bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulatory network structure and environmental signals constrain transcription factor innovation
Authors: Shepherd Matthew J. , Reynolds Mitchell , Pierce Aidan P. , Rice Alan M. , Taylor Tiffany B. 
Published: May 2023

AbstractEvolutionary innovation of transcription factors frequently drives phenotypic diversification and adaptation to environmental change. Rewiring – that is gaining or losing connections to transcriptional target genes – is a key mechanism by which transcription factors evolve and innovate. However the frequency of functional adaptation varies between different regulators, even when they are closely related. To identify factors influencing propensity for rewiring, we utilise aPseudomonas fluorescensSBW25 strain rendered incapable of flagellar mediated motility in soft-agar plates via deletion of the flagellar master regulator (fleQ). This bacterium can evolve to rescue flagellar motility via gene regulatory network rewiring of an alternative transcription factor to rescue activity of FleQ. Previously, we have identified two members (out of 22) of the RpoN-dependent enhancer binding protein (RpoN-EBP) family of transcription factors (NtrC and PFLU1132) that are capable of innovating in this way. These two transcription factors rewire repeatably and reliably in a strict hierarchy – with NtrC the only evolved rewiring route in a ΔfleQbackground, and PFLU1132 the only evolved rewiring route in a ΔfleQΔntrCbackground. However, why other members in the same transcription factor family have not been observed to rescue flagellar activity is unclear. Previous work shows that protein homology cannot fully explain this pattern, and mutations in rewired strains suggested high levels of transcription factor expression and activation drive rewiring. We predict that mutations that increase expression of the rewired transcription factor are vital to unlock rewiring potential. Here, we construct titratable expression mutant lines for 11 of the RpoN-EBPs inP. fluorescens. We show that in 5 additional RpoN-EBPs (HbcR, GcsR, DctD, AauR and PFLU2209), high expression levels result in different mutations conferring motility rescue, suggesting alternative rewiring pathways. Our results indicate that expression levels (and not protein homology) of RpoN-EBPs are a key constraining factor in determining rewiring potential. This suggests that transcription factors that can achieve high expression through few mutational changes, or transcription factors that are active in the selective environment, are more likely to innovate and contribute to adaptive gene regulatory network rewiring.
A bivalent ChAd nasal vaccine protects against SARS-CoV-2 BQ.1.1 and XBB.1.5 infection and disease in mice and hamsters
Authors: Ying Baoling , Darling Tamarand L. , Desai Pritesh , Liang Chieh-Yu , Dmitriev Igor P. , Soudani Nadia , Bricker Traci , Kashentseva Elena A. , Harastani Houda , Schmidt Aaron G. , Curiel David T. , Boon Adrianus C.M. , Diamond Michael S. 
Published: May 2023

ABSTRACTWe previously described a nasally delivered monovalent adenoviral-vectored SARS- CoV-2 vaccine (ChAd-SARS-CoV-2-S, targeting Wuhan-1 spike [S]; iNCOVACC®) that is currently used in India as a primary or booster immunization. Here, we updated the mucosal vaccine for Omicron variants by creating ChAd-SARS-CoV-2-BA.5-S, which encodes for a pre- fusion and surface-stabilized S protein of the BA.5 strain, and then tested monovalent and bivalent vaccines for efficacy against circulating variants including BQ.1.1 and XBB.1.5. Whereas monovalent ChAd-vectored vaccines effectively induced systemic and mucosal antibody responses against matched strains, the bivalent ChAd-vectored vaccine elicited greater breadth. However, serum neutralizing antibody responses induced by both monovalent and bivalent vaccines were poor against the antigenically distant XBB.1.5 Omicron strain and did not protect in passive transfer experiments. Nonetheless, nasally delivered bivalent ChAd- vectored vaccines induced robust antibody and spike-specific memory T cell responses in the respiratory mucosa, and conferred protection against WA1/2020 D614G and Omicron variants BQ.1.1 and XBB.1.5 in the upper and lower respiratory tracts of both mice and hamsters. Our data suggest that a nasally delivered bivalent adenoviral-vectored vaccine induces protective mucosal and systemic immunity against historical and emerging SARS-CoV-2 strains without requiring high levels of serum neutralizing antibody.
ImSpiRE: Image feature-aided spatial resolution enhancement method
Authors: Hua Yuwei , Zhang Yizhi , Guo Zhenming , Bian Shan , Zhang Yong 
Published: May 2023

