bluuebunny/crossref_metadata_2025_split huggingface dataset:
Developmental neuroanatomy of the Rosy Bitterling Rhodeus ocellatus (Teleostei: Cypriniformes)—A microCT study
Authors: Yi Wenjing , Mueller Thomas , Rücklin Martin , Richardson Michael K. 
Published: October 2021

ABSTRACTBitterlings are a group of teleost fish (Cyprinifromes: Acheilanathidae) notable for their brood parasitic lifestyle. Bitterling embryos develop as parasites inside the gill chamber of their freshwater mussel hosts. However, little is known about brain development in this species. Here, we have imaged the development of the brain of the Rosy Bitterling (Rhodeus ocellatus) at four embryonic stages (165, 185, 210, 235 hours post-fertilization) using micro-computed tomography (microCT) with special emphasis on developmental regionalization and brain ventricular organization. We provide a detailed neuroanatomical account of the development of the brain divisions with reference to The Atlas of Early zebrafish Brain Development and the updated prosomeric model. Segmentation and three-dimensional visualization of the ventricular system were performed in order to clarify changes in the longitudinal brain axis as a result of cephalic flexure during development. During early embryonic and larval development, we find that histological differentiation, tissue boundaries, periventricular proliferation zones, and ventricular spaces are all recognizable using microCT. Importantly, our approach is validated by the fact that the profile of CT values displayed here in the bitterling brain are consistent with genoarchitecture identified in previous studies. We also find developmental heterochrony of the inferior lobe in the Rosy Bitterling compared to the zebrafish. Our study provides a foundation for future studies of the brain development in the Rosy Bitterling, a valuable model species for studying the evolutionary adaptations associated with brood parasitism.
Complete pan-plastome sequences enable high resolution phylogenetic classification of sugar beet and closely related crop wild relatives
Authors: Sielemann Katharina , Pucker Boas , Schmidt Nicola , Viehöver Prisca , Weisshaar Bernd , Heitkam Tony , Holtgräwe Daniela 
Published: October 2021

AbstractBackgroundAs the major source of sugar in moderate climates, sugar-producing beets (Beta vulgarissubsp.vulgaris) have a high economic value. However, the low genetic diversity within cultivated beets requires introduction of new traits, for example to increase their tolerance and resistance attributes – traits that often reside in the crop wild relatives. For this, genetic information of wild beet relatives and their phylogenetic placements to each other are crucial. To answer this need, we sequenced and assembled the complete plastome sequences from a broad species spectrum across the beet generaBetaandPatellifolia, both embedded in the Betoideae (order Caryophyllales). This pan-plastome dataset was then used to determine the wild beet phylogeny in high-resolution.ResultsWe sequenced the plastomes of 18 closely related accessions representing 11 species of the Betoideae subfamily and provided high-quality plastome assemblies which represent an important resource for further studies of beet wild relatives and the diverse plant order Caryophyllales. Their assembly sizes range from 149,723 bp (Beta vulgarissubsp.vulgaris) to 152,816 bp (Beta nana), with most variability in the intergenic sequences. Combining plastome-derived phylogenies with read-based treatments based on mitochondrial information, we were able to suggest a unified and highly confident phylogenetic placement of the investigated Betoideae species.Our results show that the genusBetacan be divided into the two clearly separated sectionsBetaandCorollinae. Our analysis confirms the affiliation ofB. nanawith the otherCorollinaespecies, and we argue against a separate placement in theNanaesection. Within thePatellifoliagenus, the two diploid speciesPatellifolia procumbensandPatellifolia webbianaare, regarding the plastome sequences, genetically more similar to each other than to the tetraploidPatellifolia patellaris. Nevertheless, all threePatellifoliaspecies are clearly separated.ConclusionIn conclusion, our wild beet plastome assemblies represent a new resource to understand the molecular base of the beet germplasm. Despite large differences on the phenotypic level, our pan-plastome dataset is highly conserved. For the first time in beets, our whole plastome sequences overcome the low sequence variation in individual genes and provide the molecular backbone for highly resolved beet phylogenomics. Hence, our plastome sequencing strategy can also guide genomic approaches to unravel other closely related taxa.
Membrane Contact Sites Between Chloroplasts and Pathogen Interface Underpin Plant Focal Immune Responses
Authors: Yuen Enoch Lok Him , Savage Zachary , Adamkova Vanda , Vuolo Cristina , Zhou Yuanyang , Tumtas Yasin , Erickson Jessica Lee , Prautsch Jennifer , Balmez Andrada I. , Stuttmann Johannes , Duggan Cian , Rivetti Francesco , Molinari Camilla , Schattat Martin , Bozkurt Tolga O. 
Published: October 2021

