bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Relationship Between Preference and Switching in Flower Foraging by Bees
Authors: Papaj Daniel R. , Russell Avery L. 
Published: December 2023

AbstractIt seems self-evident that generalist foragers switch more between resources than specialists but despite diverse ecological and evolutionary implications, how variation in switching relates to variation in preference warrants additional study. Here we tested predictions based on a simple probability model, using flower-foraging bees as a model system. In laboratory assays, we presented bumble bee (Bombus impatiens) workers with flowers of two species,Tecoma stansandT. alata, from which they could collect nectar and/or pollen. We quantified landing preference and occurrence of switching between species in successive visits. Bees varied greatly in floral preference. Almost half showed statistically significant preferences for one or the other species, while the rest were generalists. As expected, generalists using both flower species switched more in successive visits than bees that were more specialized, a pattern fit to a quadratic function. However, generalist individuals switched more than expected based on null expectation. A Modified Jacob’s Index (MJI) of switching was significantly positively correlated with degree of preference: generalist bees had more negative MJI’s than specialist bees, indicating that even after the expected statistical effect of preference on switching was accounted for, they switched more than specialists. A simulation ruled out the possibility that the pattern was due to bias in MJI. Generalist-specialist differences in which food was collected (nectar versus pollen) were also ruled out. We discuss possible explanations for our observed pattern and outline possible ways in which preference and switching frequency will interact to shape pollinator behavior and the floral resource.Significance statementBehavioral preference is the subject of a large literature in areas such as foraging, mating and communication. However, a preference measure alone does not necessarily tell us if choices for one alternative are made in runs or intermingled with choices for another alternative. The distinction between preference and the sequential pattern of choices is relevant in many contexts in behavioral ecology but has been a particular focus of study in flower foraging by pollinators. Even in that literature, the relationship between preference and sequential pattern in switching warrants further examination. In our study, bees were shown to vary in preference for flowers of two species. Some were generalists; some were specialists on one or the other species. Generalist bees switched more than specialist bees, even after controlling for statistical effects of preference on switching frequency. The report of this generalist-specialist pattern in switching may be novel and has far-reaching implications throughout the field of behavioral ecology.
Mitochondrial mutation spectrum in Chordates: damage versus replication signatures, causes, and dynamics
Authors: Iliushchenko Dmitrii , Efimenko Bogdan , Mikhailova Alina G. , Shamanskiy Victor , Saparbaev Murat K. , Mazunin Ilya , Knorre Dmitrii , Kunz Wolfram S. , Kapranov Philipp , Denisov Stepan , Fellay Jacques , Khrapko Konstantin , Gunbin Konstantin , Popadin Konstantin 
Published: December 2023

AbstractTo elucidate the primary factors shaping mitochondrial DNA (mtDNA) mutagenesis, we derived a comprehensive 192-component mtDNA mutational spectrum using 86,149 polymorphic synonymous mutations reconstructed from the CytB gene of 967 chordate species. The mtDNA spectrum analysis provided numerous findings on repair and mutation processes, breaking it down into three main signatures: (i) symmetrical, evenly distributed across both strands, mutations, induced by gamma DNA polymerase (about 50% of all mutations); (ii) asymmetrical, heavy-strand-specific, C>T mutations (about 30%); and (iii) asymmetrical, heavy-strand-specific A>G mutations, influenced by metabolic and age-specific factors (about 20%). We propose that both asymmetrical signatures are driven by single-strand specific damage coupled with inefficient base excision repair on the lagging (heavy) strand of mtDNA. Understanding the detailed mechanisms of this damage is crucial for developing strategies to reduce somatic mtDNA mutational load, which is vital for combating age-related diseases.
KinAce: a web portal for exploring kinase-substrate interactions
Authors: Sekar John A. P. , Li Yan Chak , Schlessinger Avner , Pandey Gaurav 
Published: December 2023

