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Self-incompatibility (SI) is a complex mechanism that prevents plants from self-fertilizing to preserve and promote genetic variability. The angiosperm species have developed two different SI systems, the sporophytic (SSI) and the gametophytic (GSI) systems. SI is a significant impediment to steady fruit production in fruit tree species of the Rosaceae. In Rosaceae, GSI is genetically regulated via a single locus, named the 'S-locus', which includes a minimum of two polymorphic and relatively intercorrelated S genes: a pistil-expressed S-RNase gene and several pollen-expressed SFBB (S-locus F-Box Brothers) or SFB (S haplotype-specific F-box protein). This necessitates the interaction of S-RNases with the male determinants. Although genetic and molecular analyses of S genes have shown that mutations in both pistils and pollen-specific components induce self-compatibility in many species and cultivars, other genes or molecules outside the S-locus can co-participate in the male gamete rejection in GSI. However, we highlight and synthesize the most recent knowledge on different mechanisms of GSI in Rosaceae in this current review. [ABSTRACT FROM AUTHOR]

Segmented filamentous bacteria (SFB) are members of the commensal intestinal microbiome. They are known to contribute to the postnatal maturation of the gut immune system, but also to augment inflammatory conditions in chronic diseases such as Crohn's disease. Living primary tissue slices are ultrathin multicellular sections of the intestine and provide a unique opportunity to analyze tissue‐specific immune responses ex vivo. This study aimed to investigate whether supplementation of the gut flora with SFB promotes T helper 17 (Th17) cell responses in primary intestinal tissue slices ex vivo. Primary tissue slices were prepared from the small intestine of healthy Taconic mice with SFB‐positive and SFB‐negative microbiomes and stimulated with anti‐CD3/CD28 or Concanavalin A. SFB‐positive and ‐negative mice exhibited distinct microbiome compositions and Th17 cell frequencies in the intestine and complex microbiota including SFB induced up to 15‐fold increase in Th17 cell‐associated mediators, serum amyloid A (SAA), and immunoglobulin A (IgA) responses ex vivo. This phenotype could be transmitted by co‐housing of mice. Our findings highlight that changes in the gut microbiome can be observed in primary intestinal tissue slices ex vivo. This makes the system very attractive for disease modeling and assessment of new therapies. [ABSTRACT FROM AUTHOR]

Self-incompatibility (SI) is a complex mechanism that prevents plants from self-fertilizing to preserve and promote genetic variability. The angiosperm species have developed two different SI systems, the sporophytic (SSI) and the gametophytic (GSI) systems. SI is a significant impediment to steady fruit production in fruit tree species of the Rosaceae. In Rosaceae, GSI is genetically regulated via a single locus, named the ‘S-locus’, which includes a minimum of two polymorphic and relatively intercorrelated S genes: a pistil-expressed S-RNase gene and several pollen-expressed SFBB (S-locus F-Box Brothers) or SFB (S haplotype-specific F-box protein). This necessitates the interaction of S-RNases with the male determinants. Although genetic and molecular analyses of S genes have shown that mutations in both pistils and pollen-specific components induce self-compatibility in many species and cultivars, other genes or molecules outside the S-locus can co-participate in the male gamete rejection in GSI. However, we highlight and synthesize the most recent knowledge on different mechanisms of GSI in Rosaceae in this current review.

Abstract Background Segmented filamentous bacteria (SFB) are intestinal commensal microorganisms that have been demonstrated to induce the innate and adaptive immune responses in mouse and rat hosts. SFB are Gram-positive, spore-forming bacteria that fail to grow optimally under in vitro conditions due to unique metabolic requirements. Recently, SFB have been implicated in improved health and growth outcomes in commercial turkey flocks. To assess the nature and variations in SFB of turkeys and how they may differ from mammalian-associated SFB, the genome of turkey-associated SFB was compared with six representative genomes from murine hosts using an in silico approach. Results The SFB-turkey genome is 1.6 Mb with a G + C content of 26.14% and contains 1,604 coding sequences (CDS). Comparative genome analyses revealed that all the seven SFB strain possesses a common set of metabolic deficiencies and auxotrophies. Specifically, the inability of all the SFB strains to synthesize most of the amino acids, nucleotides and cofactors, emphasizing the importance of metabolite acquisition from the host intestinal environment. Among the seven SFB genomes, the SFB-turkey genome is the largest and contains the highest number of 1,604 predicted CDS. The SFB-turkey genome possesses cellular metabolism genes that are absent in the rodent SFB strains, including catabolic pathways for sucrose, stachyose, raffinose and other complex glycans. Other unique genes associated with SFB-turkey genome is loci for the biosynthesis of biotin, and degradation enzymes to recycle primary bile acids, both of which may play an important role to help turkey associated SFB survive and secure mutualism with its avian host. Conclusions Comparative genomic analysis of seven SFB genomes revealed that each strain have a core set of metabolic capabilities and deficiencies that make these bacteria challenging to culture under ex vivo conditions. When compared to the murine-associated strains, turkey-associated SFB serves as a phylogenetic outgroup and a unique member among all the sequenced strains of SFB. This turkey-associated SFB strain is the first reported non-mammalian SFB genome, and highlights the impact of host specificity and the evolution of metabolic capabilities.

