bluuebunny/crossref_metadata_2025 huggingface dataset:
PAST: latent feature extraction with a Prior-based self-Attention framework for Spatial Transcriptomics
Authors: Li Zhen , Chen Xiaoyang , Zhang Xuegong , Chen Shengquan , Jiang Rui
Published: November 2022

Rapid advances in spatial transcriptomics (ST) have revolutionized the interrogation of spatial heterogeneity and increased the demand for comprehensive methods to effectively characterize spatial domains. As a prerequisite for ST data analysis, spatial domain characterization is a crucial step for downstream analyses and biological implications. Here we propose PAST, a variational graph convolutional auto-encoder for ST, which effectively integrates prior information via a Bayesian neural network, captures spatial patterns via a self-attention mechanism, and enables scalable application via a ripple walk sampler strategy. Through comprehensive experiments on datasets generated by different technologies, we demonstrated that PAST could effectively characterize spatial domains and facilitate various downstream analyses, including ST visualization, spatial trajectory inference and pseudo-time analysis, by integrating spatial information and reference from various sources. Besides, we also show the advantages of PAST for accurate annotation of spatial domains in newly sequenced ST data and biological implications in the annotated domains.
A compound PCP scheme underlies sequential rosettes-based cell intercalation
Authors: Xu Yichi , Cheng Yunsheng , Chen Allison T. , Bao Zhirong
Published: November 2022

Sequential rosettes are a type of collective cell behavior recently discovered in theC. elegansembryo to mediate directional cell migration through sequential formation and resolution of multicellular rosettes involving the migrating cell and its neighboring cells along the way. Here we show that a Planar Cell Polarity (PCP)-related polarity scheme regulates sequential rosettes, which is distinct from the known mode of how PCP regulates multicellular rosettes in the process of convergent extension. Specifically, non-muscle myosin (NMY) localization and edge contraction are perpendicular to that of Van Gogh as opposed to colocalizing with Van Gogh. Further analyses suggest a two-component polarity scheme: one being the canonical PCP pathway with MIG-1/Frizzled and VANG-1/Van Gogh localized to the vertical edges, the other being MIG-1/Frizzled and NMY-2 localized to the midline/contracting edges. Both MIG-1/Frizzled and VANG-1/Van Gogh are required for NMY-2 localization and contraction of the midline edges, but in redundancy with LAT-1/Latrophilin, an adhesion GPCR which has not been shown to regulate multicellular rosettes. Our results establish a distinct mode of PCP-mediated cell intercalation and shed light on the versatile nature of PCP pathway.
Immune Response following FLASH and Conventional Radiation in Diffuse Midline Glioma (DMG)
Authors: Padilla Oscar , Minns Hanna E. , Wei Hong-Jian , Fan Weijia , Webster-Carrion Andrea , Tazhibi Masih , McQuillan Nicholas M. , Zhang Xu , Gallitto Matthew , Yeh Rebecca , Zhang Zhiguo , Hei Tom K. , Szalontay Luca , Pavisic Jovana , Tan Yuewen , Deoli Naresh , Garty Guy , Garvin James H. , Canoll Peter D. , Vanpouille-Box Claire , Menon Vilas , Olah Marta , Rabadan Raul , Wu Cheng-Chia , Gartrell Robyn D.
Published: November 2022

Purpose

Diffuse Midline Glioma (DMG) is a fatal tumor traditionally treated with radiotherapy (RT) and previously characterized as having a non-inflammatory tumor immune microenvironment (TIME). FLASH is a novel RT technique using ultra-high dose rate, which is associated with decreased toxicity and effective tumor control. However, the effect of FLASH and conventional (CONV) RT on the DMG TIME have not yet been explored.

Methods

Here, we perform single-cell RNA sequencing and flow cytometry on immune cells isolated from an orthotopic syngeneic murine model of brainstem DMG following the use of FLASH (90Gy/sec) or CONV (2Gy/min) dose-rate RT, and compare to unirradiated tumor (SHAM).

Results

At day 4 post-RT, FLASH exerts similar effects as CONV in the predominant microglial (MG) population, including the presence of two activated subtypes. However, at day 10 post-RT, we observe a significant increase in type 1 interferon alpha receptor (IFNAR+) in MG in CONV and SHAM compared to FLASH. In the non-resident myeloid clusters of macrophages (MACs) and dendritic cells (DCs), we find increased type 1 interferon (IFN1) pathway enrichment for CONV compared to FLASH and SHAM by scRNA-seq. We observe this trend by flow cytometry at day 4 post-RT in IFNAR+ MACs and DCs, which equalizes by day 10 post-RT. DMG control and murine survival are equivalent between RT dose rates.

