bluuebunny/crossref_metadata_2025 huggingface dataset:
Poly(ADP-ribose) binding sites on collagen I fibrils for nucleating intrafibrillar bone mineral
Authors: Zecca Marco A. , Greer Heather F. , Duer Melinda J.
Published: July 2024

Bone calcification is essential for vertebrate life. The mechanism by which mineral ions are transported into collagen fibrils to induce intrafibrillar mineral formation requires a calcium binding biopolymer that also has highly selective binding to the collagen fibril hole zones where intrafibrillar calcification begins, over other bone extracellular matrix components. Poly(ADP-ribose) has been shown to be a candidate biopolymer for this process and we show here that poly(ADP-ribose) has high affinity, highly conserved binding sites in the collagen type I C-terminal telopeptides. The discovery of these poly(ADP-ribose)-collagen binding sites gives new insights into the chemical mechanisms underlying bone calcification and possible mechanisms behind pathologies where there is dysfunctional bone calcification.
HIF-1 activated by PIM1 assembles a pathological transcription complex and regulon that drives JAK2V617F MPN disease
Authors: Kealy David , Ellerington Ruth , Bansal Suraj , Zeng Andy G.X. , Medeiros Jessie J.F. , West Katie A. , Blacknell Nicole-Mae , Hawley Catherine A. , Lukaszonek Jakub , Gawne Richard T. , Khoo Hwei Minn , Caalim Gillian , Drylie Bryce , Chatzigerou Jenny , Ferreira Bianca Lima , Fielding Adele K , Wang Guanlin , Kent David G. , Psaila Bethan , Wilkinson Adam C. , Holding Andrew N. , Hitchcock Ian S. , Mason Andrew S. , Gupta Vikas , Dick John E. , Bridge Katherine S.
Published: July 2024

Hypoxia-inducible factors (HIFs) are master transcriptional regulators, central to cellular survival under limited oxygen (hypoxia) and frequently activated within malignancy. Malignant context affects the role of HIFs within oncogenesis; however, the mechanisms regulating HIF context-specificities are not well characterised. Applying the JAK2V617F (JVF) model of myeloproliferative neoplasms (MPNs), in which HIF-1 is active in normoxia (20% O2), we sought to determine whether the modality of HIF-1 activation directs its function. We identify that HIF-1 is stabilised in JVF cells downstream of STAT1/5 signalling and upregulation of PIM1: PIM1 mediates phosphorylation of HIF-1 (Thr498/Ser500) in JVF cells that inhibits proteasomal degradation. PIM1 inhibition eradicates HIF-1 from JVF cells. Applying a single-input dual-omics output chromatin interactome methodology (DOCIA), we define JVF-specific transcription cofactors and genomic redistribution of HIF-1, and a JVF-HIF-1 regulon in primary haematopoietic stem/progenitor cells. In a cohort of 172 JVF-MPN patients, we observe significant association of the JVF-HIF-1 regulon (but strikingly, not canonical HIF-1 genes) with disease severity, progression, and patient survival. Finally, we identify a core set of JVF-HIF-1 targets significantly associated with spontaneous transformation of MPNs to AML. Our findings identify that HIF-1 activation by the JVF-PIM1 axis substantially alters its function, and that this reprogramming drives MPN disease progression, restoring the potential for targeted therapies that delineate HIF-1 activity co-opted by malignancy from essential roles within physiological oxygen homeostasis.

Key Points

HIF-1 activation via PIM1 in JAK2V617F-MPNs drives non-canonical transcription complex formation/function.

The JAK2V617F-HIF-1 regulon drives MPN disease progression, transformation to AML and worse patient outcomes.
Adult-neurogenesis allows for representational stability and flexibility in early olfactory system
Authors: Chen Zhen , Padmanabhan Krishnan
Published: July 2024

In the early olfactory system, adult-neurogenesis, a process of neuronal replacement results in the continuous reorganization of synaptic connections and network architecture throughout the animal’s life. This poses a critical challenge: How does the olfactory system maintain stable representations of odors and therefore allow for stable sensory perceptions amidst this ongoing circuit instability? Utilizing a detailed spiking network model of early olfactory circuits, we uncovered dual roles for adult-neurogenesis: one that both supports representational stability to faithfully encode odor information and also one that facilitates plasticity to allow for learning and adaptation. In the main olfactory bulb, adult-neurogenesis affects neural codes in individual mitral and tufted cells but preserves odor representations at the neuronal population level. By contrast, in the olfactory piriform cortex, both individual cell responses and overall population dynamics undergo progressive changes due to adult-neurogenesis. This leads to representational drift, a gradual alteration in sensory perception. Both processes are dynamic and depend on experience such that repeated exposure to specific odors reduces the drift due to adult-neurogenesis; thus, when the odor environment is stable over the course of adult-neurogenesis, it is neurogenesis that actually allows the representations to remain stable in piriform cortex; when those olfactory environments change, adult-neurogenesis allows the cortical representations to track environmental change. Whereas perceptual stability and plasticity due to learning are often thought of as two distinct, often contradictory processing in neuronal coding, we find that adult-neurogenesis serves as a shared mechanism for both. In this regard, the quixotic presence of adult-neurogenesis in the mammalian olfactory bulb that has been the focus of considerable debate in chemosensory neuroscience may be the mechanistic underpinning behind an array of complex computations.
Innovative Use of Depth Data to Estimate Energy Intake and Expenditure in Adélie Penguins
Authors: Dupuis Benjamin , Kato Akiko , Hicks Olivia , Wisniewska Danuta M. , Marciau Coline , Angelier Frederic , Ropert-Coudert Yan , Chimienti Marianna
Published: July 2024