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This study aimed to determine a sustainable design practice approach that can satisfy customer emotions and personal tastes, which designers need in the early stages of the SFD process, and improve environmental performance. The research was conducted through a case study and interviews. For case studies, the specific design methods of fashion brands, which have been ranked sustainable over the last 3 years in the world's top fashion magazines favored by the public, were researched. The results of the case studies were used to draw questions for the in-depth interviews. The results are as follows: first, the design approaches of SFBs were categorized into "ecofriendly materials," "functional durability design," "reuse and remanufacturing," "emotional durability design," and sustainable fashion technology. Each type's specific design approach methods were organized into a checklist for the practice of SFD and then reflected in the interview questions. From the results of the interviews, it was noted that the sustainable design approaches perceived by Korean designers were "eco-friendly materials," "reuse and remanufacturing," and "functional durability design." Moreover, it was mentioned that specific methods of emotional durability design and sustainable fashion technology need to be acquired. By applying the checklist to the interviewees, interview participants could conveniently and quickly recognize how to apply sustainable design through the inventory. This study is significant because it presents a checklist, an efficient tool for sustainable design approaches, and a sustainable design practice method that can satisfy customer emotions and personal tastes and improve environmental performance. [ABSTRACT FROM AUTHOR]

Background: Segmented filamentous bacteria (SFB) are intestinal commensal microorganisms that have been demonstrated to induce the innate and adaptive immune responses in mouse and rat hosts. SFB are Gram-positive, spore-forming bacteria that fail to grow optimally under in vitro conditions due to unique metabolic requirements. Recently, SFB have been implicated in improved health and growth outcomes in commercial turkey flocks. To assess the nature and variations in SFB of turkeys and how they may differ from mammalian-associated SFB, the genome of turkey-associated SFB was compared with six representative genomes from murine hosts using an in silico approach. Results: The SFB-turkey genome is 1.6 Mb with a G + C content of 26.14% and contains 1,604 coding sequences (CDS). Comparative genome analyses revealed that all the seven SFB strain possesses a common set of metabolic deficiencies and auxotrophies. Specifically, the inability of all the SFB strains to synthesize most of the amino acids, nucleotides and cofactors, emphasizing the importance of metabolite acquisition from the host intestinal environment. Among the seven SFB genomes, the SFB-turkey genome is the largest and contains the highest number of 1,604 predicted CDS. The SFB-turkey genome possesses cellular metabolism genes that are absent in the rodent SFB strains, including catabolic pathways for sucrose, stachyose, raffinose and other complex glycans. Other unique genes associated with SFB-turkey genome is loci for the biosynthesis of biotin, and degradation enzymes to recycle primary bile acids, both of which may play an important role to help turkey associated SFB survive and secure mutualism with its avian host. Conclusions: Comparative genomic analysis of seven SFB genomes revealed that each strain have a core set of metabolic capabilities and deficiencies that make these bacteria challenging to culture under ex vivo conditions. When compared to the murine-associated strains, turkey-associated SFB serves as a phylogenetic outgroup and a unique member among all the sequenced strains of SFB. This turkey-associated SFB strain is the first reported non-mammalian SFB genome, and highlights the impact of host specificity and the evolution of metabolic capabilities. [ABSTRACT FROM AUTHOR]

The pollination of self-incompatible diploid sweet cherry is determined by the S-locus alleles. We resolved the S-alleles of 50 sweet cherry cultivars grown in Estonia and determined their incompatibility groups, which were previously unknown for most of the tested cultivars. We used consensus primers SI-19/20, SI-31/32, PaConsI, and PaConsII followed by allele-specific primers and sequencing to identify sweet cherry S-genotypes. Surprisingly, 48% (24/50) of the tested cultivars, including 17 Estonian cultivars, carry the rare S-allele S17, which had initially been described in wild sweet cherries in Belgium and Germany. The S17-allele in Estonian cultivars could originate from 'Leningradskaya tchernaya' (S6|S17), which has been extensively used in Estonian sweet cherry breeding. Four studied cultivars carrying S17 are partly self-compatible, whereas the other 20 cultivars with S17 have not been reported to be self-compatible. The recommended pollinator of seven self-incompatible sweet cherries is of the same S-genotype, including four with S17-allele, suggesting heritable reduced effectiveness of self-infertility. We classified the newly genotyped sweet cherry cultivars into 15 known incompatibility groups, and we proposed four new incompatibility groups, 64–67, for S-locus genotypes S3|S17, S4|S17, S5|S17, and S6|S17, respectively, which makes them excellent pollinators all across Europe. Alternatively, the frequency of S17 might be underestimated in Eastern European populations and some currently unidentified sweet cherry S-alleles might potentially be S17. [ABSTRACT FROM AUTHOR]

Die DINI/nestor AG Forschungsdaten führte im November 2020 einen Workshop zum Thema Data Stewardship im Forschungsdatenmanagement[1] durch. Der Workshop befasste sich mit den unterschiedlichen Rollen, Aufgaben und Einsatzgebieten von sogenannten Data Stewards. Die einzelnen Beiträge gaben Einblicke in die inhaltlichen Aufgabenfelder und Verantwortlichkeiten von Data Stewards und boten Einsichten in die Praxis. Schnell wurde deutlich, dass Stewardship in den Wissenschaftseinrichtungen sehr unterschiedliche Formen annehmen kann[2]. Im Rahmen von DFG-geförderten Sonderforschungsbereichen bieten die Teilprojekte zur Informationsinfrastruktur (häufig INF-Projekte genannt) Unterstützung im Forschungsdatenmanagement. Zu den Aufgaben der INF-Projekte gehören sowohl die Entwicklung und Realisierung von Strategien rund um das Datenmanagement als auch der Aufbau von Infrastruktur. Der vorliegende Beitrag geht der Frage nach, was Stewardship in fächerübergreifenden, kooperativen Forschungskonstellationen bedeuten kann und inwieweit sich die zentralen Aktivitäten der INF-Projekte dem Bereich Data Stewardship zuordnen lassen. [1] Siehe dazu auch die Beschreibung des Workshops Data Stewardship im Forschungsdatenmanagement – Was ist das? Rollen, Aufgabenprofile, Einsatzgebiete: https://www.forschungsdaten.org/index.php/Wiki-Seite_des_11._Workshops_der_DINI/nestor_AG (Letzter Zugriff: 27.02.2021). [2] Hausen, Daniela, Jessica, Rosenberg, Ute, Trautwein-Bruns und Annett, Schwarz. "Data Stewards an der RWTH Aachen University – Aufbau eines Flexiblen Netzwerks." Bausteine Forschungsdatenmanagement, Nr. 2 (November 2020): 20-28, hier 22. https://doi.org/10.17192/bfdm.2020.2.8278.

