bluuebunny/crossref_metadata_2025_split huggingface dataset:
Astrocytes are active: An information theoretic approach reveals differences in Ca2+ signaling patterns among distinct astrocyte subtypes
Authors: Mennona Nicholas J. , Barile Barbara , Kang Hoony , Benfenati Valentina , Nicchia Grazia P. , O’Neill Kate M. , Losert Wolfgang 
Published: November 2023

AbstractThe discovery that astrocytes are an active, rather than a passive, component of the brain has ushered in a paradigm shift in thinking about how the brain processes information. Although the mechanisms by which astrocytes integrate information from neurons are still debated, such discourse should not distract from the importance of more completely understanding how astrocytes communicate via signals amongst themselves. This work aims to study how different astrocytes signal within their own networks. We investigate group calcium (Ca2+) dynamics in polygonal, stellate, and reactive astrocytes. These distinct and important astrocyte subtypes are present in the brain to varying degrees at different physiological states. We use an information-theoretic framework to quantify the dynamics embedded in the Ca2+ traces within astrocyte networks; specifically, we employ the Hurst exponent, cross-correlation, mutual information, and partitioned entropy to assess differences in the astrocyte signals across subtypes. To gain insights into the ability of astrocyte networks to respond to changes in the extracellular environment, we probe the networks with perturbations affecting their cytoskeletal dynamics (Latrunculin B) and energetic levels (Adenosine triphosphate). Overall, these three classes of astrocytes behave differently and respond idiosyncratically to their extracellular environment. We find that polygonal astrocytes are not quiescent, stellate astrocytes respond most strongly to ATP, and reactive astrocytes are uniquely perturbed by Latrunculin B. Interestingly, despite these distinct differences in behaviors, we find a uniform speed of information transport regardless of subtype or perturbation; this uniformity is maintained when using both cross-correlation and mutual information to assess this speed. We conclude that the differential ways astrocytes signal within our measured framework yield important insights into how astrocytes communicate and contribute to this pressing issue of understanding astrocyte information processing.
Cryo-EM structure of Slo1 with the auxiliary γ1 subunit suggests mechanism of depolarization-independent activation
Authors: Redhardt Milena , Raunser Stefan , Raisch Tobias 
Published: November 2023

AbstractMammalian Ca2+-dependent Slo K+channels are expressed with β and γ auxiliary subunits that greatly influence voltage- and Ca2+-induced gating, thereby fundamentally altering the behavior of the channel. The four γ subunits reduce the need for voltage-dependent activation, allowing Slo to open in the absence of an action potential. The mechanism of this activation has, however, remained elusive. Here, we present the cryo-EM structure of Slo1 in complex with γ1/LRRC26, revealing how the transmembrane helix of γ1 binds and presumably stabilizes the active conformation of the voltage-sensor domain. This effect is further enhanced by a polybasic stretch on the intracellular side of the membrane which locally changes the charge gradient across the membrane. Sequence differences explain why the four γ subunits possess different activation efficiencies. Simultaneous binding of γ and the unrelated β subunits is structurally possible, as both binding sites do not overlap and the γ1 LRR domains are partially flexible. Thus, our data provide a possible explanation for Slo1 regulation by γ subunits, and furthermore suggest a novel mechanism of activation of voltage-gated ion channels by auxiliary subunits and add to the growing knowledge of their complex regulation.
Local Ecological Knowledge enhances our capacity to document potential climate sentinels: a loggerhead sea turtle (Caretta caretta) case study
Authors: Early-Capistrán Michelle María , Crane Nicole L. , Crowder Larry B. , Garibay-Melo Gerardo , Seminoff Jeffrey A. , Johnston David 
Published: November 2023

