Miracle-dz/UniFAR-FTUs huggingface dataset:
The shifting importance of abiotic and biotic factors across the life cycles of wild pollinators

Organisms living in seasonal environments are exposed to different environmental conditions as they transition from one life stage to the next across their life cycle. How different life stages respond to these varying conditions is a fundamental aspect of biology and is critical for understanding how organisms will respond to environmental change. Despite the importance of animal pollinators, we lack a basic understanding of the influence of different environmental factors across their life cycles. We investigated the relative importance of climate conditions, food availability, and previous life stage abundance in a community of wild bumble bee species, asking: how do these three factors influence bee abundance at each life stage? We used a 7-year dataset to examine the importance of environmental conditions on the abundance of life stages in seven wild bumble bee species. We monitored climate conditions, the abundance of floral resources, and abundances of bees in each life stage across the active colony life cycle in a highly seasonal subalpine ecosystem in the Colorado Rocky Mountains, USA. Bee abundance at different life stages responded to environmental conditions in a consistent manner across the seven species. The survival and recruitment stage of the life cycle (assessed as abundance of overwintered queens) responded negatively to longer winters; the growth stage (assessed as abundance of workers) responded positively to floral resource availability; and the reproductive stage (assessed as abundance of males) was positively related to the abundance of the previous life stage (workers). Our long-term examination of annual bumble bees reveals a consistent set of responses in the abundance of each life stage to climate conditions, floral resource availability, and previous life stage abundance. Across species, these three factors each influenced a distinct life stage, illustrating how their relative importance can shift throughout the life cycle. The life-cycle approach we have taken with wild bumble bees highlights that important details about pollinator demography are overlooked without considering life stage-specific responses. Ultimately, it is these life-stage specific responses that shape population outcomes, not only for animal pollinators, but for many organisms living in seasonal environments.
Chronic nicotine exposure alters sperm small RNA content in a C57BL/6J mouse model: Implications for multigenerational inheritance

Multigenerational inheritance is a non-genomic form of heritability characterized by altered phenotypes in the first generation born from the exposed parent. Multigenerational factors may account for inconsistencies and gaps in heritable nicotine addiction vulnerability. Our lab previously found that F1 offspring of male C57BL/6J mice chronically exposed to nicotine exhibited altered hippocampus functioning and related learning, nicotine-seeking, nicotine metabolism, and basal stress hormones. In an effort to identify germline mechanisms underlying these multigenerational phenotypes, the current study sequenced small RNA extracted from sperm of males chronically administered nicotine using our previously established exposure model. We identified 16 miRNAs whose expression in sperm was dysregulated by nicotine exposure. A literature review of previous research on these transcripts suggested an enrichment for regulation of psychological stress and learning. mRNAs predicted to be regulated by differentially expressed sperm small RNAs were further analyzed using biological enrichment analysis, which also supported enrichment of gene expression pathways involved in hippocampus-dependent learning. Our findings point to links between nicotine-exposed F0 sperm miRNA and altered F1 phenotypes in this multigenerational inheritance model. Specifically, differentially expressed F0 sperm miRNAs may regulate the previously observed changes in F1 learning and stress. These findings provide a valuable foundation for future functional validation of these hypotheses and characterization of mechanisms underlying male-line multigenerational inheritance.
Histone H2A serine-1 phosphorylation is a chaperone dependent signal for dimerization with H2B and for enhanced deposition

