bluuebunny/crossref_metadata_2025 huggingface dataset:
Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar
Authors: Grabowski Paul P , Dang Phat , Jenkins Jerry J , Sreedasyam Avinash , Webber Jenell , Lamb Marshall , Zhang Qiong , Sanz-Saez Alvaro , Feng Yucheng , Bunting Victoria , Talag Jayson , Clevenger Josh , Ozias-Akins Peggy , Holbrook C Corley , Chu Ye , Grimwood Jane , Schmutz Jeremy , Chen Charles , Lovell John T
Published: September 2024

Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for “Line8,” a peanut genotype bred from drought-tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy.
Efflux of TolC protein to different antimicrobials can be replaced by other outer membrane proteins with similar β-barrel structures in extraintestinal pathogenic Escherichia coli
Authors: Bao Xue , Yang Chenglong , Li Tian , Wang Yanlin , Cui Ailian , Meng Xianrong , Huang Qi , Li Shaowen
Published: September 2024

Aim

As a major efflux pump system in Gram-negative bacteria, AcrAB-TolC plays a key role in the transport of multiple drug substrates and is considered a potential target for the development of novel antimicrobials. Our previous study found that TolC inactivation compromised the resistance to different antimicrobials in porcine extraintestinal pathogenic Escherichia coli (ExPEC) strain PPECC042 (WT). This study was designed to investigate the functional substitution of TolC by other outer membrane proteins (OMPs) with similar β-barrel structures in pumping out different antimicrobials.

Methods and results

In this study, we found that over-expression of several OMPs with similar β-barrel structures, OmpX, OmpC, OmpN, OmpW, and PhoE, in the ΔtolC strain restored the resistance to macrolides, quinolones, or tetracyclines to the level of WT strain. However, the introduction of any one of the five OMPs did not affect the resistance of the strains ΔacrA, ΔacrB, and ΔacrAΔtolC. Further study revealed that the efflux activity was significantly reduced in the ΔtolC strain, but not in the WT strain and the ΔtolC strains over-expressing various OMPs. Additionally, Nile red dye test and ciprofloxacin accumulation test confirmed that the lost efflux activity and drug accumulation in bacterial periplasm by TolC inactivation was restored by the over-expression of each OMP, depending on the presence of genes acrA and acrB.

Conclusion

All five OMPs can replace the TolC protein to play the efflux role in pumping out the drugs from the periplasm to the extracellular space with the help of proteins AcrA and AcrB.
Foucauldian critical thinking: An antithesis to technicization
Authors: Li Yulong , Liu Xiaojing
Published: September 2024

Challenging the way critical thinking is often considered a skill, this article explores possible discursive reasons for the skill-orientation and technicization of this concept. First, using Michel Foucault’s ‘division and rejection’ theory as a discursive analytical lens, the discussion explores the neoliberal alliance of international organizations, national governmental authorities, the media, job markets, schools, and concerned parents. It explores how this alliance promotes the discourse of skill and competence, and prepares the ground for critical thinking’s technicization. Drawing further on Foucault’s decoding of human capital as the essence of neoliberalism, the article explores the way that the technicization of critical thinking fits with a conception of human beings as a complex mix of production and consumption, where, as homo economicus, they become entrepreneurs of themselves. Second, in the light of Foucault’s discursive analytical conception of the will to truth, the article traces a possible historical underpinning of critical thinking’s technicization. It argues that power-knowledge, the dark side of Enlightenment technological rationality, creates an increasingly technical conception of the world that tampers with the criticality of critical thinking. If critical thinking does not render people aware of the power impinging on them, it loses its value and meaning. The article proposes that critical thinking should rather be conceived along the lines of a Foucauldian conception of critique: the art of not being governed, which takes inspiration from Kant’s conception of enlightenment. It explores how to practise Foucauldian critical thinking, how Foucault’s technology of the self can be enacted as the protector of subjectivity against the governmentality of power.
The progenitor star of SN 2023ixf: a massive red supergiant with enhanced, episodic pre-supernova mass loss
Authors: Qin Yu-Jing , Zhang Keming , Bloom Joshua , Sollerman Jesper , Zimmerman Erez A , Irani Ido , Schulze Steve , Gal-Yam Avishay , Kasliwal Mansi , Coughlin Michael W , Perley Daniel A , Fremling Christoffer , Kulkarni Shrinivas
Published: September 2024

