Branched swarming patterns on a synthetic medium formed by wild-type Bacillus subtilis strain 3610: detection of different cellular morphologies and constellations of cells as the complex architecture develops

Microbiology ◽  
2004 ◽  
Vol 150 (6) ◽  
pp. 1839-1849 ◽  
Author(s):  
Daria Julkowska ◽  
Michal Obuchowski ◽  
I. Barry Holland ◽  
Simone J. Séror
Keyword(s):  
Bacillus Subtilis ◽  
De Novo ◽  
Synthetic Medium ◽  
Defined Medium ◽  
Subtilis Strain ◽  
Wild Type ◽  
Rapid Movement ◽  
Complex Architecture ◽  
Forward Edge

After optimizing the conditions, including nutrients and temperature, swarming of Bacillus subtilis 3610 was obtained on a synthetic, fully defined medium. The swarms formed highly branched (dendritic) patterns, generated by successive waves of moving cells. A detailed microscopic in situ analysis of swarms 1 and 2 revealed varied cell morphologies and a remarkable series of events, with cells assembling into different ‘structures’, as the architecture of the swarm developed. Long filamentous cells begin to form before the onset of the first swarming (11 h) and are again observed at later stages in the interior of individual mature dendrites. Swarm 2, detected at 18–22 h, is accompanied by the rapid movement of a wave of dispersed (non-filamentous) cells. Subsequently at the forward edge of this swarm, individual cells begin to cluster together, gradually forming de novo the shape of a dendrite tip with progressive lengthening of this new structure ‘backwards' towards the swarm centre. In both swarms 1 and 2, after the initial clustering of cells, there is the progressive appearance of a spreading monolayer of rafts (4–5 non-filamented cells, neatly aligned). The alternative possible roles of the rafts in the development of the swarm are discussed.

scholarly journals A Viable Bacillus subtilis Strain without Functional Extracytoplasmic Function Sigma Genes

2008 ◽  
Vol 190 (7) ◽  
pp. 2633-2636 ◽  
Author(s):  
Kei Asai ◽  
Keisuke Ishiwata ◽  
Kunihiko Matsuzaki ◽  
Yoshito Sadaie
Keyword(s):  
Bacillus Subtilis ◽  
Synthetic Medium ◽  
Subtilis Strain ◽  
Quick Response ◽  
Wild Type ◽  
Deletion Mutations

ABSTRACT We constructed a Bacillus subtilis Marburg strain that harbors deletion mutations in all seven extracytoplasmic function (ECF) sigma genes. The strain shows wild-type growth at 37°C both in a complex and in a synthetic medium and exhibits wild-type sporulation. ECF sigma genes of B. subtilis are dispensable as long as no stress is imposed, although they seem to be required for quick response to stresses.

scholarly journals Improving 3-methylphenol (m-cresol) production in yeast via in vivo glycosylation or methylation

2020 ◽  
Vol 20 (8) ◽  
Author(s):  
Julia Hitschler ◽  
Eckhard Boles
Keyword(s):  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Wild Type ◽  
Biotechnological Production ◽  
Yeast Saccharomyces Cerevisiae ◽  
In Situ Extraction ◽  
Methylsalicylic Acid Synthase ◽  
In The Wild

ABSTRACT Heterologous expression of 6-methylsalicylic acid synthase (MSAS) together with 6-MSA decarboxylase enables de novo production of the platform chemical and antiseptic additive 3-methylphenol (3-MP) in the yeast Saccharomyces cerevisiae. However, toxicity of 3-MP prevents higher production levels. In this study, we evaluated in vivo detoxification strategies to overcome limitations of 3-MP production. An orcinol-O-methyltransferase from Chinese rose hybrids (OOMT2) was expressed in the 3-MP producing yeast strain to convert 3-MP to 3-methylanisole (3-MA). Together with in situ extraction by dodecane of the highly volatile 3-MA this resulted in up to 211 mg/L 3-MA (1.7 mM) accumulation. Expression of a UDP-glycosyltransferase (UGT72B27) from Vitis vinifera led to the synthesis of up to 533 mg/L 3-MP as glucoside (4.9 mM). Conversion of 3-MP to 3-MA and 3-MP glucoside was not complete. Finally, deletion of phosphoglucose isomerase PGI1 together with methylation or glycosylation and feeding a fructose/glucose mixture to redirect carbon fluxes resulted in strongly increased product titers, with up to 897 mg/L 3-MA/3-MP (9 mM) and 873 mg/L 3-MP/3-MP as glucoside (8.1 mM) compared to less than 313 mg/L (2.9 mM) product titers in the wild type controls. The results show that methylation or glycosylation are promising tools to overcome limitations in further enhancing the biotechnological production of 3-MP.

