bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole-genome sequencing of major malaria vectors revealed an evolution of new insecticide resistance variants in a longitudinal study in Burkina Faso
Authors: Kientega Mahamadi , Clarkson Chris S , Traoré Nouhoun , Hui Tin-Yu J , O’Loughlin Samantha , Millogo Abdoul-Azize , Epopa Patric S , Yao Franck A , Belem Adrien M G , Brenas Jon , Miles Alistair , Burt Austin , Diabaté Abdoulaye
Published: November 2023

Intensive deployment of insecticide based malaria vector control tools results in the rapid evolution of phenotypes resistant to these chemicals. Understanding this process on the genomic level is essential for the deployment of successful interventions. Using whole genome sequencing data of 1409 individualAn. Gambiaes.l. collected from 2012 to 2017, we investigated the change in genetic structure and the evolution of the insecticide resistance variants in natural populations over time and space. The results showed similar and constant nucleotide diversity and negative Tajima’s D betweenAn. gambiaes.s. andAn. coluzzii. PCA andFSTshowed a clear genetic structure in theAn. gambiaes.l. species. Genome-wideFSTand H12 scans identified genomic regions under divergent selection and also having an implication in the adaptations to ecological changes. Novel voltage-gated sodium channel pyrethroid resistance target-site alleles (V402L, I1527T) were identified at increasing frequencies alongside the establishedkdralleles (Vgsc-L995F,Vgsc-L995SandN1570Y) within theAn. gambiaes.l. populations. Organophosphate metabolic resistance markers were also identified, at increasing frequencies, within theAn. gambiaes.s. populations from 2012 to 2017, including the SNPAce1-G280Sand its associated duplication. Variants simultaneously identified in the same vector populations raise concerns about the long-term efficacy of new-generation bednets and the recently introduced organophosphate pirimiphos-methyl indoor residual spraying. These findings highlighted the benefit of genomic malaria vector surveillance for the detection of new insecticide resistance variants, the monitoring of the existing resistance variants, and also to get insights into the evolutionary processes driving insecticide resistance.

Author Summary

Genomic surveillance of malaria vectors is crucial for understanding the genetic variation in natural vector populations and also guiding the implementation of novel and innovative vector control tools. Application of sequencing technologies in vector studies provide insights on the genetic and evolutionary phenomena of vectors that could have impact on vector control strategies. By analyzing the whole genome data of 1409 wildAn. gambiaes.l. mosquito collected between 2012 and 2017, we showed an emergence of novel insecticide resistance markers alongside increasing frequencies of existing insecticide resistance variants over time in Burkina Faso. We showed the benefit of genomic surveillance of malaria vectors for the monitoring of the insecticide resistance variants and also providing insights into the evolutionary processes driving insecticide resistance.
Comprehensive Codon Usage Analysis Across Diverse Plant Lineages
Authors: Majeed Aasim , Rehman Wahid Ul , Kaur Amitozdeep , Das Sreemoyee , Joseph Josepheena , Singh Amandeep , Bhardwaj Pankaj
Published: November 2023

The variation of codon usage patterns in response to the evolution of organisms is an intriguing question to answer. The purpose of this study was to investigate the relevance of the evolutionary events of vascularization and seed production with the codon usage patterns in different plant lineages. We found that the optimal codons of non-vascular lineages generally end with GC, whereas those of the vascular lineages end with AU. Correspondence analysis and model-based clustering showed that the evolution of the codon usage pattern follows the evolutionary event of the vascularization more precisely than that of the seed production. The dinucleotides CpG and TpA were under-represented in all the lineages, whereas the dinucleotide TpG was found over-represented in all the lineages, except algae. Evolutionary-related lineages showed similar codon pair bias (CPB). The dinucleotide CpA showed a similar representation as those of its parent codon pairs. Although natural selection predominates over mutational pressure in determining the codon usage bias (CUB), the relative influence of mutational pressure is higher in the non-vascular lineages than in the vascular lineages.
Design of Worst-Case-Optimal Spaced Seeds
Authors: Rahmann Sven , Zentgraf Jens
Published: November 2023

Read mapping (and alignment) is a fundamental problem in biological sequence analysis. For speed and computational efficiency, many popular read mappers tolerate only a few differences between the read and the corresponding part of the reference genome, which leads to reference bias: Reads with too many difference are not guaranteed to be mapped correctly or at all, because to even consider a genomic position, a sufficiently longexactmatch (seed) must exist.

While pangenomes and their graph-based representations provide one way to avoid reference bias by enlarging the reference, we explore an orthogonal approach and consider stronger substitution-tolerant primitives, namelyspaced seedsor gappedk-mers. Given two integersk ≤ w, one considerskselected positions, described by amask, from each length-wwindow in a sequence. In the existing literature, masks with certainprobabilisticguarantees have been designed for small values ofk.