Conclusion

Our work is the first to map CONV and FLASH immune alterations of the DMG TIME with single-cell resolution. While DMG tumor control and survival are similar between CONV and FLASH, we find that changes in immune compartments differ over time. Importantly, while both RT modalities increase IFN1, we find that the timing of this response is cell-type and dose-rate dependent. These temporal differences, particularly in the context of tumor control, warrant further study.
Feeding and growth variations affectδ13C andδ15N budgets during ontogeny in a lepidopteran larva
Authors: Charberet Samuel , Maria Annick , Siaussat David , Gounand Isabelle , Mathieu Jérôme
Published: November 2022

Abstract

Isotopes are widely used in ecology to study food webs and physiology. The fractionation observed between trophic levels in nitrogen and carbon isotopes, explained by isotopic biochemical selectivity, is subject to important within-trophic level variations, leading to imprecision in trophic level estimation. Understanding the drivers of these variations is thus important to improve the study of food webs. In this study, we characterized this variation by submittingSpodoptera littoralislarvae to a gradient of starvation levels, a factor that we hypothesized would change the trophic fractionation between individuals. The various growth rates that were induced from these starvation levels resulted in a ~ 1-1.5‰ within-trophic level variation of the trophic fractionation in both carbon and nitrogen, which is substantial compared to the 3-4‰classically associated with between-trophic levels variations. Hence starved animals sampledin naturamay be ranked at a higher trophic level than they really are. We were able to gain an understanding of the effect of growth rate on isotopes fluxes between three easy-to-measure biological materials, food, organism and its wastes (frass), giving insight into physiological processes at play but also conveying helpful information to the sampling framework of field studies.
FUS modulates the level of ribosomal RNA modifications by regulating a subset of snoRNA expression
Authors: Gawade Kishor , Plewka Patrycja , Häfner Sophia J , Lund Anders H , Marchand Virginie , Motorin Yuri , Szczesniak Michal W , Raczynska Katarzyna D
Published: November 2022

FUS is a multifunctional protein involved in many aspects of RNA metabolism, including transcription, splicing, translation, miRNA processing, and replication-dependent histone gene expression. In this paper, we show that FUS depletion results in differential expression of numerous small nucleolar RNAs (snoRNAs) that guide 2’-O methylation (2’-O-Me) and pseudouridylation of specific positions in ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs). Using RiboMeth-seq and HydraPsiSeq for the profiling of 2’-O-Me and pseudouridylation status of rRNA species, we demonstrated considerable hypermodification at several sites in HEK293T and SH-SY5Y cells with FUS knockout (FUS KO) compared to wild-type cells. We observed a similar direction of changes in rRNA modification in differentiated SH-SY5Y cells with the FUS mutation (R495X) related to the severe disease phenotype of amyotrophic lateral sclerosis (ALS). Furthermore, the pattern of modification of some rRNA positions was correlated with the abundance of corresponding guide snoRNAs in FUS KO and FUS R495X cells. Our findings reveal a new role for FUS in modulating the modification pattern of rRNA molecules, that in turn might generate ribosome heterogeneity and constitute a fine-tuning mechanism for translation efficiency/fidelity. Therefore, we suggest that increased levels of 2’-O-Me and pseudouridylation at particular positions in rRNAs from cells with the ALS-linked FUS mutation may represent a possible new translation-related mechanism that underlies disease development and/or progression.
A live cell protein complementation assay for ORFeome-wide probing of human HOX interactomes
Authors: Jia Yunlong , Reboulet Jonathan , Gillet Benjamin , Hughes Sandrine , Forcet Christelle , Tribollet Violaine , Sleiman Nawal Hadj , Kundlacz Cindy , Vanacker Jean-Marc , Bleicher Françoise , Merabet Samir
Published: November 2022

Biological pathways rely on the formation of intricate protein interaction networks called interactomes. Getting a comprehensive map of interactomes implies developing tools that allow capturing transient and low affinity protein-protein interactions (PPIs) in live conditions. Here we present an experimental strategy, Cell-PCA (Cell Protein Complementation Assay), which is based on BiFC (Bimolecular Fluorescence Complementation) and high throughput sequencing for ORFeome-wide analyses of different interactomes in the same live cell context. The specificity and sensitivity of Cell-PCA was established by using a wild type and a single amino-acid mutated HOXA9 protein, and the approach was subsequently applied for seven additional human HOX proteins. These proof-of-concept experiments revealed novel molecular properties of HOX interactomes and led to the identification of a novel cofactor of HOXB13 for promoting its proliferative activity in a cancer cell context. Taken together, our work demonstrates that Cell-PCA is pertinent for revealing and, importantly, comparing interactomes between different or highly related bait proteins in the same cell context.
Effects of microRNA-mediated negative feedback on gene expression noise
Authors: Adhikary Raunak , Roy Arnab , Jolly Mohit Kumar , Das Dipjyoti
Published: November 2022

Micro-RNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally in eukaryotes by binding with target mRNAs and preventing translation. miRNA-mediated feedback motifs are ubiquitous in various genetic networks which control cellular decision-making. A key question is how such a feedback mechanism may affect gene expression noise. To answer this, we have developed a mathematical model to study the effects of a miRNA-dependent negative feedback loop on mean expression and noise in target mRNAs. Combining analytics and simulations, we show the existence of an expression threshold demarcating repressed and expressed regimes in agreement with earlier studies. The steady-state mRNA distributions are bimodal near the threshold, where copy numbers of mRNAs and miRNAs exhibit enhanced anticorrelated fluctuations. Moreover, variation of negative-feedback strength shifts the threshold locations and modulates the noise profiles. Notably, the miRNA-mRNA binding affinity and feedback strength collectively shape the bimodality. We also compare our model with a direct auto-repression motif, where a gene produces its own repressor. Auto-repression fails to produce bimodal mRNA distributions as found in miRNA-based indirect repression, suggesting the crucial role of miRNAs in creating phenotypic diversity. Together, we demonstrate how miRNA-dependent negative feedback modifies the expression threshold and leads to a broader parameter regime of bimodality compared to the no-feedback case.
Peyer’s Patch B cells undergo cell death via neutrophil-released toxic DNA following sterile tissue injury
Authors: Tuz Ali A , Beer Alexander , Gallert Markus , Ttoouli Dimitris , Ghosh Susmita , Sata Sai P , Kraus Andreas , Zwirnlein Franziska , Kaygusuz Viola , Lakovic Vivian , Qefalia Altea , Antler Medina , Korste Sebastian , Kaltwasser Britta , Abdelrahman Hossam , Mohamud-Yusuf Ayan , Wang Chen , Haeusler Lars , Lueong Smiths , Stenzel Martin , Frank Benedikt , Köhrmann Martin , Siveke Jens , Totzeck Matthias , Hoffmann Daniel , Grüneboom Anika , Hagemann Nina , Hasenberg Anja , Sickmann Albert , Chen Jianxu , Hermann Dirk M , Gunzer Matthias , Singh Vikramjeet
Published: November 2022