Energy governs species’ life histories and pace of living, requiring individuals to make trade-offs. However, measuring energetic parameters in the wild is challenging, often resulting in data collected from heterogeneous sources. This complicates comprehensive analysis and hampers transferability within and across case studies. We present a novel framework, combining information obtained from eco-physiology and bio-logging techniques, to estimate both energy expended and acquired on 48 Adélie penguins (Pygoscelis adeliae) during the chick-rearing stage.

We employ the machine learning algorithm random forest (RF) to predict accelerometry-estimated foraging behaviour using depth data (our proxy for energy acquisition). We also build a time-activity model calibrated with doubly labelled water data to estimate energy expenditure.

Using depth-derived time spent diving and amount of vertical movement in the sub-surface phase, we accurately predict energy expenditure (R² = 0.70). Movement metrics derived from depth data modelled with the RF algorithm were able to accurately (accuracy = 0.82) detect the same foraging behaviour predicted from accelerometry. The RF more accurately predicted accelerometry-estimated time spent foraging (R² = 0.81) compared to historical proxies like number of undulations (R² = 0.51) or dive bottom duration (R² = 0.31).

The proposed framework is accurate, reliable and simple to implement, enabling to couple energy intake and expenditure, which is crucial to further assess individual trade-offs. We provide universal guidelines for predicting these parameters based on widely used bio-logging technology in marine species. Our work allows us to revisit historical data, to study how long-term environmental changes affect animals’ energetics.

Summary statement

Using machine learning, we estimated energy expenditure and foraging activity of free-ranging Adélie penguins using depth data recorded with bio-logging devices.
Molecular Insights into AGS3’s Role in Spindle Orientation: A Biochemical Perspective
Authors: Yu Shi , Ji Jie , Liu Zhijun , Wang Wenning
Published: July 2024

The intrinsic regulation of spindle orientation during asymmetric cell division (ACD) depends on the evolutionarily conserved protein complex LGN (Pins)/NuMA (Mud)/Gα·GDP. While the role of LGN and itsDrosophilaorthologue Pins is well-established, the function of AGS3, the paralogue of LGN, in spindle orientation during cell division remains controversial. This study substantiates the contentious nature of AGS3’s function through systematic biochemical characterizations. The results confirm the high conservation of AGS3 in its functional structural domains, similar to LGN, and its comparable ability to bind partners including NuMA, Insc and Gαi3·GDP. However, in contrast to LGN, AGS3 and the microtubule-binding protein NuMA are unable to form stable hetero-hexamers or higher-order oligomeric complexes that are pivotal for effective regulation of spindle orientation. It was found that this notable difference between AGS3 and LGN stems from the N-terminal sequence preceding the conserved TPR motifs, which spans approximately 20 residues. Furthermore, our findings substantiate the disruptive effect of Insc on the oligomeric AGS3/NuMA complex, while showing no impact on the oligomeric LGN/NuMA complex. Consequently, Insc emerges as an additional regulatory factor that distinguishes the functional roles of AGS3 and LGN, leading to the impairment of AGS3’s ability to actively reorient the mitotic spindle. These results elucidate the molecular basis underlying the observed functional disparity in spindle orientation between LGN and AGS3, providing valuable insights into the regulation of cell division at the molecular level.
Long-lasting negative effects of past forestation on grassland pollination networks and their function
Authors: Hirayama Gaku S. , Inoue Taiki , Kenta Tanaka , Ishii Hiroshi S. , Ushimaru Atushi
Published: July 2024

Grasslands are facing a rapid decline worldwide. Among the primary threats to these ecosystems are changes in land use, such as land abandonment and forestation, which promote forest vegetation in detriment of grassland plant diversity. To support the conservation and restoration of grasslands, it is key to understand what ecological processes limit the recovery of their biodiversity and functions after perturbations. However, we still know little about the legacy effects of forestation on the ecological mechanisms involved in the recovery of grasslands, especially concerning long-lasting impacts on plant-pollinator interaction networks and plant reproduction.

Here, we aim to fill this gap of knowledge by comparing the plant and pollinator diversity, the degree of network generalization, the pollination success and pollen limitation of native plant species in 30 plant-pollinator networks of old-growth and restored grasslands of different ages since recovery (from 2 to 84 years). We hypothesized that past forestation would exert long-lasting legacy negative effects on plant richness and plant-pollinator networks, increasing pollen limitation for native plants, thereby delaying community recovery in restored grasslands.