Here, for the first time, we take a combinatorial approach from aworst-caseperspective. For any mask, using integer linear programs, we find least favorable distributions of sequence changes in two different senses: (1) minimizing the number of unchanged windows; (2) minimizing the number of positions covered by unchanged windows. Then, among all masks of a given shape (k, w), we find the set of best masks that maximize these minima. As a result, we obtain highly robust masks, even for large numbers of changes. Their advantages are illustrated in two ways: First, we provide a new challenge dataset of simulated DNA reads, on which current methods like bwa-mem2, minimap2, or strobealign struggle to find seeds, and therefore cannot produce alignments against the human t2t reference genome, whereas we are able to find the correct location from a few unique spaced seeds. Second, we use real DNA data from the highly diverse human HLA region, which we are able to map correctly based on a few exactly matching spaced seeds of well-chosen masks, without evaluating alignments.
Hammerhead-type FXR agonists induce an eRNA FincoR that ameliorates nonalcoholic steatohepatitis in mice
Authors: Chen Jinjing , Wang Ruoyu , Xiong Feng , Sun Hao , Kemper Byron , Li Wenbo , Kemper Jongsook Kim
Published: November 2023

The nuclear receptor, Farnesoid X Receptor (FXR/NR1H4), is increasingly recognized as a promising drug target for metabolic diseases, including nonalcoholic steatohepatitis (NASH). Protein coding genes regulated by FXR are well known, but whether FXR also acts through regulation of long non-coding RNAs (lncRNAs), which vastly outnumber protein-coding genes, remains unknown. Utilizing RNA-seq and GRO-seq analyses in mouse liver, we found that FXR activation affects the expression of many RNA transcripts from chromatin regions bearing enhancer features. Among these we discovered a previously unannotated liver-enriched enhancer-derived lncRNA (eRNA), termedFincoR. We show thatFincoRis specifically induced by the hammerhead-type FXR agonists, including GW4064 and tropifexor. CRISPR/Cas9-mediated liver-specific knockdown ofFincoRin dietary NASH mice reduced the beneficial effects of tropifexor, an FXR agonist currently in clinical trials for NASH and primary biliary cholangitis (PBC), indicating that that amelioration of liver fibrosis and inflammation in NASH treatment by tropifexor is mediated in part byFincoR. Overall, our findings highlight that pharmacological activation of FXR by hammerhead-type agonists induces a novel eRNA,FincoR, contributing to the amelioration of NASH in mice.FincoRmay represent a new drug target for addressing metabolic disorders, including NASH.
Quantitative cell morphology inC. elegansembryos reveals regulations of cell volume asymmetry
Authors: Guan Guoye , Li Zelin , Ma Yiming , Cao Jianfeng , Wong Ming-Kin , Chan Lu-Yan , Yan Hong , Tang Chao , Zhao Zhongying
Published: November 2023

The dynamics of cellular morphology throughout development are crucial for morphogenesis and organogenesis, yet their systematic characterization remains a significant challenge. By integrating both nuclear position and advanced cell membrane labeling, we develop a novel method that enables the segmentation of surfaces for over 95% of cells produced duringCaenorhabditis elegansembryogenesis. With this method, we segment eight wild-type and four perturbed embryos. The output, including cell identity, shape, volume, surface and contact area, can be visualized using our custom software. We demonstrate that signaling interactions, such as Notch and Wnt, regulate not only the asymmetry of cell fate but also the asymmetry of cell volume in conjunction with mechanical compression. Furthermore, we find that the asymmetries of fate and volume are generally interconnected.

ONE SENTENCE SUMMARY

Systematic quantification of cell morphology with resolved cell lineage and cell fate in developingC. elegansembryo uncovers multimodal regulations of cell size.

Potential Cover/Featured Image: Smiling “ghost” face ofC. elegansembryo.Center: shown are skins (colored in red, dorsal view with anterior to the bottom) of a 400-celledC. elegansembryo. Cells not covered by the skins are colored in gray, green, blue, and transparent yellow, respectively. Internal and external circles: confocal fluorescence images (GFP for cell nucleus and mCherry for cell membrane) and reconstructed cell morphologies of theC. elegansembryo from the 2- to 550-cell stages respectively, connected with images of aC. elegansadult expressing the same markers.
Plastic vasomotion entrainment
Authors: Sasaki Daichi , Imai Ken , Ikoma Yoko , Matsui Ko
Published: November 2023

