bluuebunny/crossref_metadata_2025_split huggingface dataset:
The maximum solubility product marks the threshold for condensation of multivalent biomolecules
Authors: Chattaraj Aniruddha , Loew Leslie M. 
Published: October 2022

AbstractClustering of weakly interacting multivalent biomolecules underlies the formation of membraneless compartments known as condensates. As opposed to single component (homotypic) systems, the concentration dependence of multi-component (heterotypic) condensate formation is not well understood. We previously proposed the solubility product (SP), the product of monomer concentrations in the dilute phase, as a tool for understanding the concentration dependence of multi-component systems. In the current study, we further explore the limits of the SP concept using spatial Langevin dynamics and rule-based stochastic simulations. We show, for a variety of idealized molecular structures, how the maximum SP coincides with the onset of the phase transition, i.e., the formation of large clusters. We reveal the importance of intra-cluster binding in steering the free and cluster phase molecular distributions. We also show how structural features of biomolecules shape the solubility product profiles. The interplay of flexibility, length and steric hindrance of linker regions controls the phase transition threshold. Remarkably, when solubility products are normalized to non-dimensional variables and plotted against the concentration scaled to the threshold for phase transition, the curves all coincide independent of the structural features of the binding partners. Similar coincidence is observed for the normalized clustering vs. concentration plots. Overall, the principles derived from these systematic models will help guide and interpret in vitro and in vivo experiments on the biophysics of biomolecular condensates.Significance StatementBiomolecular condensates are macroscopic intracellular structures that are composed of weakly interacting macromolecules. Because their composition can be complex, there are no simple rules for how condensates form as a function of the concentrations of their individual components. In this work, we show how the solubility product (SP), the product of monomer concentrations in the dilute phase, might serve as a tool for predicting the concentration dependence for condensation of multi-component systems. Specifically, Langevin dynamics simulations of the clustering of a series of multivalent binding partners reveals how the maximum SP is always attained at the same concentration as the appearance of large clusters. Experimental application of the SP concept should help rationalize the cellular formation of biomolecular condensates.
Generating fast-twitch myotubes in vitro using an optogenetic-based, quantitative contractility assay
Authors: Hennig Katharina , Hardman David , Barata David , Martins Inês , Bernabeu Miguel O. , Gomes Edgar R. , Roman William 
Published: October 2022

AbstractThe composition of fiber types within skeletal muscle impacts the tissue’s physiological characteristics and susceptibility to disease and ageing. In vitro systems should therefore account for fiber type composition when modelling muscle conditions. To induce fiber specification in vitro, we designed a quantitative contractility assay based on optogenetics and particle image velocimetry. We submitted cultured myotubes to long-term intermittent light stimulation patterns and characterized their structural and functional adaptations. After several days of in vitro exercise, myotubes contract faster and are more resistant to fatigue. The enhanced contractile functionality was accompanied by advanced maturation such as increased width and upregulation of neuron receptor genes. We observed an upregulation in the expression of distinct myosin heavy chain isoforms (namely, neonatal-Myh8 and fast-Myh), which induced a shift towards a fast fiber phenotype. This long-term in vitro exercise strategy can be used to study fiber specification and refine muscle disease modelling.
Reduction of embryonic E93 expression as a key factor for the evolution of insect metamorphosis
Authors: Fernandez-Nicolas Ana , Machaj Gabriela , Ventos-Alfonso Alba , Pagone Viviana , Minemura Toshinori , Ohde Takahiro , Daimon Takaaki , Ylla Guillem , Belles Xavier 
Published: October 2022

ABSTRACTThe early embryo of the cockroach Blattella germanica exhibits high E93 expression. In general, E93 triggers adult morphogenesis during postembryonic development, but in the cockroach E93 is also crucial in early embryogenesis. Moreover, the embryonic levels of E93 expression are high in hemimetabolan insects, while in holometabolans they are very low. They are also low in Thysanoptera and in Hemiptera Sternorrhyncha with postembryonic quiescent stages, as well as in Odonata, the nymph of which is very different from the adult. In ametabolans, such as the Zygentoma Thermobia domestica, E93 expression levels are very high in the early embryo, whereas during postembryonic development they are medium and relatively constant. Given that embryogenesis of hemimetabolans yields an adultiform nymph, we speculate that E93 plays some sort of adult triggering role in the embryo of these species. We conjecture that the reduction of E93 transcript levels in the embryo has been instrumental in the evolution of insect metamorphosis. The suppression of E93 expression during the nymphal period, and its concentration in the preadult stage, is consubstantial with the emergence of hemimetaboly. As such, attenuation of E93 expression in the embryo could have resulted in a larval genetic program and the emergence of holometaboly. Independent decreases of E93 expression in the embryo of Odonata, Thysanoptera, and different groups of Hemiptera Sternorrhyncha would have allowed the development of modified juvenile stages adapted to specific ecophysiological conditions.
Chemical Imaging Reveals Diverse Functions of Tricarboxylic Acid Metabolites in Root Growth and Development
Authors: Zhang Tao , Noll Sarah E. , Peng Jesus T. , Klair Amman , Tripka Abigail , Stutzman Nathan , Cheng Casey , Zare Richard N. , Dickinson Alexandra J. 
Published: October 2022