We identify the progenitor star of SN 2023ixf in Messier 101 using Keck/NIRC2 adaptive optics imaging and pre-explosion Hubble Space Telescope (HST)/Advanced Camera for Surveys (ACS) images. The supernova, localized with diffraction spikes and high-precision astrometry, unambiguously coincides with a progenitor candidate of $m_\text{F814W}=24.87\pm 0.05$ (AB). Given its reported infrared excess and semiregular variability, we fit a time-dependent spectral energy distribution (SED) model of a dusty red supergiant (RSG) to a combined data set of HST optical, ground-based near-infrared, and Spitzer Infrared Array Camera (IRAC) [3.6], [4.5] photometry. The progenitor resembles an RSG of $T_\text{eff}=3488\pm 39$ K and $\log (L/\mathrm{L}_\odot)=5.15\pm 0.02$, with a $0.13\pm 0.01$ dex ($31.1\pm 1.7$ per cent) luminosity variation at a period of $P=1144.7\pm 4.8$ d, obscured by a dusty envelope of $\tau =2.92\pm 0.02$ at $1\, \mu \text{m}$ in optical depth (or $A_\text{V}=8.43\pm 0.11$ mag). The signatures match a post-main-sequence star of $18.2_{-0.6}^{+1.3}\, \mathrm{M}_\odot$ in zero-age main-sequence mass, among the most massive SN II progenitor, with a pulsation-enhanced mass-loss rate of $\dot{M}=(4.32\pm 0.26)\times 10^{-4} \, \mathrm{M}_\odot \, \text{yr}^{-1}$. The dense and confined circumstellar material is ejected during the last episode of radial pulsation before the explosion. Notably, we find strong evidence for variations of $\tau$ or $T_\text{eff}$ along with luminosity, a necessary assumption to reproduce the wavelength-dependent variability, which implies periodic dust sublimation and condensation. Given the observed SED, partial dust obscuration remains possible, but any unobstructed binary companion over $5.6\, \mathrm{ M}_\odot$ can be ruled out.
Extreme-value modelling of the brightest galaxies at z ≳ 9
Authors: Heather Cameron , Chantavat Teeraparb , Chongchitnan Siri , Silk Joseph
Published: September 2024

Data from the JWST have revealed an intriguing population of bright galaxies at high redshifts. In this work, we use extreme-value statistics to calculate the distribution [in ultraviolet (UV) magnitude] of the brightest galaxies in the redshift range $9 \lesssim z \lesssim 16$. We combine the generalized extreme-value approach with modelling of the galaxy luminosity function. We obtain predictions of the brightest galaxies for a suite of luminosity functions, including the Schechter and double power-law functions, as well as a model parametrized by the stellar formation efficiency $f_*$. We find that the JWST data are broadly consistent with $f_*$ of $5\!\!-\!\!10{{\ \rm per\, cent}}$, and that the brightest galaxy at $z\sim 16$ will have $M_{\rm UV}\approx -23.5^{0.8}_{0.4}$. If $f_*$ is dependent on halo mass, we predict $M_{\rm UV}\approx -22.5^{0.5}_{1.5}$ for such an object. We show that extreme-value statistics not only predict the magnitude of the brightest galaxies at high redshifts, but may also be able to distinguish between models of star formation in high-redshift galaxies.
Asteroseismic signatures of core magnetism and rotation in hundreds of low-luminosity red giants
Authors: Hatt Emily J , Ong J M Joel , Nielsen Martin B , Chaplin William J , Davies Guy R , Deheuvels Sébastien , Ballot Jérôme , Li Gang , Bugnet Lisa
Published: September 2024

Red giant stars host solar-like oscillations which have mixed character, being sensitive to conditions both in the outer convection zone and deep within the interior. The properties of these modes are sensitive to both core rotation and magnetic fields. While asteroseismic studies of the former have been done on a large scale, studies of the latter are currently limited to tens of stars. We aim to produce the first large catalogue of both magnetic and rotational perturbations. We jointly constrain these parameters by devising an automated method for fitting the power spectra directly. We successfully apply the method to 302 low-luminosity red giants. We find a clear bimodality in core rotation rate. The primary peak is at $\delta \nu _{\mathrm{rot}}$ = 0.32 $\mu$Hz, and the secondary at $\delta \nu _{\mathrm{rot}}$ = 0.47 $\mu$Hz. Combining our results with literature values, we find that the percentage of stars rotating much more rapidly than the population average increases with evolutionary state. We measure magnetic splittings of 2$\sigma$ significance in 23 stars. While the most extreme magnetic splitting values appear in stars with masses $\gt $1.1 M$_{\odot }$, implying they formerly hosted a convective core, a small but statistically significant magnetic splitting is measured at lower masses. Asymmetry between the frequencies of a rotationally split multiplet has previously been used to diagnose the presence of a magnetic perturbation. We find that of the stars with a significant detection of magnetic perturbation, 43 per cent do not show strong asymmetry. We find no strong evidence of correlation between the rotation and magnetic parameters.
The VISCACHA Survey – XI. Benchmarking SIESTA: a new synthetic CMD fitting code
Authors: Ferreira Bernardo P L , Jr. João F C Santos , Dias Bruno , Maia Francisco F S , Kerber Leandro O , Gardin João Francisco , Oliveira Raphael A P , Westera Pieter , Rocha João Pedro S , Souza Stefano O , Hernandez-Jimenez Jose A , Santrich Orlando Katime , Villegas Angeles Pérez , Garro Elisa R , Baume Gustavo L , Fernández-Trincado José G , de Bórtoli Bruno , Parisi Maria Celeste , Bica Eduardo
Published: September 2024

