bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative multi-omics increase resolution of the sea urchin posterior gut gene regulatory network at single cell level
Authors: Voronov Danila , Paganos Periklis , Magri Marta S. , Cuomo Claudia , Maeso Ignacio , Gómez-Skarmeta Jose Luis , Arnone Maria Ina 
Published: May 2023

AbstractDrafting gene regulatory networks (GRNs) requires embryological knowledge pertaining to the cell type families, information on the regulatory genes, causal data from gene knockdown experiments and validations of the identified interactions by cis-regulatory analysis. We use multi-omics involving next-generation sequencing (-seq) to obtain the necessary information drafting the sea urchin posterior gut GRN. Here we present an update to the GRN using i) a single cell RNA-seq derived cell atlas highlighting the 2 day post fertilization (dpf) sea urchin gastrula cell type families, as well as the genes expressed at single cell level, ii) a set of putative cis-regulatory modules and transcription factor (TF) binding sites obtained from chromatin accessibility ATAC-seq data, and iii) interactions directionality obtained from differential bulk RNA-seq following knockdown of the TF Sp-Pdx1, a key regulator of gut patterning in sea urchins. Combining these datasets, we draft the GRN for the hindgutSp-Pdx1positive cells in the 2 dpf gastrula embryo. Overall, our data resolves the complex connectivity of the posterior gut GRN and increases the resolution of gene regulatory cascades operating within it.
Assessing diatom-associated bacteria by a specific CARD-FISH protocol
Authors: Den Tran Quoc , Simon Meinhard 
Published: May 2023

AbstractThe cell surfaces of phytoplankton algae including diatoms are usually colonized by specific bacterial populations which interact with and affect growth of the host species. Catalyzed Reported Deposition Fluorescence in situ Hybridizazion (CARD-FISH) is a well-suited technique to visualize and identify algal-associated bacterial cells. Autofluorescence and the strongly structured cell surface of the algal cell make it difficult to quantify distinct populations of the colonizing bacterial communities. To overcome these limitations, we adopted a CARD-FISH method to this specific application by reducing the algal autofluorescence by an extra ethanol treatment and by stacking epifluorescence micrographs taken at different focal planes and merging them into a composite image. Cells of the diatomThalassiosira rotulawere used as host and incubated with a consortium of different bacterial strains and a natural bacterial community. Samples were concentrated either by filtration onto polycarbonate membranes or by centrifugation and analyzed with probes CF319a, GAM42a and ROS536. The results showed easily quantifiable bacterial cells and did not reveal any significant differences in the abundance of diatom-associated bacterial populations assessed by both methods. Our CARD-FISH protocol persuasively demonstrated that bacterial populations can be easily and reliably enumerated on diatom cells and presumably also on other algal cells and autotrophic biofilms.
Predictable Modality Transitions and Amodal Representations Enable Crossmodal Statistical Learning
Authors: Pérez-Bellido Alexis , Duato Daniel , Giannelli Francesco , de Diego-Balaguer Ruth 
Published: May 2023

AbstractStatistical learning involves extracting statistical regularities from the environment. Despite the ubiquitous crossmodal relations in our environment, previous research has failed in showing crossmodal learning suggesting that statistical learning is modality-specific, occurring within but not between sensory modalities. The present study investigates under which circumstances statistical learning can occur between modalities. In the first experiment, participants viewed a stream of meaningless visual fractals and synthetic auditory stimuli. Importantly, the sequence of stimuli could be grouped into unimodal or crossmodal pairs based on their internal transitional probabilities. Using implicit and explicit measures of learning, we found that participants only learned the unimodal pairs. In the second experiment, pairs were presented in separate unimodal and crossmodal blocks. The crossmodal blocks alternated visual and auditory modalities allowing participants to anticipate the upcoming modality. This manipulation allowed significant statistical learning for the crossmodal pairs, reflected only by implicit measures. This suggests that modality transitions predictability aids correct attention deployment across sensory modalities, crucial for learning crossmodal statistical contingencies. In the third experiment, where audiovisual stimuli with semantic content were used leaving access to an amodal shared representation, participants could explicitly recognize statistical regularities between crossmodal pairs even when the upcoming modality was unpredictable. This finding suggests statistical learning between crossmodal pairs can occur when sensory-level limitations are bypassed, and when learning unfolds at an amodal level of representation. These findings challenge the view that statistical learning is strictly modality-specific, instead indicating that crossmodal statistical learning depends on attentional mechanisms and representational level.Public significance statementPrevious research has established that low-level statistical learning occurs within individual sensory modalities. However, evidence for statistical learning across modalities remains limited. This has led to the hypothesis that statistical learning operates as a modality-specific system, constrained by the perceptual properties and content of each sensory system. In this study, we demonstrate that modality transitions’ predictability enables crossmodal statistical learning, even in the absence of semantic information. Notably, this constraint does not apply to meaningful stimuli, which can be processed at an amodal level. Our findings broaden the classical neurobiological model of statistical learning by highlighting the roles of attentional mechanisms and representational levels in supporting crossmodal statistical learning.
Hypoxia delays steroid-induced developmental maturation inDrosophilaby suppressing EGF signaling
Authors: Turingan Michael J , Li Tan , Wright Jenna , Grewal Savraj S 
Published: May 2023