AbstractThe resolution of most spatially resolved transcriptomic technologies usually cannot attain the single-cell level, limiting their applications in biological discoveries. Here, we introduce ImSpiRE, an image feature-aided spatial resolution enhancement method forin situcapturing spatial transcriptome. Taking the information stored in histological images, ImSpiRE solves an optimal transport problem to redistribute the expression profiles of spots to construct new transcriptional profiles with enhanced resolution, together with imputing the gene expression profiles in unmeasured regions. Applications to multiple datasets confirm that ImSpiRE can enhance spatial resolution to the subspot level while contributing to the discovery of tissue domains, signaling communication patterns, and spatiotemporal characterization.
Resolving the paradox of local warning signal diversity with predator learning
Authors: Kuo Chi-Yun 
Published: May 2023

AbstractCoexistence of distinct warning signals at local scales has long stood as a paradox, as selection is expected to preserve only the most common signal. So far, there has not been an explanation that is both broadly applicable and testable. This study presents a novel and generalizable resolution to this paradox (the Unforgetful Predator Hypothesis) by showing that prey displaying a rarer warning signal can persist if predators have low enough forgetting rates relative to prey generation time. In addition, inducing a high level of predator avoidance facilitates warning signal diversity when prey do not compete. In the presence of prey competition, however, warning signal diversity is more likely to occur if prey elicit intermediate levels of avoidance, such that the competitive disadvantage for individuals displaying the rare signal can be offset by predation. This hypothesis can be tested by quantifying predator avoidance and forgetting rate in laboratory and field experiments. As the level of predator avoidance is also crucial in determining the fate of rare signal in communities, I performed a meta-analysis to examine the determinants of its variation and found that higher predator avoidance can be observed in the following situations – when prey unprofitability is due to toxicity rather than mere unpalatability, when predators search widely for prey and/or prey aggregate, and when predators could differentiate between unprofitable and profitable prey using only color or pattern. In addition to resolving the paradox, these findings help inform the types of communities in which distinct warning signals can stably coexist.SignificanceCoexistence of distinct warning signals within a community represents an evolutionary paradox that still awaits a resolution that is both general and testable. I used ecologically realistic simulations to show that warning signal diversity can occur if predators have long enough memory and if prey elicit either low or moderate levels of avoidance, depending on whether they compete. A meta-analysis further shows that higher levels of predator avoidance tend to occur when unprofitable prey are highly unprofitable, when predators search widely for prey, when prey aggregate, and when prey profitability could be discerned by only color or pattern. These findings offer a testable resolution to the paradox and inform the types of communities where warning signal diversity may occur.
netMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity
Authors: Li Zuqi , Melograna Federico , Hoskens Hanne , Duroux Diane , Marazita Mary L. , Walsh Susan , Weinberg Seth M. , Shriver Mark D. , Müller-Myhsok Bertram , Claes Peter , Van Steen Kristel 
Published: May 2023