AbstractInteractions between protein kinases and their substrates are critical for the modulation of complex signaling pathways. Currently, there is a large amount of information available about kinases and their substrates in disparate public databases. However, these data are difficult to interpret in the context of cellular systems, which can be facilitated by examining interactions among multiple proteins at once, such as the network of interactions that constitute a signaling pathway. We present KinAce, a user-friendly web portal that integrates and shares information about kinase-substrate interactions from multiple databases of post-translational modifications. KinAce enables the visual exploration of these interactions in systems contexts, such as pathways, domain families, and custom protein set inputs, in an interactive fashion. We expect KinAce to be useful as a knowledge discovery tool for kinase-substrate interactions, and the aggregated KinAce dataset to be useful for protein kinase studies and systems-level analyses. The portal is available athttps://kinace.kinametrix.com/.
Rapid long-distance migration of RPA on single stranded DNA occurs through intersegmental transfer utilizing multivalent interactions
Authors: Pangeni Sushil , Biswas Gargi , Kaushik Vikas , Kuppa Sahiti , Yang Olivia , Lin Chang-Ting , Mishra Garima , Levy Yaakov , Antony Edwin , Ha Taekjip 
Published: December 2023

AbstractReplication Protein A (RPA) is a single stranded DNA (ssDNA) binding protein that coordinates diverse DNA metabolic processes including DNA replication, repair, and recombination. RPA is a heterotrimeric protein with six functional oligosaccharide/oligonucleotide (OB) domains and flexible linkers. Flexibility enables RPA to adopt multiple configurations and is thought to modulate its function. Here, using single molecule confocal fluorescence microscopy combined with optical tweezers and coarse-grained molecular dynamics simulations, we investigated the diffusional migration of single RPA molecules on ssDNA under tension. The diffusion coefficientDis the highest (20,000 nucleotides2/s) at 3 pN tension and in 100 mM KCl and markedly decreases when tension or salt concentration increases. We attribute the tension effect to intersegmental transfer which is hindered by DNA stretching and the salt effect to an increase in binding site size and interaction energy of RPA-ssDNA. Our integrative study allowed us to estimate the size and frequency of intersegmental transfer events that occur through transient bridging of distant sites on DNA by multiple binding sites on RPA. Interestingly, deletion of RPA trimeric core still allowed significant ssDNA binding although the reduced contact area made RPA 15-fold more mobile. Finally, we characterized the effect of RPA crowding on RPA migration. These findings reveal how the high affinity RPA-ssDNA interactions are remodeled to yield access, a key step in several DNA metabolic processes.SignificanceReplication Protein A (RPA) binds to the exposed single stranded DNA (ssDNA) during DNA metabolism. RPA dynamics are essential to reposition RPA on ssDNA and recruit downstream proteins at the bound site. Here in this work, we perform a detailed biophysical study on dynamics of yeast RPA on ssDNA. We show that RPA can diffuse on ssDNA and is affected by tension and salt. Our observations are best explained by the intersegmental transfer model where RPA can transiently bridge two distant DNA segments for its migration over long distances. We further dissect the contributions of the trimerization core of RPA and other adjacent RPA molecules on RPA migration. This study provides detailed experimental and computational insights into RPA dynamics on ssDNA.
Umbrella toxin particles produced by Streptomyces block mycelial growth of competing species
Authors: Zhao Qinqin , Bertolli Savannah , Park Young-Jun , Tan Yongjun , Cutler Kevin J. , Srinivas Pooja , Asfahl Kyle L. , Garcia Citlali F. , Gallagher Larry A. , Li Yaqiao , Wang Yaxi , Coleman-Derr Devin , DiMaio Frank , Zhang Dapeng , Peterson S. Brook , Veesler David , Mougous Joseph D. 
Published: December 2023

AbstractTheStreptomycesare a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive. The production of these antibacterial molecules reflects the relentless competitionStreptomycesengage in with other bacteria, including otherStreptomycesspecies. Here we show that in addition to small molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein. A cryo-EM structure of these particles reveals an extended stalk topped by a ringed crown comprising the toxin repeats scaffolding five lectin-tipped spokes, leading to our naming them umbrella particles.S. coelicolorencodes three umbrella particles with distinct toxin and lectin composition, and supernatant containing these toxins specifically and potently inhibits the growth of selectStreptomycesspecies from among a diverse collection of bacteria screened. For one target,S. griseus, we find inhibition relies on a single toxin and that intoxication manifests as rapid cessation of vegetative mycelial growth. Our data show thatStreptomycesumbrella particles mediate competition between vegetative mycelia of related species, a function distinct from small molecule antibiotics, which are produced at the onset of reproductive growth and act broadly. Sequence analyses suggest this role of umbrella particles extends beyondStreptomyces, as we find umbrella loci in nearly one-thousand species across Actinobacteria.
Young adults accelerate their arms significantly faster and earlier than old adults resulting in improved center of mass dynamics during an overground slip perturbation
Authors: Lee-Confer Jonathan S. , Lo Matthew K. , Troy Karen L. 
Published: December 2023