AbstractClimate change is inducing rapid transformations in marine ecosystems, with a pronounced effect on top predators like loggerhead sea turtles (Caretta caretta). Loggerheads’ responsiveness to temperature fluctuations underscores their significance as a climate sentinel species. We present the first record of a loggerhead sea turtle in Monterey Bay, California, USA, documented through Local Ecological Knowledge (LEK) and community or citizen science (CS), highlighting the pivotal role of these approaches in documenting species occurrences beyond anticipated habitats during climatic anomalies. In rapidly changing conditions, rigorously documented CS and LEK offer a crucial complement to conventional scientific methods, providing high-quality data with extensive coverage— especially for elusive species—and yielding insights into emerging phenomena.
Pervasive relaxed selection in termite genomes
Authors: Ewart Kyle M. , Ho Simon Y. W. , Chowdhury Al-Aabid , Jaya Frederick R. , Kinjo Yukihiro , Bennett Juno , Bourguignon Thomas , Rose Harley A. , Lo Nathan 
Published: November 2023

AbstractThe genetic changes that enabled the evolution of eusociality have long captivated biologists. In recent years, attention has focussed on the consequences of eusociality on genome evolution. Studies have reported higher molecular evolutionary rates in eusocial hymenopteran insects compared with their solitary relatives. To investigate the genomic consequences of eusociality in termites, we sequenced genomes from three of their non-eusocial cockroach relatives. Using a phylogenomic approach, we found that termite genomes experienced lower rates of synonymous mutations than those of cockroaches, possibly as a result of longer generation times. We identified higher rates of nonsynonymous mutations in termite genomes than in cockroach genomes, and identified pervasive relaxed selection in the former (24–31% of the genes analysed) compared with the latter (2–4%). We infer that this is due to a reduction in effective population size, rather than gene-specific effects (e.g., indirect selection of caste-biased genes). We found no obvious signature of increased genetic load in termites, and postulate efficient purging at the colony level. Additionally, we identified genomic adaptations that may underpin caste formation, such as genes involved in post-translational modifications. Our results provide insights into the evolution of termites and the genomic consequences of eusociality more broadly.
Activation of the Maternal Genome Through Asymmetric Distribution of Oocyte-Genome-Associated Histone H3.3
Authors: Wen Duancheng , Rosenwaks Zev 
Published: November 2023

AbstractUpon fertilization, the typically silent and epigenetically repressed oocyte genome undergoes activation, yet the precise mechanism remains unclear. The histone variant H3.3 is evenly distributed throughout the oocyte genome, suggesting its involvement in repression. This study reveals that oocyte-genome-associated H3.3 (oH3.3) undergoes asymmetric segregation among four-cell stage blastomeres, persisting in only two blastomeres through the blastocyst stage. These oH3.3-retaining blastomeres maintain a repressive state characterized by high levels of the chromatin marker H3K9me2. Intriguingly, single-cell RNA-seq analysis revealed asymmetric transcriptional activation between paternal and maternal genomes, with the maternal genome being considerably less active. We propose a model wherein oH3.3 and associated oocyte DNA co-segregate during mitosis, allowing two blastomeres to inherit oH3.3 and a strand of oocyte DNA from maternal chromatids. Meanwhile, the other blastomeres acquire newly synthesized DNA associated with the nascent histone H3, which lacks oocyte-specific repressive modifications. Consequently, full maternal genome activation occurs in two of the four-cell stage blastomeres, while the remaining two, which retain oH3.3, remain partially repressed. This study uncovers a previously unrecognized H3.3 mediated mechanism for maternal genome activation.
Complete phylogeny ofMicrathenaspiders suggests multiple dispersal events among Neotropical rainforests, islands, and landmasses, and indicates Andean orogeny promotes speciation
Authors: Magalhaes Ivan L. F. , Martins Pedro H. , Faleiro Bárbara T. , Vidigal Teofânia H. D. A. , Santos Fabrício R. , Carvalho Leonardo S. , Santos Adalberto J. 
Published: November 2023

