Bacillus cereus growth and biofilm formation: the impact of substratum, iron sources, and transcriptional regulator Sigma 54

Biofilms are surface-associated communities of microbial cells embedded in a matrix of extracellular polymers. It is generally accepted that the biofilm growth mode represents the most common lifestyle of microorganisms. Next to beneficial biofilms used in biotechnology applications, undesired biofilms can be formed by spoilage and pathogenic microorganisms in food production environments. Bacillus cereus is a foodborne human pathogen able to cause two types of food poisoning, emetic and diarrheal. B. cereus can persist in factory environments in the form of biofilms, which can become a source of food contamination. This thesis adds to the knowledge about (a)biotic factors and conditions that affect B. cereus biofilm formation, including the effect of type of substratum such as polystyrene and stainless steel, with the latter supporting the highest biofilm formation for all tested strains including two reference strains and 20 food isolates. The ability of B. cereus to use a variety of iron sources was subsequently studied in these 22 strains and linked to the genes encoding iron transport systems present in the respective genomes, revealing significant diversity in the capacity to use complex and non-complex iron sources for growth and biofilm formation. For spore forming Bacilli, biofilm formation and sporulation are two intertwined cellular processes and studies in wet and dry (air-exposed) biofilms revealed differences in sporulation rate and efficacy, with biofilm-derived spores showing higher heat resistance than their planktonic counterparts. Additionally, comparative phenotype and transcriptome analysis of B. cereus wild type and a Sigma 54 deletion mutant provided insight into the pleiotropic role of this transcriptional regulator in B. cereus biofilm formation and physiology in general. Taken together, this knowledge improves our understanding of the biofilm lifecycle of this notorious food-borne human pathogen and provides clues which can help to reduce the domestication of this microorganism in production environments.</p

Draft Whole-Genome Sequences of 11 Bacillus cereus Food Isolates

Bacillus cereus is a foodborne pathogen causing emetic and diarrheal-type syndromes. Here, we report the whole-genome sequences of 11 B. cereus food isolates.</p

THE SPREAD OF CHALCEDONISM IN TAYK AND ITS INFLUENCE ON THE FORMATION OF THE HISTORICal AND CULTURAL ENVIRONMENT

In 451, after the Ecumenical Council of Chalcedon, Chalcedonism spread in Armenia, especially in Tayk. With its spread, Georgian penetrated there having an impact on the historic and cultural life and the ethnic image of the region. A part of the Armenians, breaking away from the Armenian Church, became Georgian-speaking. The study aims to analyze the process and the ethno-religious environment resulted from the impact of the new confession. In Tayk, a bishop’s seat was founded as early as the 4th century by Gregory the Illuminator, and it continued to be a diocese of the Armenian Apostolic Church, which is testified by the fact that the names of the bishops of Tayk have been remembered at church meetings etc. until the 9th — 10thcenturies. Chalcedonism and Georgian writing and literature rooted in the region as late as the 9th — 10th centuries, when the Bagratunis, the local ruling elite, accepted the Chalcedonian confession. As a result, the population of Tayk and their rulers were called ‘Georgians’ or ‘Iberians’ in both Armenian and foreign records. In Tayk, even church ceremonies were performed in Georgian, though Armenian was also used

ISSAID/EMQN Best Practice Guidelines for the Genetic Diagnosis of Monogenic Autoinflammatory Diseases in the Next-Generation Sequencing Era

Abstract Background Monogenic autoinflammatory diseases are caused by pathogenic variants in genes that regulate innate immune responses, and are characterized by sterile systemic inflammatory episodes. Since symptoms can overlap within this rapidly expanding disease category, accurate genetic diagnosis is of the utmost importance to initiate early inflammation-targeted treatment and prevent clinically significant or life-threatening complications. Initial recommendations for the genetic diagnosis of autoinflammatory diseases were limited to a gene-by-gene diagnosis strategy based on the Sanger method, and restricted to the 4 prototypic recurrent fevers (MEFV, MVK, TNFRSF1A, and NLRP3 genes). The development of best practices guidelines integrating critical recent discoveries has become essential. Methods The preparatory steps included 2 online surveys and pathogenicity annotation of newly recommended genes. The current guidelines were drafted by European Molecular Genetics Quality Network members, then discussed by a panel of experts of the International Society for Systemic Autoinflammatory Diseases during a consensus meeting. Results In these guidelines, we combine the diagnostic strength of next-generation sequencing and recommendations to 4 more recently identified genes (ADA2, NOD2, PSTPIP1, and TNFAIP3), nonclassical pathogenic genetic alterations, and atypical phenotypes. We present a referral-based decision tree for test scope and method (Sanger versus next-generation sequencing) and recommend on complementary explorations for mosaicism, copy-number variants, and gene dose. A genotype table based on the 5-category variant pathogenicity classification provides the clinical significance of prototypic genotypes per gene and disease. Conclusions These guidelines will orient and assist geneticists and health practitioners in providing up-to-date and appropriate diagnosis to their patients