Lymphocyte contraction (LC) in central immune organs is a concomitant of sterile tissue injury, for example after stroke. Intestinal Peyer’s patches (PP) harbor large numbers of B cells, but how sterile tissue injury leads to LC in PP has not been explored. We observed rapid and macroscopically evident shrinkage of PP after stroke and myocardial infarction. Light-sheet fluorescence microscopy and flow cytometry revealed a strong reduction in the number of PP-resident B cells. Mechanistically, tissue injury triggered the activation of neutrophils that released B cell-toxic neutrophil extracellular traps (NETs) decorated with citrullinated histone-H3. Antibody-mediated or genetically induced neutrophil-loss, NETs-degradation or blockade of their generation completely reversed B cell loss and preserved the tissue architecture of PP. We also found NET-like elements in human post-stroke plasma. Hence, we propose that targeting NET-generation or -function counteracts post-injury B cell contraction in PP and thereby maintains immune homeostasis at mucosal barriers.

In brief

High numbers of B cells reside in the intestinal Peyer’s patches. Tuz et al. revealed that in response to sterile tissue injury, activated neutrophils release histone-decorated DNA into the circulation which induces B cell death. The loss of B cells results in the shrinkage of Peyer’s patches and reduced amounts of secretory IgA.

Highlights

Stroke and myocardial infarction induce the melting of Peyer’s patch

Light-sheet microscopy and cytometry revealed B cell loss in Peyer’s patch

Post-injury activated neutrophils release NETs and trigger B cell death

Inhibition of NETs rescues B cell loss and degeneration of Peyer’s patch
Stomatal density affects rice mesophyll cell size and shape and modulates a conserved pattern of cells through the leaf
Authors: Jen Sloan , Saranrat Im-Chai , Ngai Qi Yang , Yi Xiao , Jodie Armand , Wilson Matthew J. , Xin-Guang Zhu , Fleming Andrew J.
Published: November 2022

The structure of the mesophyll influences how light, CO2and water travels inside a leaf, affecting the rates of both photosynthesis and transpiration. Recent studies in wheat and Arabidopsis have shown that the structure of the mesophyll is influenced by the density and activity of stomata, consistent with the hypothesis that gas flow via stomata can modulate internal cell growth and separation to co-ordinate leaf structure and function. To investigate whether this also occurs in rice, a staple food crop for a large fraction of the world’s population, we examined mesophyll structure in rice mutants with altered stomatal density. Our data show that stomatal function modulates mesophyll structure in rice. Variation in the degree of mesophyll lobing made a major contribution to altered mesophyll structure, suggesting that modified leaf gas flux through stomata influences an aspect of cell shape directly linked to gas exchange capacity in rice. In addition, our analysis revealed a previously unreported underlying pattern in cell size, shape and axiality across layers of the rice mesophyll, which further investigation revealed is present in a range of rice species and cultivars. The potential origin and significance of this mesophyll patterning are discussed.

HIGHLIGHT

We describe a previously unreported cellular pattern in rice leaves and show that it is modulated by stomata. These results shed new light on leaf structure and function.
Complete mitochondrial genome and draft chloroplastic genome of Northern AtlanticHaslea ostrearia(Gaillon/Bory) Simonsen, 1974 (Naviculaceae, Bacillariophyceae)
Authors: Peticca Aurelie , Fodil Mostefa , Gateau Helene , Mouget Jean-Luc , Sabot Francois , Chenais Benoit , Casse Nathalie
Published: November 2022

The first completed, circular mitochondrial genome and the first draft chloroplastic genome of Northern Atlantic blue diatomHaslea ostrearia(Naviculaceae, Bacillariophyceae) are described. The mitochondrial genome is composed of 38,696 bases and contains 64 genes, including 31 protein-coding genes (CDS), 2 ribosomal RNA (rRNA) genes and 23 transfer RNA (tRNA) genes. For the chloroplast, the genome is composed of 130,200 bases with 169 genes (131 CDS, 6 rRNA genes, 31 tRNA genes, and 1 transfermessenger RNA (tmRNA) gene). Phylogenetic trees suggest the proximity of allH. ostreariastrains yet available and the possibility to use these genomes as future references.
Neurobehavioral precursors of compulsive cocaine-seeking in dual fronto-striatal circuits
Authors: Jones Jolyon A. , Belin-Rauscent Aude , Jupp Bianca , Fouyssac Maxime , Sawiak Stephen J. , Zuhlsdorff Katharina , Zhukovsky Peter , Hebdon Lara , Sanchez Clara Velazquez , Robbins Trevor W. , Everitt Barry J. , Belin David , Dalley Jeffrey W.
Published: November 2022