We present a novel code, named SIESTA (Statistical matchIng between rEal and Synthetic sTellar popuLations), designed for performing statistical isochrone fitting to colour–magnitude diagrams (CMDs) of single stellar populations by leveraging comparisons between the observed stellar distribution and predictions from synthetic populations, simulated on top of a grid of isochrones. These synthetic populations encompass determinant factors such as the cluster’s initial mass function (IMF), the presence of non-resolved binaries, as well as the expected photometric errors, and observational completeness (or the observed luminosity function). Employing Markov Chain Monte Carlo within a Bayesian framework, SIESTA allows for the determination of a cluster’s age, metallicity, distance, colour excess, and binary fraction (with masses exceeding a certain ratio). In this study, we rigorously benchmark the SIESTA code utilizing synthetic populations and evaluate its performance against observations from the VISCACHA Survey in the Small Magellanic Cloud, focusing on five star clusters: Lindsay 114, NGC 152, Lindsay 91, Lindsay 113, and NGC 121. These clusters were chosen for their diverse age range, spanning from 0.04 to 10 Gyr. Our findings demonstrate the capability of the SIESTA code to accurately represent the observed CMDs of these clusters. Furthermore, we compare the results obtained with SIESTA to previous characterizations of these clusters, highlighting the consistency between the derived metallicity and spectroscopic determinations from various sources.
Identification of transcription factor co-binding patterns with non-negative matrix factorization
Authors: Rauluseviciute Ieva , Launay Timothée , Barzaghi Guido , Nikumbh Sarvesh , Lenhard Boris , Krebs Arnaud Regis , Castro-Mondragon Jaime A , Mathelier Anthony
Published: September 2024

Transcription factor (TF) binding to DNA is critical to transcription regulation. Although the binding properties of numerous individual TFs are well-documented, a more detailed comprehension of how TFs interact cooperatively with DNA is required. We present COBIND, a novel method based on non-negative matrix factorization (NMF) to identify TF co-binding patterns automatically. COBIND applies NMF to one-hot encoded regions flanking known TF binding sites (TFBSs) to pinpoint enriched DNA patterns at fixed distances. We applied COBIND to 5699 TFBS datasets from UniBind for 401 TFs in seven species. The method uncovered already established co-binding patterns and new co-binding configurations not yet reported in the literature and inferred through motif similarity and protein-protein interaction knowledge. Our extensive analyses across species revealed that 67% of the TFs shared a co-binding motif with other TFs from the same structural family. The co-binding patterns captured by COBIND are likely functionally relevant as they harbor higher evolutionarily conservation than isolated TFBSs. Open chromatin data from matching human cell lines further supported the co-binding predictions. Finally, we used single-molecule footprinting data from mouse embryonic stem cells to confirm that the COBIND-predicted co-binding events associated with some TFs likely occurred on the same DNA molecules.
The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site
Authors: Turnbull Kathryn , Paternoga Helge , von der Weth Esther , Egorov Artyom A , Pochopien Agnieszka A , Zhang Yujie , Nersisyan Lilit , Margus Tõnu , Johansson Marcus J O , Pelechano Vicent , Wilson Daniel N , Hauryliuk Vasili
Published: September 2024

The efficiency of translation termination is determined by the nature of the stop codon as well as its context. In eukaryotes, recognition of the A-site stop codon and release of the polypeptide are mediated by release factors eRF1 and eRF3, respectively. Translation termination is modulated by other factors which either directly interact with release factors or bind to the E-site and modulate the activity of the peptidyl transferase center. Previous studies suggested that the Saccharomyces cerevisiae ABCF ATPase New1 is involved in translation termination and/or ribosome recycling, however, the exact function remained unclear. Here, we have applied 5PSeq, single-particle cryo-EM and readthrough reporter assays to provide insight into the biological function of New1. We show that the lack of New1 results in ribosomal stalling at stop codons preceded by a lysine or arginine codon and that the stalling is not defined by the nature of the C-terminal amino acid but rather by the identity of the tRNA isoacceptor in the P-site. Collectively, our results suggest that translation termination is inefficient when ribosomes have specific tRNA isoacceptors in the P-site and that the recruitment of New1 rescues ribosomes at these problematic termination contexts.
Machine learning unravels inherent structural patterns in Escherichia coli Hi-C matrices and predicts chromosome dynamics
Authors: Bera Palash , Mondal Jagannath
Published: September 2024

High dimensional nature of the chromosomal conformation contact map (‘Hi-C Map’), even for microscopically small bacterial cell, poses challenges for extracting meaningful information related to its complex organization. Here we first demonstrate that an artificial deep neural network-based machine-learnt (ML) low-dimensional representation of a recently reported Hi-C interaction map of archetypal bacteria Escherichia coli can decode crucial underlying structural pattern. The ML-derived representation of Hi-C map can automatically detect a set of spatially distinct domains across E. coli genome, sharing reminiscences of six putative macro-domains previously posited via recombination assay. Subsequently, a ML-generated model assimilates the intricate relationship between large array of Hi-C-derived chromosomal contact probabilities and respective diffusive dynamics of each individual chromosomal gene and identifies an optimal number of functionally important chromosomal contact-pairs that are majorly responsible for heterogenous, coordinate-dependent sub-diffusive motions of chromosomal loci. Finally, the ML models, trained on wild-type E. coli show-cased its predictive capabilities on mutant bacterial strains, shedding light on the structural and dynamic nuances of ΔMatP30MM and ΔMukBEF22MM chromosomes. Overall our results illuminate the power of ML techniques in unraveling the complex relationship between structure and dynamics of bacterial chromosomal loci, promising meaningful connections between ML-derived insights and biological phenomena.
Structural basis for the concerted antiphage activity in the SIR2–HerA system
Authors: Liao Fumeng , Yu Guimei , Zhang Chendi , Liu Zhikun , Li Xuzichao , He Qiuqiu , Yin Hang , Liu Xiang , Li Zhuang , Zhang Heng
Published: September 2024