The presence of global synchronization of vasomotion induced by oscillating visual stimuli was identified in the mouse brain. Endogenous autofluorescence was used and the vessel “shadow” was quantified to evaluate the magnitude of the frequency-locked vasomotion. This method allows vasomotion to be easily quantified in non-transgenic wild-type mice using either the wide-field macro-zoom microscopy or the deep-brain fiber photometry methods. Vertical stripes horizontally oscillating at a low temporal frequency (0.25 Hz) were presented to the awake mouse and oscillatory vasomotion locked to the temporal frequency of the visual stimulation was induced not only in the primary visual cortex but across a wide surface area of the cortex and the cerebellum. The visually induced vasomotion adapted to a wide range of stimulation parameters. Repeated trials of the visual stimulus presentations resulted in the entrainment of the amplitude of the vasomotion. Horizontally oscillating visual stimulus is known to induce horizontal optokinetic response (HOKR). The amplitude of the eye movement is known to increase with repeated training sessions and the flocculus region of the cerebellum is known to be essential for this learning to occur. Here, we show a strong correlation between the average HOKR performance gain and the vasomotion entrainment magnitude in the cerebellar flocculus. Therefore, the plasticity of vasomotion and neuronal circuits appeared to occur in parallel. Efficient energy delivery by the entrained vasomotion may contribute to meeting the energy demand for increased coordinated neuronal activity and the subsequent neuronal circuit reorganization.
Epigenetic vulnerabilities of leukemia harboring inactivating EZH2 mutations
Authors: Alqazzaz Mona A. , Luciani Genna M. , Vu Victoria , Machado Raquel Martinez , Szewczyk Magdalena M. , Adamson Ella C. , Cheon Sehyun , Li Fengling , Arrowsmith Cheryl H. , Minden Mark D. , Barsyte-Lovejoy Dalia
Published: November 2023

Epigenetic regulators such as the polycomb repressive complex 2 (PRC2) play a critical role in both normal development and carcinogenesis. Mutations and functional dysregulation of PRC2 complex components such as EZH2 are implicated in various forms of cancer and associated with poor prognosis. This study investigated the epigenetic vulnerabilities of acute myeloid leukemia (AML) and myelodysplastic/myeloproliferative disorders (MDS/MPN) by performing a chemical probe screen in patient cells. Paradoxically, we observed increased sensitivity to EZH2 and EED inhibitors in AML and MDS/MPN patient cells harboringEZH2mutations. Expression analysis indicated that EZH2 inhibition elicited upregulation of pathways responsible for cell death and growth arrest, specifically in patient cells with mutant EZH2. The identifiedEZH2mutations had drastically reduced catalytic activity, resulting in lower cellular H3K27me3 levels and were associated with decreased EZH2 and PRC2 component EED protein levels. Overall, this study provides an important understanding of the role of EZH2 dysregulation in blood cancers and may indicate disease etiology for these poor prognosis AML and MDS/MPN cases.
A UHPLC–MS/MS method for determination of N-acylethanolamines in cerebrospinal fluid
Authors: Ismoilova Visolakhon , Wretlind Asger , Hooshmand Kourosh , Simonsen Anja Hviid , Hasselbalch Steen Gregers , Quigley Cristina Legido
Published: November 2023

N-acylethanolamines (NAEs) and primary fatty amides (PFAMs) are of a great interest due to the range of physiological effects they exhibit, potentially serving as neuromodulators. However, they are present at nano and picomolar concentrations in human cerebrospinal fluid (CSF) samples, posing challenges for detection and measurement using conventional Ultra-high performance liquid chromatography systems coupled to tandem mass spectrometry (UHPLC-MS).

UHPLC-MS was used in dynamic multiple reaction monitoring (dMRM) mode. Seven deuterated NAEs internal standards were used to develop the method. Six solvent combinations were tested for extraction efficiency, accuracy, precision, matrix effect, linearity, limits of detection. Lastly the method was applied to CSF from healthy individuals (n=33) to estimate their natural range of concentrations.

Extraction with acetonitrile/acetone showed the highest efficiency and recovery. The presented method was able to measure the following 17 NAEs and PFAMs in human CSF: linoleoyl ethanolamide, heptadecanoyl ethanolamide, stearoyl ethanolamide, palmitoyl ethanolamide, dihomolinolenoyl ethanolamide, eicosatrienoic acid ethanolamide, behenamide, octadecanamide, lauramide, tetradecanamide, erucamide, linoleamide, palmitamide, myristic monoethanolamide, pentadecanoyl ethanolamide, oleamide and palmitoleoyl ethanolamide. In healthy individuals the concentrations ranged three-fold from pg/mL to mg/mL. Further studies could apply this method to clinical CSF samples.
Dollo parsimony overestimates ancestral gene content reconstructions
Authors: Gàlvez-Morante Alex , Guéguen Laurent , Natsidis Paschalis , Telford Maximilian J. , Richter Daniel J.
Published: November 2023

Ancestral reconstruction is a widely-used technique that has been applied to understand the history of gain and loss of gene families over evolutionary time scales, and to produce hypotheses on how these gains and losses may have influenced the evolutionary trajectories of extant organisms.

Ancestral gene content can be reconstructed via different phylogenetic methods, such as maximum likelihood or Bayesian inference, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character can only be gained once in evolutionary history. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence (including random sequence similarity and parallel gene gains), non-orthologous homology or lateral gene transfer. The aim of this study is to test Dollo parsimony’s suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach which allows a gene family to be gained more than once within a tree.