Multiple histone chaperones and histone modifications are involved in the folding, transport, and re-lease of histones onto newly replicated DNA. Little is known about histone H2A-H2B pre-deposition his-tone modifications and their regulation of histone deposition. We previously showed that H2A serine 1 phosphorylation (H2AS1ph) is enriched on the soluble egg histones and on zygotic chromatin in Xenopus embryos. Here, we demonstrate that H2AS1 phosphorylation is required for a timely incorporation of H2A-H2B into the pronuclear chromatin. Our analysis revealed that exogenous H2AS1A-H2B dimers were poorly incorporated into pronuclei in egg extract compared with wildtype and H2AS1E-H2B dimers. Chaperone-mediated deposition using histones purified from pronuclei showed that neither Nap1 nor Nucleoplasmin (Npm2) histone deposition was directly affected by endogenous histone posttranslational modification. We further demonstrate that H2AS1 phosphorylation was dependent on Npm2 and required H2B. Surprisingly, Nap1 was incapable of promoting H2AS1 phosphorylation. These results suggest that serine 1 phosphorylation signals a specific state of H2A-H2B dimer bound by Nucleoplasmin. Neither Npm2 nor Nap1 exhibited preference for binding H2AS1A or H2AS1E mutant histones or dimers with H2B in vitro. We propose that H2AS1 phosphorylation is a pre-deposition modification that signals for the proper dimerization of H2A-H2B, which in turn activates downstream effectors leading to H2A-H2B deposition.
Improved sequence mapping using a complete reference genome and lift-over

By combining fast lift-over and selective re-mapping, levioSAM2 enables efficient and accurate read mapping and variant calling leveraging complete reference genomes. Complete, telomere-to-telomere (T2T) genome assemblies promise improved analyses and the discovery of new variants, but many essential genomic resources remain associated with older reference genomes. Thus, there is a need to translate genomic features and read alignments between references. Here we describe a method called levioSAM2 that performs fast and accurate lift-over between assemblies using a whole-genome map. In addition to enabling the use of several references, we demonstrate that aligning reads to a high-quality reference (for example, T2T-CHM13) and lifting to an older reference (for example, Genome reference Consortium (GRC)h38) improves the accuracy of the resulting variant calls on the old reference. By leveraging the quality improvements of T2T-CHM13, levioSAM2 reduces small and structural variant calling errors compared with GRC-based mapping using real short- and long-read datasets. Performance is especially improved for a set of complex medically relevant genes, where the GRC references are lower quality.
The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein import

Yeast cells employ the cytosolic ubiquitin system to increase the capacity of the mitochondrial import machinery during phases of metabolic transitions. Mitochondria play a key role in cellular energy metabolism. Transitions between glycolytic and respiratory conditions induce considerable adaptations of the cellular proteome. These metabolism-dependent changes are particularly pronounced for the protein composition of mitochondria. Here, we show that the yeast cytosolic ubiquitin conjugase Ubc8 plays a crucial role in the remodeling process when cells transition from respiratory to fermentative conditions. Ubc8 is a conserved and well-studied component of the catabolite control system that is known to regulate the stability of gluconeogenic enzymes. Unexpectedly, we found that Ubc8 also promotes the assembly of the translocase of the outer membrane of mitochondria (TOM) and increases the levels of its cytosol-exposed receptor subunit Tom22. Ubc8 deficiency results in compromised protein import into mitochondria and reduced steady-state levels of mitochondrial proteins. Our observations show that Ubc8, which is controlled by the prevailing metabolic conditions, promotes the switch from glucose synthesis to glucose usage in the cytosol and induces the biogenesis of the mitochondrial TOM machinery to improve mitochondrial protein import during phases of metabolic transition. Graphical Abstract
Loss of Myosin-1e biases MMTV-PyMT induced breast cancer towards a differentiated and secretory state