AbstractMulti-view data offer advantages over single-view data for characterizing individuals, which is crucial in precision medicine toward personalized prevention, diagnosis, or treatment follow-up. Here, we develop a network-guided multi-view clustering framework named netMUG to identify actionable subgroups of individuals. This pipeline first adopts sparse multiple canonical correlation analysis to select multi-view features possibly informed by extraneous data, which are then used to construct individual-specific networks (ISNs). Finally, the individual subtypes are automatically derived by hierarchical clustering on these network representations. We applied netMUG to a dataset containing genomic data and facial images to obtain BMI-informed multi-view strata and showed how it could be used for a refined obesity characterization. Benchmark analysis of netMUG on synthetic data with known strata of individuals indicated its superior performance compared with both baseline and benchmark methods for multi-view clustering. In addition, the real-data analysis revealed subgroups strongly linked to BMI and genetic and facial determinants of these classes. NetMUG provides a powerful strategy, exploiting individual-specific networks to identify meaningful and actionable strata. Moreover, the implementation is easy to generalize to accommodate heterogeneous data sources or highlight data structures.Author summaryIn recent years, we see the increasing possibility of collecting data from multiple modalities in various fields, requesting novel methods to exploit the consensus among different data types. As exemplified in systems biology or epistasis analyses, the interactions between features may contain more information than the features themselves, thereby necessitating the use of feature networks. Furthermore, in real-life scenarios, subjects, such as patients or individuals, may originate from diverse populations, which underscores the importance of subtyping or clustering these subjects to account for their heterogeneity. In this study, we present a novel pipeline for selecting the most relevant features from multiple data types, constructing a feature network for each subject, and obtaining a subgrouping of samples informed by a phenotype of interest. We validated our method on synthetic data and demonstrated its superiority over several state-of-the-art multi-view clustering approaches. Additionally, we applied our method to a real-life, large-scale dataset of genomic data and facial images, where it effectively identified a meaningful BMI subtyping that complemented existing BMI categories and offered new biological insights. Our proposed method has wide applicability to complex multi-view or multi-omics datasets for tasks such as disease subtyping or personalized medicine.
Diversity of the bacterial and viral communities in the tropical horse tick,Dermacentor nitensin Colombia
Authors: Holguin-Rocha Andres F. , Calle-Tobon Arley , Vásquez Gissella M. , Astete Helvio , Fisher Michael L. , Tobon-Castano Alberto , Velez-Tobon Gabriel , Maldonado-Ruiz L. Paulina , Silver Kristopher , Park Yoonseong , Londono-Renteria Berlin 
Published: May 2023

AbstractTicks are obligatory hematophagous ectoparasites that transmit pathogens among various vertebrates, including humans. The composition of the microbial and viral communities in addition to the pathogenic microorganisms is highly diverse in ticks, but the factors driving the diversity are not well understood. The tropical horse tick,Dermacentor nitens, is distributed throughout the Americas and it is recognized as a natural vector ofBabesia caballiandTheileria equi, the causal agents of equine piroplasmosis. We characterized the bacterial and viral communities associated with partially-fedD. nitensfemales collected by a passive survey on horses from field sites representing three distinct geographical areas in Colombia (Bolivar, Antioquia, and Cordoba). RNA-seq and sequencing of the V3 and V4 hypervariable regions of the 16S rRNA gene were performed using the Illumina-Miseq platform. A total of 356 operational taxonomic units (OTUs) were identified, in which the presumed endosymbiotic Francisellaceae/Francisellaspp. was predominantly found. Nine contigs corresponding to six different viruses were identified in three viral families: Chuviridae, Rhabdoviridae, and Flaviviridae. Differences in the relative abundance of the microbial composition among the geographical regions were found to be independent of the presence ofFrancisella-Like Endosymbiont (FLE). The most prevalent bacteria found on each region wereCorynebacteriumin Bolivar,Staphylococcusin Antioquia, andPseudomonasin Cordoba.Rickettsia-like endosymbionts, mainly recognized as the etiological agent of rickettsioses in Colombia were detected in the Cordoba samples. Metatranscriptomics revealed 13 contigs containing FLE genes, suggesting a trend of regional differences. These findings suggest regional distinctions among the ticks and their bacterial compositions.
ILC2 cells promote lung cancer and accumulate in tumors concomitantly with immune-suppressive cells in humans and mice
Authors: Bahhar Ilham , Eş Zeynep , Köse Oğuzhan , Turna Akif , Gunluoglu Mehmet Zeki , Çakır Aslı , Duralı Deniz , Magnusson Fay C. 
Published: May 2023