Only some individuals using drugs recreationally eventually become addicted, and persist in drug seeking and taking despite adverse consequences. The neurobehavioral determinants of this individual vulnerability have not been fully elucidated. We report that in drug naïve rats the future tendency to develop compulsive cocaine seeking is characterised by behavioral stickiness-related functional hypoconnectivity between the prefrontal cortex and posterior dorsomedial striatum in combination with impulsivity-related structural alterations in the infralimbic cortex, anterior insula and nucleus accumbens. These findings show that the vulnerability to develop compulsive cocaine seeking behavior stems from pre-existing structural or functional changes in two distinct cortico-striatal systems that underlie deficits in impulse control and goal-directed behavior.
Computational design of BclxL inhibitors that target transmembrane domain interactions
Authors: Duart Gerard , Elazar Assaf , Weinstein Jonathan J. , Gadea-Salom Laura , Ortiz-Mateu Juan , Fleishman Sarel J. , Mingarro Ismael , Martinez-Gil Luis
Published: November 2022

Several methods have been developed to explore interactions among water-soluble proteins or regions of proteins. However, techniques to target transmembrane domains have not been examined thoroughly. Here we developed a novel computational approach to design transmembrane sequences that specifically modulate protein-protein interactions in the membrane. To illustrate this method we demonstrated that BclxL can interact with other members of the Bcl2 family through the transmembrane domain and that these interactions are necessary for BclxL control of cell death. Next, we designed sequences that specifically recognize and sequester the transmembrane domain of BclxL. Hence, we were able to prevent BclxL intra-membrane interactions and cancel its anti-apoptotic effect. These results advance our understanding of protein-protein interactions in membranes and provide new means to modulate them. Moreover, the success of our approach may trigger the development of a new generation of inhibitors targeting interactions between transmembrane domains.
Ibex: Variational autoencoder for single-cell BCR sequencing
Authors: Borcherding Nicholas , Sun Bo , DeNardo David , Brestoff Jonathan R.
Published: November 2022

B cells are critical for adaptive immunity and are governed by the recognition of an antigen by the B cell receptor (BCR), a process that drives a coordinated series of signaling events and modulation of various transcriptional programs. Single-cell RNA sequencing with paired BCR profiling could offer insights into numerous physiological and pathological processes. However, unlike the plethora of single-cell RNA analysis pipelines, computational tools that utilize single-cell BCR sequences for further analyses are not yet well developed. Here we report Ibex, which vectorizes the amino acid sequence of the complementarity-determining region 3 (cdr3) of the immunoglobulin heavy and light chains, allowing for unbiased dimensional reduction of B cells using their BCR repertoire. Ibex is implemented as an R package with integration into both the Seurat and Single-Cell Experiment framework, enabling the incorporation of this new analytic tool into many single-cell sequencing analytic workflows and multimodal experiments.

Availability and Implementation

Ibex is available as an R package athttps://github.com/ncborcherding/Ibex. Reproducible code and data for the figure appearing in the manuscript are available athttps://github.com/ncborcherding/Ibex.manuscript. A companion TCR-based approach is available athttps://github.com/ncborcherding/Trex.
Neural signatures of reading-related orthographic processing in braille
Authors: Liu Yun-Fei , Rapp Brenda , Bedny Marina
Published: November 2022

Blind readers use a tactile reading systems consisting of raised dot arrays: braille/⠃⠗⠇. How does the human brain implement reading by touch? The current study looked for signatures of reading-specific orthographic processes in braille, separate from low-level somatosensory responses and semantic retrieval. Of specific interest were responses in posterior parietal cortices (PPC), because of their role in high-level tactile perception. Congenitally blind, proficient braille readers read real words and pseudowords by touch while undergoing fMRI. We leveraged the system of contractions in English braille, where one or more braille cells can represent combinations of English print letters (e.g., “ing” ⠬, “one” ⠐⠕), making it possible to separate physical and uncontracted letter-length. All words in the study consisted of 4 braille cells, but their corresponding Roman spellings varied from 4 to 7 letters (e.g., “con-c-er-t” ⠒⠉⠻⠞. contracted: 4 cells; uncontracted: 7 letters). We found that the bilateral supramarginal gyrus (SMG) in the PPC increased its activity as the uncontracted word length increased. By contrast, in the hand region of primary somatosensory cortex (S1), activity increased as a function of a low-level somatosensory feature: dot-number per word. The PPC also showed greater response to pseudowords than real words and distinguished between real and pseudowords in multi-voxel-pattern analysis. Parieto-occipital, early visual and ventral occipito-temporal, as well as prefrontal cortices also showed sensitivity to the real-vs-pseudoword distinction. We conclude that PPC is involved in sublexical orthographic processing for braille, possibly due to braille’s tactile modality.