Expression of the unconventional myosin, Myosin-1e (Myo1e), has been shown to contribute to tumor progression in the MMTV-PyMT mouse model of mammary tumorigenesis and is associated with poor outcome in breast cancer patients. However, the specific effects of Myo1e expression on the mammary tumor cells remain unidentified. Here, we used Myo1e-KO and wild-type (WT) MMTV-PyMT mice on a pure genetic background to further investigate the molecular and cellular effects of Myo1e expression. Myo1e-WT tumors were characterized by an increased abundance of intra-epithelial macrophages and lower amounts of the extracellular matrix. Transcriptomic profiling of WT and Myo1e-KO tumors identified a pattern of differential expression of tumor suppressor and tumor-promoting genes that was consistent with the observed differences in tumor progression and morphology between the genotypes, and also revealed differential expression of genes associated with secretion and cell-cell adhesion. In agreement with the RNA-seq findings, Myo1e-expressing tumor cells exhibited increased proliferation and elevated nuclear enrichment of YAP1 transcriptional activator compared to Myo1e-KO tumor cells. To investigate tumor cell-autonomous effects of Myo1e expression, we used the epithelial cell line PY-230 derived from the MMTV-PyMT-induced mouse tumor to create Myo1e-depleted cells by Crispr-mediated genome editing. Cells deficient in Myo1e had increased expression of genes encoding milk components compared to the wild-type cells. Electric cell-substrate impedance sensing (ECIS) measurements showed that depletion of Myo1e in PY-230 cells resulted in increased resistance to electrical current indicating enhanced epithelial barrier function. Overall, we find that Myo1e expression biases tumors towards a less-differentiated, pro-tumorigenic state, and that depletion of Myo1e is associated with a pro-secretory, more differentiated state.
Spontaneous Action and Everyday Practice in the Fashion Business

The specific nature of fashion industry change results in creativity and in the cyclical char acter of organisational processes that take place in the fashion business. Nevertheless routine activities are key factors in improving and maintaining everyday processes. This gives rise to the practice of day-to-day activities. Change to routine activities may be initiated by either planned or spontaneous actions. However, even spontaneous actions may be akin to the goals of the company and its brand identity. The objective of the present study was to examine spontaneous actions as categories of the institutionalization of practice. A comparative case study was conducted, key findings of which have implications for fashion business research and changes in management theory. If spontaneous actions are purposive, then they may become institutionalized within the framework of reproduced practice
Top-down modulation of the retinal code via histaminergic neurons of the hypothalamus

The mammalian retina is considered an autonomous circuit, yet work dating back to Ramon y Cajal indicates that it receives inputs from the brain. How such inputs affect retinal processing has remained unknown. We identified brain-to-retina projections of histaminergic neurons from the mouse hypothalamus, which densely innervated the dorsal retina. Histamine application, or chemogenetic activation of histaminergic axons, altered spontaneous and light-evoked activity of various retinal ganglion cells (RGCs), including direction-selective RGCs. These cells exhibited broader directional tuning and gained responses to high motion velocities. Such changes could improve vision when objects move fast across the visual field (e.g. while running), which fits with the known increased activity of histaminergic neurons during arousal. In humans, an antihistamine drug non-uniformly modulated visual sensitivity across the visual field, indicating an evolutionary conserved function of the histaminergic system. Our findings expose a previously unappreciated role for brain-to-retina projections in modulating retinal function.
Chromoanagenesis in the asy1 meiotic mutant of Arabidopsis

Chromoanagenesis is a catastrophic event that involves localized chromosomal shattering and reorganization. In this study, we report a case of chromoanagenesis resulting from defective meiosis in the MEIOTIC ASYNAPTIC MUTANT 1 (asy1) background in Arabidopsis thaliana. We provide a detailed characterization of the genomic structure of this individual with a severely shattered segment of chromosome 1. We reveal more than 300 candidate novel DNA junctions in the affected region, confirming that asy1-related defective meiosis is a potential trigger for chromoanagenesis. This is the first example of chromoanagenesis associated with female meiosis and indicates the potential for genome evolution during oogenesis.
Characterization of the cluster MabR prophages of Mycobacterium abscessus and Mycobacterium chelonae