ABSTRACTIt is now clear that group 2 innate lymphoid cells (ILC2) play crucial and sometimes opposing roles in the lung, such as restoring barrier function and integrity after viral infections or, on the contrary, exacerbating inflammation and tissue damage in allergic asthma. However, their role in lung cancer is still unclear. Here, we report that human non-small cell lung cancer patients bear increased frequencies of ILC2s in tumors, normal lung tissue and peripheral blood (PB) as compared to PB from healthy donors (HDs). Frequencies of Foxp3+regulatory T cells were also increased in NSCLC patients, concomitantly with ILC2s. In mice bearing heterotopic lung cancer, adoptive transfer of ILC2s led to increased tumor growth and reduced survival. The frequencies of monocytic myeloid-derived suppressor cells (M-MDSCs) were found to be increased in the tumors of mice that received ILC2s as compared to controls. Overall, our results indicate that ILC2 cells play a pro-tumoral role in lung cancer potentially by recruiting immune-suppressive cells to the tumors.
Evaluation of three sets of advanced backcrosses of eggplant with wild relatives from different genepools under low N fertilization conditions
Authors: Villanueva Gloria , Plazas Mariola , Gramazio Pietro , Moya Reyes D. , Prohens Jaime , Vilanova Santiago 
Published: May 2023

AbstractThe development of new cultivars with improved nitrogen use efficiency (NUE) is key for implementing sustainable agriculture practices. Crop wild relatives (CWRs) provide valuable genetic resources for breeding programs aimed at achieving this goal. In this study, three eggplant (Solanum melongena) accessions together with their advanced backcrosses (ABs; BC3 to BC5 generations) with introgressions from the wild relativesS. insanum,S. dasyphyllum, andS. elaeagnifoliumwere evaluated for 22 morpho-agronomic, physiological, and N use efficiency (NUE) traits under low nitrogen fertilization conditions. The threeS. melongenarecurrent parents were also evaluated under control (normal) N fertilization. Reduction of N fertilization in the parents resulted in decreased chlorophyll content-related traits, aerial biomass, stem diameter and yield, and increased NUE, nitrogen uptake efficiency (NUpE), and nitrogen utilization efficiency (NUtE). However, the decrease in yield was moderate, ranging between 62.6% and 72.6%. A high phenotypic variation was observed within each of the three sets of ABs under low nitrogen conditions, with some individuals displaying improved transgressive characteristics over the recurrent parents. Genotyping with the SPET 5k probes platform revealed a high, although variable, degree of recovery of the recurrent parent genome in the ABs and allowed the identification of 16 QTLs. Different allelic effects were observed for the introgressed QTL alleles. Several candidate genes were identified in the QTL regions associated with plant growth, yield, fruit size, and NUE-related parameters. Our results show that eggplant materials with introgressions from CWRs can result in a dramatic impact in eggplant breeding for a more sustainable agriculture.
Nuclear export is a limiting factor in eukaryotic mRNA metabolism
Authors: Müller Jason M. , Moos Katharina , Baar Till , Zumer Kristina , Tresch Achim 
Published: May 2023

AbstractThe eukaryotic mRNA life cycle includes transcription, nuclear mRNA export and degradation. To quantify all these processes simultaneously, we perform thiol-linked alkylation after metabolic labeling of RNA with 4-thiouridine (4sU), followed by sequencing of RNA (SLAM-seq) in the nuclear and cytosolic compartments. We develop a model that reliably quantifies mRNA synthesis, nuclear export, and nuclear and cytosolic degradation rates on a genome-wide scale. We find that nuclear degradation of polyadenylated mRNA is negligible and nuclear mRNA export is slow, while cytosolic mRNA degradation is comparatively fast. Consequently, an mRNA molecule generally spends most of its life in the nucleus. We also observe large differences in the nuclear export rates of different 3’UTR transcript isoforms. Furthermore, we identify genes whose expression is abruptly induced upon metabolic labeling. These transcripts are exported substantially faster than average mRNAs, suggesting the existence of alternative export pathways. Our results highlight nuclear mRNA export as a limiting factor in mRNA metabolism and gene regulation.
Evaluation of a set of eggplant (Solanum melongena) lines with introgressions ofS. incanumunder water stress conditions
Authors: Flores-Saavedra Martín , Gramazio Pietro , Vilanova Santiago , Mircea Diana M. , Ruiz-González Mario X. , Vicente Óscar , Prohens Jaime , Plazas Mariola 
Published: May 2023