AbstractCommunication between cellular organelles is essential for mounting effective innate immune responses to eliminate pathogens. In plants, the transport of cellular organelles to pathogen penetration sites and their assembly around the host membrane delineating plant-pathogen interface are well-documented. However, whether organelles associate with these specialized plant-pathogen membrane interfaces and the extent to which this process contributes to immunity remain unknown. Here, we discovered defense-related membrane contact sites (MCS) comprising a membrane tethering complex between chloroplasts and the extrahaustorial membrane (EHM) surrounding the pathogen haustorium. The assembly of this membrane tethering complex relies on the association between the chloroplast outer envelope protein CHLOROPLAST UNUSUAL POSITIONING 1 (CHUP1), and its plasma membrane-associated partner, KINESIN-LIKE PROTEIN FOR ACTIN-BASED CHLOROPLAST MOVEMENT 1 (KAC1). Our biochemical assays revealed that CHUP1 and KAC1 interact, while infection cell biology demonstrated their co-accumulation in foci where chloroplasts contact the EHM. Genetic depletion of CHUP1 or KAC1 reduces the deposition of callose—a cell wall material typically deployed to fortify pathogen penetration resistance—around the haustorium, without affecting other core immune processes. Our findings suggest that the chloroplast-EHM attachment complex positively regulates plant focal immunity, revealing the key components and their potential roles in the targeted deposition of defense components at the pathogen interface. These results advance our understanding of organelle-mediated immune responses and highlight the significance of MCS in plant-pathogen interactions.
Connexins evolved after early chordates lost innexin diversity
Authors: Welzel Georg , Schuster Stefan 
Published: October 2021

AbstractGap junction channels are formed by two unrelated protein families. Non-chordates use the primordial innexins, while chordates use connexins that superseded the gap junction function of innexins. Chordates retained innexin-homologs, but N-glycosylation prevents them from forming gap junctions. It is puzzling why chordates seem to exclusively use the new gap junction protein and why no chordates should exist that use non-glycosylated innexins to form gap junctions. Here, we identified glycosylation sites of 2270 innexins from 152 non-chordate and 274 chordate species. Among all chordates, we found not a single innexin without glycosylation sites. Surprisingly, the glycosylation motif is also widespread among non-chordate innexins indicating that glycosylated innexins are not a novelty of chordates. In addition, we discovered a loss of innexin diversity during the early chordate evolution. Most importantly, the most basal living chordates, which lack connexins, exclusively possess innexins with glycosylation sites. A bottleneck effect might thus explain why connexins have become the only protein used to form chordate gap junctions.
Peroxisome-derived hydrogen peroxide can modulate the sulfenylation profiles of key redox signaling proteins
Authors: Lismont Celien , Revenco Iulia , Li Hongli , Costa Cláudio F. , Lenaerts Lisa , Hussein Mohamed A. F. , De Bie Jonas , Knoops Bernard , Van Veldhoven Paul P. , Derua Rita , Fransen Marc 
Published: October 2021