SummaryAnimals often grow and develop in unpredictable environments where factors like food availability, temperature, and oxygen levels can fluctuate dramatically. To ensure proper sexual maturation into adulthood, juvenile animals need to adapt their growth and developmental rates to these fluctuating environmental conditions. Failure to do so can result in impaired maturation and incorrect body size. Here we describe a mechanism by whichDrosophilalarvae adapt their development in low oxygen (hypoxia). During normal development, larvae grow and increase in mass until they reach critical weight (CW), after which point a neuroendocrine circuit triggers the production of the steroid hormone ecdysone from the prothoracic gland (PG), which promotes maturation to the pupal stage. However, when raised in hypoxia (5% oxygen), larvae slow their growth and delay their maturation to the pupal stage. We find that, although hypoxia delays the attainment of CW, the maturation delay occurs mainly because of hypoxia acting late in development to suppress ecdysone production. This suppression operates through a distinct mechanism from nutrient deprivation, occurs independently of HIF-1 alpha and does not involve modulation of PTTH, the main neuropeptide that initiates ecdysone production in the PG. Instead, we find that hypoxia lowers the expression of the EGF ligand, spitz, and that the delay in maturation occurs due to reduced EGFR/ERK signaling in the PG. Our study sheds light on how animals can adjust their development rate in response to changing oxygen levels in their environment. Given that hypoxia is a feature of both normal physiology and many diseases, our findings have important implications for understanding how low oxygen levels may impact animal development in both normal and pathological situations.
Anionic phospholipids stimulate the proton pumping activity of the plant plasma membrane P-type H+-ATPase
Authors: Paweletz Laura C. , Holtbrügge Simon L. , Löb Malina , De Vecchis Dario , Schäfer Lars V. , Pomorski Thomas Günther , Justesen Bo Højen 
Published: May 2023

AbstractThe activity of membrane proteins depends strongly on the surrounding lipid environment. Here, we characterize the lipid stimulation of the plant plasma membrane H+-ATPase AHA2 upon purification and reconstitution into liposomes of defined lipid compositions. We show that the proton pumping activity of AHA2 is stimulated by anionic phospholipids, especially by phosphatidylserine. Molecular dynamics simulations revealed several preferential contact sites for anionic phospholipids in the transmembrane domain of AHA2. These contact sites are partly conserved across functionally different P-type ATPases from several organisms, suggesting a general regulation mechanism by the membrane lipid environment. Our findings highlight the fact that anionic lipids play an important role in the control of H+-ATPase activity.
A sensory-motor decoder that transforms neural responses in extrastriate area MT into smooth pursuit eye movements
Authors: Behling Stuart , Lisberger Stephen G. 
Published: May 2023

AbstractVisual motion drives smooth pursuit eye movements through a sensory-motor decoder that uses multiple parallel components and neural pathways to transform the population response in extrastriate area MT into movement. We evaluated the decoder by challenging pursuit in monkeys with reduced motion reliability created by reducing coherence of motion in patches of dots. Reduced dot coherence caused deficits in both the initiation of pursuit and steady-state tracking, revealing the paradox of steady-state eye speeds that fail to accelerate to target speed in spite of persistent image motion. We recorded neural responses to reduced dot coherence in MT and found a decoder that transforms MT population responses into eye movements. During pursuit initiation, decreased dot coherence reduces MT population response amplitude without changing the preferred speed at the peak of the population response. The successful decoder reproduces the measured eye movements by multiplication of (i) the estimate of target speed from the peak of the population response with (ii) visual-motor gain based on the amplitude of the population response. During steady-state tracking, the decoder that worked for pursuit initiation failed. It predicted eye acceleration to target speed even when monkeys’ eye speeds were steady at a level well below target speed. We can account for the effect of dot coherence on steady-state eye speed if sensorymotor gain also modulates the eye velocity positive feedback that normally sustains perfect steadystate tracking. Then, poor steady-state tracking persists because of balance between deceleration caused by low positive feedback gain and acceleration driven by MT.
Mutual inclusivity improves decision-making by smoothing out choice’s competitive edge
Authors: Leng Xiamin , Frömer Romy , Summe Thomas , Shenhav Amitai 
Published: May 2023