Results showed that restored grasslands exhibited significantly lower plant richness, less specialized (more generalized) interaction networks, lower pollination success and pollen-limited seed reproduction of native plants compared to old-growth grasslands. Meanwhile, the degree of network specialization and pollination success gradually increased with time after grassland restoration initiated. Overall, network generalization, which was caused by low plant richness, reduced pollination and reproduction success in native grassland plants, and degraded pollination networks and functions could recover in restored grasslands with continuous management. These findings imply that plant diversity restoration was slow because of the negative feedbacks associated with low plant richness and consequently, generalized plant-pollinator interaction networks, which diminished native plant reproduction in restored grasslands.

Synthesis and applicationsOur findings suggest that the recovery of specialized plant-pollinator networks by enhancing plant diversity is essential for restoring pollination function. For quicker grassland restoration, it may be effective to facilitate the establishment of highly specialized pollination networks by seeding or planting diverse native plants collected from neighbouring areas while avoiding genetic contamination.
Reproductive output of old polygynous males is limited by seminal fluid, not sperm number
Authors: Sanghvi Krish , Shandilya Sucheta , Brown Alana , Todorova Biliana , Jahn Martin , Gascoigne Samuel J.L. , Camilleri Tara-Lyn , Pizzari Tommaso , Sepil Irem
Published: July 2024

Advancing male age can lead to reproductive senescence, which in males is thought to be largely driven by declines in the numbers of sperm transferred by old males. This decline is predicted to be particularly pronounced in polygynous species, where males become sperm limited over a mating sequence. However, males also transfer seminal fluid to females, and little is known about the contribution of seminal fluid to constrain the reproductive output of old, multiply-mating males. UsingDrosophila melanogaster, we investigated whether age-related variation in male reproductive output is driven by differential limitation of sperm or seminal fluid, over a series of experimental matings. Consistent with reproductive senescence, old males produced fewer offspring than young males. However, this pattern was not driven by sperm limitation, with old males having more sperm and transferring similar numbers of sperm to a female, compared to young males. Yet surprisingly, females stored fewer sperm when mated to old than young males. Notably, females mated to old multiply-mating males produced more offspring when supplemented with seminal fluid, suggesting that fertility of old males over successive matings was limited by seminal fluid availability. Generally, our study indicates that germline maintenance might be prioritised over somatic maintenance as hypothesized by the disposable soma theory of ageing, and that seminal fluid senescence is a key contributor of reproductive decline with age. While other factors such as differential sperm viability and female post-mating responses could have also influenced our results, our study highlights the under-appreciated role of seminal fluid in mediating male reproductive senescence in polygynous species.

Significance statement

A key assumption in ageing research is that old males are less fertile than young males, and that this reduced fertility is partly driven by old males producing fewer sperm. However, senescence in male fertility can be caused via other ejaculate-mediated pathways, which we investigate using fruit flies. Contrary to expectations, we reveal that senescence in male fertility is not because of declines in male sperm reserves, but is instead due to age-related changes in seminal fluid and differences in female sperm storage with male age. These declines in the reproductive output of old, multiply-mating males are alleviated by supplementing females with “extra” seminal fluid. Our study demonstrates that male reproductive senescence is reversible, highlighting the underappreciated role of seminal fluid in modulating senescence in polygynous species. These results have potential for improving animal fertility and our understanding of sexual selection.
iTome Volumetric Serial Sectioning Apparatus for TEM
Authors: Peale David R. , Hess Harald , Lee P. R. , Cardona Albert , Bock Davi D. , Schneider-Mizell Casey , Fetter Richard D. , Lee Wei-Ping , Robinson Camenzind G. , Iyer Nirmala , Managan Claire
Published: July 2024

An automated ultra-microtome capable of sectioning thousands of ultrathin sections onto standard TEM slot grids was developed and used to section: a completeDrosophila melanogasterfirst-instar larva, three sections per grid, into 4,866 34-nm-thick sections with a cutting and pickup success rate of 99.74%; 30 microns of mouse cortex measuring roughly 400 um x 2000 um at 40 nm per slice; and a full adultDrosophilabrain and ventral nerve column into 9,300 sections with a pickup success rate of 99.95%. The apparatus uses optical interferometers to monitor a reference distance between the cutting knife and multiple sample blocks. Cut sections are picked up from the knife-boat water surface while they are still anchored to the cutting knife. Blocks without embedded tissue are used to displace tissue-containing sections away from the knife edge so that the tissue regions end up in the grid slot instead of on the grid rim.
Uridine Phosphorylase-1 supports metastasis of mammary cancer by altering immune and extracellular matrix landscapes of the lung
Authors: Whyte Declan , Voorde Johan Vande , Sumpton David , Dhayade Sandeep , Dornier Emmanuel , Moore Madeleine , Novo David , Peters Jasmine , Wiesheu Robert , Mackey John B.G. , McFarlane Amanda J. , Fercoq Frédéric , Fisher Sophie , Caballero Carolina Dehesa , Gilroy Kathryn , Redmond Keara L. , Mitchell Louise E. , Anderson Eve , Thomson Gemma , Dzierozynski Lindsey N. , Saab Juan J. Apiz , Lewis Caroline A. , Muir Alexander , Halbrook Christopher J. , Strathdee Douglas , Jackstadt Rene , Nixon Colin , Dunne Philip , Steele Colin W. , Carlin Leo M. , Macpherson Iain R. , Roberts Edward W. , Coffelt Seth B. , Blyth Karen , Sansom Owen J. , Norman Jim C. , Clarke Cassie J.
Published: July 2024