AbstractThe Neotropical region is the most diverse on the planet, largely due to its mosaic of tropical rainforests. Multiple tectonic and climatic processes have been hypothesized to play a role in generating this diversity; these include Andean orogeny, closure of the Panama Isthmus, the hypothesized GAARlandia land bridge, and putative historical connections among currently isolated forests.Micrathenaspiny spiders (Araneidae) include ∼120 species distributed mostly in forests from Mexico to Argentina, including the Antilles. Here, we use it as a model to study the biogeographic history of Neotropical rainforests by estimating a complete, dated phylogeny using morphological data for all species and molecular data for a subsample of 79 species. This resulted in a phylogeny that is mostly robust and supports most of the previously recognized species groups, although with uncertainty in the phylogenetic position of some species, especially those lacking sequences. The genus began diversifying about 25 million years ago. We use an event-based approach and biogeographic stochastic mapping to estimate ancestral distributions and the timing and direction of dispersal events, and to identify areas where diversity was generated, while accounting for phylogenetic uncertainty. Andean cloud forests generated the majority of species through in-situ speciation, but the Amazon was the major source of species for adjacent areas through dispersal; on the other extreme, the Dry Diagonal received species from other areas but generated very little diversity. Species exchange between Central and South America was intense, with ∼23 dispersal events beginning at least 20 million years ago, indicating thatMicrathenadispersed between these continents before closure of the Isthmus of Panama. We also inferred ∼4 over-water dispersal events from Central and North America to the Antilles, which happened in the last 20 million years, and thus much after the proposed age of the GAARlandia land bridge. We identified an important species exchange route between the Amazon and the Atlantic forests. Sampling all species of the genus was fundamental to some of the conclusions above, especially in identifying the Andes as the area that generated the majority of species. This study highlights the importance of a solid and complete taxonomic sampling in biogeographic studies.
Intra-breath oscillometry detects ventilation inhomogeneity in Cystic Fibrosis children
Authors: Blake Tamara L , Robinson Paul D , Deery Maddison T , Wainwright Claire E , Hantos Zoltan , Sly Peter D 
Published: November 2023

AbstractBackgroundVentilation inhomogeneity (VI) is measured in patients with Cystic Fibrosis (CF) by lung clearance index (LCI) using the Multiple Breath Washout (MBW). In young children, feasibility is often low within busy clinical settings. Intra-breath oscillometry (IB-OSC) measures respiratory system reactance (Xrs), which is determined by the same physiological principles. Given the high feasibility of IB-OSC in young children (>80%), we aimed to explore whether Xrs variables reflected VI as measured by LCI.MethodsPaired measurements of IB-OSC (TremoFLO C-100, 10Hz signal) and Nitrogen (N2) MBW (Exhalyzer D) were performed in 97 children with CF. Abnormal LCI was defined as ≥7.1. IB-OSC Xrs variables at end-expiration (XeE), end-inspiration (XeI), volume-dependence of Xrs (ΔX) and ΔX corrected for tidal volume (ΔX/VT) were compared between those with normal and abnormal LCI. Receiver operator characteristic (ROC) analysis was performed to identify cut-off values to detect abnormal LCI.Results115 acceptable paired IB-OSC and MBW measurements were achieved by 85 children (male 61%, median age 7.8yrs [25th-75th% 5.8-11.9]). 52 (45%) measurements of LCI were abnormal. All Xrs variables where significantly decreased (more negative) in children with abnormal LCI compared to normal (XeE -2.98v-0.81; XeI -2.10v-1.00; ΔX -0.25v0.12; ΔX/VT -0.54v0.22; all p<0.001). Cut-off values for ΔX and ΔX/VT provided the best sensitivity and specificity for detecting abnormal LCI.ConclusionThese results suggest that novel IB-OSC variables can detect abnormal VI as measured by N2MBW-LCI. This technique may allow us to detect and monitor early changes to lung function in busy CF clinics more easily.
On theindependent irritabilityof goldfish eggs and embryos – a living communication on the rhythmic yolk contractions in goldfish
Authors: Layague Sanchez Paul Gerald , Wang Chen-Yi , Li Ing-Jia , Ota Kinya G. 
Published: November 2023