AbstractEver since the first characterization of peroxisomes, a central theme has been their involvement in cellular hydrogen peroxide (H2O2) metabolism. While the reputation of H2O2 drastically changed from an exclusively toxic molecule to a signaling messenger, the regulatory role of peroxisomes in these signaling events is still largely underappreciated. This is mainly because the number of known protein targets of peroxisome-derived H2O2 is rather limited and testing of specific targets is predominantly based on knowledge previously gathered in related fields of research. To gain a broader and more systematic insight into the role of peroxisomes in redox signaling, an unbiased approach is urgently needed. To accomplish this goal, we have combined a previously developed cell system in which peroxisomal H2O2 production can be modulated with a yeast AP-1-like-based sulfenome mining strategy to inventory protein thiol targets of peroxisome-derived H2O2 in different subcellular compartments. Using this unbiased approach, we were able to identify specific and common targets of peroxisome-derived and exogenous H2O2 in peroxisomes, the cytosol, and mitochondria. We also observed that the sulfenylation kinetics profiles of key targets belonging to different protein families can vary considerably. In addition, we obtained compelling but indirect evidence that peroxisome-derived H2O2 may oxidize at least some of its targets through a redox relay mechanism. In conclusion, given that sulfenic acids function as key intermediates in H2O2 signaling, the findings presented in this study provide initial but critical insight into how peroxisomes may be integrated in the cellular H2O2 signaling network.HighlightsYAP1C-trapping is a robust tool to assess the peroxisomal H2O2-dependent sulfenomeExogenous and peroxisome-derived H2O2 have both common and distinct targetsANXA2, PRDX1, and SKP1 are major targets of peroxisome-derived H2O2The sulfenylation kinetics profiles of key redox-active proteins vary considerablyProduction of H2O2 inside peroxisomes directly impacts the mitochondrial sulfenome
Longitudinal dynamics of human B-cell response at single-cell level in response to Tdap vaccination
Authors: Khatri Indu , Diks Annieck M. , van den Akker Erik B. , Oosten Liesbeth E.M. , Zwaginga Jaap Jan , Reinders Marcel J.T. , van Dongen Jacques J.M. , Berkowska Magdalena A. 
Published: October 2021

AbstractAdaptation of the immune system to mount an adequate immune response against pathogens is a crucial function of the adaptive immune system. To better characterize a successful vaccination response, we performed longitudinal (days 0, 5, 7, 10, and 14 after Boostrix vaccination) analysis of the single cell transcriptome as well as the B-cell receptor (BCR) repertoire (scBCR-rep) in plasma cells of an immunized donor and compared it with baseline B cell characteristics as well as flow cytometry findings.Based on the flow cytometry knowledge and literature findings, we discriminated individual B cell subsets in the transcriptomics data and traced over-time maturation of plasmablasts/plasma cells (PB/PCs) and identified the pathways associated with the plasma cell maturation. We observed that the repertoire in PB/PCs differed from the baseline B cell repertoire e.g. regarding expansion of unique clones in post-vaccination visits, high usage of IGHG1 in expanded clones, increased class switching events post-vaccination represented by clonotypes spanning multiple IGHC classes and positive selection of CDR3 sequences over time. Importantly, the Variable gene family-based clustering of BCRs represented a similar measure as the gene-based clustering, however, certainly improved the clustering of BCRs, as BCRs from duplicated Variable gene families could be clustered together. Finally, we developed a query tool to dissect the immune response to the components of Boostrix vaccine. Using this tool, we could identify the BCRs related to anti-tetanus and anti-pertussis toxoid.Collectively, we developed a workflow which allows description of key features of an ongoing immune response, such as activation of PB/PCs, Ig class switching, somatic hypermutation, and clonal expansion, all of which are hallmarks of antigen exposure.
A sense-antisense RNA interaction promotes breast cancer metastasis via regulation of NQO1 expression
Authors: Culbertson Bruce , Garcia Kristle , Markett Daniel , Asgharian Hosseinali , Chen Li , Fish Lisa , Navickas Albertas , Yu Johnny , Woo Brian , Nanda Scott , Rabinowitz Joshua , Goodarzi Hani 
Published: October 2021

AbstractAntisense RNAs are ubiquitous in human cells, yet the role that they play in healthy and diseased states remains largely unexplored. Here, we developed a computational framework to catalog and profile antisense RNAs and applied it to poorly and highly metastatic breast cancer cell lines. We identified one antisense RNA that plays a functional role in driving breast cancer progression by upregulating the redox enzyme NQO1, and hence named NQO1-antisense RNA or NQO1-AS. This upregulation occurs via a stabilizing interaction between NQO1-AS and its complementary region in the 3’UTR of NQO1 mRNA. By increasing expression of NQO1 protein, breast cancer cells are able to tolerate higher levels of oxidative stress, enabling them to colonize the lung. During this process the cancer cells become dependent on NQO1 to protect them from ferroptosis. We have shown that this dependence can be exploited therapeutically in xenograft models of metastasis. Together, our findings establish a previously unknown role for NQO1-AS in the progression of breast cancer by serving as a post-transcriptional regulator of RNA processing and decay for its sense mRNA.
Low heritability and high phenotypic plasticity of salivary cortisol in response to environmental heterogeneity in a wild pinniped
Authors: Nagel Rebecca , Kaiser Sylvia , Stainfield Claire , Toscani Camille , Fox-Clarke Cameron , Paijmans Anneke J. , Castro Camila Costa , Vendrami David L. J. , Forcada Jaume , Hoffman Joseph I. 
Published: October 2021