In situ and de novo biosynthesis of vitamin C in wild type and transgenic tomato hairy roots: A precursor feeding study

Plant Science ◽  
2009 ◽  
Vol 177 (1) ◽  
pp. 28-34 ◽  
Author(s):  
Ana Laura Wevar Oller ◽  
Elizabeth Agostini ◽  
Silvia R. Milrad ◽  
María I. Medina
Keyword(s):  
Vitamin C ◽  
Hairy Roots ◽  
De Novo ◽  
Transgenic Tomato ◽  
Wild Type ◽  
Precursor Feeding ◽  
Feeding Study ◽  
De Novo Biosynthesis

scholarly journals Virulence of a Phosphoribosylaminoimidazole Carboxylase-DeficientCandidaalbicans Strain in an Immunosuppressed Murine Model of Systemic Candidiasis

2001 ◽  
Vol 69 (4) ◽  
pp. 2542-2548 ◽  
Author(s):  
Matthew Donovan ◽  
Jon J. Schumuke ◽  
William A. Fonzi ◽  
Sheri L. Bonar ◽  
Karen Gheesling-Mullis ◽  
...  
Keyword(s):  
Parent Strain ◽  
De Novo ◽  
Synthetic Medium ◽  
Wild Type ◽  
Gene Encoding ◽  
Site Specific ◽  
De Novo Purine Biosynthesis ◽  
Exogenous Addition ◽  
Novel Target ◽  
Immunosuppressed Mice

ABSTRACT The relative pathogenicities of three Candida albicans strains differing in the function ofADE2 (the gene encoding phosphoribosylaminoimidazole carboxylase) were evaluated in a murine candidiasis model. C. albicans strain CAI7 (ade2/ade2), previously constructed by site-specific recombination, was avirulent in immunosuppressed mice compared to the parent strain, CAF2-1, and a heterozygous ADE2/ade2 strain obtained by transforming CAI7 with a wild-type allele. The reduced virulence of CAI7 was correlated with the inability to proliferate in either synthetic medium or serum without the exogenous addition of >10 μg of adenine/ml. The loss of virulence upon site-specific disruption of the ade2 locus, and the restoration of wild-type virulence with the repair of just one ade2 allele, confirmed that the ADE2 gene and de novo purine biosynthesis were required for Candida pathogenicity. The potential of the phosphoribosylaminoimidazole carboxylase enzyme as a novel target for antifungal drug discovery is discussed.

scholarly journals Influence of Bacillus subtilis strain on abscisic acid content in ABA-deficient barley mutant and its wild type

2021 ◽  
Vol 2(26) ◽  
pp. 28-40
Author(s):  
Z.A. Akhtyamova ◽  
◽  
T.N. Arkhipova ◽  
E.V. Martynenko ◽  
T.V. Nuzhnaya ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Abscisic Acid ◽  
Leaf Area ◽  
Photochemical Quenching ◽  
Bacterial Suspension ◽  
Subtilis Strain ◽  
Deficient Mutant ◽  
Wild Type ◽  
Promoting Effect ◽  
Shoot Mass