AbstractArm motions reduce the likelihood of falling from a slip in young adults, and injuries to older adults from falls are known to occur from a frontal plane fall. Therefore, the purpose of this study was to quantify the frontal plane trunk and arm motion in older and younger adults during a slip. Eleven older adults (age: 72.0 ± 5.0) and 11 younger adults (age: 25.17 ± 5.94) were subjected to a slip during walking. 27% of the older adults and 11% of the younger adults experienced a fall from the slip incident. The arm excursion did not significantly differ between groups, however younger adults’ average peak arm abduction occurred 310 ms prior to older adults (p = 0.03). There were no significant differences in peak trunk between groups. The arm abduction acceleration was significantly higher in younger adults compared to older adults (3593.2 ± 1144.8 vs. 2309.8 ± 1428.5 degrees/s2, p = 0.03). Furthermore, young adults exhibited a significantly reduced CoM excursion compared to old adults (4.55 ± 3.45 vs. 10.27 ± 6.62 cm, p < 0.01). Young adults may have exhibited lower fall rates due to the significantly higher acceleration of their arms compared to old adults.
Uncovering network mechanism underlying thalamic deep brain stimulation
Authors: Tian Yupeng , Bello Edward , Crompton David , Paraskevopoulos Zoe , Kalia Suneil K. , Hodaie Mojgan , Lozano Andres M. , Hutchison William D. , Johnson Matthew D. , Popovic Milos R. , Milosevic Luka , Lankarany Milad 
Published: December 2023

AbstractThalamic ventral intermediate nucleus (Vim) is the primary surgical target of deep brain stimulation (DBS) for reducing symptoms of essential tremor. High-frequency Vim-DBS (≥100Hz) has been clinically effective, generating two experimentally-observed features in Vim spiking activity: 1) a large transient excitatory response (lasting <1s), followed by 2) a suppressed steady-state consisting of oscillations. Yet, mechanisms underlying these observations have not been fully understood by previous studies. In this work, we developed a network rate model and a novel parameter optimization method that accurately fit in-vivo single-unit recordings of Vim in human patients with essential tremor receiving a wide range of DBS frequencies (5∼200Hz). Our model incorporates both the DBS-induced synaptic plasticity of Vim neurons, and the recurrent connections among excitatory and inhibitory neurons in Vim-network. We hypothesized that besides inducing synaptic depression, the therapeutic mechanism of high-frequency Vim-DBS could be to engage more inhibitory neurons in stabilizing the underlying circuits.Graphical abstract
A One-Step Plasma Assisted Synthesis of Gold Nanoparticles and Simultaneous Linker-Free Conjugation with Nestin: An In Vitro Study of Cellular toxicity
Authors: Shokri Babak , Aalikhani Kimia , Sanavandi Melika , Shafiee Mojtaba , Rabbani Hodjattallah , Fazli Ghazaleh , Sadeghi Nilufar 
Published: December 2023

ABSTRACTWe introduce a method for conjugating antigens to gold nanoparticles (GNPs) while synthesizing them using gas plasma, which eliminates the need for chemical linkers intended to facilitate the conjugation procedure for immunotherapy purposes. We report a physical approach to conjugate antigen Nestin (NES) as a marker in malignant tumors to GNPs. Two approaches were used to perform the conjugation of GNPs and NES. The first method involved using citrate to synthesize GNPs, and then NES was conjugated onto the GNPs surface by plasma. In the second method, GNPs were simultaneously synthesized and linker-freely conjugated to NES by plasma treatment.Enzyme-linked immunosorbent assaywith the protocol defined in this study,Zeta-sizer, Ultraviolet-visible spectroscopy, andTransmission Electron Microscopyresults confirmed NES conjugation to GNPs. In addition, the toxicity of the prepared samples was investigated in vitro using peripheral blood mononuclear cells (PBMCs) andflow cytometry, which proved the non-toxicity of the samples.Abstract Figure
Solar Bird Banding: Notes on Changes in Avian Behavior While Mist-netting During an Eclipse
Authors: DeNiro Adara , Kittelberger Kyle D. , Samani Atoosa M. , Hakkı Şekercioğlu Çağan 
Published: December 2023