Mycobacterium abscessus is an emerging pathogen of concern in cystic fibrosis and immunocompromised patients and is considered one of the most drug-resistant mycobacteria. The majority of clinical M. abscessus isolates carry one or more prophages that are hypothesized to contribute to virulence and bacterial fitness. The prophage McProf was identified in the genome of the Bergey strain of M. chelonae, and is distinct from previously described prophages of M. abscessus. The McProf genome increases intrinsic antibiotic resistance of M. chelonae and drives expression of the intrinsic antibiotic resistance gene, whiB7, when superinfected by a second phage. The prevalence of McProf-like genomes was determined in sequenced mycobacterial genomes. Related prophage genomes were identified in the genomes of 25 clinical isolates of M. abscessus and assigned to the novel cluster, MabR. The MabR genomes share less than 10% gene content with previously described prophages; however, share features typical of prophages, including polymorphic toxin immunity (PT-Imm) systems.
Aperiodic brain activity and response to anesthesia vary in disorders of consciousness

The analysis of human EEG has traditionally focused on oscillatory power, which is characterized by peaks above an aperiodic component in the power spectral density. This study investigates the aperiodic EEG component of individuals in a disorder of consciousness (DOC); how it changes in response to exposure to anesthesia; and how it relates to the brain’s information richness and criticality. High-density EEG was recorded from 43 individuals in a DOC, with 16 of these individuals undergoing a protocol of propofol anesthesia. The aperiodic component was defined by the spectral slope of the power spectral density. Our results demonstrate that the EEG aperiodic component is more informative about the participants’ level of consciousness than the oscillatory component. Importantly, the pharmacologically induced change in the spectral slope from 30-45 Hz positively correlated with individual’s pre-anesthetic level of consciousness. The pharmacologically induced loss of information-richness and criticality was associated with individual’s pre-anesthetic aperiodic component. During exposure to anesthesia, the aperiodic component was correlated with 3-month recovery status for individuals with DOC. The aperiodic EEG component has been historically neglected; this research highlights the necessity of considering this measure for the assessment of individuals in DOC and future research that seeks to understand the neurophysiological underpinnings of consciousness.
Rac rather than Rho drives the early transcriptional response to extracellular matrix stiffness and mediates repression of ATF3

The Rho family GTPases, Rac and Rho, play critical roles in transmitting mechanical information contained within the extracellular matrix (ECM) to the cell. Rac and Rho have well described roles in regulating stiffness-dependent actin remodeling, proliferation and motility. However, much less is known about the relative roles of these GTPases in stiffness-dependent transcription, particularly at the genome-wide level. Here, we selectively inhibited Rac and Rho in mouse embryonic fibroblasts cultured on deformable substrata and used RNA sequencing to elucidate and compare the contribution of these GTPases to the early transcriptional response to ECM stiffness. Surprisingly, we found that Rac activation is almost exclusively responsible for the initial transcriptional response to ECM stiffness. We also identified Activating Transcription Factor 3 (ATF3) as a major target of stiffness/Rac signaling and show that ATF3 repression by ECM stiffness connects the stiffness-dependent activation of Rac to the induction of cyclin D1.
Utilising hippocampal neuronal calcium activity in mouse CA1 for a multimodal optical brain-computer interface

The hippocampus has been proposed to integrate information from multiple sensory modalities, supporting a comprehensive “cognitive map” for both spatial and non-spatial information. Previous studies have demonstrated decoding of hippocampal spatial information in real time by recording neuronal action potentials with electrodes. However, decoding of hippocampal non-spatial information robustly in real-time has not been previously shown. Here, we utilise the advantages of widefield optical calcium imaging to construct an optical brain-computer interface (BCI) driven by calcium activity of large neuronal ensembles (∼600 neurons) to decode spatial, visual and auditory information effectively in real time. We developed a high speed end-to-end analysis workflow with advanced machine learning techniques for decoding. This methodology achieves high decoding accuracy and provides a “cognitive translation” approach that may be applied to both research and clinical applications to allow direct neural communication with animals and patients with impairment of function.
Localization of chemical synapses and modulatory release sites in the cardiac ganglion of the crab, Cancer borealis

