bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying population resistance to climatic variability: The invasive spotted lanternfly grape pest is buffered against temperature extremes in California
Authors: Lewkiewicz Stephanie M. , Seibold Benjamin , Helmus Matthew R.
Published: December 2023

Temperature time series data are a composition of average trends and stochastic variability that together shape population dynamics. However, models of temperature-dependent species often overlook variability, focusing solely on growth rate under average conditions. When models omit variability, they can inaccurately predict the dynamics that underlie the establishment of invasive pests sensitive to temperature fluctuations. Here, we conduct a stochastic modeling study of spotted lanternfly (Lycorma delicatula), a univoltine grape pest, which has invaded grape growing regions of the eastern U.S. due to human transport leading to frequent establishment of populations in urban and suburban areas. As spotted lanternfly continues to be transported to new grape growing regions and climate change alters variability, it is vital to predict its establishment potential. Although it overwinters as diapausing eggs, experiments suggest that diapause is plastic and not necessary for survival. We developed a deterministic stage-age-structured partial differential equation model of diapausing and non-diapausing populations. We derived a new metric quantifying population resistance to climatic variability defined as the level of stochasticity that leads to negative growth compared to average conditions. We simulated growth rate and resistance to variability across a range of average temperature conditions and stochasticity. We then analyzed how variability and diapause interact with survival, fecundity, and development to affect population dynamics. Finally, we estimated establishment potential across all U.S. cities. Diapausing populations were typically more resistant than non-diapausing populations because diapause enhances overwintering egg survival during winter cold waves, while allowing accelerated development and increased fecundity during summer and fall heat waves. Establishment potential is especially underestimated in important grape growing regions of California if models of diapausing populations omit variability. By quantifying population resistance to climatic variability, we gain a fuller understanding of invasive species establishment in today’s stochastic and changing climate.
Biosynthesis of the proteins containing neurotoxinβ-N-methylamino-L-alanine in marine diatoms
Authors: Zheng Xianyao , Li Aifeng , Qiu Jiangbing , Yan Guowang , Zhao Peng , Li Min , Meng Fanping
Published: December 2023

Neurotoxinβ-N-methylamino-L-alanine (BMAA) has been deemed a pathogenic factor for human neurodegenerative diseases. It is an important issue to disclose the biosynthesis mechanism of BMAA in marine diatoms. In the present study, the iron (Fe) limitation (1/3 × Fe) was found to suppress the growth of diatoms but stimulate the production of BMAA-containing proteins, maximum 7.7 fold inThalassiosira minima. Transcriptome analysis showed that energy metabolism, protein biosynthesis and carbon fixation functions were mainly affected by the Fe limitation in the diatom. Analysis of subcellular distribution of BMAA showed that BMAA-containing proteins were mainly detected in the endoplasmic reticulum and the Golgi apparatus. Combination results of the responses of the diatom to Fe deficiency and co-culture with cyanobacteria in our previous study, we speculate that cysteine embedded in peptide chains and methylamine produced by the diatom itself are possibly catalyzed by the cysteine synthase (cysK) to form the BMAA structure in situ. Spiked methylamine in culture media significantly stimulated the production of BMAA, and BMAA amounts were correlated with the expression of cysK gene in different diatoms. The reduced ubiquitination-mediated proteolysis and vesicle trafficking precision through the COPII system would aggravate the accumulation of BMAA-containing proteins in the diatom.

Significance Statement

With the detection of neurotoxin BMAA in diverse marine diatoms, the pathogenic risk of BMAA has been further concerned to human neurodegenerative diseases such as Alzheimer’s disease. Interestingly, BMAA-containing proteins are the dominant forms of this neurotoxin in diatoms. It is a keystone issue to disclose the biosynthesis mechanism of BMAA in marine diatoms. We found Fe-limitation could stimulate the production of BMAA-containing proteins in diatoms and explored its biosynthesis using transcriptomics in this study. Results suggested that cysteine embedded in peptides and methylamine in cytoplasm were catalyzed by the cysteine synthase (cysK) to form BMAA. This study hints that the biosynthesis of BMAA would be improved by the worldwide prevalence of iron deficiency in the coastal waters.
A common regulatory switch controls a suite of C4 traits in multiple cell types
Authors: Camo-Escobar Daniel , Alcalá-Gutiérrez Carlos , Palafox-Figueroa Ernesto , Guillotin Bruno , Hernández-Coronado Marcela , Coyac-Rodríguez José L. , Cerbantez-Bueno Vincent E. , Vélez-Ramírez Aarón , de Folter Stefan , Birnbaum Kenneth D. , Ortiz-Ramírez Carlos
Published: December 2023