AbstractIndividuals are unique in how they interact with and respond to their environment. Correspondingly, unpredictable challenges or environmental stressors often produce an individualized response of the hypothalamic-pituitary-adrenal axis and its downstream effector cortisol. We used a fully crossed, repeated measures design to investigate the factors shaping individual variation in baseline cortisol in Antarctic fur seal pups and their mothers. Saliva samples were collected from focal individuals at two breeding colonies, one with low and the other with high density, during two consecutive years of contrasting food availability. Mothers and pups were sampled concurrently at birth and shortly before weaning, while pups were additionally sampled every 20 days. We found that heritability was low for baseline cortisol, while within-individual repeatability and among-individual variability were high. A substantial proportion of the variation in baseline cortisol could be explained in pups and mothers by a combination of intrinsic and extrinsic factors including sex, weight, day, season, and colony of birth. Our findings provide detailed insights into the individualization of endocrine phenotypes and their genetic and environmental drivers in a wild pinniped. Furthermore, the strong associations between cortisol and life history traits that we report in fur seals could have important implications for understanding the population dynamics of species impacted by environmental change.
Artificial reefs geographical location matters more than shape, age and depth for sessile invertebrate colonization in the Gulf of Lion (NorthWestern Mediterranean Sea)
Authors: Blouet Sylvain , Bramanti Lorenzo , Guizien Katell 
Published: October 2021

AbstractArtificial reefs (ARs) have been used to support fishing activities. Sessile invertebrates are essential components of trophic networks within ARs, supporting fish productivity. However, colonization by sessile invertebrates is possible only after effective larval dispersal from source populations, usually in natural habitat. While most studies focused on short term colonization by pioneer species, we propose to test the relevance of geographic location, shape, age and depth of immersion on the ARs long term colonization by species found in natural stable communities in the Gulf of Lion. We recorded the presence of five sessile invertebrates species, with contrasting life history traits and regional distribution in the natural rocky habitat, on ARs with different shapes deployed during two immersion time periods (1985 and the 2000s) and in two depth ranges (<20m and >20m). At the local level (∼5kms), neither shape, depth nor immersion duration differentiated ARs assemblages. At the regional scale (>30kms), colonization patterns differed between species, resulting in diverse assemblages. This study highlights the primacy of geographical positioning over shape, immersion duration and depth in ARs colonization, suggesting it should be accounted for in maritime spatial planning.
Progressive chromatin silencing of ABA biosynthesis gene permits seed germination in Arabidopsis
Authors: Yang Deyue , Zhao Fengli , Zhu Danling , Chen Xi , Kong Xiangxiong , Wu Yufeng , Chen Min , Du Jiamu , Qu Li-jia , Wu Zhe 
Published: October 2021

AbstractSeed germination represents a major developmental switch in plants that is vital to agricultural, but how this process is controlled at the chromatin level remains obscure. Here we demonstrate that successful germination in Arabidopsis requires a chromatin mechanism that progressively silences NCED6, which encodes a rate-limiting enzyme for abscisic acid (ABA) biosynthesis, through the cooperative action of the RNA-binding protein RZ-1 and the polycomb repressive complex 2 (PRC2). Simultaneous inactivation of RZ-1 and PRC2 blocks germination and synergistically derepresses NCEDs and hundreds of genes. At NCED6, by promoting H3 deacetylation and suppressing H3K4me3, RZ-1 facilitates transcriptional silencing and also a H3K27me3 accumulation process that occurs during seed germination and early seedling growth. Genome-wide analysis reveals RZ-1 is preferentially required for transcriptional silencing of many PRC2 targets early during seed germination when H3K27me3 is not yet established. We propose RZ-1 confers a novel silencing mechanism to compensate and coordinate with PRC2. Our work highlights the progressive chromatin silencing of ABA biosynthesis genes via synergized action of the RNA-binding protein RZ1 and PRC2, which is vital for seed germination.
Expression analysis and single-nucleotide polymorphisms of MLPH and PMEL17 genes associated with melanin deposition in Xuefeng black-bone chickens
Authors: Dengyuying  , Pengcanyang  , Liuxu  , Hechangqing  , Guosongchang  , Quxiangyong  
Published: October 2021