BackgroundHeat stress has negative effects on the intestinal health of humans and animals. However, the impact of heat stress on intestinal microbial and metabolic changes remains elusive. Here, we investigated the cecal microbial and metabolic profiles in mice in response to heat stress.MethodsThe mouse heat stress model was constructed by simulating a high-temperature environment. Twenty mice were randomly assigned to two groups, the control group (CON, 25°C) and the heat treatment group (HS, 40°C from 13:00 to 15:00 every day for 7 days). Serum and cecal contents were collected from the mice for serum biochemical analysis, 16S rRNA high-throughput sequencing, and non-targeted metabolomics.ResultsBoth core body temperature and water intake were significantly increased in the HS group. Serum biochemical indicators were also affected, including significantly increased triglyceride and decreased low-density lipoprotein in the heat stress group. The composition and structure of intestinal microbiota were remarkably altered in the HS group. At the species level, the relative abundance of Candidatus Arthromitus sp. SFB-mouse-Japan and Lactobacillus murinus significantly reduced, while that of Lachnospiraceae bacterium 3-1 obviously increased after HS. Metabolomic analysis of the cecal contents clearly distinguished metabolite changes between the groups. The significantly different metabolites identified were mainly involved in the fatty acid synthesis, purine metabolism, fatty acid metabolism, cyanoamino acid metabolism, glyceride metabolism, and plasmalogen synthesis.ConclusionIn summary, high temperature disrupted the homeostatic balance of the intestinal microbiota in mice and also induced significant alterations in intestinal metabolites. This study provides a basis for treating intestinal disorders caused by elevated temperature in humans and animals and can further formulate nutritional countermeasures to reduce heat stress-induced damage.

Background: Heat stress has negative effects on the intestinal health of humans and animals. However, the impact of heat stress on intestinal microbial and metabolic changes remains elusive. Here, we investigated the cecal microbial and metabolic profiles in mice in response to heat stress. Methods: The mouse heat stress model was constructed by simulating a high-temperature environment. Twenty mice were randomly assigned to two groups, the control group (CON, 25°C) and the heat treatment group (HS, 40°C from 13:00 to 15:00 every day for 7 days). Serum and cecal contents were collected from the mice for serum biochemical analysis, 16S rRNA high-throughput sequencing, and non-targeted metabolomics. Results: Both core body temperature and water intake were significantly increased in the HS group. Serum biochemical indicators were also affected, including significantly increased triglyceride and decreased low-density lipoprotein in the heat stress group. The composition and structure of intestinal microbiota were remarkably altered in the HS group. At the species level, the relative abundance of Candidatus Arthromitus sp. SFB-mouse-Japan and Lactobacillus murinus significantly reduced, while that of Lachnospiraceae bacterium 3-1 obviously increased after HS. Metabolomic analysis of the cecal contents clearly distinguished metabolite changes between the groups. The significantly different metabolites identified were mainly involved in the fatty acid synthesis, purine metabolism, fatty acid metabolism, cyanoamino acid metabolism, glyceride metabolism, and plasmalogen synthesis. Conclusion: In summary, high temperature disrupted the homeostatic balance of the intestinal microbiota in mice and also induced significant alterations in intestinal metabolites. This study provides a basis for treating intestinal disorders caused by elevated temperature in humans and animals and can further formulate nutritional countermeasures to reduce heat stress-induced damage. [ABSTRACT FROM AUTHOR]

Das "Scheitern" und die zentralen Herausforderungen bei der Entwicklung und Etablierung einer Informationsinfrastruktur fürs Forschungsdatenmanagement (FDM) sind Themenbereiche, die üblicherweise ungern diskutiert werden. Diese können jedoch zu Unzufriedenheit in dem ganzen Sonderforschungsbereich (SFB) führen, insbesondere aber auch zu Frustration bei den Mitarbeiterinnen und Mitarbeitern der Informationsinfrastruktur (INF)-Teilprojekte. Die Probleme und Herausforderungen manifestieren sich auf verschiedenen Ebenen, die wir in diesem Beitrag etwas näher beleuchten wollen. Die Diskussion am World-Café-Tisch lässt sich in folgende Bereiche bündeln: (i) Fehlender Zugang zu Bedarfen, (ii) unklare Rollen und Governance, (iii) Nachnutzung statt Neuentwicklung. Aufgrund des Projektcharakters von SFBs kann das "Scheitern" wesentliche Auswirkungen haben. Die in diesem Beitrag ausformulierten Stolpersteine sollten jedoch nicht notwendigerweise als vollständiges Scheitern von INF-Vorhaben betrachtet werden. Vielmehr hilft ein Wechsel auf die Perspektive von Forschenden: "Man hat unter bestimmten Annahmen und Rahmenbedingungen eine Entwicklung betrieben. Geht das Experiment schief, dann müssen die Annahmen und Rahmenbedingungen angepasst werden." Das Gelingen eines Infrastrukturprojektes hängt in komplexer Weise von vielen Faktoren ab. Eine gepflegte Kommunikation zwischen den Beteiligten, ein offenes Mindset auf allen Seiten und eine klare Verteilung der Rollen scheinen hier besonders wichtig.