Understanding the mechanisms that facilitate early events in metastatic seeding is key to developing therapeutic approaches to reduce metastasis – the leading cause of cancer-related death. Using whole animal screens in genetically engineered mouse models of cancer we have identified circulating metabolites associated with metastasis. Specifically, we highlight the pyrimidine uracil as a prominent metastasis-associated metabolite. Uracil is generated by neutrophils expressing the enzyme uridine phosphorylase-1 (UPP1), and neutrophil specificUpp1expression is increased in cancer. Altered UPP1 activity influences expression of adhesion molecules on the surface of neutrophils, leading to decreased neutrophil motility in the pre-metastatic lung. Furthermore, we find that UPP1-expressing neutrophils suppress T-cell proliferation, and the UPP1 product uracil can increase fibronectin deposition in the extracellular microenvironment. Consistently, knockout or inhibition of UPP1 in mice with mammary tumours increases the number of T-cells and reduces fibronectin content in the lung and decreases the proportion of mice that develop lung metastasis. These data indicate that UPP1 influences neutrophil behaviour and extracellular matrix deposition in the lung and suggest that pharmacological targeting of this pathway could be an effective strategy to reduce metastasis.
Intervening to preserve function in ischemic cardiomyopathy with a porous hydrogel and extracellular matrix composite in a rat myocardial infarction model
Authors: Hayashi Yasunari , Fujii Taro , Kim Seungil , Badylak Stephen F. , D’Amore Antonio , Wagner William R.
Published: July 2024

A variety of hydrogels have been developed for intramyocardial injection therapy after myocardial infarction. Some of these biomaterials have incorporated bioactive substances that promote local tissue regeneration and integration, while others have emphasized the mechanical role of the injectate in providing functional benefit. In this study, we incorporated two bioactive features, porosity, and extracellular matrix derived hydrogel (ECM), into a mechanically optimized, thermoresponsive, degradable hydrogel (poly(N-isopropylacrylamide-co-N-vinylpyrrolidone-co-MAPLA) copolymer) and evaluated whether injection of this biomaterial could abrogate the remodeling process in a rat ischemic cardiomyopathy model. After myocardial infarction by coronary artery ligation, rats were randomly divided into four groups: group NP (non-porous hydrogel) without either ECM or porosity, group PM (porous hydrogel) from the same synthetic copolymer with mannitol beads as porogens, and group PME with porosity and ECM digest added to the synthetic copolymer. A group with PBS injection alone served as a control. Intramyocardial injections were made 3 days after myocardial infarction. Serial echocardiography was assessed over time, and histological assessments were performed eight weeks after infarction. Results demonstrated improved echocardiographic function and neovascularization in the PME group compared to the other hydrogels and PBS injection. The PME group also demonstrated significant improvement in LV geometry and macrophage polarization (towards M2) compared to the PBS group, whereas these differences were not observed in the NP or PM groups versus the control. These results demonstrate that further functional improvement may be achieved in hydrogel injection therapy for ischemic cardiomyopathy by incorporating porosity and ECM digest, representing a combination of mechanical and biological effects.
Exenatide administration time determines the effects on blood pressure dipping indb/dbmice via modulation of food intake and sympathetic activity
Authors: Chacon Aaron N. , Su Wen , Hou Tianfei , Guo Zhenheng , Gong Ming C.
Published: July 2024

Abstract

Type 2 diabetics have an increased prevalence of hypertension and nondipping blood pressure (BP), which worsen cardiovascular outcomes. Exenatide, a short acting glucagon-like peptide-1 receptor agonist (GLP-1RA) used to treat type 2 diabetes, also demonstrates blood pressure (BP)-lowering effects. However, the mechanisms behind this and the impact of administration timing on BP dipping remain unclear. We investigated the effects of exenatide intraperitoneal injected at light onset (ZT0) or dark onset (ZT12) in diabetic (db/db) mice and nondiabetic controls. Using radio-telemetry and BioDAQ cages, we continuously monitored BP and food intake. Db/db mice exhibited non-dipping BP and increased food intake. ZT0 exenatide administration restored BP dipping by specifically lowering light-phase BP, while ZT12 exenatide reversed dipping by lowering dark-phase BP. These effects correlated with altered food intake patterns, and importantly, were abolished when food access was removed. Additionally, urinary norepinephrine excretion, measured by HPLC, was significantly reduced 6 hours post-exenatide at both ZT0 and ZT12, suggesting sympathetic nervous system involvement. Notably, combining exenatide with either ganglionic blocker mecamylamine or α-blocker prazosin did not enhance BP reduction beyond the individual effects of each blocker. These findings reveal that exenatide, when administered at light onset, restores BP dipping in db/db mice by suppressing light-phase food intake and sympathetic activity. Importantly, the efficacy of exenatide is dependent on food availability and its timing relative to circadian rhythms, highlighting the potential for chronotherapy in optimizing GLP-1RA- based treatments for type 2 diabetes and hypertension.

