consumer behavior.

Design/methodology/approach

The study applied a quantitative technique using a survey method by distributing self-administered questionnaires among the Indian households who have purchased energy efficient air conditioners in the past six months or had enquired to do so. The study collected data from three select regions: Delhi and NCR, Punjab and Tri-city. The collected data of 424 respondents have been analyzed using confirmatory factor analysis and structural equation modeling.

Findings

The study posits that normative factors such as subjective norms and personal norms have a relatively higher influence on purchase intention. Despite the significant existence of environmental concern, the study did not find environmental concern directly influencing purchase intention.

Research limitations/implications

The sample size of the study is too small and pertains to specific regions. Thus, it could hinder the generalizability of the results. Advertisement appeals should be related with enhancement of self-esteem in terms of making responsible and valuable contribution to environment protection through the purchase of energy efficient air conditioner.

Originality/value

There are a few studies in the Indian context studying consumer’s purchase intention toward energy efficient air conditioners to which this study adds. The study provides an important contribution to marketers in developing strategies for increasing purchase intention toward energy efficient air conditioners in view of their stage in the product life cycle, diffusion of product and influence of normative factors.
Big textual data research for operations management: topic modelling with grounded theory
Authors: Odacioglu Eyyub Can , Zhang Lihong , Allmendinger Richard , Shahgholian Azar
Published: December 2023

Purpose

There is a growing need for methodological plurality in advancing operations management (OM), especially with the emergence of machine learning (ML) techniques for analysing extensive textual data. To bridge this knowledge gap, this paper introduces a new methodology that combines ML techniques with traditional qualitative approaches, aiming to reconstruct knowledge from existing publications.

Design/methodology/approach

In this pragmatist-rooted abductive method where human-machine interactions analyse big data, the authors employ topic modelling (TM), an ML technique, to enable constructivist grounded theory (CGT). A four-step coding process (Raw coding, expert coding, focused coding and theory building) is deployed to strive for procedural and interpretive rigour. To demonstrate the approach, the authors collected data from an open-source professional project management (PM) website and illustrated their research design and data analysis leading to theory development.

Findings

The results show that TM significantly improves the ability of researchers to systematically investigate and interpret codes generated from large textual data, thus contributing to theory building.

Originality/value

This paper presents a novel approach that integrates an ML-based technique with human hermeneutic methods for empirical studies in OM. Using grounded theory, this method reconstructs latent knowledge from massive textual data and uncovers management phenomena hidden from published data, offering a new way for academics to develop potential theories for business and management studies.
Deformation mechanism and dimension optimization methods of PTFE oil seals for shafts in a wide temperature range cycle
Authors: Xing Yangtao , Zhai Fugang , Li Shengnan , Gui Peng
Published: December 2023

Purpose

This paper aims to study the deformation mechanism of polytetrafluoroethylene (PTFE) oil seal under a wide temperature range cycle.

Design/methodology/approach

This study categorizes the oil seal operation into three states: assembly, heating-up and cooling. The deformation equation for the oil seal is developed for each state, considering the continuity between them. The investigation of the oil seal’s deformation trends and mechanisms is performed using the ANSYS Workbench.

Findings

The assembling process results in a radial shrinkage of the skeleton, causing the centroid to move toward the axis. During heating-up, the outer diameter of the skeleton slightly expands, whereas the inner diameter sharply contracts toward the axis, leading to a further reduction in the centroid’s distance from the axis. Upon cooling, both the inner and outer diameters continue to contract toward the axis, causing the centroid to persist in its movement toward the axis. Consequently, after undergoing a heating-up and cooling cycle ranging from 20°C to 180°C, the outer diameter of the PTFE oil seal reduces by 0.92 mm from its original deformation, ensuring minimal contact between the skeleton and housing. As a result of the reduced static friction torque at the skeleton, the oil seal rotates along the shaft.

Originality/value

The deformation mechanism of PTFE oil seals under a wide temperature range cycle was investigated, aiming to address the concerns related to the rotation along the shaft and leakage.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-05-2023-0142/
Institutions, technology and resource integration in the value co-creation process: a study of service-dominant logic in higher education
Authors: Adi Stanislaus Puji Setyanto , Ghinahana Salmanda , Yudianto Bernardinus Realino , Wibowo Alexander Joseph Ibnu
Published: December 2023

Purpose

This paper analyzes the value creation process in terms of the relationships between institutions, technology, integration of resources and contextual value. The study was conducted within an online learning setting in higher education, and utilized service-dominant logic as a basis for analysis.

Design/methodology/approach

A total of 349 responses were collected through an online survey. After removing data from respondents who did not meet the criteria and outliers, 280 responses were analyzed. Furthermore, six hypotheses were tested using structural equation modeling (SEM) techniques.

Findings

The results confirm that institutions are proven to influence technology and resource integration. The technology significantly affects resource integration and value-in-context. Likewise, resource integration determines value-in-context remarkably. On the other hand, this study found no evidence of the impact of institutions on value-in-context.

Research limitations/implications

The study has been conducted in the Jabodetabek area, with a sample size of only 280. An extensive survey, including a larger sample size, may reveal a broader glimpse of the value co-creation process of students in higher education institutions. Only three antecedents of contextual value have been explored, namely institutions, technology and resource integration. More strengthening and detailed findings could be derived if the antecedents of the contextual value addressed could be added. In the sampling, the researchers have used non-probability sampling for collecting data due to various constraints. The use of the probabilistic sampling method might have given some new insights to the study and made the sample more representative. The convenient sampling method employed in this study may limit the generalization of this study's findings. Therefore, the findings of the hypothesis test only apply to the selected sample data. Another limitation of the study is that the survey respondents represented an urban Indonesian perspective. So, replication of this study in different areas (e.g. west, east and central Indonesia) would help to generalize the findings. In this study, there is no evidence that institutions have a direct impact on contextual value. The authors suggest reexamining the relationship between institutions and contextual value in future studies.

Originality/value

In particular, the authors have succeeded in designing a new empirical model in higher education based on the perspective of service-dominant logic (S-D logic). This finding further strengthens the existence of the perspective of S-D logic as a new general theory of the market.