Recently, a novel two-gene bacterial defense system against phages, encoding a SIR2 NADase and a HerA ATPase/helicase, has been identified. However, the molecular mechanism of the bacterial SIR2–HerA immune system remains unclear. Here, we determine the cryo-EM structures of SIR2, HerA and their complex from Paenibacillus sp. 453MF in different functional states. The SIR2 proteins oligomerize into a dodecameric ring-shaped structure consisting of two layers of interlocked hexamers, in which each subunit exhibits an auto-inhibited conformation. Distinct from the canonical AAA+ proteins, HerA hexamer alone in this antiphage system adopts a split spiral arrangement, which is stabilized by a unique C-terminal extension. SIR2 and HerA proteins assemble into a ∼1.1 MDa torch-shaped complex to fight against phage infection. Importantly, disruption of the interactions between SIR2 and HerA largely abolishes the antiphage activity. Interestingly, binding alters the oligomer state of SIR2, switching from a dodecamer to a tetradecamer state. The formation of the SIR2–HerA binary complex activates NADase and nuclease activities in SIR2 and ATPase and helicase activities in HerA. Together, our study not only provides a structural basis for the functional communications between SIR2 and HerA proteins, but also unravels a novel concerted antiviral mechanism through NAD+ degradation, ATP hydrolysis, and DNA cleavage.
ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation
Authors: Karlström Victor , Sagredo Eduardo A , Planells Jordi , Welinder Charlotte , Jungfleisch Jennifer , Barrera-Conde Andrea , Engfors Linus , Daniel Chammiran , Gebauer Fátima , Visa Neus , Öhman Marie
Published: September 2024

ADAR3 is a catalytically inactive member of the family of adenosine deaminases acting on RNA (ADARs). Here we have investigated its function in the context of the developing mouse brain. The expression of ADAR3 gradually increases throughout embryogenesis and drops after birth. Using primary cortical neurons, we show that ADAR3 is only expressed in a subpopulation of in vitro differentiated neurons, which suggests specific functions rather than being a general regulator of ADAR editing in the brain. The analysis of the ADAR3 interactome suggested a role in mRNA stability and translation, and we show that expression of ADAR3 in a neuronal cell line that is otherwise ADAR3-negative changes the expression and stability of a large number of mRNAs. Notably, we show that ADAR3 associates with polysomes and inhibits translation. We propose that ADAR3 binds to target mRNAs and stabilizes them in non-productive polysome complexes. Interestingly, the expression of ADAR3 downregulates genes related to neuronal differentiation and inhibits neurofilament outgrowth in vitro. In summary, we propose that ADAR3 negatively regulates neuronal differentiation, and that it does so by regulating mRNA stability and translation in an editing-independent manner.
Modulation of dynamic DNA G-quadruplex structures in the hTERT promoter region by ligands
Authors: Karna Deepak , Liang Lin , Sharma Grinsun , Mandal Shankar , Asamitsu Sefan , Kawamoto Yusuke , Hashiya Kaori , Bando Toshikazu , Sugiyama Hiroshi , Mao Hanbin
Published: September 2024

Small molecules can inhibit cellular processes such as replication and transcription by binding to the promoter regions that are prone to form G-quadruplexes. However, since G-quadruplexes exist throughout the human genome, the G-quadruplex binders suffer from specificity issues. To tackle this problem, a G-quadruplex binder (Pyridostatin, or PDS) is conjugated with a ligand (Polyamide, or PA) that can specifically recognize DNA sequences flanking the G-quadruplex forming region. The binding mechanism of this hybrid ligand to the hTERT promoter region (hTERT 5–12) is then elucidated using optical tweezers. During mechanical unfolding processes, different intermediate structures of hTERT 5–12 in presence of PDS, PA, or PA-PDS conjugate are observed. These intermediate structures are consistent with two folding patterns of G-quadruplexes in the hTERT 5–12 fragment. While the duplex DNA binder PA facilitates the folding of a hairpin-G-quadruplex structure, the PDS assists the formation of two tandem G-quadruplexes. Both replication stop assay in vitro and dual luciferase assay in vivo established the effectiveness of the PA-PDS conjugate for hTERT 5–12 targeting. We expect such a ligand dependent folding dynamics will provide guidelines to the development of drugs that not only target hTERT expressions, but also other oncogenes via interactions with specific G-quadruplex structures formed in their promotor regions.
PARP1-TRIM44-MRN loop dictates the response to PARP inhibitors
Authors: Kim Yonghyeon , Min Sunwoo , Kim Soyeon , Lee Seo Yun , Park Yeon-Ji , Heo Yungyeong , Park Soon Sang , Park Tae Jun , Lee Jae-Ho , Kang Ho Chul , Ji Jae-Hoon , Cho Hyeseong
Published: September 2024

PARP inhibitors (PARPi) show selective efficacy in tumors with homologous recombination repair (HRR)-defects but the activation mechanism of HRR pathway in PARPi-treated cells remains enigmatic. To unveil it, we searched for the mediator bridging PARP1 to ATM pathways by screening 211 human ubiquitin-related proteins. We discovered TRIM44 as a crucial mediator that recruits the MRN complex to damaged chromatin, independent of PARP1 activity. TRIM44 binds PARP1 and regulates the ubiquitination-PARylation balance of PARP1, which facilitates timely recruitment of the MRN complex for DSB repair. Upon exposure to PARPi, TRIM44 shifts its binding from PARP1 to the MRN complex via its ZnF UBP domain. Knockdown of TRIM44 in cells significantly enhances the sensitivity to olaparib and overcomes the resistance to olaparib induced by 53BP1 deficiency. These observations emphasize the central role of TRIM44 in tethering PARP1 to the ATM-mediated repair pathway. Suppression of TRIM44 may enhance PARPi effectiveness and broaden their use even to HR-proficient tumors.
The Serine Shunt enables formate conversion to formaldehyde in vivo
Authors: Schann Karin , Wenk Sebastian
Published: September 2024

