bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grazers and predators mediate the post-settlement bottleneck in Caribbean octocoral forests
Authors: Wells Christopher D. , Benz Joseph , Tonra Kaitlyn J. , Anderson Emily R. , Lasker Howard R. 
Published: August 2022

AbstractCaribbean octocorals have not suffered the decades long decline in abundance that has plagued reef-building scleractinian corals. Their success and the formation of octocoral forests has been attributed to their continuing recruitment to reef habitats. Assessing the processes controlling recruitment is essential to understanding the success of octocorals and predicting their future. Benthic grazers on coral reefs can facilitate the growth and recruitment of corals by reducing the abundance of competitive algal turfs and macroalgae or hinder corals through predation of coral tissue and recruits. We assessed the effects of grazing by fishes and the sea urchinDiadema antillarumand mesofaunal predation on octocoral recruitment in a series of manipulative experiments using varying grazer/predator exclusion and inclusion conditions inin situandex situexperiments. Exposure to fish and urchin grazing significantly reduced survival and recruitment of single-polyp octocorals, while turf-associated mesofauna did not significantly affect neither recruitment nor survival. We also found a positive relationship between octocoral recruitment and turf algae, a potential related response to the deleterious effect of grazing exposure. These data suggest that grazers and predators mediate the mortality bottleneck characteristic of recruitment. Thus, the declines in the abundance of grazing fishes and urchins throughout the Caribbean may have contributed to the increase in abundance of octocorals in the Caribbean, concurrent with the loss of scleractinians.
The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe
Authors: Masunaga Aki , Mansfield Michael J , Tan Yongkai , Liu Andrew W , Bliznina Aleksandra , Barzaghi Paolo , Hodgetts Tamara L , Ferrández-Roldán Alfonso , Cañestro Cristian , Onuma Takeshi A , Plessy Charles , Luscombe Nicholas M 
Published: August 2022

AbstractAppendicularian tunicates are some of the most abundant mesozooplankton organisms with key roles in marine trophic webs and global carbon flux. Like most appendicularians with cosmopolitan distributions, Oikopleura dioica Fol, 1872 is considered a single species worldwide based on morphological features that distinguish them from other appendicularians. Despite their abundance however, there are still only ∼70 described appendicularian species, compared with over 2,800 ascidian tunicates. Here we perform a molecular phylogenetic, morphological, and reproductive assessment of O. dioica specimens collected from the Ryukyu Archipelago, mainland Japan, and Europe. The specimens are morphologically very similar, with only detailed examination of the oikoplastic epithelium and quantitative measurements revealing minor distinguishing characteristics. Phylogenetic analyses of the ribosomal gene loci and mitochondrial cytochrome oxidase I (COI) gene strongly indicate that they form three separate genetic clades despite their morphological similarities. Finally, in vitro crosses between the Ryukyu and mainland Japanese specimens show total prezygotic reproductive isolation. Our results reveal that the current taxonomic O. dioica classification likely hides multiple cryptic species, highlighting the genetic diversity and complexity of their population structures. Cryptic organisms are often hidden under a single species name because their morphological similarities make them difficult to disinguish and their correct identification is fundamental to understanding Earth’s biodiversity. O. dioica is an attractive model to understand how morphological conservation can be maintained despite pronounced genetic divergence.
CRISPR/Cas9 mutants delineate roles ofPopulus FTandTFL1/CEN/BFTfamily members in growth, dormancy release and flowering
Authors: Sheng Xiaoyan , Mahendra R. Ayeshan , Wang Chieh-Ting , Brunner Amy M. 
Published: August 2022