AbstractMelanin deposition related genes such as MLPH and PMEL17 play an important role in black-bone chicken. This study was aimed to identify and associate SNPs in the MLPH and PMEL17 genes with melanin content of pectoral muscle (MCPM) in Xuefeng black-bone chicken. A total of 120 Xuefeng black-bone chickens at 120-day-old were randomly selected to measure blackness of pectoral muscle (BPM), according to the degree of BPM selected 22 high blackness (HB) and 22 low blackness (LB) chickens to determine the MCPM, and extract DNA and mRNA. The results indicated that the MCPM in the HB group was higher than in the LB group (P < 0.01), and the L value in the HB group was lower than in the LB group (P < 0.01). And we measured the mRNA expression levels of MLPH and PMEL17 genes in pectoral muscle by quantitative real-time PCR. The results revealed that the mRNA expression levels of MLPH gene (P < 0.05) and PMEL17 gene (P < 0.01) in the HB group was higher than in the LB group, and the mRNA relative expression level of MLPH and PMEL17 genes with MCPM was positive correlation (P < 0.01). And the sequencing results found that a total of 17 SNPs were found in MLPH gene, the C-1411T was associated with MCPM (P < 0.05), there was no difference in MCPM among other locus (P > 0.05). And there were 10 SNPs in PMEL17 gene, the G-1843C, C-2812T, and G-2794A were associated with MCPM (P < 0.05), there was no difference in the MCPM among other locus (P > 0.05). These SNPs could be molecular markers for breeding selection of blackness traits.
Development of a highly sensitive luciferase-based reporter system to study two-step protein secretion in cyanobacteria
Authors: Russo David A. , Zedler Julie A. Z. , Conradi Fabian D. , Schuergers Nils , Jensen Poul Erik , Mullineaux Conrad W. , Wilde Annegret , Pohnert Georg 
Published: October 2021

AbstractCyanobacteria, ubiquitous oxygenic photosynthetic bacteria, interact with the environment and their surrounding microbiome through the secretion of a variety of small molecules and proteins. The release of these compounds is mediated by sophisticated multi-protein complexes, also known as secretion systems. Genomic analyses indicate that protein and metabolite secretion systems are widely found in cyanobacteria; however little is known regarding their function, regulation and secreted effectors. One such system, the type IVa pilus system (T4aPS), is responsible for the assembly of dynamic cell surface appendages, type IVa pili (T4aP), that mediate ecologically relevant processes such as phototactic motility, natural competence and adhesion. Several studies have suggested that the T4aPS can also act as a two-step protein secretion system in cyanobacteria akin to the homologous type II secretion system in heterotrophic bacteria. To determine whether the T4aP are involved in two-step secretion of non-pilin proteins, we developed a NanoLuc-based quantitative secretion reporter for the model cyanobacterium Synechocystis sp. PCC 6803. The NLuc reporter presented a wide dynamic range with at least one order of magnitude more sensitivity than traditional immunoblotting. Application of the reporter to a collection of Synechocystis T4aPS mutants demonstrated that two-step protein secretion in cyanobacteria is independent of T4aP. In addition, our data suggest that secretion differences typically observed in T4aPS mutants are likely due to a disruption of cell envelope homeostasis. This study opens the door to explore protein secretion in cyanobacteria further.ImportanceProtein secretion allows bacteria to interact and communicate with the external environment. Secretion is also biotechnologically relevant, where it is often beneficial to target proteins to the extracellular space. Due to a shortage of quantitative assays, many aspects of protein secretion are not understood. Here we introduce a NanoLuc (NLuc)-based secretion reporter in cyanobacteria. NLuc is highly sensitive and can be assayed rapidly and in small volumes. The NLuc reporter allowed us to clarify the role of type IVa pili in protein secretion and identify mutations that increase secretion yield. This study expands our knowledge on cyanobacterial secretion and offers a valuable tool for future studies of protein secretion systems in cyanobacteria.