Microbial valorization of CO2-derived substrates has emerged as a promising approach to address climate change and resource scarcity. Formate, which can be efficiently produced from CO2, shows great potential as a sustainable feedstock for biotechnological production. However, the scope of formate assimilation pathways is restricted by the limited number of natural formate-assimilating enzymes. To overcome this limitation, several new-to-nature routes for formate assimilation based on its reduction to formaldehyde have been proposed, but they suffer from low catalytic efficiencies and cannot yet support bacterial growth. Here, we propose the Serine Shunt as a novel formate reduction route and demonstrate its activity in vivo. In this pathway, formate is attached to glycine to form serine, which is subsequently cleaved into formaldehyde and glycine, thereby effectively converting formate to formaldehyde. Unlike other formate reduction routes, the Serine Shunt mainly utilizes natural reactions with favorable enzyme kinetics, while requiring the same amount of ATP and NADPH as the most efficient new-to-nature route. We implemented the Serine Shunt in engineered Escherichia coli strains using a stepwise approach by dividing the pathway into metabolic modules. After validating the individual module activities, we demonstrated the in vivo activity of the complete Serine Shunt by measuring intracellular formaldehyde production with a green fluorescent protein (GFP) sensor and coupling its activity to cell growth. Our results indicate that the Serine Shunt could be applied as a novel formate reduction route in methylotrophic hosts relevant for biotechnology.
Sample Size Impact (SaSii): an R script for estimating optimal sample sizes in population genetics and population genomics studies
Authors: Scaketti Matheus , Sujii Patricia Sanae , Alves-Pereira Alessandro , Schwarcz Kaiser Dias , Francisconi Ana Flávia , Moro Matheus Sartori , Martins Kauanne Karolline Moreno , de Jesus Thiago Araujo , de Souza Guilherme Brener Ferreira , Zucchi Maria Imaculada
Published: September 2024

Obtaining large sample sizes for genetic studies can be challenging, time-consuming, and expensive. However, small sample sizes may generate biased or imprecise results. Many studies have suggested the minimum sample size necessary to obtain robust and reliable results, but it is not possible to define one ideal minimum sample size that fits all studies. Here, we aim to present SaSii (Sample Size Impact), a R script to help researchers to define minimum sample size and to indicate minimum sample size patterns for some taxa groups. The patterns were obtained by analyzing previously published datasets with SaSii and can be used as a starting point for the sample design of population genetics and genomic studies. Our results showed that it is possible to estimate an adequate sample size that accurately represents the real population and does not require the scientist to take time to write any program code, extract and sequence samples or use population genetics programs, making it easier to gather this information. We also confirmed that sample sizes of five to twenty-five for SNP and fifteen to thirty for SSR can be used for most plant species, giving a better direction for new studies.
Deficiency in transmitter release triggers homeostatic transcriptional changes that increase presynaptic excitability
Authors: Cypranowska Caroline A , Bakshinska Dariya , Feldthouse Maya , Choi Yoon Gi , Li Rachel , Newman Zachary L , Isacoff Ehud Y
Published: September 2024

Weakening of synaptic transmission at the Drosophila larval neuromuscular junction triggers two forms of homeostatic compensation, one that increases the probability of glutamate release per action potential (Pr) and another that increases motoneuron (MN) activity. We investigated the molecular changes in MNs that underlie the increase in MN activity. RNA-seq analysis on MNs whose glutamate release is weakened by knockdown of components of the MN transmitter release machinery reveals a reduction in expression of a group of genes that encode potassium channels and their positive modulators. These results identify a mechanism of compensation for weakened synaptic transmission by MNs, which engages a transcriptional program in those cells to increase firing and, thereby, ensure sufficient locomotory drive.
Sec18 side-loading is essential for universal SNARE recycling across cellular contexts
Authors: Khan Yousuf A. , White K. Ian , Pfuetzner Richard A. , Singal Bharti , Esquivies Luis , Mckenzie Garvey , Liu Fang , DeLong Katherine , Choi Uchoer B. , Montabana Elizabeth , Mclaughlin Theresa , Wickner William T. , Brunger Axel T.
Published: September 2024