AbstractDecisions form a central bottleneck to most tasks, one that people often experience as costly. Past work proposes mitigating those costs by lowering one’s threshold for deciding. Here, we test an alternative solution, one that targets the basis for most choice costs: that choosing one option sacrifices others (mutual exclusivity). Across 5 studies (N = 462), we test whether this tension can be relieved by framing choices as inclusive (allowing selection of more than one option, as in buffets). We find that inclusivity makes choices more efficient, by selectively reducing competition between potential responses as participants accumulate information for each of their options. Inclusivity also made participants feel less conflicted, especially when they couldn’t decide which good option to keep or which bad option to get rid of. These inclusivity benefits were also distinguishable from the effects of manipulating decision threshold (increased urgency), which improved choices but not experiences thereof.
Transposable elements impact the population divergence of rice blast fungusMagnaporthe oryzae
Authors: Lin Lianyu , Sun Ting , Guo Jiayuan , Lin Lili , Chen Meilian , Wang Zhe , Bao Jiandong , Norvienyeku Justice , Zhang Dongmei , Han Yijuan , Lu Guodong , Rensing Christopher , Zheng Huakun , Zhong Zhenhui , Wang Zonghua 
Published: May 2023

ABSTRACTDynamic transposition of transposable elements (TEs) in fungal pathogens have significant impact on genome stability, gene expression, and virulence to the host. InMagnaporthe oryzae, genome plasticity resulting from TE insertion is a major driving force leading to the rapid evolution and diversification of this fungus. Despite their importance inM. oryzaepopulation evolution and divergence, our understanding of TEs in this context remains limited. Here we conducted a genome-wide analysis of TE transposition dynamics in the 11 most abundant TE families inM. oryzaepopulations. Our results show that these TEs have specifically expanded in recently isolatedM. oryzaerice populations, with the presence/absence polymorphism of TE insertions highly concordant with population divergence on Geng/Japonicaand Xian/Indicarice cultivars. Notably, the genes targeted by clade-specific TEs showed clade-specific expression patterns and are involved in the pathogenic process, suggesting a transcriptional regulation of TEs on targeted genes. Our study provides a comprehensive analysis of TEs inM. oryzaepopulations and demonstrates a crucial role of recent TE bursts in adaptive evolution and diversification of theM. oryzaerice-infecting lineage.IMPORTANCEM. oryzaeis the causal agent of the destructive blast disease, which caused massive loss of yield annually worldwide. The fungus diverged into distinct clades during adaptation toward two rice subspecies, Xian/indica and Geng/japonica. Although the role of TEs in the adaptive evolution was well established, mechanisms underlying how TEs promote the population divergence ofM. oryzaeremains largely unknown. In this study, we reported that TEs shape the population divergence ofM. oryzaeby differentially regulating gene expression between Xian/Indica-infecting and Geng/Japonica-infecting populations. Our results revealed a TE insertion mediated gene expression adaption that led to the divergence ofM. oryzaepopulation infecting different rice subspecies.
The gut microbiome mediates adaptation to scarce food in Coleoptera
Authors: Moldovan Oana Teodora , Carrell Alyssa A. , Bulzu Paul Adrian , Levei Erika , Bucur Ruxandra , Sitar Cristian , Faur Luchiana , Mirea Ionu□ Cornel , □enilă Marin , Cadar Oana , Podar Mircea 
Published: May 2023

AbstractBeetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles’ microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibulae adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineagesSpiroplasmaorWolbachia. All beetles had relatively high levels of fermentativeCarnobacteriumandVagococcusinvolved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.
Stable expression ofHelicobacter pylori cagAoncoprotein in brinjal
Authors: Mehran Mohammad Javad , Barzigar Rambod , Sathish Kumar Basaralu Yadurappa , Haraprasad Nanjundappa , Fakrudin Bashasab , Paul Sayan , Ramasamy Rajesh Kumar , Malla Sudhakar 
Published: May 2023