The animal gut is a major site affecting productivity via its role in mediating functions like food conversion and pathogen colonization. Live microorganisms like probiotics are widely used to improve poultry productivity. However, given that chicks receive their microbiota from the environment at-hatch, a bacterial treatment that can stimulate gut immune maturation in early life can benefit animal health. Thus, our lab has begun investigating alternative means to improve poultry health via single inoculation with microbial spores. In this study, we orally-inoculated day-old chicks with ileal scrapings (ISs) enriched for spores via chloroform treatment (SPORE) or non-treated (CON). At 3, 7, and 14 days post-inoculation (dpi), gut permeability was measured via FITC-dextran assay in serum. Additionally, small intestinal scrapings (SISs) were tested for in vitro Salmonella killing and total IgA. Lastly, distal ileum was either fixed or flash-frozen for microscopy or kinome peptide array, respectively. Using bacterial 16S rRNA gene sequencing, SPORE and CON inocula were highly-similar in bacterial composition. However, spores were detected in SPORE but not in CON inoculum. Segmented filamentous bacteria (SFB) filaments were observed in the distal ileum in SPORE birds as early as 3 dpi and all birds at 7 and 14 dpi. Additionally, SFB were detected via PCR in the ceca, colonizing all SPORE birds at 3 dpi. At 3 dpi, SPORE birds exhibited lower gut permeability vs. CON. In SPORE birds, SISs induced greater Salmonella growth in vitro at 3 dpi yet significantly-reduced Salmonella load at 7 and 14 dpi compared to CON in an IgA-independent manner. SPORE distal ileal tissue exhibited unique upregulation of several immunometabolic processes vs. CON birds, including innate (Toll-like receptor, JAK-STAT) and adaptive (T/B cell receptor, TH17 differentiation) immune pathways, PI3K/Akt signaling, mTOR signaling, and insulin-related pathways. Collectively, these data suggest oral inoculation with ileal spores generally-improved gut health.Importance: We report that ileal, spore-forming commensal microbes have potent effects on ileum immunometabolism. Additionally, we identify a functional ileal phenotype in spore-treated chickens, which matched several of the observed immunometabolic changes and was associated with SFB colonization in the ileum.

Modulation instability is one of the consequences of the water medium's inclination. It causes surface water waves to run into phenomena of splitting and merging in their propagation. An increase in wave amplitude follows this phenomenon, which can encourage the appearance of extreme waves. It is known that the Benjamin Bona Mahony (BBM) wave has modulation instability in its propagation, with the envelope evolving by the equation Nonlinear Schrodinger (NLS) equation dynamic. One of the NLS equation solution is known as Soliton on Finite Background (SFB). SFB is a continuation of the Benjamin-Feir nonlinear terms. Here, the probe of the BBM wave dynamics is conducted by transforming the complex amplitudes form of SFB variable into the polar form of displaced phase-amplitude. It was done to observe changes in the amplitude of the wave in a complex plane with phases that depend only on position. The description of the dynamics of the SFB can be illustrated through Argand diagrams. It was found that the modulation frequency affects the SFB phase: the smaller the modulation frequency, the higher the phase angle. Also, it is found that the phenomenon of SFB phase singularity occurs in extreme waves for certain frequency modulation intervals.

In more than 60 families of angiosperms, the self- and cross-fertilization is avoided through a complex widespread genetic system called self-incompatibility (SI). One of the major puzzling issues concerning the SI is the evolution of this system in species with complex polyploid genomes. Among plums, one of the first fruits species to attract human interest, polyploid species represent enormous genetic potential, which can be exploited in breeding programs. However, molecular studies in these species are very scarce due to the complexity of their genome. In order to study the SFB gene [the male component of gametophytic self-incompatibility system (GSI)] in plum species, 36 plum accessions belonging to diploid and hexaploid species were used. A total of 19 different alleles were identified; 1 of them was revealed after analyzing sequences. Peptide sequence analysis allowed identifying the five domains features of the SFB gene. Polymorphism analysis showed a subtle difference between domesticated and open pollinated Tunisian accessions and suggested a probable influence of the ploidy level. Divergence analysis between studied sequences showed that a new specificity may appear after 5.3% of divergence at synonymous sites between pairs of sequences in Prunus insititia, 6% in Prunus cerasifera, 8% and 9% in Prunus domestica and Prunus salicina respectively. Furthermore, sites under positive selection, the ones more likely to be responsible for specificity determination, were identified. A positive and significant Pearson correlation was found between the divergence between sequences, divergence time, fixed substitutions (MK test), and PSS number. These results supported the model assuming that functionally distinct proteins have arisen not as a result of chance fixation of neutral variants, but rather as a result of positive Darwinian selection. Further, the role that plays recombination can not be ruled out, since a rate of 0.08 recombination event per polymorphic sites was identified. [ABSTRACT FROM AUTHOR]

Tetraploid sour cherry (Prunus cerasus L.) exhibits gametophytic self-incompatibility (GSI) whereby the specificity of self-pollen rejection is controlled by alleles of the stylar and pollen specificity genes, S-RNase and SFB (S haplotype-specific F-box protein gene), respectively. As sour cherry selections can be either self-compatible (SC) or self-incompatible (SI), polyploidy per se does not result in SC. Instead the genotype-dependent loss of SI in sour cherry is due to the accumulation of non-functional S-haplotypes. The presence of two or more non-functional S-haplotypes within sour cherry 2x pollen renders that pollen SC. Two new S-haplotypes from sour cherry, S(33) and S(34), that are presumed to be contributed by the P. fruticosa species parent, the complete S-RNase and SFB sequences of a third S-haplotype, S(35), plus the presence of two previously identified sweet cherry S-haplotypes, S(14) and S(16) are described here. Genetic segregation data demonstrated that the S(16)-, S(33)-, S(34)-, and S(35)-haplotypes present in sour cherry are fully functional. This result is consistent with our previous finding that 'hetero-allelic' pollen is incompatible in sour cherry. Phylogenetic analyses of the SFB and S-RNase sequences from available Prunus species reveal that the relationships among S-haplotypes show no correspondence to known organismal relationships at any taxonomic level within Prunus, indicating that polymorphisms at the S-locus have been maintained throughout the evolution of the genus. Furthermore, the phylogenetic relationships among SFB sequences are generally incongruent with those among S-RNase sequences for the same S-haplotypes. Hypotheses compatible with these results are discussed.