The C4 photosynthetic pathway provided a major advantage to plants growing in hot, dry environments, including the ancestors of our most productive crops. Two traits were essential for the evolution of this pathway: increased vein density and the functionalization of bundle sheath cells for photosynthesis. Although GRAS transcriptional regulators, including SHORT ROOT (SHR), have been implicated in mediating leaf patterning in both C3 and C4 species, little is known about what controls the specialized features of the cells that mediate C4 metabolism and physiology. We show in the model monocot,Setaria viridis, that SHR regulates components of multiple cell identities, including chloroplast biogenesis and photosynthetic gene expression in bundle sheath cells, a central feature of C4 plants. Furthermore, we found that it also contributes to the two-cell compartmentalization of the characteristic four-carbon shuttle pathway. Disruption of SHR function clearly reduced photosynthetic capacity and seed yield in mutant plants under heat stress. Together, these results show how cell identities are remodeled bySHRto host the suite of traits characteristic of C4 regulation, which are a main engineering target in non-C4 crops to improve climate resilience.
Development of a robotic cluster for automated and scalable cell therapy manufacturing
Authors: Melocchi Alice , Schmittlein Brigitte , Jones Alexis L. , Ainane Yasmine , Rizvi Ali , Chan Darius , Dickey Elaine , Pool Kelsey , Harsono Kenny , Szymkiewicz Dorothy , Scarfogliero Umberto , Bhatia Varun , Sivanantham Amlesh , Kreciglowa Nadia , Hunter Allison , Gomez Miguel , Tanner Adrian , Uboldi Marco , Batish Arpit , Balcerek Joanna , Kutova-Stoilova Mariella , Paruthiyil Sreenivasan , Acevedo Luis A. , Stadnitskiy Rachel , Carmichael Sabrina , Aulbach Holger , Hewitt Matthew , De Mollerat Du Jeu Xavier , Robilant Benedetta di , Parietti Federico , Esensten Jonathan H.
Published: December 2023

The production of commercial autologous cell therapies such as chimeric antigen receptor T cells requires complex manual manufacturing processes. Skilled labor costs and challenges in manufacturing scale-out have contributed to high prices for these products. Here, we present a robotic system that uses industry-standard cell therapy manufacturing equipment to automate the steps involved in cell therapy manufacturing. The robotic cluster consists of a robotic arm and customized modules, allowing the robot to manipulate a variety of standard cell therapy instruments and materials such as incubators, bioreactors, and reagent bags. This system enables existing manual manufacturing processes to be rapidly adapted to robotic manufacturing, without having to adopt a completely new technology platform. Proof-of-concept for the robotic cluster’s expansion module was demonstrated by activating and expanding human CD8+ T cells. The robotic cultures showed comparable cell yields, viability, and identity to those manually performed. Such modular robotic solutions may support scale-up and scale-out of cell therapies that are developed using classical manual methods in academic laboratories and biotechnology companies.
Grid cells perform path integration in multiple reference frames during self-motion-based navigation
Authors: Peng Jing-Jie , Throm Beate , Jazi Maryam Najafian , Yen Ting-Yun , Monyer Hannah , Allen Kevin
Published: December 2023

With their periodic firing pattern, grid cells are considered a fundamental unit of a neural network performing path integration. The periodic firing patterns of grid cells have been observed mainly during behaviors with little navigational demands, and the firing patterns of grid cells in animals navigating 2D environments using path integration are largely unknown. Here, we recorded the activity of grid cells in mice performing the AutoPI task, a task assessing homing based on path integration. Using artificial deep neural networks to decode the animal’s moment-to-moment movement vectors, we found that grid cells perform path integration over short trajectories and change their reference frames within single trials. More specifically, grid cell modules re-anchor to a task-relevant object via a translation of the grid pattern. The code for movement direction in grid modules drifts as the animal navigates using self-motion cues, and this drift predicts the homing direction of the mouse. These results reveal the computations in grid cell circuits during self-motion-based navigation.
Identification of ligands binding to MB327-PAM-1, a binding pocket relevant for resensitization of nAChRs
Authors: Kaiser Jesko , Gertzen Christoph G.W. , Bernauer Tamara , Nitsche Valentin , Höfner Georg , Niessen Karin V. , Seeger Thomas , Paintner Franz F. , Wanner Klaus T. , Steinritz Dirk , Worek Franz , Gohlke Holger
Published: December 2023

Desensitization of nicotinic acetylcholine receptors (nAChRs) can be induced by overstimulation with acetylcholine (ACh) caused by an insufficient degradation of ACh after poisoning with organophosphorus compounds (OPCs). Currently, there is no generally applicable treatment for OPC poisoning that directly targets the desensitized nAChR. The bispyridinium compound MB327, an allosteric modulator of nAChR, has been shown to act as a resensitizer of nAChRs, indicating that drugs binding directly to nAChRs can have beneficial effects after OPC poisoning. However, MB327 also acts as an inhibitor of nAChRs at higher concentrations and can thus not be used for OPC poisoning treatment. Consequently, novel, more potent resensitizers are required. To successfully design novel ligands, the knowledge of the binding site is of utmost importance. Recently, we performedin silicostudies to identify a new potential binding site of MB327, MB327-PAM-1, for which a more affine ligand, UNC0646, has been described. In this work, we performed ligand-based screening approaches to identify novel analogs of UNC0646 to help further understand the structure-affinity relationship of this compound class. Furthermore, we used structure-based screenings and identified compounds representing four new chemotypes binding to MB327-PAM-1. One of these compounds, cycloguanil, is the active metabolite of the antimalaria drug proguanil and shows a higher affinity towards MB327-PAM-1 than MB327. Furthermore, cycloguanil can reestablish the muscle force in soman-inhibited rat muscles. These results can act as a starting point to develop more potent resensitizers of nAChR and to close the gap in the treatment after OPC poisoning.
ETS1, a target gene of the EWSR1::FLI1 fusion oncoprotein, regulates the expression of the focal adhesion protein TENSIN3
Authors: Ebegboni Vernon Justice , Jones Tamara L. , Brownmiller Tayvia , Zhao Patrick X. , Pehrsson Erica C. , Sundara Rajan Soumya , Caplen Natasha J.
Published: December 2023