SNARE proteins drive membrane fusion as their core domains zipper into a parallel four-helix bundle1,2. After fusion, these bundles are disassembled by the AAA+ protein Sec18/NSF and its adaptor Sec17/ α-SNAP3,4to make them available for subsequent rounds of membrane fusion. SNARE domains are often flanked by C-terminal transmembrane or N-terminal domains5. Previous structures of the NSF–α-SNAP–SNARE complex revealed SNARE domain threaded through the D1 ATPase ring6, posing a topological constraint as SNARE transmembrane domains would prevent complete substrate threading as suggested for other AAA+ systems7. Here,in vivomass-spectrometry reveals N-terminal SNARE domain interactions with Sec18, exacerbating this topological issue. Cryo-EM structures of a yeast SNARE complex, Sec18, and Sec17 in a non-hydrolyzing condition shows SNARE Sso1 threaded through the D1 and D2 ATPase rings of Sec18, with its folded, N-terminal Habc domain interacting with the D2 ring. This domain does not unfold during Sec18/NSF activity. Cryo-EM structures under hydrolyzing conditions revealed substrate-released and substrate-free states of Sec18 with a coordinated opening in the side of the ATPase rings. Thus, Sec18/NSF operates by substrate side-loading and unloading topologically constrained SNARE substrates.
Unbiased preclinical phenotyping reveals neuroprotective properties of pioglitazone
Authors: Harding Edward C. , Chen Hsiao-Jou Cortina , Shepilov Dmytro , Zhang Stefanie O. , Rowley Christine , Mali Iman , Chen Jiahui , Stewart Natasha , Swinden Dean , Washer Sam J. , Bassett Andrew R. , Merkle Florian T.
Published: September 2024

Animal models are essential for assessing the preclinical efficacy of candidate drugs, but animal data often fails to replicate in human clinical trials. This translational gulf is due in part to the use of models that do not accurately replicate human disease processes and phenotyping strategies that do not capture sensitive, disease-relevant measures. To address these challenges with the aim of validating candidate neuroprotective drugs, we combined a mouse prion (RML scrapie) model that recapitulates the key common features of human neurodegenerative disease including bona fide neuronal loss, with unbiased and machine learning-assisted behavioural phenotyping. We found that this approach measured subtle, stereotyped, and progressive changes in motor behaviour over the disease time course that correlated with the earliest detectable histopathological changes in the mouse brain. To validate the utility of this model system, we tested whether the anti-diabetic drug pioglitazone could slow prion disease progression. Pioglitazone crosses the blood-brain-barrier and has been shown to reduce neurodegenerative disease severity in other mouse models. We found that in addition to significantly slowing the emergence of early-stage clinical signs of neurodegeneration, pioglitazone significantly improved motor coordination throughout the disease time course and reduced neuronal endoplasmic reticulum stress. Together, these findings suggest that pioglitazone could have neuroprotective properties in humans, confirm the utility of the scrapie mouse model of neurodegeneration, and provide generalisable experimental and analysis methods for the generation of data-rich behavioural data to accelerate and improve preclinical validation.
Diversity and ecological roles of RNA viral communities in the cryosphere of the Tibetan Plateau
Authors: Liu Yongqin , Zhang Zhihao , Jiao Nianzhi , Zhu Yongguan , Zhang Rui , Dominguez-Huerta Guillermo , Wang Haina , Feng Meilin , Wen Rong , Ji Mukan , Zheng Qiang , Liu Pengfei , Yao Tandong
Published: September 2024

RNA viruses play crucial roles in modulating host communities, but their diversity and ecological roles in the cryosphere are poorly understood. We investigated the RNA virome from the cryosphere of the Tibetan Plateau (TPC), the largest area of the cryosphere in the mid-low latitude regions, which includes 79 metatranscriptomes from ecosystems including glaciers, proglacial lake sediments, permafrost wetland and upland soils. We obtained 8,799 RNA-dependent RNA polymerase encoding contigs, which clustered into 5,333 viral species, adding more than 4,900 new RNA viral species to the global RNA virome database. The recovered RNA viruses primarily infect prokaryotes, distinctively different from the dominance of eukaryotic RNA viruses in oceanic ecosystems. In addition to the known taxa such as Leviviricetes, we identified novel clades of putative prokaryotic RNA viruses, which greatly extended our understanding of their diversity. We further expanded the host of RNA virus by 20 additional prokaryotic phylum- or class-level taxonomic groups. Moreover, the TPC RNA viruses encoded dozens of auxiliary metabolic genes that could reprogram the metabolisms of diverse hosts, including photosynthesis in glacier eukaryotic algae and cyanobacteria, which may exert great impacts on glacier dynamics through modulating host adaptation. Furthermore, we identified potential pathogenic RNA viruses in various cryosphere environments, though their overall risks are low. This study provides the first comprehensive view of cryosphere RNA virome, highlighting their high diversity, vital ecological functions, and potential health impacts.
Cell morphology and gene expression: tracking changes and complementarity across time and cell lines
Authors: Lejal Vanille , Rouquié David , Taboureau Olivier
Published: September 2024

Effective drug discovery relies on combining target knowledge with functional assays and multi-omics data to understand chemicals’ molecular actions. However, the relationship between cell morphology and gene expression over time and across cell lines remains unclear. To explore this, we analyzed Cell Painting and L1000 data for 106 compounds across three cell lines from osteoblast, lung, and breast tumors (U2OS, A549, and MCF7) at three time points (6h, 24h, 48h) using a 10µM concentration. We found significant time and cell line effects in Cell Painting data, with less pronounced effects in transcriptomics. Using Weighted Gene Co-expression Network Analysis (WGCNA) and enrichment analysis, we identified connections between cell morphology and gene deregulation for chemicals with similar biological effects (e.g., HDAC and CDK inhibitors). These findings suggest that while Cell Painting shows distinct patterns, both technologies offer complementary insights into compound-induced cellular changes, enhancing drug discovery and chemical risk assessment.
A Benchmark for Virus Infection Reporter Virtual Staining in Fluorescence and Brightfield Microscopy
Authors: Wyrzykowska Maria , Maggiora Gabriel della , Deshpande Nikita , Mokarian Ashkan , Yakimovich Artur
Published: September 2024