The ability to produce phytohormones and influence their metabolism in plants is an important property of rhizosphere bacteria that determines their plant growth promoting effect. Since abscisic acid (ABA) reduces stomatal conductance and increases the ability of tissues to conduct water, maintenance of water balance in lettuce plants on the background of activation of their growth was associated with the accumulation of ABA under the influence of bacteria. The aim of the study is to test the hypothesis that the growth-stimulating effect of bacteria on plants depends on their ability to synthesize the hormone ABA. The plants were grown on a light platform; seedlings were treated with a bacterial suspension simultaneously with planting. The ABA content, the relative water content, the chlorophyll content, the level of non-photochemical quenching, the leaf area and the weight of the shoots were measured. The level of transcripts of the HvNCED1, HvNCED2, and HvCYP707A1 genes responsible for ABA metabolism in barley was assessed using real-time PCR. Comparison of the ABA-deficient mutant of barley and plants of its wild type revealed the stimulation of the growth of plants of both genotypes upon bacterial treatment. The shoot mass and leaf area of the untreated mutant with bacteria were about 30 % less compared to Steptoe. The stimulating effect of bacteria was manifested in an increase in leaf area by 15 % in Steptoe and by 35 % in Az 34; shoot mass – by 18 % and 41 %, respectively. As a result, the phenotype difference between plants of two genotypes decreased. In the deficient mutant, the ABA level increased under the influence of Bacillus subtilis IB-22 more than twice. It was due to the ability of bacteria to produce ABA and reduce the activity of ABA degradation in barley plants. The results obtained in this study indicate that certain bacterial strains are able to increase the level of ABA in plants, compensating for the genetically determined deficiency of this hormone.

scholarly journals Draft Genome Sequences of Bacillus subtilis Strain DKU_NT_01 Isolated from Traditional Korean Food Containing Soybean (Chung-gook-jang)

2017 ◽  
Vol 5 (31) ◽  
Author(s):  
Man-Seok Bang ◽  
Hee-Won Jeong ◽  
Yea-Jin Lee ◽  
Ha-Yeong Oh ◽  
Su Ji Lee ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
De Novo ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Subtilis Strain ◽  
Whole Genome ◽  
Genome Sequences ◽  
Coding Sequences ◽  
Content Type ◽  
Korean Food

ABSTRACT Here, we report the whole-genome sequence of Bacillus subtilis strain DKU_NT_01 isolated from traditional Korean food containing soybean (chung-gook-jang). The de novo genome of Bacillus subtilis strain DKU_NT_01 has one contig and G+C content of 55.4%, is 4,954,264 bp in length, and contains 5,011 coding sequences (CDSs).

Arabidopsis 4-COUMAROYL-COA LIGASE 8 contributes to the biosynthesis of the benzenoid ring of coenzyme Q in peroxisomes

2019 ◽  
Vol 476 (22) ◽  
pp. 3521-3532
Author(s):  
Eric Soubeyrand ◽  
Megan Kelly ◽  
Shea A. Keene ◽  
Ann C. Bernert ◽  
Scott Latimer ◽  
...  
Keyword(s):  
Oxidative Metabolism ◽  
Time Course ◽  
Reverse Genetics ◽  
De Novo ◽  
Coenzyme Q ◽  
Control Level ◽  
Wild Type ◽  
Fluorescent Reporters ◽  
Coa Ligase ◽  
Peroxisomal Targeting

Plants have evolved the ability to derive the benzenoid moiety of the respiratory cofactor and antioxidant, ubiquinone (coenzyme Q), either from the β-oxidative metabolism of p-coumarate or from the peroxidative cleavage of kaempferol. Here, isotopic feeding assays, gene co-expression analysis and reverse genetics identified Arabidopsis 4-COUMARATE-COA LIGASE 8 (4-CL8; At5g38120) as a contributor to the β-oxidation of p-coumarate for ubiquinone biosynthesis. The enzyme is part of the same clade (V) of acyl-activating enzymes than At4g19010, a p-coumarate CoA ligase known to play a central role in the conversion of p-coumarate into 4-hydroxybenzoate. A 4-cl8 T-DNA knockout displayed a 20% decrease in ubiquinone content compared with wild-type plants, while 4-CL8 overexpression boosted ubiquinone content up to 150% of the control level. Similarly, the isotopic enrichment of ubiquinone's ring was decreased by 28% in the 4-cl8 knockout as compared with wild-type controls when Phe-[Ring-13C6] was fed to the plants. This metabolic blockage could be bypassed via the exogenous supply of 4-hydroxybenzoate, the product of p-coumarate β-oxidation. Arabidopsis 4-CL8 displays a canonical peroxisomal targeting sequence type 1, and confocal microscopy experiments using fused fluorescent reporters demonstrated that this enzyme is imported into peroxisomes. Time course feeding assays using Phe-[Ring-13C6] in a series of Arabidopsis single and double knockouts blocked in the β-oxidative metabolism of p-coumarate (4-cl8; at4g19010; at4g19010 × 4-cl8), flavonol biosynthesis (flavanone-3-hydroxylase), or both (at4g19010 × flavanone-3-hydroxylase) indicated that continuous high light treatments (500 µE m−2 s−1; 24 h) markedly stimulated the de novo biosynthesis of ubiquinone independently of kaempferol catabolism.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Jacobsen syndrome and neonatal bleeding: report on two unrelated patients