In order to test our hypothesis, we first compared the performance of the two approaches on a series of artificial datasets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, which were more pronounced at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.
Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation
Authors: Ramnauth Anthony D. , Tippani Madhavi , Divecha Heena R. , Papariello Alexis R. , Miller Ryan A. , Nelson Erik D. , Pattie Elizabeth A. , Kleinman Joel E. , Maynard Kristen R. , Collado-Torres Leonardo , Hyde Thomas M. , Martinowich Keri , Hicks Stephanie C. , Page Stephanie C.
Published: November 2023

The dentate gyrus of the hippocampus is important for many cognitive functions, including learning, memory, and mood. Here, we investigated age-associated changes in transcriptome-wide spatial gene expression in the human dentate gyrus across the lifespan. Genes associated with neurogenesis and the extracellular matrix were enriched in infants, while gene markers of inhibitory neurons and cell proliferation showed increases and decreases in post-infancy, respectively. While we did not find evidence for neural proliferation post-infancy, we did identify molecular signatures supporting protracted maturation of granule cells. We also identified a wide-spread hippocampal aging signature and an age-associated increase in genes related to neuroinflammation. Our findings suggest major changes to the putative neurogenic niche after infancy and identify molecular foci of brain aging in glial and neuropil enriched tissue.
Multiple focal pulvinar projection fields in the macaque cortex
Authors: Froesel Mathilda , Clavagnier Simon , Goudard Quentin , Zhu Qi , Vanduffel Wim , Ben Hamed Suliann
Published: November 2023

The pulvinar, the largest nucleus of the thalamus, is functionally heterogeneous and involved in multiple cognitive functions. It has been proposed to act as a functional hub of cortical processes due to its extensive reciprocal connectivity with the cortex. However, its role in cognition is not fully understood yet. Here, we posit that an improved understanding of its functional connectivity with the cortex is needed to better capture the cognitive functions of this nucleus. To address this question, we characterize the pulvino-cortical functional connectivity along the ventro-dorsal, antero-posterior and medio-lateral axes, using awake resting state data from ten adult macaques. We first report two global cortical functional connectivity gradients along the antero-posterior and ventro-dorsal pulvinar gradients, that match remarkably well the structural connectivity gradients described by anatomical approaches. In addition to these global gradients, multiple local cortical pulvinar projection fields can be identified at the sulci level such as in the lateral sulcus (LS), the intraparietal sulcus (IPS), the principal sulci (PS) and the anterior cingulate cortex (ACC). For most sulci, we show that functional pulvino-cortical projection fields follow the major anatomical axis of these different sulci (e.g. the ventro-dorsal axis for the LS and the antero-posterior axis for the IPS). Other sulci, such as the superior temporal sulcus, the posterior cingulate cortex or the central sulcus, display multiple projection fields from the pulvinar. Although substantial inter-individual differences exist, the general functional connectivity patterns are remarkably consistent across hemispheres and individuals. Overall, we propose that these multiple pulvinar projection fields correspond to a fundamental principle of pulvino-cortical connectivity and that a better understanding of this connectional organization will shed light on the function of pulvino-cortical interactions and the role of the pulvinar in cognition at large.
Refinement of the “CandidatusAccumulibacter” Genus Based on a Metagenomic Analysis of Biological Nutrient Removal (BNR) Pilot-Scale Plants Operated with Reduced Aeration
Authors: Stewart Rachel D. , Myers Kevin S. , Amstadt Carly , Seib Matt , McMahon Katherine D. , Noguera Daniel R.
Published: November 2023

Members of the “CandidatusAccumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 “Ca. Accumulibacter” species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most “Ca. Accumulibacter” MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the “Ca. Accumulibacter” diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium and high-quality MAGs for 5 of the 18 “Ca. Accumulibacter” species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA,ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized “Ca. Accumulibacter” species for which we propose the new species designation “Ca. Accumulibacter jenkinsii” sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, “Ca. A. necessarius” and “Ca. A. propinquus” accounted for more than 40% of the “Ca. Accumulibacter” community, whereas the newly proposed “Ca. A. jenkinsii” accounted for about 5% of the “Ca. Accumulibacter” community.

IMPORTANCE

One of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the “CandidatusAccumulibacter” genus in pilot-scale plants operating with minimal aeration. We identified the “Ca.Accumulibacter” species enriched under these conditions, including one novel species for which we propose “Ca.Accumulibacter jenkinsii” sp. nov. as its designation. Furthermore, the MAGs obtained for 5 additional “Ca.Accumulibacter” species further refine the phylogeny of the “Ca.Accumulibacter” genus and provide new insight into its diversity within unconventional biological nutrient removal systems.
Characteristics of putative keystones in the healthy adult human gut microbiome as determined by correlation network analysis
Authors: Bauchinger Franziska , Seki David , Berry David
Published: November 2023

Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa.