Graphic Abstract

Article Highlights

Maintaining a normal blood pressure (BP) circadian rhythm is vital for cardiovascular health, but diabetes often disrupts this rhythm. The effect of exenatide, a GLP-1 receptor agonist (GLP-1RA), on BP rhythm in diabetes is uncertain.

This study investigates the impact of exenatide administration timing on BP patterns in diabetic db/db mice.

Findings indicate that exenatide given at the onset of rest restores normal BP dipping, while at the start of the active phase worsens BP rhythm by modulating food intake and sympathetic activity.

Timing GLP-1 RA administration may optimize BP control and provide cardiovascular benefits for type 2 diabetes patients.
Tks5 interactome reveals ER-associated machinery translation in invadosomes
Authors: Normand Léa , Bonnard Benjamin , Sala Margaux , Di-Tommaso Sylvaine , Dourthe Cyril , Raymond Anne-Aurélie , Dupuy Jean-William , Mercier Luc , Goetz Jacky G. , Moreau Violaine , Henriet Elodie , Saltel Frédéric
Published: July 2024

The ability to progress and invade through the extracellular matrix is a characteristic shared by both normal and cancer cells through the formation of structures called invadosomes gathering invadopodia and podosomes. These invadosomes are plastic and dynamic structures that can adopt different organizations depending on the cell types and the environment such as rosettes, dots or linear invadosomes. In this study, we used the specific invadosome marker Tks5 (SH3PXD2A), to identify common features in these different organizations. Tks5 immunoprecipitation coupled with mass spectrometry analysis allowed us to identify common proteins in these different models. We identified elements of the translation machinery, in particular the EIF4B protein, but also endoplasmic reticulum (ER) proteins as part of the invadosome structure. Providing new data on invadosome molecular composition through Tks5 interactome, we identified that ER-associated translation machinery is recruited to invadosome and involved in their formation, persistence and function in all types of invadosomes.

Invadosomes are invasive F-actin structures exhibiting different organizations that degrade the extracellular matrix. The study uses their universal marker, Tks5, to provide new data about invadosome molecular composition and reveal the role of ER-associated translation machinery in invadosome formation and function.
3D directional tuning in the orofacial sensorimotor cortex during natural feeding and drinking
Authors: Hosack Victoria B. , Arce-McShane Fritzie I.
Published: July 2024

Directional tongue movements are essential for vital behaviors, such as feeding and speech, to position food for chewing and swallowing safely and to position the tongue for accurate sound production. While directional tuning has been well-studied in the arm region of the sensorimotor cortex during reaching tasks, little is known about how 3D tongue direction is encoded in the orofacial region during natural behaviors. Understanding how tongue direction is represented in the brain has important implications for improving rehabilitation for people with orolingual dysfunctions. The goal of this study is to investigate how 3D direction of tongue movement is encoded in the orofacial sensorimotor cortex (OSMCx) during feeding and drinking, and how this process is affected by the loss of oral sensation. Using biplanar video-radiography to track implanted markers in the tongue of behaving non-human primates (Macaca mulatta), 3D positional data was recorded simultaneously with spiking activity in primary motor (MIo) and somatosensory (SIo) areas of the orofacial cortex using chronically implanted microelectrode arrays. In some sessions, tasks were preceded by bilateral nerve block injections to the sensory branches of the trigeminal nerve. Modulation to the 3D tongue direction was found in a majority of MIo but not SIo neurons during feeding, while the majority of neurons in both areas were modulated to the direction of tongue protrusion during drinking. Following sensory loss, the proportion of directionally tuned neurons decreased and shifts in the distribution of preferred direction were observed in OSMCx neurons. Overall, we show that 3D directional tuning of MIo and SIo to tongue movements varies with behavioral tasks and availability of sensory information.
Multi-dimensional demarcation of phylogenetic groups of plant 14-3-3 isoforms using biochemical signatures
Authors: Sedlov Ilya A. , Sluchanko Nikolai N.
Published: July 2024

Interaction of dimeric 14-3-3 proteins with numerous phosphotargets regulates various physiological processes in plants, from flowering to transpiration and salt tolerance. Several genes express distinct 14-3-3 ‘isoforms’, particularly numerous in plants, but comparative studies of all 14-3-3 isoforms for a given organism have not been undertaken. Here we systematically investigated twelve 14-3-3 isoforms from the model plantArabidopsis thaliana, uniformly capable of homodimerization at high protein concentration. We unexpectedly discovered that, at physiological protein concentrations, four isoforms representing a seemingly more ancestral, epsilon phylogenetic group (iota, mu, omicron, epsilon) demonstrate an outstanding monomerization propensity and enhanced surface hydrophobicity, which is uncharacteristic for eight non-epsilon isoforms (omega, phi, chi, psi, upsilon, nu, kappa, lambda). Further analysis revealed that dramatically lowered thermodynamic stabilities entail aggregation of the epsilon-group isoforms at near-physiological temperatures and provoke their proteolytic degradation. Structure-inspired single mutations in 14-3-3 iota could rescue non-epsilon behavior, thereby pinpointing key positions responsible for the phylogenetic demarcation. Combining two major demarcating positions (namely, 27th and 51st in omega) and multi-dimensional differences in biochemical properties identified here, we developed a predictor strongly supporting categorization of abundant 14-3-3 isoforms widely across plant groups, from Eudicots to Monocots, Gymnosperms and Lycophytes. In particular, our approach fully recapitulates the phylogenetic epsilon/non-epsilon demarcation in Eudicots and supports the presence of isoforms of both types in more primitive plant groups such asSelaginella, thereby refining solely sequence-based analysis in evolutionarily distant species and providing novel insights into the evolutionary history of the epsilon phylogenetic group.