AbstractVegetative and reproductive phase change and phenology are economically and ecologically important traits. Trees typically require several years of growth before flowering and once mature, seasonal control of the transition to flowering and flower development is necessary to maintain vegetative meristems and for reproductive success. Members of two related gene subfamilies,FLOWERING LOCUST (FT)andTERMINAL FLOWER1 (TFL1)/CENTRORADIALIS (CEN)/BROTHER OF FT AND TFL1 (BFT), have antagonistic roles in flowering in diverse species and roles in vegetative phenology in trees, but many details of their functions in trees have yet to be resolved. Here, we used CRISPR/Cas9 to generate single and double mutants involving the fivePopulus FTandTFL1/CEN/BFTgenes.ft1mutants exhibited wild-type-like phenotypes in long days and short days, but after chilling to release dormancy showed delayed bud flush and GA3could compensate for theft1mutation. After rooting and generating some phytomers in tissue culture, bothcen1andcen1ft1mutants produced terminal as well as axillary flowers, indicating that thecen1flowering phenotype is independent ofFT1. Some axillary meristems initially generated phytomers and in potted plants, the timing of flowering in these shoots correlated with upregulation ofFT2in maturing leaves, suggesting that, in long days,CEN1antagonizesFT2promotion of flowering but enablesFT2promotion of shoot growth by maintaining indeterminacy of the shoot apical meristem.CEN1showed distinct circannual expression patterns in vegetative and reproductive tissues and comparison with the expression patterns ofFT1andFT2suggest that the relative levels ofCEN1compared toFT1andFT2regulate multiple phases of vegetative and reproductive seasonal development.
Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1 in promoting post-transcriptional transgene silencing
Authors: Bazin Jérémie , Elvira-Matelot Emilie , Blein Thomas , Jauvion Vincent , Bouteiller Nathalie , Cao Jun , Crespi Martin D. , Vaucheret Hervé 
Published: August 2022

AbstractBesides regulating splicing, the conserved spliceosome component SmD1 was shown to promote posttranscriptional silencing of sense transgenes (S-PTGS). Here, we show that the conserved spliceosome component PRP39a also plays a role in S-PTGS. However, PRP39a and SmD1 actions appear distinct in both splicing and S-PTGS. Indeed, RNA-seq analysis of prp39a and smd1 mutants identified different sets of deregulated mRNAs and non-coding RNAs, both at expression level and alternative splicing genome-wide. Moreover, double mutant analyses involving prp39a or smd1 and RNA quality control (RQC) mutants revealed genetic interactions of SmD1 and PRP39a with distinct nuclear RQC machineries, suggesting synergistic rather than redundant roles in the RQC/PTGS interplay. Supporting this hypothesis, a prp39a smd1 double mutant exhibited enhanced suppression of S-PTGS compared with single mutants. Because no major changes in the expression of PTGS or RQC components or in small RNA production were identified in prp39a and smd1 mutants, and because prp39a and smd1 mutations do not alter PTGS triggered by inverted-repeat transgenes directly producing dsRNA (IR-PTGS), PRP39a and SmD1 seem to synergistically promote a step specific to S-PTGS. We propose that, independent of their specific roles in splicing, PRP39a and SmD1 limit 3’-to-5’ and 5’-to-3’ degradation of transgene aberrant RNAs, respectively, thus favoring the export of aberrant RNAs to the cytoplasm where their transformation into dsRNA initiates S-PTGS.
Distantly related hepaciviruses share common entry factor, Claudin-1
Authors: Toon Kamilla , Kalemera Mphatso D , Palor Machaela , Rose Nicola J. , Takeuchi Yasuhiro , Grove Joe , Mattiuzzo Giada 
Published: August 2022