Significance statement

Blind readers use tactile reading systems of raised dot arrays: braille. To identify signatures of orthographic processing for reading by touch, and dissociate it from tactile and linguistic process, we leveraged the system of contractions in English braille, where one or more braille characters represents combinations of English print letters. Blind proficient braille readers read real words and pseudowords during fMRI scans. While all words consisted of 4 braille characters, the uncontracted spelling ranged from 4-7 letters. Activity in bilateral-posterior-parietal cortices, just posterior to primary-somatosensory cortex, increased with uncontracted word length, independent of tactile complexity (number of raised dots per word). By contrast, primary-somatosensory activity increased with tactile complexity. The posterior-parietal cortices contribute to tactile reading.
An untargeted metabolomics approach to characterize dissolved organic matter in groundwater of the Samail Ophiolite
Authors: Seyler Lauren M. , Kraus Emily A. , McLean Craig , Spear John R. , Templeton Alexis S. , Schrenk Matthew O.
Published: November 2022

The process of serpentinization supports life on Earth and gives rise to the habitability of other worlds in our Solar System. While numerous studies have provided clues to the survival strategies of microbial communities in serpentinizing environments on the modern Earth, characterizing microbial activity in such environments remains challenging due to low biomass and extreme conditions. Here, we use an untargeted metabolomics approach to characterize dissolved organic matter in groundwater in the Samail Ophiolite, the largest and best characterized example of actively serpentinizing uplifted ocean crust and mantle. We found that dissolved organic matter composition is strongly correlated with both fluid type and microbial community composition, and that the fluids that were most influenced by serpentinization contained the greatest number of unique compounds, none of which could be identified using the current metabolite databases. Using metabolomics in conjunction with metagenomic data, we detected numerous products and intermediates of microbial metabolic processes and identified potential biosignatures of microbial activity, including pigments, porphyrins, quinones, fatty acids, and metabolites involved in methanogenesis. Metabolomics techniques like the ones used in this study may be used to further our understanding of life in serpentinizing environments, and aid in the identification of biosignatures that can be used to search for life in serpentinizing systems on other worlds.
An IS-mediated, RecA-dependent, bet-hedging strategy inBurkholderia thailandensis
Authors: Lowrey Lillian C. , Kent Leslie A. , Rios Bridgett M. , Ocasio Angelica B. , Cotter Peggy A.
Published: November 2022

Adaptation to fluctuating environmental conditions is difficult to achieve. Phase variation mechanisms can overcome this difficulty by altering genomic architecture in a subset of individuals, creating a phenotypically heterogeneous population with subpopulations optimized to persist when conditions change, or are encountered, suddenly. We have identified a phase variation system inBurkholderia thailandensisthat generates a genotypically and phenotypically heterogeneous population. Genetic analyses revealed that RecA-mediated homologous recombination between a pair of insertion sequence (IS)2-like elements duplicates a 208.6 kb region that contains 157 coding sequences. RecA-mediated homologous recombination also resolves merodiploids, and hence copy number of the region is varied and dynamic within populations. We showed that the presence of two or more copies of the region is advantageous for growth in a biofilm, and a single copy is advantageous during planktonic growth. While IS elements are well-known to contribute to evolution through gene inactivation, polar effects on downstream genes, and altering genomic architecture, we believe that this system represents a rare example of IS element-mediated evolution in which the IS elements provide homologous sequences for amplification of a chromosomal region that provides a selective advantage under specific growth conditions, thereby expanding the lifestyle repertoire of the species.
Managing invasive hybrids through habitat restoration in an endangered salamander system
Authors: Cooper Robert D. , Shaffer H. Bradley
Published: November 2022

Invasive species present one of the greatest threats to the conservation of biodiversity. When invasives hybridize with endangered native taxa, they introduce novel challenges ranging from the identification of hybrids in the field, to hybrid vigor and the erosion of species identity as genotypes are lost. Across a large swath of central California, a hybrid swarm consisting of admixed endangered California tiger salamanders (“CTS”,Ambystoma californiense) and introduced barred tiger salamander (Ambystoma mavortium) has replaced native populations, threatening CTS with genomic extinction. Here we employ a large-scale, genomically-informed field ecological experiment to test whether habitat restoration can reinstate natural selection favoring native salamander genotypes. We constructed 14 large, semi-natural ponds and manipulated their hydroperiods to evaluate larval survival and mass at metamorphosis. Consistent with earlier work, we found overwhelming evidence of hybrid superiority which persisted across all hydroperiod treatments. Short duration ponds substantially reduced the mass and survival probability of both native and hybrid larvae, likely exerting strong selective pressure in the wild. We identified 86 candidate genes, representing 1.8% of 4,723 screened loci, that significantly responded to this hydroperiod-driven selection. In contrast to previous mesocosm-based studies, native CTS never exhibited greater fitness than hybrids, suggesting that hydroperiod management alone will not shift selection to favor native genotypes. However, shortening pond hydroperiod may represent a cost-effective strategy to limit the overall productivity of ponds with non-native genotypes, complimenting additional strategies such as targeted hybrid removal. At a broader level, our experimental approach leverages extensive ecological knowledge, modern genomic tools, and a naturalistic,in situreplicated design to critically evaluate and expand the potential toolkit that managers can use to address this, and other recalcitrant biological invasions. We believe that this strategy may be an important tool for managing the growing number of complex invasion scenarios threatening global biodiversity.
Multi-omics analysis identifies symbionts and pathogens of blacklegged ticks (Ixodes scapularis) from a Lyme disease hotspot in southeastern Ontario, Canada
Authors: Paulson Amber R. , Lougheed Stephen C. , Huang David , Colautti Robert I.
Published: November 2022