Significance

Despite over 30 years of research, systematic comparative studies on the regulatory plant 14-3-3 proteins have not been undertaken, making phylogenetic classification of numerous plant 14-3-3 isoforms in different species unreliable. Working on twelve purifiedArabidopsis14-3-3 isoforms, we have discovered a set of biochemical signatures that can be used to robustly and widely categorize epsilon and non-epsilon plant 14-3-3 isoforms, also identifying at least two amino acid positions responsible for such multi-dimensional demarcation.
Thalamic Influence Over Adaptive Cortical Dynamics Across Conscious States
Authors: Müller Eli J. , Munn Brandon R. , Baracchini Giulia , Fulcher Ben D. , Medel Vicente , Redinbaugh Michelle J. , Saalmann Yuri B. , Brunton Bingni W. , Brunton Steven L. , Shine James M.
Published: July 2024

The human brain must support both stable and flexible neural dynamics in order to adapt to changing contexts that are inherently non-linear. The thalamus has been linked to the coordination of these opposing dynamical regimens in the cerebral cortex, however existing methodological approaches have not integrated sufficient neurobiological details with a sensitive measure of neural dynamics that permits sensitivity to time-series non-linearities. Inspired by the field of fluid dynamics, we use a novel approach to show that spontaneous fMRI data exhibits non-trivial fluctuations in predictability over time, akin to a river that has sections of smooth and predictable (laminar) versus rough and unpredictable (non-laminar) fluid flow. We use a combination of pharmacological fMRI, macaque electrophysiology and a large-scale biophysical model of the thalamocortical system to provide robust evidence that the thalamus provides versatile control over globally linear dynamics in the cerebral cortex that characterize conscious states.
SID-2 localises to extracellular vesicles in parasitic nematodes and does not function in environmental RNAi
Authors: Blow Frances , Jeffrey Kate , Chow Franklin Wang-Ngai , Nikonorova Inna A. , Barr Maureen M. , Cook Atlanta G. , Prevo Bram , Cheerambathur Dhanya K. , Buck Amy H.
Published: July 2024

In the free-living nematodeCaenorhabditis elegansthe transmembrane protein SID-2 imports double-stranded RNA into intestinal cells to trigger systemic RNA interference (RNAi), allowing organisms to sense and respond to environmental cues such as the presence of pathogens. This process, known as environmental RNAi, has not been observed in the most closely related parasites that are also within clade V. Previous sequence-based searches failed to identifysid-2orthologs in available clade V parasite genomes. In this study we identifiedsid-2orthologues in these parasites using genome synteny and protein structure-based comparison, following identification of a SID-2 orthologue in extracellular vesicles from the murine intestinal parasitic nematodeHeligmosomoides bakeri. Expression of GFP-taggedH. bakeriSID-2 inC. elegansshowed comparable localisation to the intestinal apical membrane as seen for GFP-taggedC. elegansSID-2 and further showed mobility in intestinal cells in vesicle-like structures. We tested the capacity ofH. bakeriSID-2 to functionally complement environmental RNAi in aC. elegansSID-2 null mutant and show thatH. bakeriSID-2 does not rescue the phenotype in this context. Therefore, our work identifies SID-2 as a highly abundant nematode EV protein whose ancestral function may be unrelated to environmental RNA and rather highlights an association with extracellular vesicle-mediated communication in free-living and parasitic nematodes.
Heat pre-treatment reduces multiplicity of plasmid transformations in yeast during electroporation, without diminishing the transformation efficiency
Authors: Wäneskog Marcus , Hoch-Schneider Emma Elise , Garg Shilpa , Kronborg Cantalapiedra Christian , Schaefer Elena , Krogh Jensen Michael , Damgaard Jensen Emil
Published: July 2024

High-throughput DNA transformation techniques are invaluable when creating high-diversity mutant libraries, and the success rate of any protein engineering endeavors is directly dependent on both the size and diversity of the mutant library that is to be screened. It is also widely accepted that in both bacteria and yeast there is an inverse correlation between the DNA transformation efficiency and the likelihood of transforming multiple DNA molecules into each cell. However, most successful high-throughput mutant screening efforts require high quality libraries, i.e., libraries comprised of cells with a clear phenotype-to-genotype relationship (one genotype/cell). Thus, DNA transformation methods with a high multiplicity of transformation are highly undesirable and detrimental to most mutant screening assays. Here we describe a simple, robust, and highly efficient yeast plasmid DNA transformation methodology, using a dual heat-shock and electroporation approach (HEEL) that generates more than 2 x 107plasmid-transformed yeast cells per reaction, while simultaneously increasing the fraction of mono-transformed cells from 20% to more than 70% of the transformed population. By also using an automated yeast genotyping workflow coupled with a dual-barcoding approach, consisting of a SNP and high-diversity barcode (10N), we can consistently identify and enumerate unique plasmid genotypes within a heterogeneous population merely through Sanger sequencing. We demonstrate here that the size and quality of a transformed library no longer need to be inversely correlated when transforming large mutant DNA libraries in yeast using highly efficient DNA electroporation methods.