Involvement of the Modifier Gene of a Human Mendelian Disorder in a Negative Selection Process

BACKGROUND:Identification of modifier genes and characterization of their effects represent major challenges in human genetics. SAA1 is one of the few modifiers identified in humans: this gene influences the risk of renal amyloidosis (RA) in patients with familial Mediterranean fever (FMF), a Mendelian autoinflammatory disorder associated with mutations in MEFV. Indeed, the SAA1 alpha homozygous genotype and the p.Met694Val homozygous genotype at the MEFV locus are two main risk factors for RA. METHODOLOGY/PRINCIPAL FINDINGS:HERE, WE INVESTIGATED ARMENIAN FMF PATIENTS AND CONTROLS FROM TWO NEIGHBORING COUNTRIES: Armenia, where RA is frequent (24%), and Karabakh, where RA is rare (2.5%). Sequencing of MEFV revealed similar frequencies of p.Met694Val homozygotes in the two groups of patients. However, a major deficit of SAA1 alpha homozygotes was found among Karabakhian patients (4%) as compared to Armenian patients (24%) (p = 5.10(-5)). Most importantly, we observed deviations from Hardy-Weinberg equilibrium (HWE) in the two groups of patients, and unexpectedly, in opposite directions, whereas, in the two control populations, genotype distributions at this locus were similar and complied with (HWE). CONCLUSIONS/SIGNIFICANCE:The excess of SAA1alpha homozygotes among Armenian patients could be explained by the recruitment of patients with severe phenotypes. In contrast, a population-based study revealed that the deficit of alpha/alpha among Karabakhian patients would result from a negative selection against carriers of this genotype. This study, which provides new insights into the role of SAA1 in the pathophysiology of FMF, represents the first example of deviations from HWE and selection involving the modifier gene of a Mendelian disorder

A principal component approach to structure formation with massive neutrinos

It will soon become possible to study the evolution of large scale structures with tomographic weak lensing surveys, such as DES and LSST. This will provide a powerful way of constraining the current cosmological model, LCDM, which assumes that neutrinos have zero mass. On linear scales, any small departure of the growth dynamics from the LCDM prediction can be described in terms of two functions of time and scale. Zhao et al derived the principal components of these two functions that will be best constrained by DES and LSST. This thesis demonstrates the possibility of using these principal components to derive the expected constraints on the neutrino mass. It also discusses the effects of neutrino mass on the evolution of cosmological perturbations, and their effect on observables, such as the matter density contrast and the CMB spectrum

Palynological studies of some species of the genus Cuscuta with emphasis on taxonomy

The main objective of this research was to conduct a comparative pollen morphological analysis of some representatives of the genus Cuscuta in relation to taxonomy. Investigations of 38 species and 1 variation revealed that not only the number, but the colpi length, as well as the exine ornamentation (at the SEM level), can be regarded as a diagnostic feature. For all the taxa studied, the common zonocolpate type of pollen was observed, represented by three variations: I) colpi long; II) colpi of medium length; III) colpi short. In combination with colpi length, variations in the number of colpi were also identified, such as: I) 3(4)-zonocolpate pollen grains with long colpi (in most of the species studied from subgenera Grammica and Cuscuta , as well as in C. monogyna from the subgenus Monogynella ); II) 4(3)-zonocolpate pollen grains, with long colpi ( C. cristata from subgenus Grammica ); III) 3-zonocolpate pollen grains both with long colpi and colpi of medium length ( C. abyssinic a from subgenus Cuscuta and C. africana , C. angulata from subgenus Pachystigma ); IV) 3-zonocolpate pollen grains with colpi of medium length were noted for species from all four subgenera ( C. cassytoides , C. lupuliformis from subgenus Monogynella , C. kotschyana from subgenus Cuscuta , C. nitida from subgenus Pachystigma and C. jalapensis , C. rostrata , C. suaveolens from subgenus Grammica ); V) 3–4- or 4-zonocolpate, with short colpi ( C. lehmanniana and C. gigantea from subgenus Monogynella respectively); VI) 5–6-zonocolpate, with short colpi ( C. reflexa from subgenus Monogynella ). Using SEM, three main types of exine ornamentation were also identified: perforate, foveolate and reticulate. The last type in the vast majority of the cases was presented in combination with echinae (rarely with spines or granules). The data revealed that the presence of the significant similarity of palyno-morphological characteristics in representatives of the subgenera Cuscuta , Pachystigma and Grammica , with the exception of the species Lepidanche adpressa (syn. C. compacta ), makes it difficult to create an identification key at the level of individual subgenera. Pollen features can be most clearly used only to distinguish the subgenus Monoginella , reflecting its certain isolation within the entire Cuscuta genus. The presence of a highly specialized reticulate exine ornamentation in Lepidanche adpressa (syn. C. compacta ), not identified for the pollen of any of the studied taxa of the subgenus Grammica , indicates a significant proximity of this species to the subgenus Monogynella . For the species C. reflexa , the obtained palyno-morphological data are consistent with the previous opinion about the separation of this species, as well as its more advanced position within the genus Cuscuta