Innate immunity is maintained in part by antigen presenting cells (APCs) including dendritic cells, macrophages, and B cells. APCs interact with T cells to link innate and adaptive immune responses. By displaying bacterial and tumorigenic antigens on their surface via major histocompatibility complexes, APCs can directly influence the differentiation of T cells. Likewise, T cell activation, differentiation, and effector functions are modulated by APCs utilizing multiple mechanisms. The objective of this review is to describe how APCs interact with and influence the activation of T cells to maintain innate immunity during exposure to microbial infection and malignant cells. How bacteria and cancer cells take advantage of some of these interactions for their own benefit will also be discussed. While this review will cover a broad range of topics, a general focus will be held around pathogens, cancers, and interactions that typically occur within the gastrointestinal tract.

The intestinal microbiota is a complex ecosystem implicated in host health and disease. Inflammatory bowel disease (IBD) is a multifactorial chronic disorder of the gastrointestinal mucosa. Even though the exact mechanisms are still unknown, the intestinal microbiota is crucial in IBD development. We previously showed that murine norovirus (MNV) induces colitis in the Il10 -deficient (Il10 −/−) mouse model of IBD in a microbiota-dependent manner. Thus, in this study we analyzed whether distinct minimal bacterial consortia influence the outcome of MNV-triggered colitis in Il10 −/− mice. Gnotobiotic Il10 −/− mice associated with Oligo-Mouse-Microbiota 12 (OMM12) or Altered Schaedler Flora (ASF) developed little to no inflammatory lesions in the colon and cecum. MNV infection exacerbated colitis severity only in ASF-colonized mice, but not in those associated with OMM12. Four weeks after MNV infection, inflammatory lesions in ASF-colonized Il10 −/− mice were characterized by epithelial hyperplasia, infiltration of inflammatory cells, and increased barrier permeability. Co-colonization of ASF-colonized Il10 −/− mice with segmented filamentous bacteria (SFB) abolished MNV-induced colitis, whereas histopathological scores in SFB-OMM12-co-colonized mice stayed unchanged. Moreover, SFB only colonized mice associated with ASF. The SFB-mediated protective effects in ASF-colonized mice involved enhanced activation of intestinal barrier defense mechanisms and mucosal immune responses in the chronic and acute phase of MNV infection. SFB colonization strengthened intestinal barrier function by increasing expression of tight junction proteins, antimicrobial peptides and mucus. Furthermore, SFB colonization enhanced the expression of pro-inflammatory cytokines such as Tnf α, Il1 β, and Il12a , as well as the expression of the regulatory cytokine Tgf β. Altogether, our results showed that MNV-triggered colitis depends on the microbial context. [ABSTRACT FROM AUTHOR]

Segmented filamentous bacteria (SFB) are a group of host-adapted, commensal organisms that attach to the ileal epithelium of vertebrate and invertebrate hosts. A genetic relative of the genus Clostridium, these morphologically unique bacteria display a replication and differentiation lifecycle initiated by epithelial tissue binding and filamentation. SFB intimately bind to the surface of absorptive intestinal epithelium without inducing an inflammatory response. Rather, their presence impacts the generation of innate and differentiation of acquired immunity, which impact the clearance of extracellular bacterial or fungal pathogens in the gastrointestinal and respiratory tracts. SFB have recently garnered attention due to their role in promoting adaptive and innate immunity in mice and rats through the differentiation and maturation of Th17 cells in the intestinal tract and production of immunoglobulin A (IgA). SFB are the first commensal bacteria identified that impact the maturation and development of Th17 cells in mice. Recently, microbiome studies have revealed the presence of Candidatus Arthromitus (occasionally designated as Candidatus Savagella), a proposed candidate species of SFB, in higher proportions in higher-performing flocks as compared to matched lower-performing flocks, suggesting that SFB may serve to establish a healthy gut and protect commercial turkeys from pathogens resulting in morbidity and decreased performance. In this review we seek to describe the life cycle, host specificity, and genetic capabilities of SFB, such as bacterial metabolism, and how these factors influence the host immunity and microbiome. Although the role of SFB to induce antigen-specific Th17 cells in poultry is unknown, they may play an important role in modulating the immune response in the intestinal tract to promote resistance against some infectious diseases and promote food-safety. This review demonstrates the importance of studying and further characterizing commensal, host-specific bacteria in food-producing animals and their importance to animal health.

Segmented filamentous bacteria (SFB) are commensal organisms that grow by anchoring a specialized holdfast structure to the intestinal walls of a variety of animals. Interaction of SFB with Peyer’s patches in mice promotes the post-natal maturation of the immune system. We previously reported that the colonization of SFB in humans mainly occurs by 36 months of age, and is difficult to be detected afterward. In this study, we measured the level of SFB in intestinal fluids of human children. SFB were found via qPCR to represent a small fraction of the whole SFB-positive microbiota (105 SFB in 1011 total bacteria). Bacteria with filamentous segmented morphology were observed in intestinal fluids via fluorescent in situ hybridization, and from gut biopsies via scanning electron microscopy. SFB-specific DNA and peptide fragments were also identified via multiple displacement amplification PCR and mass spectrometry. There was an overall positive correlation between the presence of SFB and the titer of total secretory immunoglobulin A (sIgA), which is more apparent in intestinal fluids of the age group of 8–36 months. Afterward there was a decline of SFB in numbers correlated with a reduction of total sIgA. RT-qPCR analysis of the terminal ileal biopsies revealed that the expression of Th17 pathway genes were induced in SFB-positive samples, while the markers of T and B cell receptor signaling pathways were also upregulated. Collectively, these data suggest that SFB is a rare member of microbiota, and may play an important role in the development of human gut immunity.