AbstractUnderstanding how plants grow is critical for agriculture and fundamental for illuminating principles of multicellular development 1. Here, we apply chemical mapping of the developing maize root using desorption electrospray ionization mass spectrometry imaging (DESI-MSI) 2. This technique reveals a range of small molecule distribution patterns across the gradient of stem cell differentiation in the root. To understand the developmental logic of these patterns, we examined tricarboxylic acid (TCA) cycle metabolites. In both Arabidopsis and maize, TCA metabolites are enriched in developmentally opposing regions, suggesting that stem-cell specific TCA metabolite localization may be conserved in evolutionarily divergent species. We find that these metabolites, particularly succinate, aconitate, citrate, and α-ketoglutarate, control root development in diverse and distinct ways. Critically, the effects of metabolites on stem cell behavior can be independent of their canonical role in ATP production. These results present new insights into development and suggest practical means for controlling plant growth.
Transcriptomic remodeling of the retina in a Zebrafish model of Retinitis Pigmentosa
Authors: Santhanam Abirami , Shihabeddin Eyad , Wei Haichao , Wu Jiaqian , O’Brien John 
Published: October 2022

AbstractInherited retinal degenerative diseases such as Retinitis Pigmentosa (RP) result in progressive loss of photoreceptors until an individual is completely blind. A hallmark of these diseases is progressive structural and functional remodeling of the remaining retinal neurons as rod photoreceptors are lost. While many studies focus on regenerative or bionic therapies to restore vision, extensive remodeling of retinal cell types throughout the course of retinal degenerative diseases stands as a barrier for successful implementation of these strategies. As a window onto the molecular basis of remodeling, we have performed a comparative analysis of single-cell transcriptome data from adult Zebrafish retina of wild-type and a P23H mutant rhodopsin model of RP. In addition to providing a benchmark atlas of retinal cell type transcriptomes in the wild-type adult Zebrafish retina, we find transcriptional changes in essentially all retinal cell types in the P23H model. Increased oxidative stress is evident not only in the rods but also in cones, retinal pigmented epithelium (RPE) and to a lesser extent in amacrine and bipolar cells. Metabolic changes increasing oxidative metabolism and glycolysis are found in rods and cones, while evidence of increased activity of the mitochondrial electron transport chain is found in retinal ganglion cells (RGCs). Evidence of synaptic remodeling is found throughout the retina, with changes to increase synaptic transmission in photoreceptors and bipolar cells, increased ionotropic glutamate receptors in amacrine and ganglion cells, and dendritic and axon remodeling throughout. Surprisingly, RPE, cones and bipolar cells in the P23H retinas also have increased expression of genes involved in circadian rhythm regulation. While this model system undergoes continuous regeneration, ongoing remodeling impacts the entire retina. This comprehensive transcriptomic analysis provides a molecular road map to understand how the retina remodels in the context of chronic retinal degeneration with ongoing regeneration.
Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutation of Staphylococcus aureus DNA Polymerase PolC
Authors: Nelson-Rigg Rachel , Fagan Sean P. , Jaremko William J. , Pata Janice D. 
Published: October 2022

ABSTRACTThe emergence and spread of antibiotic resistance in bacterial pathogens are serious and ongoing threats to public health. Since chromosome replication is essential to cell growth and pathogenesis, the essential DNA polymerases in bacteria have long been targets of antimicrobial development, although none have yet advanced to the market. Here we use transient-state kinetic methods to characterize the inhibition of the PolC replicative DNA polymerase from Staphylococcus aureus by ME-EMAU, a member of the 6-anilinouracil compounds that specifically target PolC enzymes, which are found in low-GC content Gram-positive bacteria. We find that ME-EMAU binds to S. aureus PolC with a dissociation constant of 14 nM, more than 200-fold tighter than the previously reported inhibition constant, which was determined using steady-state kinetic methods. This tight binding is driven by a very slow off rate, 0.006 s-1. We also characterized the kinetics of nucleotide incorporation by PolC containing a mutation of phenylalanine 1261 to leucine (F1261L). The F1261L mutation decreases ME-EMAU binding affinity by at least 3500-fold, but also decreases the maximal rate of nucleotide incorporation by 11.5-fold. This suggests that bacteria acquiring this mutation would be likely to replicate slowly and be unable to out-compete wild-type strains in the absence of inhibitor, reducing the likelihood of the resistant bacteria propagating and spreading resistance.
Exploring the meaningfulness of integrated reporting: a framing perspective
Authors: Okwuosa Innocent , Atkins Jill 
Published: October 2022