Detecting virus-infected cells in light microscopy requires a reporter signal commonly achieved by immunohistochemistry or genetic engineering. While classification-based machine learning approaches to the detection of virus-infected cells have been proposed, their results lack the nuance of a continuous signal. Such a signal can be achieved by virtual staining. Yet, while this technique has been rapidly growing in importance, the virtual staining of virus-infected cells remains largely uncharted. In this work, we propose a benchmark and datasets to address this. We collate microscopy datasets, containing a panel of viruses of diverse biology and reporters obtained with a variety of magnifications and imaging modalities. Next, we explore the virus infection reporter virtual staining (VIRVS) task employing U-Net and pix2pix architectures as prototypical regressive and generative models. Together our work provides a comprehensive benchmark for VIRVS, as well as defines a new challenge at the interface of Data Science and Virology.
Learning is a fundamental source of behavioral individuality
Authors: Manna Riddha , Brea Johanni , Braga Gonçalo Vasconcelos , Modirshanechi Alireza , Tomić Ivan , Jakšić Ana Marija
Published: September 2024

Learning and memory are thought to be essential for our individual uniqueness and sense of self (1). Yet, individuality is rarely studied in the context of behaviors that depend on learning. While it is established that such behaviors can vary across individuals, it remains unknown whether their variation stems from learning or from classical sources of individuality, the de-velopmental stochasticity, environment and genetics (2–12). To answer this fundamental ques-tion, we measured behavior in thousands of flies in the presence and absence of learning, and compared the extent of their individuality. We discover an excess of non-normally distributed individual behavior only in flies that experienced learning, even though they were genetically identical, raised under the same conditions and exposed to the same environment as the non-learning flies. By tracking each fly’s decision-making process, we find that learning does not simply change individual behavior, but it also diversifies it. We could recreate the emergence of this excess of individuality using computer simulations of behaving flies only when we enabled reinforced learning. Although individual experience and genetics shaped behavioral biases, we demonstrated that behavior can diverge due to learning even in individuals that share biases. Our results thus establish learning as the fundamental source of individuality, rather than a phenotypic outcome of genetics, environment, or development.
Validation studies and multi-omics analysis of Zhx2 as a candidate quantitative trait gene underlying brain oxycodone metabolite (oxymorphone) levels and behavior
Authors: Lynch William B. , Miracle Sophia A. , Goldstein Stanley I. , Beierle Jacob A. , Bhandari Rhea , Gerhardt Ethan T. , Farnan Ava , Nguyen Binh-Minh , Wingfield Kelly K. , Kazerani Ida , Saavedra Gabriel A. , Averin Olga , Baskin Britahny M. , Ferris Martin T. , Reilly Christopher A. , Emili Andrew , Bryant Camron D.
Published: September 2024

Sensitivity to the subjective reinforcing properties of opioids has a genetic component and can predict addiction liability of opioid compounds. We previously identifiedZhx2as a candidate gene underlying increased brain concentration of the oxycodone (OXY) metabolite oxymorphone (OMOR) in BALB/cJ (J) versus BALB/cByJ (By) females that could increase OXY state-dependent reward. A large structural intronic variant is associated with a robust reduction of Zhx2 expression in J mice, which we hypothesized enhances OMOR levels and OXY addiction-like behaviors. We tested this hypothesis by restoring theZhx2loss-of-function in Js (MVKO) and modeling the loss-of-function variant through knocking out theZhx2coding exon (E3KO) in Bys and assessing brain OXY metabolite levels and behavior. Consistent with our hypothesis, Zhx2 E3KO females showed an increase in brain OMOR levels and OXY-induced locomotor activity. However, contrary to our hypothesis, state-dependent expression of OXY-CPP was decreased in E3KO females and increased in E3KO males. We also overexpressed Zhx2 in the livers and brains of Js and observed Zhx2 overexpression in select brain regions that was associated with reduced OXY state-dependent learning. Integrative transcriptomic and proteomic analysis of E3KO mice identified astrocyte function, cell adhesion, extracellular matrix properties, and endothelial cell functions as pathways influencing brain OXY metabolite concentration and behavior. These results supportZhx2as a quantitative trait gene underlying brain OMOR concentration that is associated with changes in OXY behavior and implicate potential quantitative trait mechanisms that together inform our overall understanding ofZhx2in brain function.
Inhibition of Soluble Epoxide Hydrolase Ameliorates Cerebral Blood Flow Autoregulation and Cognition in Alzheimer’s Disease and Diabetes-Related Dementia Rat Models
Authors: Tang Chengyun , Border Jane J. , Zhang Huawei , Gregory Andrew , Bai Shan , Fang Xing , Liu Yedan , Wang Shaoxun , Hwang Sung Hee , Gao Wenjun , Morgan Gilbert C. , Smith Jhania , Bunn David , Cantwell Cameron , Wagner Karen M. , Morisseau Christophe , Yang Jun , Shin Seung Min , O’Herron Philip , Bagi Zsolt , Filosa Jessica A. , Dong Yanbin , Yu Hongwei , Hammock Bruce D. , Roman Richard J. , Fan Fan
Published: September 2024