Ticks in the familyIxodidaeare important vectors of zoonoses including Lyme disease (LD), which is caused by spirochete bacteria from theBorreliella(Borrelia)burgdorferisensu lato (Bbsl) complex. The blacklegged tick (Ixodes scapularis) continues to expand across Canada, creating hotspots of elevated LD risk at the leading edge of its expansion range. Current efforts to understand the risk of pathogen transmission associated withI. scapularisin Canada focus primarily on targeted screens, while variation in the tick microbiome remains poorly understood. Using multi-omics consisting of 16S metabarcoding and ribosome-depleted, whole-shotgun RNA transcriptome sequencing, we examined the microbial communities associated with adultI. scapularis(N = 32), sampled from four tissue types (whole tick, salivary glands, midgut, and viscera) and three geographical locations within a LD hotspot near Kingston, Ontario, Canada. The communities consisted of both endosymbiotic and known or potentially pathogenic microbes, including RNA viruses, bacteria, and aBabesiasp. intracellular parasite. We show that β-diversity is significantly higher between individual tick salivary gland and midgut bacterial communities, compared to whole ticks; while linear discriminant analysis (LDA) effect size (LEfSe) determined that the three potentially pathogenic bacteria detected by V4 16S rDNA sequencing also differed among dissected tissues only, including aBorreliafrom theBbslcomplex,Borrelia miyamotoi, andAnaplasma phagocytophilum. Importantly, we find co-infection ofI. scapularisby multiple microbes, in contrast to diagnostic protocols for LD, which typically focus on infection from a single pathogen of interest (B. burgdorferisensu stricto).

IMPORTANCE

A vector of human health concern, blacklegged ticks,Ixodes scapularis, transmit pathogens that cause tick-borne diseases (TBDs), including Lyme disease (LD). Several hotspots of elevated LD risk have emerged across Canada asI. scapularisexpands its range. Focusing on a hotspot in southeastern Ontario, we used high-throughput sequencing on whole ticks and dissected salivary glands and midguts. Compared to whole ticks, analysis of salivary glands and midguts revealed greater β-diversity among microbiomes that are less dominated byRickettsiaendosymbiont bacteria and enriched for pathogenic bacteria including aBbsl-associatedBorrelia,Borrelia miyamotoi, andAnaplasma phagocytophilum. We also find evidence of co-infection ofI. scapularisin this region by multiple microbes. Overall, our study highlights the challenges and opportunities associated with the surveillance of the microbiome ofI. scapularisfor pathogen detection using metabarcoding and metatranscriptome approaches.
BatCount: A software program to count moving animals
Authors: Bentley Ian , Kuczynska Vona , Eddington Valerie M. , Armstrong Mike , Kloepper Laura N.
Published: November 2022

One of the biggest challenges with species conservation is collecting accurate and efficient information on population sizes, especially from species that are difficult to count. Bats worldwide are declining due to disease, habitat destruction, and climate change, and many species lack reliable population information to guide management decisions. Current approaches for estimating population sizes of bats in densely occupied colonies are time-intensive, may negatively impact the population due to disturbance, and/or have low accuracy. Research-based video tracking options are rarely used by conservation or management agencies for animal counting due to the perceived training required to operate. In this paper, we present BatCount, a free software program created in direct consultation with end-users designed to automatically count aggregations of bats at cave roosts with a streamlined and user-friendly interface. We report on the software package and provide performance metrics for different recording habitat conditions. Our analysis demonstrates that BatCount is an efficient and reliable option for counting bats in flight and has important implications for range- and species-wide population monitoring. Furthermore, this software can be extended to count any organisms moving across a camera including birds, mammals, fish or insects.
Surfactants or scaffolds? RNAs of different lengths exhibit heterogeneous distributions and play diverse roles in RNA-protein condensates
Authors: Sanchez-Burgos Ignacio , Herriott Lara , Collepardo-Guevara Rosana , Espinosa Jorge R.
Published: November 2022

Biomolecular condensates, thought to form via liquid–liquid phase separation of intracellular mixtures, are multicomponent systems that can include diverse types of proteins and RNAs. RNA is a critical modulator of RNA-protein condensate stability, as it induces an RNA-concentration dependent reentrant phase transition—increasing stability at low RNA concentrations and decreasing it at high concentrations. Beyond concentration, RNAs inside condensates can be heterogeneous in length, sequence, and structure. Here, we use multiscale simulations to understanding how different RNA parameters interact with one another to modulate the properties of RNA-protein condensates. To do so, we perform residue/nucleotide-resolution coarse-grained Molecular Dynamics simulations of multicomponent RNA-protein condensates containing RNAs of different lengths and concentrations, and either FUS or PR25proteins. Our simulations reveal that RNA length regulates the reentrant phase behaviour of RNA-protein condensates: increasing RNA length sensitively rises the maximum value that the critical temperature of the mixture reaches, and the maximum concentration of RNA that the condensate can incorporate before beginning to become unstable. Strikingly, RNA of different lengths are organised heterogeneously inside condensates, which allows them to enhance condensate stability via two distinct mechanisms: shorter RNA chains accumulate at the condensate’s surface acting as natural biomolecular surfactants, whilst longer RNA chains concentrate inside the core to saturate their bonds and enhance the density of molecular connections in the condensate. Using a patchy particle model, we demonstrate that the combined impact of RNA length and concentration on condensate properties is dictated by the valency, binding affinity, and polymer length of the various biomolecules involved. Our results postulate that diversity on RNA parameters within condensates allows RNAs to increase condensate stability by fulfilling two different criteria: maximizing enthalpic gain and minimizing interfacial free energy; hence, RNA diversity should be considered when assessing the impact of RNA on biomolecular condensates regulation.
Accurate Detection of Incomplete Lineage Sorting via Supervised Machine Learning
Authors: Rosenzweig Benjamin , Kern Andrew , Hahn Matthew
Published: November 2022