The mechanistic basis for the metastasis of Ewing sarcomas remains poorly understood, as these tumors harbor few mutations beyond the chromosomal translocation that initiates the disease. Instead, the epigenome of Ewing sarcoma (EWS) cells reflects the regulatory state of genes associated with the DNA binding activity of the fusion oncoproteins EWSR1::FLI1 or EWSR1::ERG. In this study, we examined the EWSR1::FLI1/ERG’s repression of transcription factor genes, concentrating on those that exhibit a broader range of expression in tumors than in EWS cell lines. Focusing on one of these target genes,ETS1, we detected EWSR1::FLI1 binding and an H3K27me3 repressive mark at this locus. Depletion of EWSR1::FLI1 results in ETS1’s binding of promoter regions, substantially altering the transcriptome of EWS cells, including the upregulation of the gene encoding TENSIN3 (TNS3), a focal adhesion protein. EWS cell lines expressing ETS1 (CRISPRa) exhibited increased TNS3 expression and enhanced movement compared to control cells. The cytoskeleton of control cells and ETS1-activated EWS cell lines also differed. Specifically, control cells exhibited a distributed vinculin signal and a network-like organization of F-actin. In contrast, ETS1-activated EWS cells showed an accumulation of vinculin and F-actin towards the plasma membrane. Interestingly, the phenotype of ETS1-activated EWS cell lines depleted of TNS3 resembled the phenotype of the control cells. Critically, these findings have clinical relevance asTNS3expression in EWS tumors positively correlates with that ofETS1.

Significance

ETS1’s transcriptional regulation of the gene encoding the focal adhesion protein TENSIN3 in Ewing sarcoma cells promotes cell movement, a critical step in the evolution of metastasis.

Graphical abstract
A novel framework to build saliva-based DNA methylation biomarkers: quantifying systemic chronic inflammation as a case study
Authors: Schmunk Lisa J. , Call Toby P. , McCartney Daniel L. , Javaid Hira , Hastings Waylon J. , Jovicevic Vanja , Kojadinović Dragoljub , Tomkinson Natacha , Zlamalova Eliska , McGee Kirsty C. , Sullivan Jack , Campbell Archie , McIntosh Andrew M , Óvári Veronika , Wishart Karl , Behrens Christian E. , Stone Emma , Gavrilov Miloš , Thompson Rob ,   Hurdle bio-infrastructure team, Jackson Thomas , Lord Janet M. , Stubbs Thomas M. , Marioni Riccardo E. , Martin-Herranz Daniel E.
Published: December 2023

Accessible and non-invasive biomarkers that measure human ageing processes and the risk of developing age-related disease are paramount in preventative healthcare. In this study, we describe a novel framework to train saliva-based DNA methylation (DNAm) biomarkers that are reproducible and biologically interpretable. By leveraging a reliability dataset with replicates across tissues, we demonstrate that it is possible to transfer knowledge from blood DNAm data to saliva DNAm data using DNAm proxies of blood proteins (EpiScores). We then apply these methods to create a new saliva-based epigenetic clock (InflammAge) that quantifies systemic chronic inflammation (SCI) in humans. Using a large blood DNAm human cohort with linked electronic health records and over 18,000 individuals (Generation Scotland), we demonstrate that InflammAge significantly associates with all-cause mortality, disease outcomes, lifestyle factors and immunosenescence; in many cases outperforming the widely used SCI biomarker C-reactive protein (CRP). We propose that our biomarker discovery framework and InflammAge will be useful to improve our understanding of the molecular mechanisms underpinning human ageing and to assess the impact of gero-protective interventions.
Human telomere length is chromosome specific and conserved across individuals
Authors: Karimian Kayarash , Groot Aljona , Huso Vienna , Kahidi Ramin , Tan Kar-Tong , Sholes Samantha , Keener Rebecca , McDyer John F. , Alder Jonathan K. , Li Heng , Rechtsteiner Andreas , Greider Carol W.
Published: December 2023