Segmented filamentous bacteria (SFB) modulate the ontogeny of the immune system, and their presence can significantly affect mouse models of disease. Until recently, the inability to successfully culture SFB has made controlled studies on the mechanisms by which these bacteria exert their influence problematic. Here, we report a new method for selecting SFB from complex microbial mixtures, providing researchers a simple and cost-effective means to prepare pure infective inocula for prospective studies and also to compare individual SFB isolates.

Segmented filamentous bacteria (SFB) are a group of host-adapted, commensal organisms that attach to the ileal epithelium of vertebrate and invertebrate hosts. A genetic relative of the genus Clostridium , these morphologically unique bacteria display a replication and differentiation lifecycle initiated by epithelial tissue binding and filamentation. SFB intimately bind to the surface of absorptive intestinal epithelium without inducing an inflammatory response. Rather, their presence impacts the generation of innate and differentiation of acquired immunity, which impact the clearance of extracellular bacterial or fungal pathogens in the gastrointestinal and respiratory tracts. SFB have recently garnered attention due to their role in promoting adaptive and innate immunity in mice and rats through the differentiation and maturation of Th17 cells in the intestinal tract and production of immunoglobulin A (IgA). SFB are the first commensal bacteria identified that impact the maturation and development of Th17 cells in mice. Recently, microbiome studies have revealed the presence of Candidatus Arthromitus (occasionally designated as Candidatus Savagella), a proposed candidate species of SFB, in higher proportions in higher-performing flocks as compared to matched lower-performing flocks, suggesting that SFB may serve to establish a healthy gut and protect commercial turkeys from pathogens resulting in morbidity and decreased performance. In this review we seek to describe the life cycle, host specificity, and genetic capabilities of SFB, such as bacterial metabolism, and how these factors influence the host immunity and microbiome. Although the role of SFB to induce antigen-specific Th17 cells in poultry is unknown, they may play an important role in modulating the immune response in the intestinal tract to promote resistance against some infectious diseases and promote food-safety. This review demonstrates the importance of studying and further characterizing commensal, host-specific bacteria in food-producing animals and their importance to animal health. [ABSTRACT FROM AUTHOR]

The sour cherry is known to exhibit the phenomenon of gametophytic self-incompatibility which prevents self-fertilization. In sour cherry, besides self-incompatible cultivars, there often occur self-compatible cultivars. This is due to the occurrence of natural mutations of theS-RNaseorSFBgenes and, consequently, loss of functionality ofS-alleles. Here we present the results of the identification ofS-haplotypes of 21 cultivars of sour cherry from various regions of Europe. The analyses were performed using methods based on the amplification of intron I and intron II of theS-RNasegene and fragments specific to the individual alleles of theS-RNaseorSFBgenes. The tested cultivars were found to contain 15S-haplotypes:S1, S1ʹ,S4, S6,S6m, S6m2,S9, S12,S13, S13ʹ,S26, S35,S36a, S36b, andS36b2. The most frequently occurringS-haplotypes wereS13ʹ(61.9%),S36a(57.1%), andS26(47.6%). On the basis of the results, 17 of the 21 cultivars were deduced to be self-compatible. The results will be of use in the production of sour cherry fruit by facilitating the selection of suitable pollinating cultivars. The results are also expected to be useful in the breeding of new cultivars of sour cherry when selecting genotypes for crosses. [ABSTRACT FROM PUBLISHER]

Ten years ago, we discovered that microbiota composition controls intestinal T cell homeostasis and alters T cell responses of mice in different animal facilities. Here I discuss how these discoveries, reported in Cell Host & Microbe in 2008, came to be and contributed to our understanding of microbiota immune effects. [ABSTRACT FROM AUTHOR]

Prunus avium is primarily cultivated for its fruit, sweet cherries. However, it is also used to produce high-quality timber. In a P. avium seed orchard, gametophytic self-incompatibility is a restriction for free pollen flow and should be considered when establishing basic forest materials. In this study, S-locus diversity and cross-incompatibility of wild cherry individuals in clonal banks established for breeding for timber production were investigated. Wild cherry trees (140) with outstanding forest growth habit, collected in northern Spain, grafted and planted in two clonal banks, were genotyped at the S-locus. The self-incompatibility S-locus genes, S- RNase and SFB, were analysed by PCR. Twenty-two S-haplotypes, resulting in 72 different S-genotypes, were identified. The genotypes were grouped into 33 incompatibility groups and 39 unique genotypes. This initial S-locus analysis revealed large genetic diversity of wild cherry trees from the Spanish northern deciduous forest, and provides useful information for seed orchard design. Wild P. avium displays significantly more genetic diversity than what is detected in local cultivars, revealing a narrowing of genetic diversity during local domestication. [ABSTRACT FROM AUTHOR]