Alzheimer’s Disease and Alzheimer’s Disease-related dementias (AD/ADRD) pose major global healthcare challenges, with diabetes mellitus (DM) being a key risk factor. Both AD and DM-related ADRD are characterized by reduced cerebral blood flow, although the exact mechanisms remain unclear. We previously identified compromised cerebral hemodynamics as early signs in TgF344-AD and type 2 DM-ADRD (T2DN) rat models. Genome-wide studies have linked AD/ADRD to SNPs in soluble epoxide hydrolase (sEH). This study explored the effects of sEH inhibition with TPPU on cerebral vascular function and cognition in AD and DM-ADRD models. Chronic TPPU treatment improved cognition in both AD and DM-ADRD rats without affecting body weight. In DM-ADRD rats, TPPU reduced plasma glucose and HbA1C levels. Transcriptomic analysis of primary cerebral vascular smooth muscle cells from AD rats treated with TPPU revealed enhanced pathways related to cell contraction, alongside decreased oxidative stress and inflammation. Both AD and DM-ADRD rats exhibited impaired myogenic responses and autoregulation in the cerebral circulation, which were normalized with chronic sEH inhibition. Additionally, TPPU improved acetylcholine-induced vasodilation in the middle cerebral arteries (MCA) of DM-ADRD rats. Acute TPPU administration unexpectedly caused vasoconstriction in the MCA of DM-ADRD rats at lower doses. In contrast, higher doses or longer durations were required to induce effective vasodilation at physiological perfusion pressure in both control and ADRD rats. Additionally, TPPU decreased reactive oxygen species production in cerebral vessels of AD and DM-ADRD rats. These findings provide novel evidence that chronic sEH inhibition can reverse cerebrovascular dysfunction and cognitive impairments in AD/ADRD, offering a promising avenue for therapeutic development.
Synaptic imbalance and increased inhibition impair motor function in SMA
Authors: Fletcher Emily V. , Chalif Joshua I. , Rotterman Travis M. , Pagiazitis John G. , Van Alstyne Meaghan , Sivakumar Nandhini , Rabinowitz Joseph E. , Pellizzoni Livio , Alvarez Francisco J. , Mentis George Z.
Published: September 2024

Movement is executed through the balanced action of excitatory and inhibitory neurotransmission in motor circuits of the spinal cord. Short-term perturbations in one of the two types of transmission are counteracted by homeostatic changes of the opposing type. Prolonged failure to balance excitatory and inhibitory drive results in dysfunction at the single neuron, as well as neuronal network levels. However, whether dysfunction in one or both types of neurotransmission leads to pathogenicity in neurodegenerative diseases characterized by select synaptic deficits is not known. Here, we used mouse genetics, functional assays, morphological methods, and viral-mediated approaches to uncover the pathogenic contribution of unbalanced excitation-inhibition neurotransmission in a mouse model of spinal muscular atrophy (SMA). We show that vulnerable motor circuits in the SMA spinal cord fail to respond homeostatically to the reduction of excitatory drive and instead increase inhibition. This imposes an excessive burden on motor neurons and further restricts their recruitment to activate muscle contraction. Importantly, genetic or pharmacological reduction of inhibitory synaptic drive improves neuronal function and provides behavioural benefit in SMA mice. Our findings identify the lack of excitation-inhibition homeostasis as a major maladaptive mechanism in SMA, by which the combined effects of reduced excitation and increased inhibition diminish the capacity of premotor commands to recruit motor neurons and elicit muscle contractions.
Computational model of primitive nervous system controlling chemotaxis in early multicellular heterotrophs
Authors: Vasilenko Egor O. , Sinitskiy Anton V.
Published: September 2024

Abstract

This paper presents a model to study a hypothetical role of a simple nervous systems in chemotaxis in early multicellular heterotrophs. The model views the organism as a network of motor units connected by flexible fibers and driven by realistic neuron excitation functions. Through numerical simulations, we identified the parameters that maximize the survival time of the modeled organism, focusing on its ability to efficiently locate and consume food. This synchronization enhances the ability of the modeled organism to navigate toward food and avoid harmful conditions. The model is described using basic mechanical principles and highlights the relationship between motor activity and energy balance. Our results suggest that even early prototypes of neural networks might provide significant survival advantages by optimizing movement and energy use. This study offers insights into how the first primitive nervous systems might have functioned. By publishing the code used in the simulations, we hope to contribute to the toolkit of computational methods and models used for exploration of neural origin and evolution.
Elimination of the neuroparsin neuroendocrine cells in Drosophila virilis using the UAS-Gal4 system shows that neuroparsin is not important for reproduction in this species.
Authors: Veenstra Jan Adrianus
Published: September 2024

Neuroparsin is a common insect neurohormone produced in large neuroendocrine cells in the brain and is important in mosquito reproduction. Although it is present in many flies including many Drosophila species, it was lost from D. melanogaster and a few closely related species. Three different lines of transgenic D. virilis were produced: One that expresses the yeast transcription factor gal4 under the control of the neuroparsin promoter (NP-gal4), while others codes for proteins under the control of the gal4 promoter, either enhanced green fluorescent protein (UAS-eGFP) or the D. virilis ortholog of reaper, an apoptosis inducing protein (UAS-rpr). Crosses between UAS-eGFP and NP-gal4 revealed that expression of NP-gal4 was correct. Crosses between UAS-rpr and NP-gal4 completely eliminated the neuroparsin neuroendocrine cells, but were without effect on reproduction.