AbstractAs access to irrigation water becomes increasingly limited, introgression of relevant genomic regions from drought-tolerant wild genotypes is a promising breeding strategy for crop plants. In this study, nine eggplant (Solanum melongena) introgression lines (ILs) covering altogether 71.6% of the genome of the donor wild relative parentS. incanumwere evaluated for drought tolerance under water stress conditions. Plants at the five true leaves stage were irrigated at either 100% (control) or 30% (water stress) field capacity for 14 days, and growth and biochemical traits were measured. Reduced irrigation resulted in decreased growth and increased levels of stress markers such as proline and malondialdehyde. Most ILs had lower growth and biomass production than the cultivated parent under both conditions. However, the wild alleles for two QTLs related to stem and root dry weight (dwt8anddwr6%) conferred improved tolerance to water stress. In addition, severalS. incanumalleles had a positive effect on important traits that may improve yield under drought conditions, such as leaf water content (lwc12%), water use efficiency (wue1%) and chlorophyll content (chl2andchl8%). Fine-mapping of the QTLs for tolerance and reducing linkage drag with regions affecting growth will be crucial for significantly improving eggplant drought tolerance through introgression breeding.
Drivers of plankton community structure in intermittent and continuous coastal upwelling systems–from microscale in-situ imaging to large scale patterns
Authors: Schmid Moritz S , Sponaugle Su , Sutherland Kelly R , Cowen Robert K 
Published: May 2023

AbstractEastern Boundary Systems support major fisheries whose early life stages depend on upwelling production. Upwelling can be highly variable at the regional scale, with substantial repercussions for new productivity and microbial loop activity. A holistic assessment of plankton community structure is challenging due to the range in body forms and sizes of the taxa. Thus, studies that integrate the classic trophic web based on new production with the microbial loop are rare. Underwater imaging can overcome this limitation, and together with machine learning, enables fine resolution studies spanning large spatial scales. We used the In-situ Ichthyoplankton Imaging System (ISIIS) to investigate the drivers of plankton community structure in the northern California Current, sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA, respectively. The non-invasive imaging of particles and plankton (250μm –15cm) over 1644km (30 transects) in the winters and summers of 2018 and 2019 yielded 1.194 billion classified plankton images. The imaged plankton community ranged from protists, crustaceans, and gelatinous taxa to larval fishes. To assess community structure, >2000 single-taxon distribution profiles were analyzed using high resolution spatial correlations. Co-occurrences on the NH line were consistently significantly higher off-shelf while those at TR tended to be highest on-shelf. Taxa co-occurrences at TR increased significantly with upwelling strength and in 2019 TR summer co-occurrences were similar to those on the NH line. Random Forests models identified the concentrations of microbial loop taxa such as protists,Oithonacopepods, and appendicularians as important drivers of co-occurrences at NH line, while at TR, cumulative upwelling and chlorophyll a were of the highest importance. Our results indicate that the microbial loop is actively driving plankton community structure in intermittent upwelling systems such as the NH line and may induce temporal stability. Where upwelling is more continuous such as at TR, primary production may dominate patterns of community structure, obscuring the underlying role of the microbial loop. Future changes in upwelling strength are likely to disproportionately affect plankton community structure in continuous upwelling regions, while high microbial loop activity enhances community structure resilience.
Draft genome sequence of Stenotrophomonas goyisp. nov., a novel bacterium associated with the algaChlamydomonas reinhardtii
Authors: Torres María Jesus , Fakhimi Neda , Dubini Alexandra , González-Ballester David 
Published: May 2023

ABSTRACTStenotrophomonas goyisp. nov. has been isolated from a contaminated algal culture (Chlamydomonas reinhardtii). Its genome has been fully sequenced (4,487,389 base pairs) and a tentative annotation is provided (4,147 genes). The genome information suggests thatS. goyisp. nov. is unable to use sulfate and nitrate as sulfur and nitrogen sources, respectively. Growth tests have confirmed the dependence of the sulfur-containing amino acids methionine and cysteine. The potential biotechnological interest of this bacteria is discussed here and in a related research paper (Fakhimi et al., 2023b).