Shepherd's purse ( Capsella bursa-pastoris), native to Europe, is commonly consumed fresh and sometimes inadequately washed before consumption in Korea. The objective of this study was to characterize isolates of spore-forming bacilli (SFB) in samples of fresh Shepherd's purse. Three genera were identified: Bacillus (9 species), Paenibacillus (3 species), and Brevibacillus (1 species). None of the genes of the hemolysin BL (HBL) and nonhemolytic enterotoxin (NHE) complexes, or of the emetic toxin, was detected in the 25 SFB isolates, except for 2 Bacillus pseudomycoides isolates, where all 3 genes of the HBL enterotoxin complex were detected. There were significant sequence variations between the 2 species ( Bacillus cereus and B. pseudomycoides) in the 3 genes of the HBL enterotoxin complex. These findings may provide insights into the diverse characteristics of the B. pseudomycoides HBL enterotoxin complex. Antibiotic resistance was assessed using 8 antibiotics. Among the 25 SFB isolates, 11 showed resistance to antibiotics, of which 5 were multiresistant. Assessment of the spoilage potential showed that all 25 SFB isolates could produce enzymes that can cause spoilage of foods. In conclusion, our findings may serve as integrative information for food research and industrial sectors. [ABSTRACT FROM AUTHOR]

Plum ( Prunus L.) is a species which exhibits a gametophytic self-incompatibility system 'GSI' as the majority of species belonging to the Rosaceae family. The self-incompatibility system is genetically controlled by a single and multiallelic locus named the S locus which contains at least two linked genes, one is expressed in pistil named S-RNase gene, the second is expressed in pollen called SFB gene ( S-haplotype-specific F-box). In this work, 16 Tunisian plums cultivars were considered. The PCR amplification of the SFB gene and the automatic sequencing of amplicons have identified the SFB alleles of each variety. The analysis of both nucleotide and peptide sequences shows the high degree of polymorphism in SFB alleles. Moreover, the mutational events show a high proportion of transversions and nonsynonymous mutations. Furthermore, sequence analysis has proved that the intragenic recombination can occur within the SFB gene. Regions characterizing the SFB gene: the F-Box conserved domain, and three variable and two hypervariable regions were detected. These (hyper) variable regions seem to be hydrophilic or at least not strongly hydrophobic. Dendrograms were basically constructed on nucleotide, and peptide sequences provide relationships and similarity of cultivars representing the same allele independently from geographic origin and provide a valuable scenario on the evolutionary history of the SFB gene. Moreover, the neutrality tests show that the SFB gene is the seat of positive selection that plays in favor of the rare alleles. Finally, the study of the relationship between the SFB gene and the S-RNase gene shows that both genes are contiguous and have an opposite transcription direction. To conclude, the study of self-incompatibility genes, as ideal markers of the self-incompatibility system, forms an essential node for understanding the origin and evolution of this system. [ABSTRACT FROM AUTHOR]

Self-incompatible Prunus species show a gametophytic self-incompatibility system, but self-compatibility is an interesting horticultural trait in these fruit tree species. Self-compatibility has recently attracted a particular attention since molecular approaches have been applied to the elucidation of the interacting pollen–pistil mechanism and to the identification of the genes involved in pistil–pollen recognition. Both mutations of the S -RNase gene expressed in the pistil and the SFB gene expressed in the pollen have been reported to explain breakdown of the incompatibility system in Prunus . Stylar-part mutations have revealed that ribonuclease activity of the S -RNases is required to inhibit pollen growth and have shown different activity levels for some S -RNases. The self-compatibility observed in some cultivars has been reported to be due to a defective pollen S -function, such as in sweet cherry, apricot, Japanese apricot and peach. Breakdown of self-incompatibility has also been associated with mutations affecting modifier genes unlinked to the S -locus, such as in sweet cherry, apricot, Japanese plum, and almond. Additionally, a double phenotypic expression of the same S -genotype has been observed in Japanese plum, sweet cherry and almond. The nature of these different mutations has only been identified in a few cases, including deletions, insertions, shift mutations and, more recently, epigenetic alterations. [ABSTRACT FROM AUTHOR]

Segmented filamentous bacteria (SFB) are Gram-positive, anaerobic, spore-forming commensals that reside in the gut of many animal species. Described more than forty years ago, SFB have recently gained interest due to their unique ability to modulate the host immune system through induction of IgA and Th17 cells. Here, we describe a collection of methods to detect and quantify SFB and SFB adhesion in intestinal mucosa, as well as SFB-specific CD4 T cells in the lamina propria. In addition, we describe methods for purification of SFB from fecal material of SFB-monoassociated gnotobiotic mice. Using these methods we examine the kinetics of SFB colonization and Th17 cell induction. We also show that SFB colonize unevenly the intestinal mucosa and that SFB adherence occurs predominantly in the terminal ileum and correlates with an increased proportion of SFB-specific Th17 cells. [ABSTRACT FROM AUTHOR]

T helper 17 (Th17) cells regulate mucosal barrier defenses but also promote multiple autoinflammatory diseases. Although many molecular determinants of Th17 cell differentiation have been elucidated, the transcriptional programs that sustain Th17 cells in vivo remain obscure. The transcription factor RORγt is critical for Th17 cell differentiation; however, it is not clear whether the closely related RORα, which is co-expressed in Th17 cells, has a distinct role. Here, we demonstrated that although dispensable for Th17 cell differentiation, RORα was necessary for optimal Th17 responses in peripheral tissues. The absence of RORα in T cells led to reductions in both RORγt expression and effector function among Th17 cells. Cooperative binding of RORα and RORγt to a previously unidentified Rorc cis -regulatory element was essential for Th17 lineage maintenance in vivo. These data point to a non-redundant role of RORα in Th17 lineage maintenance via reinforcement of the RORγt transcriptional program. [Display omitted] • RORα is required for sustained Th17 responses in vivo • RORα shares genomic binding sites with RORγt • RORα binding depends on RORγt, whereas RORγt can bind ROREs in the absence of RORα • A Rorc (t) +11 kb cis -element is required for RORα-maintained RORγt expression in vivo The transcription factor RORα is recognized for contributing to Th17 cell differentiation and pathogenesis, but the underlying mechanisms are unclear. Hall, Pokrovskii, et al. find that RORα reinforces the RORγt transcriptional program by binding to a cis -regulatory element within the Rorc locus that maintains RORγt expression in vivo , thus potentiating inflammatory disease. [ABSTRACT FROM AUTHOR]