Short telomeres cause age-related disease and long telomeres predispose to cancer; however, the mechanisms regulating telomere length are unclear. To probe these mechanisms, we developed a nanopore sequencing method, Telomere Profiling, that is easy to implement, precise, and cost effective with broad applications in research and the clinic. We sequenced telomeres from individuals with short telomere syndromes and found similar telomere lengths to the clinical FlowFISH assay. We mapped telomere reads to specific chromosome end and identified both chromosome end-specific and haplotype-specific telomere length distributions. In the T2T HG002 genome, where the average telomere length is 5kb, we found a remarkable 6kb difference in lengths between some telomeres. Further, we found that specific chromosome ends were consistently shorter or longer than the average length across 147 individuals. The presence of conserved chromosome end-specific telomere lengths suggests there are new paradigms in telomere biology that are yet to be explored. Understanding the mechanisms regulating length will allow deeper insights into telomere biology that can lead to new approaches to disease.
Stable chromosome configuration and loop-based polarization in animal symbionts
Authors: Viehboeck Tobias , Weber Philipp M. , Krause Nicole , Varoquaux Nelle , Boccard Frédéric , Junier Ivan , Bulgheresi Silvia , Lioy Virginia S.
Published: December 2023

Chromosome partitioning precedes the division of the cytoplasm, and its evolution is linked with the positioning of the division plane. So far, bacterial chromosome biology has heavily focused on transversally dividing, free-living ones. Here, we determined the chromosome organization of three longitudinally dividingNeisseriaceaeexclusively inhabiting the oral cavity of mammals. We showed that in all three multicellular bacteria the origin of DNA replication is invariably located at the host-attached (proximal) pole. Next, 3C-seq revealed loop-based folding of theoriregion inAlysiella filiformisandSimonsiella muelleri. Moreover, genes involved in cell motility, piliation and signal transduction mechanisms were specifically looped when transcriptionally and translationally active cells adhered to a substrate, but not when cultured in liquid. Overall, we propose that proximal positioning of theoriand loop-based folding of its surrounding DNA may mediate localized translation of proteins involved in host colonization.
Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain
Authors: Navratna Vikas , Kumar Arvind , Rana Jaimin K. , Mosalaganti Shyamal
Published: December 2023

InC. elegans, inter-cellular transport of the small non-coding RNA causing systemic RNA interference (RNAi) is mediated by the transmembrane protein SID1, encoded by thesid1gene in the systemic RNA interference-defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the cholesterol uptake family (ChUP). Although systemic RNAi is not an evolutionarily conserved process, thesidgene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs ofsidgene products – hSIDT1 and hSIDT2 – mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra- cytosolic domain (ECD) of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain (TMD) exists as two modules – a flexible lipid binding domain (LBD) and a rigid TMD core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in cholesterol uptake (ChUP) family members.
Genotypic and Phenotypic Analyses of Two Distinct Sets ofPseudomonas aeruginosaUrinary Tract Isolates
Authors: Ebrahim HA , Haldenby S , Moore MP , Dashti AA , Floyd RV , Fothergill JL
Published: December 2023

Urinary tract infections (UTIs) are associated with a high burden of morbidity, mortality, and cost.Pseudomonas aeruginosaemploys a myriad of virulence factors, including biofilm formation and motility mechanisms, to cause infections including persistent UTIs.P. aeruginosais highly resistant to antibiotics and the World Health Organization has identified it as a pathogen for which novel antimicrobials are urgently required. Genotypic and phenotypic characterization ofP. aeruginosafrom UTIs are underreported. In addition, the rise of antimicrobial resistance (AMR) is a cause for concern, particularly in many countries where surveillance is severely lacking.

22P. aeruginosaUTI isolates were sourced from the United Kingdom (UK) and Kuwait. To establish the phenotypes of UK isolates, growth analysis, biofilm formation assays, motility assays, and antibiotic disc diffusion assays were performed. Whole genome sequencing, antimicrobial susceptibility assays, andin silicodetection of AMR-associated genes were conducted on both sets of isolates.

In terms of their phenotypic characteristics and genomic composition, the UTI isolates varied. Multiple resistance genes associated with resistance to various classes of antibiotics, such as aminoglycosides, fluoroquinolones, and β-lactams, particularly in isolates from Kuwait. Extreme antibiotic resistance was detected in the isolates obtained from Kuwait, indicating that the country may be an antibiotic resistance hotspot.

This study highlights that isolates from UTIs are diverse and can display extremely high resistance. Surveillance in countries such as Kuwait are currently limited and this study suggest the need for greater surveillance.
Fast inhibition slows and desynchronizes mouse auditory efferent neuron activity
Authors: Fischl Matthew , Pederson Alia , Voglewede Rebecca , Cheng Hui , Drew Jordan , Cadenas Lester Torres , Weisz Catherine J.C.
Published: December 2023

The encoding of acoustic stimuli requires precise neuron timing. Auditory neurons in the cochlear nucleus (CN) and brainstem are well-suited for accurate analysis of fast acoustic signals, given their physiological specializations of fast membrane time constants, fast axonal conduction, and reliable synaptic transmission. The medial olivocochlear (MOC) neurons that provide efferent inhibition of the cochlea reside in the ventral brainstem and participate in these fast neural circuits. However, their modulation of cochlear function occurs over time scales of a slower nature. This suggests the presence of mechanisms that restrict MOC inhibition of cochlear function. To determine how monaural excitatory and inhibitory synaptic inputs integrate to affect the timing of MOC neuron activity, we developed a novel in vitro slice preparation (‘wedge-slice’). The wedge-slice maintains the ascending auditory nerve root, the entire CN and projecting axons, while preserving the ability to perform visually guided patch-clamp electrophysiology recordings from genetically identified MOC neurons. The ‘in vivo-like’ timing of the wedge-slice demonstrates that the inhibitory pathway accelerates relative to the excitatory pathway when the ascending circuit is intact, and the CN portion of the inhibitory circuit is precise enough to compensate for reduced precision in later synapses. When combined with machine learning PSC analysis and computational modeling, we demonstrate a larger suppression of MOC neuron activity when the inhibition occurs with in vivo-like timing. This delay of MOC activity may ensure that the MOC system is only engaged by sustained background sounds, preventing a maladaptive hyper-suppression of cochlear activity.