Rhythms play an important role in the precise spatiotemporal regulation of biological processes during development and patterning of embryos. We here investigate the rhythmic contractions of the yolk during early development of the goldfishCarassius auratus. We quantify these contractions and record robust and persistent rhythmic yolk movements that are not seen in closely-related species (common carpCyprinus carpioand zebrafishDanio rerio). We report that yolk contractions are an intrinsic emergent property of the egg, i.e. goldfish eggs are independently irritable / excitable. These contractions do not require sperm entry / fertilization nor cell division, and they notably emerge at a precise time — suggesting that goldfish eggs are able to measure elapsed time from what we infer to be egg activation. We further show that these rhythmic contractions persist even in yolk in isolation. As the yolk itself is known to confer critical cues for early dorsoventral (DV) patterning of teleost embryos, we hypothesize that its contractions in goldfish may influence the patterning process of this species. Indeed, we find that embryos of the naturally more ventralized twin-tail goldfish strainOrandadisplay altered yolk contraction dynamics (i.e. faster contractions). We also present that the period of yolk contractions is independent ofChdS, a key gene involved in DV pattening and linked to the twin-tail phenotype, but is instead a trait that is maternal in origin. We aim to uncover whether the yolk contractions happening during early development of domesticated goldfish are the licensing process which permit the emergence of novel patterning phenotypes naturally-observed in this species (e.g. twin-tail and dorsal-finless strains) and which instead have not been found among closely-related species (e.g. common carp) whose yolks do not contract.This manuscript is here published as a living communication (as described in Gnaiger (2021)). The authors intend to share findings when they are available, encourage feedback and discussion, and invite knowledge exchange and collaboration.
Emergent functional behaviors of ribozymes in oxychlorine brines indicate Mars could host a unique niche for molecular evolution
Authors: Hoog Tanner G. , Pawlak Matthew R. , Gaut Nathaniel J. , Baxter Gloria C. , Bethel Thomas A. , Adamala Katarzyna P. , Engelhart Aaron E. 
Published: November 2023

ABSTRACTMars is a particularly attractive candidate among known astronomical objects to potentially host life. Results from space exploration missions have provided insights into Martian geochemistry indicating oxychlorine species, particularly perchlorate, are ubiquitous features of the Martian geochemical landscape. Perchlorate presents potential obstacles for known forms of life due to its toxicity. However, it can also provide potential benefits, such as producing brines by deliquescence, like those thought to exist on present-day Mars. Here we show perchlorate brines support folding and catalysis of functional RNAs, while inactivating representative protein enzymes. Additionally, we show perchlorate and other oxychlorine species enable new ribozyme functions, including homeostasis-like regulatory behavior, copying of structured RNAs, and the first ribozyme-catalyzed chlorination of organic molecules. We suggest nucleic acids are uniquely well-suited to hypersaline Martian environments. Furthermore, Martian near-or subsurface oxychlorine brines, and brines found in potential lifeforms, could provide a unique niche for biomolecular evolution.
ReptiLearn: A Smart Home Cage for Behavioral Experiments in Reptiles
Authors: Eisenberg Tal , Shein-Idelson Mark 
Published: November 2023