PurposeThe purpose of the study is to explain why there is a conflict in the meaningfulness of integrated reporting (IR) between International Integrated Reporting Council (IIRC) and analysts and institutional investors using framing theory and suggest a way forward for a meaningful IR to analysts and institutional investors.Design/methodology/approachThe study used qualitative research design in which data was collected from IIRC's document and 21 semi-structured interviews of analysts and fund managers conducted between 2014 and 2015 after the introduction of IIRC framework. This period coincided with prior studies that provide conflicting evidence over the meaningfulness of IR between IIRC and analysts and fund managers.FindingsThe findings show that the IIRC from inception uses a preparer-centred frame where it predominantly interprets IR as meaningful from the perspective of preparers of information under ideal conditions, and as such also meaningful to fund managers and analysts. On the other hand, the fund managers and analysts from the onset use a user-centred frame where they interpret IR as not meaningful from their perspective as users of the information under pragmatic conditions. The context making it difficult to reconcile the differentiated frames are the timeframe; absence of trust relationship and balance in reporting.Research limitations/implicationsThe study is limited by its qualitative nature meaning that generalisation of findings may not apply. Its data is also limited to IIRC IR Framework, analysts and fund managers as opposed to wider stakeholders.Practical implicationsThe practical implication of the findings suggests that if IR is to be made meaningful to analysts and fund managers, the promoters must reconcile the differentiations in frames employed by both the IIRC, analysts and institutional investors. Without this reconciliation IR may not serve the information needs of the intended primary users.Originality/valueThe study uses framing theory to show that time frame, emotional connectedness and data financialisation are attributes that make IR to be considered meaningful to analysts and fund managers. In addition, it provides insight into how the use of organisational and market context influences the framing of the meaningfulness of IR.
Passengers' service perceptions emerging from user-generated content during the pandemic: the case of leading low-cost carriers
Authors: Saydam Mehmet Bahri , Olorunsola Victor Oluwafemi , Rezapouraghdam Hamed 
Published: October 2022

PurposeAlthough a vast amount of research has been started to gauge customer satisfaction using surveys, the influence of COVID-19 on passengers' satisfaction has not received enough attention. Hence, the primary purpose of this research is to determine the dominant themes that emerged from airline travelers' online reviews and to determine attributes that are pertinent to the satisfaction of passengers flying with low-cost carriers (LCC) during the COVID-19 outbreak. In addition, this study investigates whether the salient themes of passengers' overall experiences vary by traveler origin, which may give more insight into airline sector market segmentation.Design/methodology/approachLeximancer software was used to construct concepts from words, followed by themes in the data analysis.FindingsThe analyses revealed eight themes in descriptions of “travel experiences” for airline passengers. These are “flights,” “staff,” “service,” “hygiene,” “cancellations,” “legroom,” “COVID-19” and “test”. Negative reviews associated with “cancellations,” “refund,” “waiting” and “baggage” (handling) concepts.Originality/valueThe findings provide important information about airline passengers' overall experiences. Limited studies have comprehensively considered various satisfaction categories of airline travelers using online reviews.
Malignant melanoma treatment using brachytherapy: Two case reports and 15 case series
Authors: Ishiguro Akihiro , Ogata Dai , Okuma Kae , Kashihara Tairo , Murakami Naoya , Hiki Kojiro , Yamakawa Kohei , Jinnai Shunichi , Takahashi Akira , Namikawa Kenjiro , Igaki Hiroshi , Yamazaki Naoya 
Published: October 2022

AbstractMalignant melanoma (MM) is usually resistant to radiotherapy. Brachytherapy may be an option in patients with bleeding or pain, and those in whom surgery is difficult. Brachytherapy has few side effects and can be used in combination with external beam radiotherapy or chemotherapy. We summarize the demographic and clinical characteristics of 15 patients who received brachytherapy for MM at our hospital and describe two of these representative cases. Patient 1 had an approximately 10‐mm, dark‐red nodule near the external urethral meatus. Excision was not performed to preserve urethral function. A gradual improvement was observed after 48 Gy of remote afterloading system (RALS) brachytherapy and nivolumab therapy. Patient 2 had a 38‐mm, black tumor on the vagina. Post‐resection, RALS brachytherapy was administered to treat the residual black macule and a lesion quickly disappeared. In all 15 cases, nine patients received radiotherapy for local control and six patients received palliative radiotherapy to reduce symptoms such as bleeding and pain. The irradiation site was the vagina in six patients, lymph node metastasis in five, head and neck in two, skin or subcutaneous metastases in two, and the anus in one. Treatment effect for local control and palliative care was 75% and 83% of patients, respectively. In particular, disappearance of the tumor or disappearance of symptoms was observed in half of the cases of brachytherapy to the vagina. On the other hand, brachytherapy was not very effective for lymph node metastases. Immediately after radiotherapy, eight (53%) patients experienced dermatitis or mucositis. Due to the histological and structural characteristics of mucosal melanoma of the luminal organs, brachytherapy may be an effective therapy. Hence, widespread use of brachytherapy with an appropriate irradiation technique aiming for local control and palliative care in case of unresectable MM should be considered.
Increasing prevalence of severe fires change the structure of arthropod communities: Evidence from a meta‐analysis
Authors: Bieber Blyssalyn V. , Vyas Dhaval K. , Koltz Amanda M. , Burkle Laura A. , Bey Kiaryce S. , Guzinski Claire , Murphy Shannon M. , Vidal Mayra C. 
Published: October 2022