AbstractHelicobacter pyloriis closely connected to upper gastrointestinal tract diseases including gastric cancer. Transgenic plants are found to be successful in expressing the bacterial antigens, which could elicit an immune response when consumed. The Cytotoxicity-associated immunodominant antigen protein (cagA) ofH. pyloriis kindred with pathogenicity and cancer risk. We expressed thecagAtransgenically in the brinjal. We amplified thecagAgene fromH. pyloristrain 26695 chromosomal DNA and transformed it into brinjal callus derived from leaf explants using the pBI121 expression vector. The stable expression and accumulation of the recombinantcagAgene were confirmed by using quantitative real-time PCR, western blot analysis and ELISA. The RT-PCR, western blot and ELISA showed stable expression ofcagAgene in the transgenic lines B3, B5, B11, B17 and B21. Among them, B11 and B17 samples showed higher expression of thecagAcompared to the other samples. Besides, the immunohistochemistry assay showed the abundant expression ofcagAprotein in the parenchymal regions of the transgenic plants. Out of the 52 plants, a set five plants were found to be positive forcagAexpression. Our experimental outcomes can be used further to design the vaccines againstH. pylorifrom the transgenic brinjal plants.
Factors influencing the detergent-free membrane protein isolation using synthetic nanodisc-forming polymers
Authors: Krishnarjuna Bankala , Sharma Gaurav , Ravula Thirupathi , Ramamoorthy Ayyalusamy 
Published: May 2023

AbstractThe detergent-free isolation of membrane proteins using synthetic polymers is becoming the desired approach for functional and structural studies of membrane proteins. Since the expression levels for many membrane proteins are low and a high yield of functionalized reconstituted membrane proteins is essential forin vitrostudies, it is crucial to optimize the experimental conditions for a given polymer to effectively solubilize target membranes/proteins. The factors that affect membrane solubilization and subsequently the isolation of a target membrane protein include polymer concentration, polymer charge, temperature, pH, and concentration of divalent metal ions. Therefore, it is important to have knowledge about the efficacy of different types of polymers in solubilizing cell membranes. In this study, we evaluate the efficacy of inulin-based non-ionic polymers in solubilizingE. colimembranes enriched with rat flavin mononucleotide binding-domain (FBD) of cytochrome-P450-reductase (CPR) and rabbit cytochrome-b5 (Cyt-b5) under various solubilization conditions. Our results show that a 1:1 (w/w) membrane:polymer ratio, low temperature, high pH and sub-millimolar concentration of metal ions favor the solubilization ofE. colimembrane enriched with FBD or Cyt-b5. Conversely, the presence of excess divalent metal ions affected the final protein levels in the polymer-solubilized samples. We believe that the results from this study provides knowledge to assess and plan the use of non-ionic polymers in membrane protein studies.
Pathogenic bacteria experience pervasive RNA polymerase backtracking during infection
Authors: Browning Kaitlyn R. , Merrikh Houra 
Published: May 2023

AbstractPathogenic bacteria and their eukaryotic hosts are in a constant arms race. Hosts have numerous defense mechanisms at their disposal that not only challenge the bacterial invaders, but have the potential to disrupt molecular transactions along the bacterial chromosome. However, it is unclear how the host impacts association of proteins with the bacterial chromosome at the molecular level during infection. This is partially due to the lack of a method that could detect these events in pathogens while they are within host cells. We developed and optimized a system capable of mapping and measuring levels of bacterial proteins associated with the chromosome while they are actively infecting the host (referred to as PIC-seq). Here, we focused on the dynamics of RNA polymerase (RNAP) movement and association with the chromosome in the pathogenic bacteriumSalmonella entericaas a model system during infection. Using PIC-seq, we found that RNAP association patterns with the chromosome change during infection genome-wide, including at regions that encode for key virulence genes. Importantly, we found that infection of a host significantly increases RNAP backtracking on the bacterial chromosome. RNAP backtracking is the most common form of disruption to RNAP progress on the chromosome. Interestingly, we found that the resolution of backtracked RNAPs via the anti-backtracking factors GreA and GreB is critical for pathogenesis, revealing a new class of virulence genes. Altogether, our results strongly suggest that infection of a host significantly impacts transcription by disrupting RNAP movement on the chromosome within the bacterial pathogen. The increased backtracking events have important implications not only for efficient transcription, but also for mutation rates as stalled RNAPs increase the levels of mutagenesis.
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development
Authors: Kim Sunghyun , Koppitch Kari , Parvez Riana K. , Guo Jinjin , Achieng MaryAnne , Schnell Jack , Lindström Nils O. , McMahon Andrew P. 
Published: May 2023

SummaryMammalian kidneys maintain fluid homeostasis through the cellular activity of nephrons and the conjoined collecting system. Each epithelial network originates from distinct progenitor cell populations that reciprocally interact during development. To extend our understanding of human and mouse kidney development, we profiled chromatin organization (ATAC-seq) and gene expression (RNA-seq) in developing human and mouse kidneys. Data were analyzed at a species level and then integrated into a common, cross-species multimodal data set. Comparative analysis of cell types and developmental trajectories identified conserved and divergent features of chromatin organization and linked gene activity, revealing species- and cell-type specific regulatory programs. Identification of human-specific enhancer regions linked through GWAS studies to kidney disease highlights the potential of developmental modeling to provide clinical insight.