Significance Statement

Auditory brainstem neurons are specialized for speed and fidelity to encode rapid features of sound. Extremely fast inhibition contributes to precise brainstem sound encoding. This circuit also projects to medial olivocochlear (MOC) efferent neurons that suppress cochlear function to enhance detection of signals in background sound. Using a novel brain slice preparation with intact ascending circuitry, we show that inhibition of MOC neurons can also be extremely fast, with the speed of the circuit localized to the cochlear nucleus. In contrast with the enhancement of precision afforded by fast inhibition in other brainstem auditory circuits, inhibition to MOC neurons instead has a variable onset that delays and desynchronizes activity, thus reducing precision for a slow, sustained response to background sounds.
Cannabidiol improves learning and memory deficits and alleviates anxiety in 12-month-old SAMP8 Mice
Authors: Goodland Monica N. , Banerjee Subhashis , Niehoff Michael L. , Young Benjamin J. , Macarthur Heather , Butler Andrew A. , Morley John E. , Farr Susan A.
Published: December 2023

Cannabidiol (CBD) has gained a lot of interest in recent years for its purported medicinal properties. CBD has been investigated for the treatment of anxiety, depression, epilepsy, neuroinflammation, and pain. Recently there has been an interest in CBD as a possible treatment for age-related disorders such as Alzheimer’s disease and related disorders (ADRD). Here we tested the hypothesis that chronic CBD administration would improve learning and memory in the SAMP8 mouse model of Alzheimer’s disease. SAMP8 mice aged 11 months (at the start of the study) were administered vehicle or CBD (3 or 30 mg/Kg) daily via oral gavage for 2 months. Vehicle-treated young SAMP8 mice (age 3 months at the start of the study) served as unimpaired controls. After 30 days of treatment (4 and 12 months of age), learning and memory, activity, anxiety, strength and dexterity were assessed. High dose CBD treatment significantly improved learning and memory of the 12-month-old mice in the T maze. Novel object recognition memory was also improved by CBD in aged CBD treated mice. Aged CBD treated mice also displayed less anxiety in the elevated plus maze test compared to controls. However, activity and strength levels were similar between groups. Biochemical analysis revealed decreased markers of oxidative stress, providing a possible mechanism by which CBD treatment impacts learning, memory, and anxiety. These results highlight the potential use of CBD as a therapeutic for age related cognitive impairment and dementia.
Cryo-EM structure of the bacterial effector protein SipA bound to F-actin reveals a unique mechanism for filament stabilization
Authors: Guo Emily Z. , Chou Steven Z. , Lara-Tejero Maria , Galán Jorge E.
Published: December 2023

The bacterial pathogenSalmonellaspp. modulates cellular processes by delivering effector proteins through its type III secretion systems. Among these effectors, SipA facilitates bacterial invasion and promotes intestinal inflammation. The mechanisms by which this effector carries out these functions are incompletely understood, although SipA’s ability to modulate actin dynamics is central to some of these activities. Here, we report the cryo-EM structure of SipA bound to filamentous actin. The structure shows that this effector stabilizes actin filaments through unique interactions of its carboxy-terminal domain with four actin subunits. Furthermore, our structure-function studies revealed that SipA’s actin-binding activity is independent of its ability to stimulate intestinal inflammation. Overall, these studies illuminate critical aspects ofSalmonellapathogenesis and provide unique insight into the mechanisms by which a bacterial effector modulates actin dynamics.
Survivin Mediates Mitotic Onset in HeLa Cells Through Activation of the Cdk1-Cdc25B Axis
Authors: Cánovas Pedro M.
Published: December 2023