AbstractUnderstanding behavior and its evolutionary underpinnings is crucial for unraveling the complexities of brain function. Traditional approaches strive to reduce behavioral complexity by designing short-term, highly constrained behavioral tasks with dichotomous choices in which animals respond to defined external perturbation. In contrast, natural behaviors evolve over multiple time scales and under minimally constrained conditions in which actions are selected through bi-directional interactions with the environment and without human intervention. Recent technological advancements have opened up new possibilities for more natural experimental designs by replacing stringent experimental control with accurate multidimensional behavioral analysis. However, these approaches have been tailored to fit only a small number of species. This specificity limits the experimental opportunities offered by species diversity. Further, it hampers comparative analyses which are essential for extracting overarching behavioral principles and for examining behavior from an evolutionary perspective. To address this limitation, we developed ReptiLearn - a versatile, low-cost, Python-based solution, optimized for conducting automated long-term experiments in the home cage of reptiles, without human intervention. In addition, this system offers unique features such as precise temperature measurement and control, live prey reward dispensers, engagement with touch screens, and remote control through a user-friendly web interface. Finally, ReptiLearn incorporates low-latency closed-loop feedback allowing bi-directional interactions between animals and their environments. Thus, ReptiLearn provides a comprehensive solution for researchers studying behavior in ectotherms and beyond, bridging the gap between constrained laboratory settings and natural behavior in non-conventional model systems. We demonstrate the capabilities of ReptiLearn by automatically training the lizardPogona vitticepson a complex spatial learning task requiring association learning, displaced reward learning and reversal learning.
Seven-up acts in neuroblasts to specify adult central complex neuron identity and initiate neuroblast decommissioning
Authors: Dillon Noah R. , Manning Laurina , Hirono Keiko , Doe Chris Q. 
Published: November 2023

AbstractAn open question in neurobiology is how diverse neuron cell types are generated from a small number of neural stem cells. In theDrosophilalarval central brain, there are eight bilateral Type 2 neuroblast (T2NB) lineages that express a suite of early temporal factors followed by a different set of late temporal factors and generate the majority of the central complex (CX) neurons. The early-to-late switch is triggered by the orphan nuclear hormone receptor Seven-up (Svp), yet little is known about this Svp-dependent switch in specifying CX neuron identities. Here, we (i) birthdate the CX neurons P-EN and P-FN (early and late, respectively); (ii) show that Svp is transiently expressed in all early T2NBs; and (iii) show that loss of Svp expands the population of early born P-EN neurons at the expense of late born P-FN neurons. Furthermore, in the absence of Svp, T2NBs fail decommissioning and abnormally extend their lineage into week-old adults. We conclude that Svp is required to specify CX neuron identity, as well as to initiate T2NB decommissioning.SummarySeven-up acts in Type 2 neuroblasts to specify adult central complex columnar neuron identity and to initiate neuroblast decommissioning.
The pH-responsive SmrR-SmrT system modulatesC. difficileantimicrobial resistance, spore formation, and toxin production
Authors: Wetzel Daniela , Carter Zavier A. , Monteiro Marcos P. , Edwards Adrianne N. , McBride Shonna M. 
Published: November 2023

ABSTRACTClostridioides difficileis an anaerobic gastrointestinal pathogen that spreads through the environment as dormant spores. To survive, replicate, and sporulate in the host intestine,C. difficilemust adapt to a variety of conditions in its environment, including changes in pH, the availability of metabolites, host immune factors, and a diverse array of other species. Prior studies showed that changes in intestinal conditions, such as pH, can affectC. difficiletoxin production, spore formation, and cell survival. However, little is understood about the specific genes and pathways that facilitate environmental adaptation and lead to changes inC. difficilecell outcomes. In this study, we investigated two genes,CD2505andCD2506,that are differentially regulated by pH to determine if they impactC. difficilegrowth and sporulation. Using deletion mutants, we examined the effects of both genes (hereinsmrRandsmrT) on sporulation frequency, toxin production, and antimicrobial resistance. We determined that SmrR is a repressor ofsmrRTthat responds to pH and suppresses sporulation and toxin production through regulation of the SmrT transporter. Further, we showed that SmrT confers resistance to erythromycin and lincomycin, establishing a connection between the regulation of sporulation and antimicrobial resistance.IMPORTANCEC. difficileis a mammalian pathogen that colonizes the large intestine and produces toxins that lead to severe diarrheal disease.C. difficileis a major threat to public health due to its intrinsic resistance to antimicrobials and its ability to form dormant spores that are easily spread from host to host. In this study, we examined the contribution of two genes,smrRandsmrTon sporulation, toxin production, and antimicrobial resistance. Our results indicate that SmrR repressessmrTexpression, while production of SmrT increases spore and toxin production, as well as resistance to antibiotics.