IMPORTANCE

The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance. By employing a robust workflow based on bootstrapping and subsampling techniques, we identify putative keystone species at the genus and species level. This emphasizes the importance of considering taxonomic resolution when investigating correlations. The potential impact of keystones on community stability provides valuable insights for systematic microbiome manipulation. Furthermore, the observed clusters of co-occurring taxa align well with recent findings and emphasize the reproducibility and relevance of the identified patterns in microbial community composition. We are able to add a functional dimension to the analysis with the identification of distinct transcriptional states in putative keystone taxa, highlighting their functional versatility and adaptability.
Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling
Authors: Cohen Natalie R. , Krinos Arianna I. , Kell Riss M. , Chmiel Rebecca J. , Moran Dawn M. , McIlvin Matthew R. , Lopez Paloma Z. , Barth Alexander , Stone Joshua , Alanis Brianna A. , Chan Eric W. , Breier John A. , Jakuba Michael V. , Johnson Rod , Alexander Harriet , Saito Mak A.
Published: November 2023

Protists (microeukaryotes) are key contributors to marine carbon cycling, influencing the transfer of energy to higher trophic levels and the vertical movement of carbon to the ocean interior. Their physiology, ecology, and interactions with the chemical environment are still poorly understood in offshore ecosystems, and especially in the deep ocean. Using the Autonomous Underwater Vehicle (AUV)Clio, the microbial community along a 1,050 km transect in the western North Atlantic Ocean was surveyed at 10-200 m vertical depth increments to capture metabolic microeukaryote signatures spanning a gradient of oligotrophic, continental margin, and productive coastal ecosystems. Plankton biomass was collected along the surface of this transect and across depth features, and taxonomy and metabolic function were examined using a paired metatranscriptomic and metaproteomic approach. A shift in the microeukaryote community composition was observed from the euphotic zone through the mesopelagic and into the bathypelagic ocean. A diverse surface assemblage consisting of haptophytes, stramenopiles, dinoflagellates and ciliates was represented in both the transcript and protein fractions, with foraminifera, radiolaria, picozoa, and discoba proteins enriched at >200 m depth, and fungal proteins emerging in waters >3,000 m depth. In the broad microeukaryote community, nitrogen stress biomarkers were found in productive coastal sites, with phosphorus stress biomarkers in offshore waters where Saharan dust input is thought to supply iron and nitrogen. This multi-omics dataset broadens our understanding of how microeukaryotic taxa and their functional processes are structured along environmental gradients of temperature, light, macronutrients, and trace metals.
Short-term social isolation acts on hypothalamic neurons to promote social behavior in a sex- and context-dependent manner
Authors: Zhao Xin , Chae Yurim , Smith Destiny , Chen Valerie , DeFelipe Dylan , Sokol Joshua W , Sadangi Archana , Tschida Katherine
Published: November 2023

Social animals, including both humans and mice, are highly motivated to engage in social interactions. Short-term social isolation promotes social behavior, but the neural circuits through which it does so remain incompletely understood. Here, we sought to identify neurons that promote social behavior in single-housed female mice, which exhibit increased rates of social investigation, social ultrasonic vocalizations (USVs), and mounting during same-sex interactions that follow a period of short-term (3-day) isolation. We first used immunostaining for the immediate early gene Fos to identify a population of neurons in the preoptic hypothalamus (POA) that increase their activity in single-housed females following same-sex interactions (POAsocialneurons) but not in single-housed females that did not engage in social interactions. TRAP2-mediated chemogenetic silencing of POAsocialneurons in single-housed females significantly attenuates the effects of short-term isolation on social investigation, USV production, and mounting. In contrast, caspase-mediated ablation of POAsocialneurons in single-housed females robustly attenuates mounting but does not decrease social investigation or USV production. Optogenetic activation of POAsocialneurons in group-housed females promotes social investigation and USV production but does not recapitulate the effects of short-term isolation on mounting. To understand whether a similar population of POAsocialneurons promotes social behavior in single-housed males, we performed Fos immunostaining in single-housed males following either same-sex or opposite-sex social interactions. These experiments revealed a population of POA neurons that increase Fos expression in single-housed males following opposite-sex, but not same-sex, interactions. Chemogenetic silencing of POAsocialneurons in single-housed males during interactions with females reduces mounting but does not affect social investigation or USV production. These experiments identify a population of hypothalamic neurons that promote social behavior following short-term isolation in a sex- and social context-dependent manner.
Short communication: Accounting for nuclear and mito genome in dairy cattle breeding - a simulation study
Authors: Mafra Fortuna Gabriela , Zumbach B.J. , Johnsson M. , Pocrnic I. , Gorjanc G.
Published: November 2023