Sporulation dynamics and spore heat resistance in wet and dry biofilms of Bacillus cereus

Environmental conditions and growth history can affect the sporulation process as well as subsequent properties of formed spores. The sporulation dynamics was studied in wet and air-dried biofilms formed on stainless steel (SS) and polystyrene (PS) for Bacillus cereus ATCC 10987 and the undomesticated food isolate B. cereus NIZO 4080. After harvesting and maturation, the wet heat resistance of spores obtained from these biofilms was tested and compared to planktonic and agar plate-derived spores. Drying/air exposure of the preformed 24 h old biofilms accelerated spore formation for both strains and resulted in higher final spore percentages. Prolonged dry incubation of more than three days triggered germination of spores in the biofilms of ATCC 10987. Spores harvested from wet biofilms on SS displayed the highest heat resistance compared to liquid, agar plate and PS biofilm derived spores. The D95 °C values for these spores were 17 and 22 min for NIZO 4080 and ATCC 10987, respectively, which was 2 and 1.2 fold higher compared to planktonic spores of these strains. Spores obtained from dried biofilms of ATCC 10987 displayed reduced heat resistance compared to wet biofilm spores. The results indicate that environmental conditions encountered by biofilms affect sporulation dynamics and spore heat resistance, thus affecting subsequent quality issues and safety risks related to these biofilms

Pollen typification and palynotaxonomy of subfamily Salsoloideae Ulbr. (Chenopodiaceae Vent.) in the flora of South Transcaucasia

The article presents the results of a comparative palyno-morphological analysis of the representatives of the Salsoloideae subfamily (Chenopodiaceae) in South Transcaucasia. Out of 25 species belonging to 13 genera of Salsoloideae subfamily in South Transcaucasia, pollen morphology of 23 species from 12 genera was investigated, as well as an analysis of the pollen characteristics was conducted. Data on five key features of pollen (on LM level) were statistically analyzed including pollen diameter, pore number, pore diameter, exine thickness, and mesoporium width. The results indicated that within the Salsoloideae subfamily of South Transcaucasian flora the first three features may be considered diagnostic. The application of a scanning electron microscope (SEM) has revealed the fourth diagnostic feature of the pollen within the Salsoloideae subfamily, specifically, the number of spinules on the unit surface of the pollen, which enables, in several cases, to conduct intergeneric or interspecific differentiation. Based on the obtained data, typification of pollen within the Salsoloideae subfamily of South Transcaucasia was carried out for the first time. As a result, two morphological types and four subtypes combined in two palynogroups were distinguished. The subdivision into palynogroups is based on differences in the size of pollen grains. Only species Climacoptera crassa with pollen of average sizes (26–33/29 μm in diameter) is included into the monotypic Palynogroup I, all other investigated species with small pollen grains (10–25 (27)/22 μm in diameter) are joined in Palynogroup II. Allocation of species into two different Types of Palynogroup II is based on the presence of a significant difference in the size of small pollen grains of individual species. In particular, species with relatively large pollen grains (> 20 μm in diameter) are included in Type 1, while species with relatively small ones (≤ 20 μm in diameter) are joined in Type 2. And finally, the distribution of species into the subtypes and variations of Palynogroup II is based on differences in pore number and size. The identified key palyno-morphological features made it possible in some cases to specify the taxonomic boundaries, as well as the relationship between taxa within the subfamily Salsoloideae

Some notes on the types of pollen aperture in the genus Crocus L. (Iridaceae)

Crocus L. (Iridaceae) is systematically a very problematic genus due to the lack of clear distinctive features, wide range of habitats and the heterogeneity of morphological features. This genus is also highly heterogeneous from a karyological point of view. Apart from the most common spiraperturate pollen grains in Crocus, the authors frequently mentioned a number of other aperture types for individual species (subspecies, variations, etc.), i.e. polyrugoidate, nonaperturate (inaperturate), polyaperturate, with more or less extensive furrows, with short furrows, etc. The purpose of this work is to perform a palyno-morphological analysis of pollen aperture types noted in the genus Crocus. The reason for the study is a significant disagreement among researchers when describing the types of pollen apertures in the genus Crocus. An analysis of the literature, as well as the results of our previous studies, showed that the genus Crocus is characterized by inaperturate (nonaperturate), polyaperturoidate, spiraperturate and net-like pollen apertures. The similar net-like apertures were observed for some representatives of the subgenus Scorpiris Sach of the genus Iris L., in particular, in Iris atropatana Grossh. In our opinion, this aperture type can serve as a link between the genus Crocus and the subgenus Scorpiris of the genus Iris. We suggest, that the spiraperturate pollen type mentioned most often for the representatives of the genus Crocus can be considered the basic type within the genus. On the other hand, formless aperture-like areas are genetically unstable transitory variations, which occurred arbitrarily due to mutations. Finally, “polyrugoidate” (or with net-like apertures) pollen type noted in the literature for C. chrysanthus subsp. punctatus F.Candan et N.Özhatay may be considered to be more advanced in the genus Crocu