Gene tree discordance due to incomplete lineage sorting or introgression has been described in numerous genomic datasets. Among distantly related taxa, however, it is difficult to differentiate these biological sources of discordance from discordance due to errors in gene tree reconstruction, even when supervised machine learning techniques are used to infer individual gene trees. Here, rather than applying machine learning to the problem of inferring single tree topologies, we develop a model to infer important properties of a particular internal branch of the species tree via genome-scale summary statistics extracted from individual alignments and inferred gene trees. We show that our model can effectively predict the presence/absence of discordance, estimate the probability of discordance, and infer the correct species tree topology in the presence of multiple, common sources of error. While gene tree topology counts are the most salient predictors of discordance at short time scales, other genomic features become relevant for distantly related species. We validate our approach through simulation, and apply it to data from the deepest splits among metazoans. Our results suggest that the base of Metazoa experienced significant gene tree discordance, implying that discordant traits among current taxa can be explained without invoking homoplasy. In addition, we find support for Porifera as the sister clade to the rest of Metazoa. Overall, these results demonstrate how machine learning can be used to answer important phylogenetic questions, while marginalizing over individual gene tree—and even species tree—topologies.
Essential Gene Phenotypes Reveal Antibiotic Mechanisms and Synergies inAcinetobacter baumannii
Authors: Ward Ryan D. , Tran Jennifer S. , Banta Amy B. , Bacon Emily E. , Rose Warren E. , Peters Jason M.
Published: November 2022

The emergence of multidrug-resistant Gram-negative bacteria underscores the need to define genetic vulnerabilities in relevant pathogens. The Gram-negative pathogen,Acinetobacter baumannii, poses an urgent threat by evading antibiotic treatment through both intrinsic and acquired mechanisms. Antibiotics kill bacteria by targeting essential gene products, but antibiotic-essential gene interactions have not been studied systematically inA. baumannii. Here, we use CRISPR interference (CRISPRi) to comprehensively phenotypeA. baumanniiessential genes. We show that certain essential genes are acutely sensitive to knockdown, providing a set of promising therapeutic targets. Screening our CRISPRi library against last-resort antibiotics revealed essential pathways that modulate beta-lactam resistance, an unexpected link between NADH dehydrogenase function and polymyxin killing, and the genetic basis for synergy between polymyxins and rifamycins. Our results demonstrate the power of systematic genetic approaches to identify weaknesses in Gram-negative pathogens and uncover antibiotic mechanisms that better inform combination therapies.

Significance

Acinetobacter baumanniiis a hospital-acquired pathogen that is resistant to common antibiotic treatments.A. baumanniiinfections, we need to identify promising therapeutic targets and effective antibiotic combinations. Here, we characterize genes critical forA. baumanniiviability and their interactions with antibiotics. We find that genes involved in proton gradient formation required for oxygen-dependent energy generation are central toA. baumanniiphysiology and represent appealing drug targets. We show that polymyxins interact with proton gradient genes, explaining how these antibiotics inhibit growth at sub-lethal concentrations and their efficacy in combination therapies. Our studies reveal antibiotic-gene interactions inA. baumanniithat can inform future therapies.
Preferential consumption of benthic cyanobacterial mats by Caribbean parrotfishes
Authors: Manning Joshua C. , McCoy Sophie J.
Published: November 2022

Cyanobacteria are ubiquitous on coral reefs and perform important ecosystem functions. Benthic cyanobacterial mats (BCMs) have become increasingly abundant on degraded reefs. While epilithic and endolithic benthic cyanobacteria are the primary trophic resource for many parrotfishes, mat-forming benthic cyanobacteria are generally considered unpalatable to reef fishes. Regardless, recent studies have documented substantial grazing of BCMs by reef fishes, including parrotfishes. Here, we observed foraging in five Caribbean parrotfishes on the fringing coral reefs of Bonaire, Netherlands, to investigate BCM consumption relative to other benthic substrates. All species overwhelmingly targeted reef substrates composed of algal turfs and crustose coralline algae, which are typically associated with epilithic and endolithic microalgal and cyanobacterial communities. Additionally, three species preferentially consumed BCMs. As such, our work is consistent with and provides direct evidence supporting the recently proposed trophic role for parrotfishes as microphages. Contrasting observations of reef fishes avoiding substrates dominated by BCMs on other reefs suggests variation in the palatability of BCMs to grazing reef fishes, or species-specific differences in preference for these potentially nutritional trophic resources.
memento: Generalized differential expression analysis of single-cell RNA-seq with method of moments estimation and efficient resampling
Authors: Kim Min Cheol , Gate Rachel , Lee David S. , Lu Andrew , Gordon Erin , Shifrut Eric , Marson Alexander , Ntranos Vasilis , Ye Chun Jimmie
Published: November 2022