Mitochondria play a significant role in numerous cellular processes through proteins encoded by both nuclear genome (nDNA) and mito genome (mDNA). While the variation in nDNA is influenced by mutations and recombination of parental genomes, the variation in mDNA is solely driven by mutations. In addition, mDNA is inherited in a haploid form, from the dam. Cattle populations show significant variation in mDNA between and within breeds. Past research suggests that variation in mDNA accounts for 1-5% of the phenotypic variation in dairy traits. Here we simulated a dairy cattle breeding program to assess the impact of accounting for mDNA variation in pedigree-based and genome-based genetic evaluations on the accuracy of estimated breeding values for mDNA and nDNA components. We also examined the impact of alternative definitions of breeding values on genetic gain, including nDNA and mDNA components that both impact phenotype expression, but mDNA is inherited only maternally. We found that accounting for mDNA variation increased accuracy between +0.01 and +0.05 for different categories of animals, especially for young bulls (+0.05) and females without genotype data (between +0.01 and +0.03). Different scenarios of modelling and breeding value definition impacted genetic gain. The standard approach of ignoring mDNA variation achieved competitive genetic gain. Modelling, but not selecting on mDNA expectedly reduced genetic gain, while optimal use of mDNA variation recovered the genetic gain.
Antagonistic conflict between transposon-encoded introns and guide RNAs
Authors: Žedaveinytė Rimantė , Meers Chance , Le Hoang C. , Mortman Edan E. , Tang Stephen , Lampe George D. , Pesari Sanjana R. , Gelsinger Diego R. , Wiegand Tanner , Sternberg Samuel H.
Published: November 2023

TnpB nucleases represent the evolutionary precursors to CRISPR-Cas12 and are widespread in all domains of life, presumably due to the critical roles they play in transposon proliferation. IS605-family TnpB homologs function in bacteria as programmable homing endonucleases by exploiting transposon-encoded guide RNAs to cleave vacant genomic sites, thereby driving transposon maintenance through DSB-stimulated homologous recombination. Whether this pathway is conserved in other genetic contexts, and in association with other transposases, is unknown. Here we uncover molecular mechanisms of transposition and RNA-guided DNA cleavage by IS607-family elements that, remarkably, also encode catalytic, self-splicing group I introns. After reconstituting and systematically investigating each of these biochemical activities for a candidate ‘IStron’ derived fromClostridium botulinum, we discovered sequence and structural features of the transposon-encoded RNA that satisfy molecular requirements of a group I intron and TnpB guide RNA, while still retaining the ability to be faithfully mobilized at the DNA level by the TnpA transposase. Strikingly, intron splicing was strongly repressed not only by TnpB, but also by the secondary structure of ωRNA alone, allowing the element to carefully control the relative levels of spliced products versus functional guide RNAs. Our results suggest that IStron transcripts have evolved a sensitive equilibrium to balance competing and mutually exclusive activities that promote transposon maintenance while limiting adverse fitness costs on the host. Collectively, this work explains how diverse enzymatic activities emerged during the selfish spread of IS607-family elements and highlights molecular innovation in the multi-functional utility of transposon-encoded noncoding RNAs.
Season-specific dominance broadly stabilizes polymorphism under symmetric and asymmetric multivoltinism
Authors: Brud Evgeny
Published: November 2023

Seasonality causes intraannual fitness changes in multivoltine populations (defined as having multiple generations per year). While it is well-known that seasonally balanced polymorphism is established by overdominance in geometric mean fitness, an unsettled aspect of the deterministic theory is the relative contribution of various season-specific dominance mechanisms to the potential for polymorphism. In particular, the relative importance of seasonally-reversing and non-reversing schemes remains unclear. Here I analyze the parameter space for the discrete generation two-season multivoltine model and conclude that, in general, a substantial fraction of stabilizing schemes are non-reversing with the season (∼25-50%). In addition, I derive the approximate equilibrium allele frequency cycle under bivoltinism, and find that the amplitude of allelic oscillation is maximized by non-reversing dominance if the selection coefficients are roughly symmetric. Lastly, I derive conditions for the intralocus evolution of dominance. These predict a long-term trend toward maximally beneficial reversal. Overall, the results counter the disproportionate emphasis placed on dominance reversal as a stabilizing mechanism and clarify that non-reversing dominance is expected to frequently characterize seasonally fluctuating alleles under both weak and strong selection, especially in their early history. I conclude that seasonally alternating selection regimes are easily able to maintain allelic variation without restrictive assumptions on either selection coefficients or dominance parameters.
Particulate organic matter drives spatial variation in denitrification potential at the field scale
Authors: Stuchiner Emily R. , Jernigan Wyatt A. , Zhang Ziliang , Eddy William C. , DeLucia Evan H. , Yang Wendy H.
Published: November 2023