2021 ◽  
Vol 47 (1) ◽  
Author(s):  
Gregorio Serra ◽  
Luigi Memo ◽  
Vincenzo Antona ◽  
Giovanni Corsello ◽  
Valentina Favero ◽  
...  
Keyword(s):  
Developmental Delay ◽  
De Novo ◽  
Comparative Genomic ◽  
Fish Analysis ◽  
Variable Degree ◽  
Jacobsen Syndrome ◽  
Contiguous Gene ◽  
Clinical Consequences ◽  
11Q Deletion

Abstract Introduction In 1973, Petrea Jacobsen described the first patient showing dysmorphic features, developmental delay and congenital heart disease (atrial and ventricular septal defect) associated to a 11q deletion, inherited from the father. Since then, more than 200 patients have been reported, and the chromosomal critical region responsible for this contiguous gene disorder has been identified. Patients’ presentation We report on two unrelated newborns observed in Italy affected by Jacobsen syndrome (JBS, also known as 11q23 deletion). Both patients presented prenatal and postnatal bleeding, growth and developmental delay, craniofacial dysmorphisms, multiple congenital anomalies, and pancytopenia of variable degree. Array comparative genomic hybridization (aCGH) identified a terminal deletion at 11q24.1-q25 of 12.5 Mb and 11 Mb, in Patient 1 and 2, respectively. Fluorescent in situ hybridization (FISH) analysis of the parents documented a de novo origin of the deletion for Patient 1; parents of Patient 2 refused further genetic investigations. Conclusions Present newborns show the full phenotype of JBS including thrombocytopenia, according to their wide 11q deletion size. Bleeding was particularly severe in one of them, leading to a cerebral hemorrhage. Our report highlights the relevance of early diagnosis, genetic counselling and careful management and follow-up of JBS patients, which may avoid severe clinical consequences and lower the mortality risk. It may provide further insights and a better characterization of JBS, suggesting new elements of the genotype-phenotype correlations.

scholarly journals Associations between Amplification (1q) and Prior Cancer in a Real-World De Novo Myeloma Cohort

2021 ◽  
Author(s):  
Elizabeth B Lamont ◽  
Andrew J Yee ◽  
Stuart L Goldberg ◽  
David S Siegel ◽  
Andrew D Norden
Keyword(s):  
Real World ◽  
Fluorescent In Situ Hybridization ◽  
De Novo ◽  
Chromosome 1 ◽  
Second Malignancies ◽  
Cancer History ◽  
Screening Strategies ◽  
Cytogenetic Testing

Abstract Genomic biomarkers inform treatment in multiple myeloma (MM) making patient clinical data a potential window into MM biology. We evaluated de novo MM patients for associations between specific MM cytogenetic patterns and prior cancer history. Analyzing a MM real-world dataset (RWD), we identified a cohort of 1,769 patients with fluorescent in-situ hybridization (FISH) cytogenetic testing at diagnosis. Fully 241 patients (0.14) had histories of prior cancer(s). Amplification of the long arm of chromosome 1 [amp(1q)] varied by prior cancer history (0.31 with prior cancer vs 0.24 without; p = .02). No other MM translocations, amplifications, or deletions were associated with prior cancers. Amp(1q) and cancer history remained strongly associated in a logistic regression adjusting for patient demographic and disease attributes. The results merit follow-up regarding carcinogenic treatment effects and screening strategies for second malignancies. Broadly the findings suggest analyses of patient-level phenotypic-genomic RWD may accelerate cancer research through hypothesis generating studies.

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