Significance

With the recent expansion of artificial intelligence in the field of synthetic biology there has never been a greater need for high-quality data and reliable measurements of phenotype-to-genotype relationships. However, one major obstacle to creating accurate computer-based models is the current abundance of low-quality phenotypic measurements originating from numerous high-throughput, but low-resolution assays. Rather than increasing the quantity of measurements, new studies should aim to generate as accurate measurements as possible. The HEEL methodology presented here aims to address this issue by minimizing the problem of multi-plasmid uptake during high-throughput yeast DNA transformations, which leads to the creation of heterogeneous cellular genotypes. HEEL should enable highly accurate phenotype-to-genotype measurements going forward, which could be used to construct better computer-based models.
Competition and cooperation: The plasticity of bacteria interactions across environments
Authors: Solowiej-Wedderburn Josephine , Pentz Jennifer T. , Lizana Ludvig , Schröder Björn , Lind Peter , Libby Eric
Published: July 2024

Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is why some species engage in cooperative interactions, whereas others compete. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By scanning thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions to the availability of environmental resources.
Characterizing Excretory-Secretory Products Proteome Across Larval Development Stages inAscaris suum
Authors: Castañeda Sergio , Adeniyi-Ipadeola Grace , Wu Yifan , Suarez-Reyes Charlie , Jain Antrix , Ramírez Juan David , Weatherhead Jill E.
Published: July 2024

Introduction

Ascaris lumbricoidesandAscaris suumare parasitic nematodes that primarily infest the small intestines of humans and pigs, respectively. Ascariasis poses a significant threat to human health and swine health. UnderstandingAscarislarval development is crucial for developing novel therapeutic interventions that will prevent ascariasis in both humans and pigs. This study aimed to characterize the excretory-secretory (ES) proteome of differentAscaris suumlarval stages (L3-egg, L3-lung, L3-trachea) to identify potential targets for intervention to preventAscaris-induced global morbidity.

Methods

Stage-specific larvae were isolated, cultured in vitro and ES-product was collected. Third-stageAscarislarvae (L3) were isolated from embryonated eggs (L3-egg), isolated from the lungs of Balb/c mice infected withAscaris suumeggs at day 8 post infection (L3-lungs) and isolated from the trachea of Balb/c mice infected withAscaris suumeggs at day 12 post infection (L3-trachea). ES products were obtained by culturing larvae. Proteomic analysis was conducted using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and bioinformatic tools including MaxQuant, Perseus, and Andromeda, following a detailed protocol available on GitHub. The analysis encompassed peptide identification, scoring, and quantification against an organism-specific database, with subsequent quality control, correlation assessment, and differential abundance determination using the Amica algorithm.

Results

A total of 58 unique proteins were identified in the ES products. Fourteen proteins were common across all stages, while others were stage-specific. Principal component analysis revealed distinct protein profiles for each stage, suggesting qualitatively different proteomes. Gene ontology analysis indicated stage-specific GO enrichment of specific protein classes, such as nuclear proteins in L3-egg ES products and metabolic enzymes in L3-lung and L3-trachea ES products.

Discussion

This study revealed stage-specific differences in the composition ofAscarisES products. Further investigation into the functional roles of these proteins and their interactions with host cells is crucial for developing novel therapeutic and diagnostic strategies against ascariasis.
NPM1 mediates genome-nucleolus interactions and the establishment of their repressive chromatin states
Authors: Gupta Shivani , Bersaglieri Cristiana , Bär Dominik , Raingeval Mathieu , Schaab Luana , Santoro Raffaella
Published: July 2024

Repressive chromatin domains are often located at the nuclear lamina (NL) or nucleolus. Although nucleolar associated domains (NADs) have been recently mapped, the mechanisms of NAD association with nucleoli and the functional significance of their localization remain unclear. Here, we show that NAD association with nucleoli is mediated by nucleophosmin (NPM1), a factor located within the granular component, the outer layer of the nucleolus. NPM1 binds NADs, interacts with the histone lysine methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of NPM1 mutant lacking the DNA binding domain (NPM1ΔDBD) caused NAD dissociation from nucleoli and H3K9me2 reduction specifically at NADs. G9a is dispensable for NAD contacts with nucleoli and interacts with NPM1ΔDBD, indicating that NADs acquire G9a-mediated H3K9me2 only after associating with NPM1 at nucleoli. The results provide mechanistic insights into how genomic domains associate with nucleoli and acquire their repressive chromatin state. Additionally, our findings suggest that the nucleolus not only serves as a scaffold for positioning repressive chromatin domains but also plays a direct role in establishing these chromatin states.
Automated pipeline processing X-ray diffraction data from dynamic compression experiments on the Extreme Conditions Beamline of PETRA III
Authors: Karnevskiy Mikhail , Glazyrin Konstantin , Yu Yuelong , Mondal Anshuman , Sanchez-Valle Carmen , Marquardt Hauke , Husband Rachel J. , O'Bannon Earl , Prescher Clemens , Barty Anton , Liermann Hanns-Peter
Published: July 2024