ABSTRACTSolar eclipses present rare celestial events that can elicit unique behavioral responses in animals, yet comprehensive studies on these phenomena, particularly concerning bird behavior, remain limited. This study, conducted at the Red Butte Canyon Research Natural Area in Utah during the annular solar eclipse on October 14, 2023, aimed to document and analyze avian activity using bird banding data. Leveraging 11 years of banding records, we observed a surprising positive peak in bird captures, indicating increased activity during the eclipse, challenging conventional expectations of decreased activity during peak totality. The unexpected, record-breaking captures on the eclipse day at this location, which also surpassed the average trend in captures over time for 18 other banding days in mid-October, highlights the complexity of bird behavior during celestial events. This study marks the first known published effort to conduct bird banding during a solar eclipse. Quantitative analyses, including species composition and capture trends, contribute to a nuanced understanding of avian responses to the eclipse. This study underscores the importance of empirical research in unraveling the intricacies of how birds navigate and adapt to unique environmental conditions created by solar eclipses.
Disease signatures in the gut metagenome of a prospective family cohort of inflammatory bowel disease
Authors: Rühlemann Malte , Waschina Silvio , Wacker Eike Matthias , Rausch Philipp , Schaan Ana , Zafroon Zaira , Franzpötter Katrin , Jacobs Gunnar , Ellinghaus David , Kruse Robert , Bergemalm Daniel , Halfvarson Jonas , Ziemann Malte , Görg Siegfried , Lieb Wolfgang , Schreiber Stefan , Poyet Mathilde , Bang Corinna , Franke Andre , Groussin Mathieu 
Published: December 2023

AbstractInflammatory bowel disease (IBD) is associated with dysbiotic microbiomes. However, whether microbiomes of family members of IBD patients harbour microbial disease signatures of IBD is unknown. Here, we generate shotgun metagenomic data of an IBD family cohort and treatment-naive IBD cases, which we combine with published IBD metagenomes, to perform a meta-analysis of IBD-microbiome associations. Our study reveals microbial shifts that are specific to IBD or IBD subtypes (Crohn’s disease and ulcerative colitis). We find that IBD cohorts share signatures of association with disease irrespective of geography, and we report novel species-level identifications of microbial taxa that are universal markers of Crohn’s disease. We further demonstrate that the microbiome of healthy family members at high risk for IBD represent transitional states between the microbiome of unrelated healthy controls and IBD cases, and harbor diversity, compositional and ecological features that are also observed among IBD microbiomes. Overall, our study provides valuable insights into the intricate relationship between the gut microbiome and IBD, with implications for better predicting disease onset among individuals with high susceptibility for IBD.
Complex genomes of early nucleocytoviruses revealed by ancient origins of viral aminoacyl-tRNA synthetases
Authors: Kijima Soichiro , Hikida Hiroyuki , Delmont Tom O. , Gaïa Morgan , Ogata Hiroyuki 
Published: December 2023