High spatiotemporal variability in soil nitrous oxide (N2O) fluxes challenges quantification and prediction of emissions to evaluate the climate change mitigation outcomes of sustainable agricultural practices. Triggers for large, short-lived N2O emission pulses, such as rainfall and fertilization, alter soil oxygen (O2) and nitrate (NO3−) availability to favor N2O production via denitrification. However, the organic C (OC) needed to fuel denitrification may exhibit subfield variation that constrains the potential for high denitrification rates to occur, leading to spatial variation in N2O hot moments. We tested the hypothesis that the particulate organic matter (POM) fraction of soil organic matter controls subfield variation in denitrification potential by regulating availability of dissolved organic C (DOC), the form of OC used by denitrifiers. Among 20 soil samples collected across a maize field in central Illinois, USA, we found that potential denitrification rate was best predicted by POM C concentration (R2= 0.35). Using multiple linear regression analysis that included other soil properties as explanatory variables, we found that POM C fraction of bulk soil (mg POM C g−1SOC) was the most important predictor based on regression coefficient size (P < 0.01). Our results, which provide support for our hypothesis, suggest that consideration of the link between C and N cycling may be a key to predicting spatiotemporal variation in soil N2O emissions when denitrification is the dominant N2O source process.
scSemiProfiler: Advancing Large-scale Single-cell Studies through Semi-profiling with Deep Generative Models and Active Learning
Authors: Wang Jingtao , Fonseca Gregory , Ding Jun
Published: November 2023

Abstract

Single-cell sequencing is a crucial tool for dissecting the cellular intricacies of complex diseases. Its prohibitive cost, however, hampers its application in expansive biomedical studies. Traditional cellular deconvolution approaches can infer cell type proportions from more affordable bulk sequencing data, yet they fall short in providing the detailed resolution required for single-cell-level analyses. To overcome this challenge, we introduce “scSemiProfiler”, an innovative computational framework that marries deep generative models with active learning strategies. This method adeptly infers single-cell profiles across large cohorts by fusing bulk sequencing data with targeted single-cell sequencing from a few rigorously chosen representatives. Extensive validation across heterogeneous datasets verifies the precision of our semi-profiling approach, aligning closely with true single-cell profiling data and empowering refined cellular analyses. Originally developed for extensive disease cohorts, “scSemiProfiler” is adaptable for broad applications. It provides a scalable, cost-effective solution for single-cell profiling, facilitating in-depth cellular investigation in various biological domains.
Genetic labeling of embryonically-born dentate granule neurons in young mice using thePenkCremouse line
Authors: Mortessagne Pierre , Cartier Estelle , Balia Maddalena , Fèvre Murielle , Corailler Fiona , Herry Cyril , Abrous Djoher Nora , Battefeld Arne , Pacary Emilie
Published: November 2023

The dentate gyrus (DG) of the hippocampus is a mosaic of dentate granule neurons (DGNs) accumulated throughout life. While many studies focused on the morpho-functional properties of adult-born DGNs, much less is known about DGNs generated during development, and in particular those born during embryogenesis. One of the main reasons for this gap is the lack of methods available to specifically label and manipulate embryonically-born DGNs. Here, we have assessed the relevance of thePenkCremouse line as a genetic model to target this embryonically-born population. In young animals,PenkCreexpression allows to tag neurons in the DG with positional, morphological and electrophysiological properties characteristic of DGNs born during the embryonic period. In addition, PenkCre+ cells in the DG are distributed in both blades along the entire septo-temporal axis. This model thus offers new possibilities to explore the functions of this underexplored population of embryonically-born DGNs.
Fast and efficient root phenotyping via pose estimation
Authors: Berrigan Elizabeth M. , Wang Lin , Carrillo Hannah , Echegoyen Kimberly , Kappes Mikayla , Torres Jorge , Ai-Perreira Angel , McCoy Erica , Shane Emily , Copeland Charles D. , Ragel Lauren , Georgousakis Charidimos , Lee Sanghwa , Reynolds Dawn , Talgo Avery , Gonzalez Juan , Zhang Ling , Rajurkar Ashish B. , Ruiz Michel , Daniels Erin , Maree Liezl , Pariyar Shree , Busch Wolfgang , Pereira Talmo D.
Published: November 2023

Image segmentation is commonly used to estimate the location and shape of plants and their external structures. Segmentation masks are then used to localize landmarks of interest and compute other geometric features that correspond to the plant’s phenotype. Despite its prevalence, segmentation-based approaches are laborious (requiring extensive annotation to train), and error-prone (derived geometric features are sensitive to instance mask integrity). Here we present a segmentation-free approach which leverages deep learning-based landmark detection and grouping, also known as pose estimation. We use a tool originally developed for animal motion capture called SLEAP (Social LEAP Estimates Animal Poses) to automate the detection of distinct morphological landmarks on plant roots. Using a gel cylinder imaging system across multiple species, we show that our approach can reliably and efficiently recover root system topology at high accuracy, few annotated samples, and faster speed than segmentation-based approaches. In order to make use of this landmark-based representation for root phenotyping, we developed a Python library (sleap-roots) for trait extraction directly comparable to existing segmentation-based analysis software. We show that landmark-derived root traits are highly accurate and can be used for common downstream tasks including genotype classification and unsupervised trait mapping. Altogether, this work establishes the validity and advantages of pose estimation-based plant phenotyping. To facilitate adoption of this easy-to-use tool and to encourage further development, we makesleap-roots, all training data, models, and trait extraction code available at:https://github.com/talmolab/sleap-rootsandhttps://osf.io/k7j9g/.
Re-drawing Köppen-Geiger classes with microclimate: implications for nature and society
Authors: Klinges David H. , Maclean Ilya M. D. , Scheffers Brett R.
Published: November 2023