AbstractDue to increased and broadened screening efforts, the last decade has seen a rapid expansion in the number of viral species classified into the Hepacivirus genus. Conserved genetic features of hepaciviruses suggest they have undergone specific adaptation and evolved to hijack similar host proteins for efficient propagation in the liver. Here, we developed pseudotyped viruses to elucidate the entry factors of GB virus-B (GBV-B), the first hepacivirus described in an animal, closely related to hepatitis C virus (HCV). GBV-B pseudotyped viruses (GBVBpp) were shown to be uniquely sensitive to the serum of tamarins infected with GBV-B, validating their usefulness as a surrogate for GBV-B entry studies. We screened GBVBpp infection of hepatoma cell lines CRISPR/Cas9-engineered to ablate expression of individual HCV receptors/entry factors and found that claudin-1 is essential for GBV-B infection, indicating GBV-B and HCV share a common entry factor. Our data suggest that claudin-1 facilitates HCV and GBV-B entry through distinct mechanisms since the former requires the first extracellular loop and the latter is reliant on the second extracellular loop. The implication of this sharing of claudin-1 as an entry factor between these two hepaciviruses on their tissue tropism and evolutionary relationships will be discussed.ImportanceHepatitis C virus (HCV) is a major public health burden; approximately 58 million individuals have chronic HCV infection which could lead to cirrhosis and liver cancer. To achieve the World Health Organisation target of eliminating hepatitis by 2030, new therapeutics and vaccines are needed. Understanding how HCV enters the cells will inform the design of new vaccines and treatments, targeting the first stage of HCV infection. However, the entry mechanism is complex and sparsely described. Studying the entry of related hepaciviruses will increase the knowledge of the molecular mechanisms of the first stages of HCV infection, such as the membrane fusion, and inform structure-guided HCV vaccine design; in this work we have identified a protein, Claudin-1, which facilitates the entry of HCV-related hepacivirus, but with a mechanism not described for HCV. Similar work on other hepaciviruses may unveil commonality of entry factors and possibly new mechanisms.
In silico discovery of repetitive elements as key sequence determinants of 3D genome folding
Authors: Gunsalus Laura M. , Keiser Michael J. , Pollard Katherine S. 
Published: August 2022

AbstractNatural and experimental genetic variants can modify DNA loops and insulating boundaries to tune transcription, but it is unknown how sequence perturbations affect chromatin organization genome-wide. We developed an in silico deep-learning strategy to quantify the effect of any insertion, deletion, inversion, or substitution on chromatin contacts and systematically scored millions of synthetic variants. While most genetic manipulations have little impact, regions with CTCF motifs and active transcription are highly sensitive, as expected. However, our analysis also points to noncoding RNA genes and several families of repetitive elements as CTCF motif-free DNA sequences with particularly large effects on nearby chromatin interactions, sometimes exceeding the effects of CTCF sites and explaining interactions that lack CTCF. We anticipate that our available disruption tracks may be of broad interest and utility as a measure of 3D genome sensitivity and our computational strategies may serve as a template for biological inquiry with deep learning.
Effects of early life stress and subsequent re-exposure to stress on neuronal activity in the lateral habenula
Authors: Webster Jack F. , Beerens Sanne , Wozny Christian 
Published: August 2022

AbstractEarly life stress can result in depression in humans and depressive-like behaviour in rodents. In various animal models of depression, the lateral habenula (LHb) has been shown to become hyperactive immediately after early life stress. However, whether these pathological changes persist into adulthood is less well understood. Hence, we utilised the maternal separation (MS) model of depression to study how early life stress alters LHb physiology and depressive behaviour in adult mice. We find that only a weak depressive phenotype persists into adulthood which surprisingly is underpinned by LHb hypoactivity in acute slices, accompanied by alterations in both excitatory and inhibitory signalling. However, while we find the LHb to be less active at rest, we report that the neurons reside in a sensitised state where they are more responsive to re-exposure to stress in adulthood in the form of acute restraint, thus priming them to respond to aversive events with an increase in neuronal activity mediated by changes in glutamatergic transmission. These findings thus suggest that in addition to LHb hyperactivity, hypoactivity likely also promotes an adverse phenotype. Re-exposure to stress results in the reappearance of LHb hyperactivity offering a possible mechanism to explain how depression relapses occur following previous depressive episodes.
SARS-CoV-2 specific plasma cells acquire the phenotype of long-lived plasma cells in the human bone marrow
Authors: Schulz Axel R. , Hirseland Heike , Diekmann Lisa-Marie , Reinke Simon , Hardt Sebastian , Niedobitek Antonia , Mei Henrik E. 
Published: August 2022