AbstractAminoacyl-tRNA synthetases (aaRSs), also known as tRNA ligases, are essential enzymes in translation. Owing to their functional essentiality, these enzymes are conserved in all domains of life and used as informative markers to trace the evolutionary history of cellular organisms. Unlike cellular organisms, viruses generally lack aaRSs because of their obligate parasitic nature, but several large and giant DNA viruses in the phylumNucleocytoviricotaencode aaRSs in their genomes. The discovery of viral aaRSs led to the idea that the phylogenetic analysis of aaRSs can shed light on ancient viral evolution. However, conflicting results have been reported from previous phylogenetic studies: one posited that nucleocytoviruses recently acquired their aaRSs from their host eukaryotes, while another hypothesized that the viral aaRSs have ancient origins. Here, we investigated 4,168 nucleocytovirus genomes, including metagenome-assembled genomes derived from large-scale metagenomic studies. In total, we identified 780 viral aaRS sequences in 273 viral genomes. We generated and examined phylogenetic trees of these aaRSs with a large set of cellular sequences to trace evolutionary relationships between viral and cellular aaRSs. The analyses firmly establish that the origins of some viral aaRSs predate the last common eukaryotic ancestor. Inside viral aaRS clades, we identify intricate evolutionary trajectories of viral aaRSs with horizontal transfers, losses, and displacements. Overall, these results suggest that ancestral nucleocytoviruses already developed complex genomes with an expanded set of aaRSs in the proto-eukaryotic era.
Atenolol reduces cardiac-mediated mortality in genetic mouse model of sudden unexpected death in epilepsy
Authors: Soh Ming S. , Kuanyshbek Alibek , Mohamed Syazwan Erlina S. , Lee Hian M. , McKenzie Chaseley E. , Phillips A. Marie , Hu Amanda , Scheffer Ingrid E. , Semsarian Christopher , Berkovic Samuel F. , Reid Christopher A. 
Published: December 2023

AbstractSudden Unexpected Death in Epilepsy (SUDEP) is the leading cause of premature mortality in epilepsy. Genetic cardiac risk factors, including loss-of-functionKCNH2variants, have been linked to SUDEP. We hypothesised that seizures and LQTS interact to increase SUDEP risk. To investigate this, we crossedKcnh2+/-andGabrg2R43Q/+mice that model LQTS and genetic epilepsy, respectively. Electrocorticography and electrocardiogram confirmed thatKcnh2+/-mice had a LQTS phenotype, whileGabrg2R43Q/+mice displayed spontaneous seizures. Double mutant mice (Gabrg2R43Q/+/Kcnh2+/-) had both seizure and LQTS phenotypes that were indistinguishable from the respective single mutant mice. Survival analysis revealed thatGabrg2R43Q/+/Kcnh2+/-mice experienced a disproportionate higher rate of seizure-related death. Long-term oral administration of atenolol, a cardiac-selective β-blocker, significantly improved survival in theGabrg2R43Q/+/Kcnh2+/-mice. An additional mouse model,Hcn1M294L/+/Kcnh2+/-, based on aHCN1developmental epileptic encephalopathy variant, also experienced a disproportionately higher rate of premature death that was rescued by atenolol.Kcnh2+/-mice also spent more time in ventricular arrhythmia during proconvulsant-induced seizures. Overall, the data implicates cardiac and loss-of-functionKCNH2variants as an important risk factor, and the potential repurposing of β- blockers as a prevention strategy, for SUDEP in a subset of epilepsy patients.
Protein-specific crowding accelerates aging in phase-separated droplets
Authors: Brzezinski Mateusz , Argudo Pablo G. , Scheidt Tom , Yu Miao , Lemke Edward A. , Michels Jasper J. , Parekh Sapun H. 
Published: December 2023

ABSTRACTCrowding agents, such as polyethylene glycol (PEG, are often used to mimic the cellular cytoplasm in protein assembly studies. Despite the perception that crowding agents have an inert nature, recent work has shown they are not bystanders while proteins interact. Here, we explore the diverse effects of PEG on the phase separation and maturation of proteins. We use two proteins, the FG domain of Nup98 and bovine serum albumin (BSA), which represent an intrinsically disordered protein and a protein with well-established secondary structure, respectively. PEG expedites the maturation of Nup98, enhancing denser protein packing and fortifying hydrophobic interactions which hasten beta-sheet formation and subsequent droplet gelation. In contrast for BSA, PEG appears to enhance droplet stability and limits available solvent for the protein solubilization, without inducing significant changes to the secondary structure, pointing towards a significantly different behavior of the crowding agent. Interestingly, we detect almost no presence of PEG in Nup droplets whereas PEG is detectable within BSA droplets. Our findings demonstrate a nuanced interplay between crowding agents and proteins. PEG can accelerate protein maturation in LLPS systems but its partitioning and effect on protein structure in droplets is protein specific. This suggests that crowding phenomena are specific to each protein-crowding agent pair.