The Survivin protein has roles in repairing incorrect microtubule-kinetochore attachments at prometaphase and the faithful execution of cytokinesis, both as part of thechromosomalpassengercomplex(CPC) (1). In this context, errors frequently lead to aneuploidy, polyploidy and cancer (1). Adding to these well-known roles of this protein, this paper now shows for the first time that Survivin is required for cancer cells to enter mitosis, and that, in its absence, HeLa cells accumulate at early prophase, or prior to reported before (2, 3). The early prophase blockage in cells lacking Survivin is demonstrated by the presence of an intact nuclear lamina and low Cdk1 activity (4). Interestingly, Survivin and Cdk1 form a complexin vivo. This interaction peaks at mitosis, and its molecular targeting indicates that Survivin is needed for Cdk1 to be active. In this regard, escaping the blockage induced by Survivin abrogation leads to multiple mitotic defects, ormitotic catastrophe, and eventually cell death. Mechanistically, recombinant Survivin can induce the activation of Cdk1 via Cdc25in vitro. Coincidentally, Cdk1 mislocalizes at the centrosome when Survivin is not expressed. Moreover, Survivin directly interacts with phosphatase Cdc25B, bothin vitroandin vivo, and in the absence of the former, an inactive cytosolic Cdc25B-Cdk1-Cyclin B1 complex accumulates, which coincides with the mitotic arrest induced by Survivin depletion. Finally, in agreement with a role for Survivin in the early activation of Cdk1, the G2/early prophase accumulation induced in HeLa cells by Survivin abrogation could be bypassed by a gain-of-function Cdc25B mutant, which drove cells into mitosis.
Supervised contrastive learning enhances MHC-II peptide binding affinity prediction
Authors: Shen Long-Chen , Liu Yan , Liu Zi , Zhang Yumeng , Wang Zhikang , Guo Yuming , Rossjohn Jamie , Song Jiangning , Yu Dong-Jun
Published: December 2023

Accurate prediction of major histocompatibility complex (MHC)-peptide binding affinity can improve our understanding of cellular immune responses and guide personalized immunotherapies. Nevertheless, the existing deep learning-based approaches for predicting MHC-II peptide interactions fall short of satisfactory performance and offer restricted model interpretability. In this study, we propose a novel deep neural network, termed ConBoTNet, to address the above issues by introducing the designed supervised contrastive learning and bottleneck transformer extractors. Specifically, the supervised contrastive learning pre-training enhances the model’s representative and generalizable capabilities on MHC-II peptides by pulling positive pairs closer and pushing negative pairs further in the feature space, while the bottleneck transformer module focuses on MHC-II peptide interactions to precisely identify binding cores and anchor positions in an unsupervised manner. Extensive experiments on benchmark datasets under 5-fold cross-validation, leave-one-molecule-out validation, independent testing, and binding core prediction settings highlighted the superiority of our proposed ConBoTNet over current state-of-the-art methods. Data distribution analysis in the latent feature space demonstrated that supervised contrastive learning can aggregate MHC-II-peptide samples with similar affinity labels and learn common features of similar affinity. Additionally, we interpreted the trained neural network by associating the attention weights with peptides and innovatively find both well-established and potential peptide motifs. This work not only introduces an innovative tool for accurately predicting MHC-II peptide affinity, but also provides new insights into a new paradigm for modeling essential biological interactions, advancing data-driven discovery in biomedicine.
Transcription near arrested DNA replication forks triggers ribosomal DNA copy number changes
Authors: Sasaki Mariko , Kobayashi Takehiko
Published: December 2023

DNA copy number changes as a consequence of chromosomal structural rearrangements or the production of extrachromosomal circular DNA. Here, we demonstrate that the histone deacetylase Sir2 maintains the copy number of budding yeast ribosomal RNA gene (rDNA) by suppressing the initiation of homologous recombination (HR)-mediated repair of DNA double-strand breaks (DSBs) that are formed upon DNA replication fork arrest in the rDNA. Sir2 represses the transcription from the regulatory promoter E-pro, which is located near the fork arresting site. When Sir2 is absent, transcription is stimulated by E-pro but terminated by arrested replication forks. This transcription–replication collision enhances DSB formation and induces DSB end resection and HR-mediated repair that is prone to chromosomal rDNA copy number changes and the production of extrachromosomal rDNA circles. Therefore, repression of transcription near arrested replication forks is critical for the maintenance of genome stability by directing DSB repair into the HR-independent, rearrangement-free pathway.
Species interactions drive continuous assembly of freshwater communities in stochastic environments
Authors: Tabi Andrea , Siqueira Tadeu , Tonkin Jonathan D.
Published: December 2023

Understanding the factors driving the maintenance of long-term biodiversity in changing environments is essential for improving restoration and sustainability strategies in the face of global environmental change. Biodiversity is shaped by both niche and stochastic processes, however the strength of deterministic processes in unpredictable environmental regimes is highly debated. Since communities continuously change over time and space — species persist, disappear or (re)appear — understanding the drivers of species gains and losses from communities should inform us about whether niche or stochastic processes dominate community dynamics. Applying a nonparametric causal discovery approach to a 30-year time series containing annual abundances of benthic invertebrates across 66 locations in New Zealand rivers, we found a strong asynchronous causal relationship between species gains and losses directly driven by predation indicating that niche processes dominate community dynamics. Despite the unpredictable nature of these system, environmental noise was only indirectly related to species gains and losses through altering life history trait distribution. Using a stochastic birth-death framework, we demonstrate that the negative relationship between species gains and losses can not emerge without strong niche processes. Our results showed that even in systems that are dominated by unpredictable environmental variability, species interactions drive continuous community assembly.
Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates
Authors: Alvarez-Aponte Zoila I. , Govindaraju Alekhya M. , Hallberg Zachary F. , Nicolas Alexa M. , Green Myka A. , Mok Kenny C. , Fonseca-Garcia Citlali , Coleman-Derr Devin , Brodie Eoin L. , Carlson Hans K. , Taga Michiko E.
Published: December 2023

Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids—the vitamin B12family of cofactors—are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microbes involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1,000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.
Leveraging machine learning and citizen science data to describe flowering phenology across South Africa
Authors: Stewart R. D. , Bard N. , van der Bank M. , Davies T. J.
Published: December 2023

Phenology — the timing of recurring life history events—is strongly linked to climate. Shifts in phenology have important implications for trophic interactions, ecosystem functioning and community ecology. However, data on plant phenology can be time consuming to collect and current records are biased across space and taxonomy.