The crustacean cardiac ganglion (CG) comprises nine neurons that provide rhythmic drive to the heart. The CG is the direct target of multiple modulators. Synapsin-like immunoreactivity was found clustered around the somata of the large cells (LC) and in a neuropil at the anterior branch of the CG trunk. This implicates the soma as a key site of synaptic integration, an unusual configuration in invertebrates. Proctolin is an excitatory neuromodulator of the CG and proctolin-like immunoreactivity exhibited partial overlap with putative chemical synapses near the LCs and at the neuropil. A proctolin-like projection was also found in a pair of excitatory nerves entering the CG. GABA-like immunoreactivity was nearly completely colocalized with chemical synapses near the LCs but absent at the anterior branch neuropil. GABA-like projections were found in a pair of inhibitory nerves entering the CG. Cancer borealis Allatostatin B1 (CbAST-B1), red pigment concentrating hormone (RPCH) and FLMRFamide-like immunoreactivity each had a unique pattern of staining and co-localization with putative chemical synapses. These results provide morphological evidence that synaptic input is integrated at LC somata in the CG. Our findings provide a topographical organization for some of the multiple inhibitory and excitatory modulators that alter the rhythmic output of this semi-autonomous motor circuit.
Self-similar tip growth links exocytosis profile with cell wall shape

Exocytosis plays a crucial role in regulating the growth and migration of filamentous tip-growing cells. We present a mathematical framework that infers the spatial profile of exocytosis from the cell morphology in self-similar growing cells that elongate while preserving their apical domain shapes. By applying the framework to cell wall outline data from experiments across walled cell species, we find that while tapered cells have their exocytosis concentrated at the apex, cells with flatter tip shape beyond a threshold require exocytosis to peak in an annulus region away from the apex.
Real-Time Feeding Behavior Monitoring by Electrical Penetration Graph Rapidly Reveals Host Plant Susceptibility to Crapemyrtle Bark Scale (Hemiptera: Eriococcidae)

Host range confirmation of invasive hemipterans relies on the evaluation of plant susceptibility though greenhouse or field trials, which are inefficient and time-consuming. When the green industry faces the fast-spreading threat of invasive pests such as crapemyrtle bark scale (Acanthococcus lagerstroemiae), it is imperative to timely identify potential host plants and evaluate plant resistance/susceptibility to pest infestation. In this study, we developed an alternative technology to complement the conventional host confirmation methods. We used electrical penetration graph (EPG) based technology to monitor the A. lagerstroemiae stylet-tip position when it was feeding on different plant tissues in real-time. The frequency and relative amplitude of insect feeding waveforms (recorded by EPG) were extracted by an R programming-based software written to generate eleven feeding parameters for comparative analysis between plant species. The results demonstrated that the occurrences of phloem phase and xylem phase offered conclusive evidence for host plant evaluation. Furthermore, parameters including the percentage of insects capable of accessing phloem tissue, time duration spent on initiating phloem phase and ingesting phloem sap, provided insight into why host plant susceptibility differs among similar plant species. In summary, this study developed a novel real-time diagnostic tool for quick A. lagerstroemiae host confirmation, which laid the essential foundation for effective pest management. Simple Summary Crapemyrtle bark scale (CMBS; Acanthococcus lagerstroemiae), an invasive polyphagous sap feeder in the United States, has spread across 16 U.S. states in less than two decades, posing potential risks to the Green Industry. Confirming the host range is crucial for effective pest management of invasive insects. However, host range confirmation relying on greenhouse or field trials is often inefficient and time-consuming. In this study, we used the electrical penetration graph (EPG) to monitor the stylet penetration of CMBS in plant tissue in real-time. An R programming-based application was developed to better characterize the insect feeding waveforms recorded by EPG. By analyzing EPG-based feeding parameters, we demonstrated that CMBS have difficulty accessing the phloem tissue (salivation and ingestion) of a resistant plant compared to a susceptible plant. Importantly, we hereby present CMBS typical feeding behaviors on susceptible and non-susceptible plants comparatively, which provides direct evidence for revealing unknown hosts rapidly.