Abstract

Animal ecology and evolution are shaped by environmental perturbations, which are undergoing unprecedented alterations due to climate change. Fire is one such perturbation that causes significant disruption by causing mortality and altering habitats and resources for animals. Fire regimes are changing on a global scale, but the effects of these changes on animal communities are poorly understood. Arthropods are one of the most ubiquitous and diverse animal taxa on the planet and their populations are sensitive to environmental change. Given their wide‐ranging impacts on ecosystem functioning, a better understanding of arthropod responses to changing fire regimes is critical and may also provide more general insights into how other groups might respond to fire.

Here, we provide a comprehensive meta‐analytical assessment of how fire influences the arthropod community across habitats and functional groups. Using data from 130 peer‐reviewed papers across the globe, we tested how a variety of fire characteristics, including management regime, severity and time‐since‐fire affect arthropod populations and communities across habitats.

Our results show that arthropod communities display substantial variation in response to fire and that community‐level responses are most likely to be detected within the first year. Responses also vary depending on fire characteristics and habitat. Specifically, while community metrics such as diversity were increased by low severity fires, they were reduced by high severity fires. Likewise, evenness increased after prescribed burns but was reduced after wildfire. Measures of arthropod community structure decreased following fires in deserts and forests.

Across the entire arthropod community, fire also had variable effects on community diversity. Fire tended to have a negative effect size on arthropods across life stages, but responses did vary among groups. Nearly all functional groups exhibited a negative response to fire with the exception of herbivores, for which abundance, diversity and richness increased after fire.

Our results suggest that the increasing prevalence of high‐severity wildfires are changing the structure of arthropod communities. Given their ubiquitous presence and diverse roles in terrestrial ecosystems, these community changes are likely to affect ecosystem functioning in various ways, including through increased herbivory.

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Forest disturbance and growth processes are reflected in the geographical distribution of large canopy gaps across the Brazilian Amazon
Authors: Reis Cristiano Rodrigues , Jackson Toby D. , Gorgens Eric Bastos , Dalagnol Ricardo , Jucker Tommaso , Nunes Matheus Henrique , Ometto Jean Pierre , Aragão Luiz E. O. C. , Rodriguez Luiz Carlos Estraviz , Coomes David A. 
Published: October 2022

Abstract

Canopy gaps are openings in the forest canopy resulting from branch fall and tree mortality events. The geographical distribution of large canopy gaps may reflect underlying variation in mortality and growth processes. However, a lack of data at the appropriate scale has limited our ability to study this relationship until now.

We detected canopy gaps using a unique LiDAR dataset consisting of 650 transects randomly distributed across 2500 km2 of the Brazilian Amazon. We characterized the size distribution of canopy gaps using a power law and we explore the variation in the exponent, α. We evaluated how the α varies across the Amazon, in response to disturbance by humans and natural environmental processes that influence tree mortality rates.

We observed that South‐eastern forests contained a higher proportion of large gaps than North‐western, which is consistent with recent work showing greater tree mortality rates in the Southeast than the Northwest. Regions characterized by strong wind gust speeds, frequent lightning and greater water shortage also had a high proportion of large gaps, indicating that geographical variation in α is a reflection of underlying disturbance processes. Forests on fertile soils were also found to contain a high proportion of large gaps, in part because trees grow tall on these sites and create large gaps when they fall; thus, canopy gap analysis picked up differences in growth as well as mortality processes. Finally, we found that human‐modified forests had a higher proportion of large gaps than intact forests, as we would expect given that these forests have been disturbed.

Synthesis. The proportion of large gaps in the forest canopy varied substantially over the Brazilian Amazon. We have shown that the trends can be explained by geographical variation in disturbance and growth. The frequency of extreme weather events is predicted to increase under climate change, and changes could lead to greater forest disturbance, which should be detectable as an increased proportion of large gaps in intact forests.