Here, we explore the performance of Convolutional Neural Networks (CNN) for classifying flowering phenology on a very large and taxonomically diverse dataset of citizen science images. We analyse >1.8 million iNaturalist records for plants listed in the National Botanical Gardens within South Africa, a country famed for its floristic diversity (∼21,000 species) but poorly represented in phenological databases.

We were able to correctly classify images with >90% accuracy. Using metadata associated with each image, we then reconstructed the timing of peak flower production and length of the flowering season for the 6,986 species with >5 iNaturalist records.

Our analysis illustrates how machine learning tools can leverage the vast wealth of citizen science biodiversity data to describe large-scale phenological dynamics. We suggest such approaches may be particularly valuable where data on plant phenology is currently lacking.
Lumen pressure modulation in chicken embryos
Authors: McLaren Susannah B.P. , Xiong Fengzhu
Published: December 2023

Pressure exerted by fluid contained within a lumen plays a crucial role in the growth, morphogenesis and patterning of epithelial organs. Accurate modulation of lumen pressure in the developing embryo requires sensitive and robust methods that can detect and vary pressure in the range of tens to hundreds of Pascals (Pa). Here we describe a simple, cost- effective method for setting up a pressure modulation apparatus combining a high-sensitivity pressure sensor and a water column whose height can be finely tuned. We demonstrate lumen pressure control using the developing brain of early chicken embryos.
Task-Switch Related Reductions in Neural Distinctiveness in Children and Adults: Commonalities and Differences
Authors: Schwarze Sina A. , Bonati Sara , Cichy Radoslaw M. , Lindenberger Ulman , Bunge Silvia A. , Fandakova Yana
Published: December 2023

Goal-directed behavior requires the ability to flexibly switch between task sets with changing environmental demands. Switching between tasks generally comes at the cost of slower and less accurate responses. Compared to adults, children show greater switch costs, presumably reflecting the protracted development of the ability to flexibly update task-set representations. To examine whether the distinctiveness of neural task-set representations is more strongly affected by a task switch in children compared to adults, we examined multi-voxel patterns of fMRI activation in 88 children (8–11 years, 49 girls) and 53 adults (20–30 years, 28 women) during a task-switching paradigm. Using multivariate pattern analysis (MVPA), we investigated whether task-set representations were less distinct on switch than on repeat trials across frontoparietal, cingulo-opercular, and temporo-occipital regions. Children and adults showed lower accuracy and longer response times on switch than on repeat trials, with higher accuracy costs in children. Decoding accuracy across regions was lower on switch than repeat trials, consistent with the notion that switching reduces the distinctiveness of task-set representations. Reliable age differences in switch-related representational distinctiveness reductions were absent, pointing to a remarkable degree of maturity of neural representations of task-relevant information in late childhood. However, we also observed that switch-related reductions in distinctiveness were more highly correlated across frontoparietal and cingulo-opercular regions in children than in adults, potentially reflecting the ongoing specialization of different control networks with respect to the representation of task features.

Significance statement

The ability to flexibly switch between tasks enables goal-directed behavior, but is particularly challenging for children, potentially due to protracted development in the ability to represent multiple and overlapping task rules that link stimuli to appropriate responses. We tested this hypothesis by using neuroimaging to measure brain activity during task switching in 8–11-year-olds and adults. Activation patterns in frontal, parietal, and temporal regions could tell us with above-chance accuracy which task a person was performing when the task remained the same, but not when it had switched. Adults showed greater differentiation across regions in terms of switch-related reductions in distinctiveness than children, suggesting that the relevant functional circuity is present but has not yet fully matured by late childhood.
A novelKCNJ16kidney organoid model recapitulates the disease phenotype and shows restoration of lipid accumulation upon treatment with statins
Authors: Sendino Garví E. , van Slobbe G. , Zaal E.A. , de Baaij J. H. F. , Hoenderop J.G. , Masereeuw R. , Janssen M. J. , van Genderen A. M.
Published: December 2023

Background

theKCNJ16gene has been associated with a novel kidney tubulopathy phenotype,viz.disturbed acid-base homeostasis, hypokalemia and altered renal salt transport.KCNJ16encodes for Kir5.1, which together with Kir4.1 constitutes a potassium channel located at kidney tubular cell basolateral membranes. Preclinical studies provided mechanistical links between Kir5.1 and a disease phenotype, however, the disease pathology remains poorly understood. Here, we aimed at generating and characterizing a novel advancedin vitrohuman kidney model that recapitulates the disease phenotype to investigate further the pathophysiological mechanisms underlying the disease and potential therapeutic interventions.