Scientists have long categorized the planet’s climate using the Köppen-Geiger (KG) classification to understand climate change impacts, biogeographical realms, agricultural suitability, and conservation. However, global KG maps primarily rely on macroclimate data collected by weather stations, which may not represent microclimatic conditions experienced by most life on Earth. Few studies have explored microclimate at broad scales, largely due to data and computational constraints. Here, we predicted KG classes separately from macroclimate and microclimate for over 32 million locations across six continents. Microclimate reclassified 38% of the total area, and microclimate KG classes were both more spatially variable, and encompassed a broader range of latitudes, relative to macroclimate KG classes. By redrawing the lines of climate classes, our study prompts a reevaluation of the importance of meteorological drivers of ecology across scales, shedding light on how natural, agricultural, and social systems experience and respond to global change.
Multi-parametric MRI can detect enhanced myelination in theGli1-/-mouse brain
Authors: Lee Choong H. , Holloman Mara , Salzer James L. , Zhang Jiangyang
Published: November 2023

This study investigated the potential of combining multiple MR parameters to enhance the characterization of myelin in the mouse brain. We collectedex vivomulti-parametric MR data at 7 Tesla from control andGli1−/−mice; the latter exhibit enhanced myelination at postnatal day 10 (P10) in the corpus callosum and cortex. The MR data included relaxivity, magnetization transfer, and diffusion measurements, each targeting distinct myelin properties. This analysis was followed by and compared to myelin basic protein (MBP) staining of the same samples. Although a majority of the MR parameters included in this study showed significant differences in the corpus callosum between the control andGli1−/−mice, only T2, T1/T2,and radial diffusivity (RD) demonstrated a significant correlation with MBP values. Based on data from the corpus callosum, partial least square regression suggested that combining T2, T1/T2, and inhomogeneous magnetization transfer ratio could explain approximately 80% of the variance in the MBP values. Myelin predictions based on these three parameters yielded stronger correlations with the MBP values in the P10 mouse brain corpus callosum than any single MR parameter. In the motor cortex, combining T2, T1/T2,and radial kurtosis could explain over 90% of the variance in the MBP values at P10. This study demonstrates the utility of multi-parametric MRI in improving the detection of myelin changes in the mouse brain.
A Synthetic Cytotoxic T cell Platform for Rapidly Prototyping TCR Function
Authors: Sharma Govinda , Round James , Teng Fei , Ali Zahra , May Chris , Yung Eric , Holt Robert A.
Published: November 2023

Current tools for functionally profiling T cell receptors with respect to cytotoxic potency and cross-reactivity are hampered by difficulties in establishing model systems to test these proteins in the contexts of different HLA alleles and against broad arrays of potential antigens. We have implemented and validated a granzyme-activatable sensor of T cell cytotoxicity in a novel universal prototyping platform which enables facile recombinant expression of any combination of TCR-, peptide-, and class I MHC-coding sequences and direct assessment of resultant responses. This system consists of an engineered cell platform based on the immortalized natural killer cell line, YT-Indy, and the MHC-null antigen-presenting cell line, K562. These cells were engineered using contemporary gene-editing techniques to furnish the YT-Indy/K562 pair with appropriate protein domains required for recombinant TCR expression and function in a non-T cell chassis, integrate a fluorescence-based target-centric early detection reporter of cytotoxic function, and deploy a set of protective genetic interventions designed to preserve antigen-presenting cells for subsequent capture and downstream characterization. Our data show successful reconstitution of the surface TCR complex in the YT-Indy cell line at biologically relevant levels. We also demonstrate successful induction and highly sensitive detection of antigen-specific response in multiple distinct model TCRs, with significant responses (p < 0.05 and Cohen’sd>1.9) in all cases. Additionally, we monitored destruction of targets in co-culture and found that our survival-optimized system allowed for complete preservation after 24-hour exposure to cytotoxic effectors. With this bioplatform, we anticipate investigators will be empowered to rapidly express and characterize T cell receptor responses, generate new knowledge regarding the patterns of T cell receptor recognition, and optimize novel therapeutic T cell receptors for improved cytotoxic potential and reduced cross-reactivity to undesired antigenic targets.