Presented and discussed here is the implementation of a software solution that provides prompt X-ray diffraction data analysis during fast dynamic compression experiments conducted within the dynamic diamond anvil cell technique. It includes efficient data collection, streaming of data and metadata to a high-performance cluster (HPC), fast azimuthal data integration on the cluster, and tools for controlling the data processing steps and visualizing the data using the DIOPTAS software package. This data processing pipeline is invaluable for a great number of studies. The potential of the pipeline is illustrated with two examples of data collected on ammonia–water mixtures and multiphase mineral assemblies under high pressure. The pipeline is designed to be generic in nature and could be readily adapted to provide rapid feedback for many other X-ray diffraction techniques, e.g. large-volume press studies, in situ stress/strain studies, phase transformation studies, chemical reactions studied with high-resolution diffraction etc.
Subgradient-projection-based stable phase-retrieval algorithm for X-ray ptychography
Authors: Akaishi Natsuki , Yamada Koki , Yatabe Kohei , Takayama Yuki
Published: July 2024

X-ray ptychography is a lensless imaging technique that visualizes the nanostructure of a thick specimen which cannot be observed with an electron microscope. It reconstructs a complex-valued refractive index of the specimen from observed diffraction patterns. This reconstruction problem is called phase retrieval (PR). For further improvement in the imaging capability, including expansion of the depth of field, various PR algorithms have been proposed. Since a high-quality PR method is built upon a base PR algorithm such as ePIE, developing a well performing base PR algorithm is important. This paper proposes an improved iterative algorithm named CRISP. It exploits subgradient projection which allows adaptive step size and can be expected to avoid yielding a poor image. The proposed algorithm was compared with ePIE, which is a simple and fast-convergence algorithm, and its modified algorithm, rPIE. The experiments confirmed that the proposed method improved the reconstruction performance for both simulation and real data.
Medical tourism in South East Asia: science mapping of present and future trends
Authors: Fauzi Muhammad Ashraf , Mohd Aripin Norhana , Alimin Nur Sofia Nabila , Ting Irene Wei Kiong , Wider Walton , Maidin Siti Sarah , Zainul Abideen Ahmed
Published: July 2024

Purpose

This study evaluates the knowledge structure of medical tourism within the geographical context of South East Asia. This region is one of the growing economic powerhouses in the world, and tourism activities have contributed a lot to its advancement.

Design/methodology/approach

Applying a science mapping technique using bibliometric analysis, the current and emerging themes and future trends are analyzed using bibliographic coupling and co-word analysis.

Findings

Findings show that current trends produced four themes: Fundamentals of medical tourism in Southeast Asia, determinants of tourist medical tourism visits, quality of medical and health service in Southeast Asia and impact of medical tourism on national economic growth. The future trends also produced four themes related to navigating excellence in medical tourism, medical tourism and economic growth, service quality in medical tourism services and accredited destinations in the globalized era of medical tourism.

Research limitations/implications

This study is relevant to all stakeholders, operators and local communities in Southeast Asia tourism destinations to provide the best medical tourism with the best quality service and technologies.

Originality/value

This study fills the gap by performing a bibliometric approach to reviewing medical tourism in Southeast Asia using a science mapping technique. Crucial themes are produced through topological and temporal streams that provide critical insight for future developments in medical tourism in the region.
TwinLab: a framework for data-efficient training of non-intrusive reduced-order models for digital twins
Authors: Kannapinn Maximilian , Schäfer Michael , Weeger Oliver
Published: July 2024

Purpose

Simulation-based digital twins represent an effort to provide high-accuracy real-time insights into operational physical processes. However, the computation time of many multi-physical simulation models is far from real-time. It might even exceed sensible time frames to produce sufficient data for training data-driven reduced-order models. This study presents TwinLab, a framework for data-efficient, yet accurate training of neural-ODE type reduced-order models with only two data sets.

Design/methodology/approach

Correlations between test errors of reduced-order models and distinct features of corresponding training data are investigated. Having found the single best data sets for training, a second data set is sought with the help of similarity and error measures to enrich the training process effectively.

Findings

Adding a suitable second training data set in the training process reduces the test error by up to 49% compared to the best base reduced-order model trained only with one data set. Such a second training data set should at least yield a good reduced-order model on its own and exhibit higher levels of dissimilarity to the base training data set regarding the respective excitation signal. Moreover, the base reduced-order model should have elevated test errors on the second data set. The relative error of the time series ranges from 0.18% to 0.49%. Prediction speed-ups of up to a factor of 36,000 are observed.

Originality/value

The proposed computational framework facilitates the automated, data-efficient extraction of non-intrusive reduced-order models for digital twins from existing simulation models, independent of the simulation software.