Methods

we used CRISPR/Cas9 to generateKCNJ16mutant (KCNJ16+/-andKCNJ16-/-) cell lines from healthy human induced pluripotent stem cells (iPSC)KCNJ16control (KCNJ16WT). The iPSCs were differentiated following an optimized protocol into kidney organoids in an air-liquid interface.

Results

KCNJ16-depleted kidney organoids showed transcriptomic and potential functional impairment of key voltage-dependent electrolyte and water-balance transporters. We observed cysts formation, lipid droplet accumulation and fibrosis upon Kir5.1 function loss. Furthermore, a large scale, glutamine tracer flux metabolomics analysis demonstrated thatKCNJ16-/-organoids display TCA cycle and lipid metabolism impairments. Drug screening revealed that treatment with statins, particularly the combination of simvastatin and C75, prevented lipid droplet accumulation and collagen-I deposition inKCNJ16-/-kidney organoids.

Conclusions

mature kidney organoids represent a relevantin vitromodel for investigating the function of Kir5.1. We discovered novel molecular targets for this genetic tubulopathy and identified statins as a potential therapeutic strategy forKCNJ16defects in the kidney.

Significance Statement

In this study, the use of CRISPR/Cas9 technology resulted in the establishment of aKCNJ16-depleted kidney organoid model, instrumental in elucidating the pathophysiology of the recently reportedKCNJ16-associated kidney tubulopathy. Our study substantiates the role of Kir5.1 (KCNJ16) in kidney disease, confirming already described phenotypes, as well as aiding to gain insight in the causal role of Kir5.1 loss in the disease phenotype. Our approach increases the knowledge onKCNJ16-related kidney phenotype, and it states the importance of combining CRISPR/Cas9 technology and advancedin vitromodels for complex disease modeling and therapy testing. Furthermore, we encourage the application of our approach to thein vitromodeling of rare and/or underrepresented genetic kidney diseases, for which the availability of patient material is limited.
Bi-allelic variants inWDR47lead to neuronal loss causing a rare neurodevelopmental syndrome with corpus callosum dysgenesis in humans
Authors: Bayam Efil , Tilly Peggy , Collins Stephan C. , Alvarez José Rivera , Kannan Meghna , Tonneau Lucile , Rinaldi Bruno , Lecat Romain , Schwaller Noémie , Maddirevula Sateesh , Monteiro Fabiola , Kitajima João Paulo , Kok Fernando , Kato Mitsuhiro , Hamed Ahlam A. A. , Salih Mustafa A. , Tala Saeed Al , Hashem Mais , Tada Hiroko , Saitsu Hirotomo , Friant Sylvie , Yüksel Zafer , Nakashima Mitsuko , Alkuraya Fowzan S. , Yalcin Binnaz , Godin Juliette D.
Published: December 2023

The corpus callosum (CC) is the largest interhemispheric connection that is largely formed by the axons of layer 2/3 callosal projection neurons (CPNs) through a series of tightly regulated cellular events, including neuronal specification, migration, axon extension and branching. Defects in any of those steps may prevent the proper development of the corpus callosum resulting in a spectrum of disorders collectively referred to as corpus callosum dysgenesis (CCD). Here, we report four unrelated families carrying bi-allelic variants inWDR47presenting with CCD together with other neuroanatomical phenotypes such as microcephaly, cerebellar abnormalities and hydrocephalus. Using a combination ofin vitroandin vivomouse models and complementation assays, we show that independently from its previously identified functions in neuronal migration and axonal extension, WDR47 is required for survival of callosal neurons by contributing to the maintenance of mitochondrial and microtubule homeostasis. We further provide evidence that severity of the CCD phenotype is determined by the degree of the loss of function caused by the human variants. Taken together, we identifyWDR47as a causative gene of a new neurodevelopmental syndrome characterized by corpus callosum abnormalities and other neuroanatomical malformations.
Phytochrome-dependent responsiveness to root-derived cytokinins enables coordinated elongation responses to combined light and nitrate cues
Authors: Gautrat Pierre , Buti Sara , Romanowski Andrés , Buijs Guido , Pierik Ronald
Published: December 2023

Plants growing at high densities can detect competitors through changes in the composition of light reflected by neighbours. In response to this far-red-enriched light, plants elicit adaptive shade avoidance responses for light capture, but these need to be balanced against other input signals, such as nutrient availability. Here, we used a combination of transcriptomics, growth assays and dedicated genetic and pharmacological interventions to demonstrate how Arabidopsis integrates light and nitrate signalling. We unveiled that nitrate modulates shade avoidance via a previously unknown shade response pathway that involves root-derived transZeatin (tZ). Under nitrate-sufficient conditions, tZ promotes hypocotyl elongation specifically in the presence of supplemental far-red light. This occurs via PIF transcription factors-dependent inhibition of type-AARRscytokinin response inhibitors. Our data thus reveal how plants co-regulate responses to shade cues with root-derived information about nutrient availability, and how they restrict responses to this information to specific light conditions in the shoot.