Infectious triggers are associated with the induction of transient antiphospholipid antibodies. One therefore wonders if microbes that permanently colonize us play a role in the pathogenesis of antiphospholipid syndrome (APS). The microbiota represents the collection of all microorganisms colonizing humans and is necessary for normal host physiology. The microbiota, however, is a constant stress on the immune system, which is tasked with recognizing and eliminating pathogenic microbes while tolerating commensal populations. A growing body of literature supports a critical role for the commensal-immune axis in the development of autoimmunity against colonized barriers (e.g., gut or skin) and sterile organs (e.g., pancreas or joints). Whether these interactions affect the development and sustainment of autoreactive CD4 T cells and pathogenic autoantibodies in APS is unknown. This review provides an overview of the current understanding of the commensal-immune axis in autoimmunity with a focus on the potential relevance to APS. Additionally, we discuss emerging findings supporting the involvement of the gut microbiota in a spontaneous model of APS, the (NZW × BXSB)F hybrid, and formalize hypotheses to explain how interactions between the immune system and the microbiota may influence human APS etiopathogenesis. [ABSTRACT FROM AUTHOR]

Sweet cherry is a traditional fruit crop in Spain. The introduction of modern cultivars is replacing the local varieties and genetic diversity is lost. To conserve this plant material, local varieties are being collected and characterized. As part of this objective we investigated the S-genotype of 73 local varieties. S-locus analysis was carried out by PCR analysis of S- RNase and SFB genes. PCR was done using conserved primers and fragments detection was carried out by capillary electrophoresis. Fifty-six cultivars were S-genotyped for first time and 17 had been S- RNase typed previously. The S-genotype of the 73 varieties was unambiguously determined. Ten different S-haplotypes were identified: S, S, S, S, S, S, S, S, S and S. The varieties were assigned to 17 incompatibility groups, to Group '0' of universal donors, and to Group 'SC' of self-compatible varieties. The results provide cross-compatibility information for cross design and orchard management. The results also reveal the S-locus diversity of this plant material. S-haplotypes S, S and S were the most frequent and S was only found in the Balearic Islands. Comparison of S-haplotype frequencies worldwide and within Europe showed that S is almost exclusive of southern Europe. Other S-haplotypes that are common in northern Europe, like S, S, S, were rare in the southern plant material. This geographic distribution of S-haplotypes across Europe may indicate a common origin or genetic relationship of varieties from close areas. Alternatively, there may be an association of certain S-haplotypes with adaptive traits correlated to climatic conditions in the different areas. [ABSTRACT FROM AUTHOR]

While most Japanese apricot ( Prunus mume Sieb. et Zucc.) cultivars display typical S- RNase-based gametophytic self-incompatibility, some self-compatible (SC) cultivars have also been identified. In this study, we confirmed SC of 'Zaohong' through replicated self-pollination tests. Cross-pollination tests showed that SC of 'Zaohong' was caused by a loss of pollen function, so we determined that the S-genotype of 'Zaohong' was S S. Sequence analysis of the S-haplotypes of 'Zaohong' showed no mutations which were likely to alter gene function. Furthermore, expression analysis based on RT-PCR of S-locus genes revealed no differences at the transcript level when compared with 'Xiyeqing', a self-incompatible cultivar with the same S haplotypes. In addition, except for S-locus genes, a new type of F-box gene encoding a previously uncharacterised protein with high sequence similarity (61.03-64.65 %) to Prunus SFB genes was identified. Putative structural regions of PmF- box genes have been described, corresponding to regions in PmSFB alleles, but with some sequence variations. These results suggest that SC in 'Zaohong' occurs in pollen, and that other factors outside the S-locus, including PmF- box genes, might be associated with the loss of function of pollen S genes. [ABSTRACT FROM AUTHOR]

Highlights: [•] S6ins-RNase was cloned from the self-compatible loquat cultivars. [•] Four S6-SFBs were cloned from homozygote S6 loquat seedlings. [•] A 24-nucleotide insertion was identified within S6ins-RNase open reading frame. [•] No mutation was observed in the S6-SFBs. [•] The mutation in S6ins-RNase was found to be responsible for SC in these cultivars. [ABSTRACT FROM AUTHOR]

Intertwining roles of lymphotoxin in the immune system, commensal microbiota and metabolic disease.The field of lymphotoxin biology has seen many advances in the past decade. Notably, a role for lymphotoxin as a key effector cytokine has emerged to add to its foundational contribution to lymphoid organogenesis. It is now clear that lymphotoxin contributes to host defense for a wide variety of pathogens, and the lymphotoxin receptor is a defining feature of and regulatory mechanism in both innate and adaptive immunities. Specifically, lymphotoxin contributes to Th education, licensing of IL-22 production from type 3 innate lymphoid cells, and even maintains innate myeloid populations within the fully developed lymph node. Most recently, lymphotoxin has been implicated in regulation of the microbiota and metabolic disease. Early studies revealed that lymphotoxin might influence composition of the commensal microbiota through its regulation of immunological compartmentalization in the gut. Additionally, several epidemiological studies have linked polymorphisms in lymphotoxin to metabolic disease. Studies exploring the role of lymphotoxin in metabolic disease have demonstrated that lymphotoxin may influence metabolism both directly in the liver and indirectly through regulation of gut immune responses. It now appears that lymphotoxin may bridge the gap between altered composition of the commensal microbiota and metabolism. [ABSTRACT FROM PUBLISHER]