Differential expression analysis of scRNA-seq data is central for characterizing how experimental factors affect the distribution of gene expression. However, it remains challenging to distinguish biological and technical sources of cell-cell variability and to assess the statistical significance of quantitative comparisons between groups of cells. We introducemementoto address these limitations and enable accurate and efficient differential expression analysis of the mean, variability, and gene correlation from scRNA-seq. We usedmementoto analyze 70,000 tracheal epithelial cells to identify interferon response genes with distinct variability and correlation patterns, 160,000 T cells perturbed with CRISPR-Cas9 to reconstruct gene-regulatory networks that control T cell activation, and 1.2 million PMBCs to map cell-type-specificcisexpression quantitative trait loci (eQTLs). In all cases,mementoidentified more significant and reproducible differences in mean expression but also identified differences in variability and gene correlation that suggest distinct modes of transcriptional regulation imparted by cytokines, genetic perturbations, and natural genetic variation. These results demonstratemementoas a first-in-class method for the quantitative comparisons of scRNA-seq data scalable to millions of cells and thousands of samples.
Structures of the Ndc80 complex and its interactions at the yeast kinetochore-microtubule interface
Authors: Zahm Jacob , Jenni Simon , Harrison Stephen
Published: November 2022

The conserved Ndc80 kinetochore complex, Ndc80c, is the principal link between spindle microtubules and centromere associated proteins during chromosome segregation. We used AlphaFold 2 to obtain structural predictions of the Ndc80 “loop” region and the Ndc80:Nuf2 globular head domains that interact with the Dam1 subunit of the decameric DASH/Dam1 complex (Dam1c). The predictions guided design of constructs that readily yielded crystal structures, essentially congruent with the predicted ones. The Ndc80 “loop” is a stiff, straight α-helical “switchback” structure, and flexibility within the long Ndc80c rod occurs instead at a hinge point between the globular head and the loop. Conserved stretches of the Dam1 C terminus bind Ndc80c with a short α helix followed by an extended segment such that phosphorylation of Dam1 serines 257, 265, and 292 by the mitotic kinase Ipl1/Aurora B can release this contact during error correction of mis-attached kinetochores. We integrate the structural results presented here into our current molecular model of the kinetochore-microtubule interface. The model illustrates how multiple interactions between Ndc80c, DASH/Dam1c and the microtubule lattice stabilize kinetochore attachments.
Tumor-specific CD4 T cells instruct monocyte differentiation in pancreatic ductal adenocarcinoma
Authors: Patterson Michael T. , Burrack Adam L. , Xu Yingzheng , Schmiechen Zoe C. , Schrank Patricia R. , Kennedy Ainsley E. , Firulyova Maria M. , Miller Ebony A. , Cruz-Hinojoza Eduardo , Zaitsev Konstantin , Williams Jesse W. , Stromnes Ingunn M.
Published: November 2022

Pancreatic ductal adenocarcinoma (PDA) is a lethal malignancy resistant to immunotherapy. The pancreatic tumor microenvironment is shaped and maintained by myeloid cells that outnumber tumor cells. Here, using monocyte fate-mapping PDA mouse models and human tumor tissues, we identify monocytes give rise to most heterogeneous macrophage subpopulations in PDA. We show that monocyte differentiation is governed by the local presence of CD4, but not CD8, T cells. We demonstrate that tumor specific CD4 T cells induce monocyte differentiation into antitumor MHCIIhiproinflammatory macrophages dependent on non-redundant IFNγ and CD40 signaling pathways that suppress tumor growth. Pancreatic tissue-resident macrophages exhibit an immunosuppressive pro-tumor state that is refractory to the modulatory effects of antitumor CD4 T cells. Intratumoral monocytes adopt a pro-tumor fate indistinguishable from tissue-resident macrophages following CD4 T cell depletion. Thus, tumor-specific CD4 T cell governance of monocyte fate promotes immune-mediated control of solid tumors.

Highlights

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Circulating monocytes are progenitors to most heterogeneous macrophage subsets in PDA

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Monocyte-derived macrophage acquisition of an MHCIIhiphenotype is dependent on tumor-specific CD4 T cells

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In the absence of CD4 T cells, monocyte-derived macrophages acquire tissue resident macrophage traits and tumors rapidly progress

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IFNγ and CD40 signaling are nonredundant and critical determinants of intratumoral monocyte fate
Quisinostat is a brain-penetrant radiosensitizer in glioblastoma
Authors: Cascio Costanza Lo , Margaryan Tigran , Melendez Ernesto Luna , McNamara James B. , White Connor I. , Knight William , Ganta Saisrinidhi , Opachich Zorana , Yoo Wonsuk , Sanai Nader , Tovmasyan Artak , Mehta Shwetal
Published: November 2022

In recent years, histone deacetylase inhibitors (HDACi) have garnered considerable interest for the treatment of adult and pediatric malignant brain tumors. However, owing to their broad-spectrum nature and inability to effectively penetrate the blood-brain barrier, HDACi have failed to provide significant clinical benefit to glioblastoma (GBM) patients to date. Moreover, global inhibition of HDACs results in widespread toxicity, highlighting the need for selective isoform targeting. While no isoform-specific HDACi are currently available, the second-generation hydroxamic acid-based HDACi quisinostat possesses sub-nanomolar specificity for class I HDAC isoforms, particularly HDAC1 and 2. Recently, we demonstrated that HDAC1 is the essential HDAC in GBM. Here, we provide the first report on the neuro-pharmacokinetic, pharmacodynamic and radiation-sensitizing properties of quisinostat in preclinical models of GBM. We demonstrate that quisinostat is a well-tolerated and brain-penetrant molecule that significantly extends survival when administered in combination with radiationin vivo. The pharmacokinetic-pharmacodynamic-efficacy relationship was established by correlating free drug concentrations and evidence of target modulation in the brain with survival benefit. Together, these data provide a strong rationale for clinical development of quisinostat as a radiosensitizer for the treatment of GBM.