AbstractEstablishment of long-lived plasma cells (PC) in the bone marrow (BM) is important for the development of long-term specific humoral immunity. While SARS-CoV-2-specific, resting, affinity-matured, IgG-secreting plasma cells were described in human bone marrow approx. 6-7 months after infection or vaccination, the long-term durability of these PC remains unclear. We here show that approximately 20% of SARS-CoV-2-specific human BM plasma cells, including RBD-specific PC accommodate the phenotype of long-lived plasma cells, characterized by the lack of CD19 and/or CD45. This result provides evidence in support of the emergence of persistent SARS-CoV-2 specific plasma cells in humans sustaining the durable production of specific serum IgG protecting against severe courses of COVID-19.
Functional dissociation of the language network and other cognition in early childhood
Authors: Hiersche K.J. , Schettini E. , Li J. , Saygin Z.M. 
Published: August 2022

AbstractIs language distinct from other cognition during development? Does neural machinery for language emerge from general-purpose neural mechanisms, becoming tuned for language after years of experience and maturation? Answering these questions will shed light on the origins of domain-specificity in the brain. We address these questions using precision fMRI and found young children (35 months-9 years) show domain-specific, left-lateralized language activation, and the language network is not responsive to domain-general cognitive load. Additionally, the cortically adjacent multiple demand network is selective to cognitive load, but not to language. These networks show higher within vs. between-network functional connectivity. This connectivity is stable across ages (examined cross-sectionally and longitudinally), whereas language responses increase with age and across-time within subject, reflecting a domain-specific developmental change. Overall, these findings suggest that domain-specificity, even for uniquely human cognition like language, develops early and distinctly from mechanisms that presumably support other human cognition.Significance StatementThis study provides evidence of a double dissociation between neural processors for language and domain-general cognition (specifically, cognitive load) in young children. These results refute previous claims that linguistic function emerges from domain-general mechanisms supporting non-linguistic, higher-order cognition, and with both cross-sectional and longitudinal analyses, show that the continued development of linguistic specialization is also unrelated to domain-general mechanisms that support cognitive flexibility and executive function. This work emphasizes the importance of single-subject fMRI analyses with multiple tasks to explicitly dissociate cognitive constructs, and the importance of longitudinal research for scientific rigor, even in toddlers and preschoolers who are difficult to image with fMRI.
TheSolanum americanumpangenome and effectoromics reveal new resistance genes against potato late blight
Authors: Lin Xiao , Jia Yuxin , Heal Robert , Prokchorchik Maxim , Sindalovskaya Maria , Olave-Achury Andrea , Makechemu Moffat , Fairhead Sebastian , Noureen Azka , Heo Jung , Witek Kamil , Smoker Matthew , Taylor Jodie , Shrestha Ram-Krishna , Lee Yoonyoung , Zhang Chunzhi , Park Soon Ju , Sohn Kee Hoon , Huang Sanwen , Jones Jonathan D. G. 
Published: August 2022

AbstractLate blight caused by the oomycete pathogenPhytophthora infestanscontinues to cause major worldwide losses in potato and tomato. Most accessions ofSolanum americanum, a globally distributed, wild Solanaceae plant, are highly resistant to late blight. We generated high-quality reference genomes of fourS. americanumaccessions, re-sequenced 52 accessions, and we defined variation in the NLR immune receptor genes (theS. americanumNLRome). We further screened for variation in recognition of ∼315P. infestansRXLR effectors in 52S. americanumaccessions. Using these genotypic and phenotypic data, we cloned three novel NLR-encoding genesRpi-amr4, Rpi-amr16andRpi-amr17, and determined their corresponding RXLR effector genesAvramr4(PITG_22825),Avramr16(PITG_02860) andAvramr17(PITG_04373) fromP. infestans. These genomic resources and methodology will support efforts to convert potato into a “nonhost” of late blight and can be applied to diseases of other crops.
Overlapping and specialized roles of tomato phytoene synthase isoforms PSY1 and PSY2 in carotenoid and ABA production
Authors: Ezquerro Miguel , Burbano Esteban , Rodriguez-Concepcion Manuel 
Published: August 2022

AbstractCarotenoids are plastidial isoprenoids required for photosynthesis and production of hormones such as abscisic acid (ABA) in all plants. In tomato (Solanum lycopersicum), carotenoids also provide color to flowers and ripe fruit. Phytoene synthase (PSY) catalyzes the first and main flux-controlling step of the carotenoid pathway. Three PSY isoforms are present in tomato, PSY1 to 3. Mutants have shown that PSY1 is the isoform providing carotenoids for fruit pigmentation but it is dispensable in photosynthetic tissues. No mutants are available for PSY2 or PSY3, but their expression profiles suggest a main role for PSY2 in leaves and PSY3 in roots. To further investigate isoform specialization with genetic tools, we created tomato edited lines defective in PSY1 and PSY2 in the MicroTom background. The albino phenotype of lines lacking both PSY1 and PSY2 confirmed that PSY3 does not contribute to carotenoid biosynthesis in shoot tissues. Our work further shows that carotenoid production in tomato shoots relies on both PSY1 and PSY2 but with different contributions in different tissues. PSY2 is the main isoform for carotenoid biosynthesis in leaf chloroplasts, but the supporting role of PSY1 is particularly important under high light. PSY2 also contributes to the production of carotenoids in flower petals and, to a lower extent, fruit chromoplasts. Most interestingly, our results demonstrate that fruit growth and ripening is controlled by ABA produced in the pericarp from PSY1-derived precursors whereas PSY2 provides precursors for ABA synthesis in seeds to control germination.
Cytoplasmic tail of the putative polycystin channel Pkd2 regulates its clustering in the fission yeast eisosomes
Authors: Malla Mamata , Sinha Debatrayee , Chowdhury Pritha , Bisesi Benjamin Thomas , Chen Qian 
Published: August 2022

AbstractPolycystins are a family of conserved ion channels, mutations of which lead to human genetic disorder Autosomal Dominant Polycystic Kidney Disease. The unicellular model organism fission yeast Schizosacchromyces pombe possesses single essential polycystin Pkd2 that localizes to the plasma membrane and is required for cell proliferation. Here, we carried out a functional analysis of Pkd2 based on its Alphafold predicted structure. It consisted of N-terminal lipid-binding (LBD), central transmembrane (TMD) and C-terminal cytoplasmic (CCD) domains. LBD assumes a unique immunoglobulin-fold, while TMD contains nine transmembrane helices. Both were essential. Although the mostly disordered CCD was not, its removal led to clustering of Pkd2 in eisosomes, a microdomain of the plasma membrane. Inhibiting eisosome assembly prevented the clustering but disrupting ER-PM contacts further increased it. Pkd2 shared similar structure with two other putative channels Trp663 and Trp1322, but their intracellular localization and function diverged from each other. Replacing LBD with that of Trp663 partially restored the function of Pkd2, but TMD could not be replaced by either that of Trp663 or human polycystins. We concluded that both the plasma membrane microdomains and cytoplasmic tail of Pkd2 regulate the cell surface clustering of this putative ion channel.
Pandemic uncertainty and sectoral stock returns predictability in South Africa
Authors: Fasanya Ismail Olaleke 
Published: August 2022

PurposeIn this paper, the author examines the role of uncertainty due to pandemic on the predictability of sectoral stock returns in South Africa. This is motivated by the ongoing global pandemic, COVID-19, in predicting sector stock returns.Design/methodology/approachThe study considers estimation of dynamic panel data with dynamic common correlated effects estimator and two pair-wise forecast measures, namely Campbell and Thompson (2008) and Clark and West (2007) tests in dealing with the nested predictive models.FindingsThe results show that pandemic uncertainty has a negative and statistically significant effect on the different sector returns, implying that sector stock returns decline as the pandemic outbreak becomes more pronounced. While the single predictor model consistently outperforms the historical average model both for in-sample and out-of-sample, controlling for other macroeconomic variables effect improves the forecast accuracy of infectious diseases uncertainty. These results are consistently robust to both the in-sample and out-of-sample forecast periods, outliers and heterogeneity. These results have implications for portfolio diversification strategies, which we set aside for future research.Originality/valueThe empirical literature is satiated with studies on how news can predict economic and financial variables, however, the role of uncertainty due to infectious diseases in the stock return predictability especially at the sectoral level is less understudied, this is the main contribution of the study.