Draft Genome of Tanacetum Coccineum: Genomic Comparison of Closely Related Tanacetum-Family Plants

The plant Tanacetum coccineum (painted daisy) is closely related to Tanacetum cinerariifolium (pyrethrum daisy). However, T. cinerariifolium produces large amounts of pyrethrins, a class of natural insecticides, whereas T. coccineum produces much smaller amounts of these compounds. Thus, comparative genomic analysis is expected to contribute a great deal to investigating the difference in biological defense systems, including pyrethrin biosynthesis. Here, we elucidated the 9.4-Gb draft genome of T. coccineum, consisting of 2,836,647 scaffolds and 103,680 genes. Comparative analyses of the draft genome of T. coccineum and that of T. cinerariifolium, generated in our previous study, revealed distinct features of T. coccineum genes. While the T. coccineum genome contains more numerous ribosome-inactivating protein (RIP)-encoding genes, the number of higher-toxicity type-II RIP-encoding genes is larger in T. cinerariifolium. Furthermore, the number of histidine kinases encoded by the T. coccineum genome is smaller than that of T. cinerariifolium, suggesting a biological correlation with pyrethrin biosynthesis. Moreover, the flanking regions of pyrethrin biosynthesis-related genes are also distinct between these two plants. These results provide clues to elucidation of species-specific biodefense systems, including the regulatory mechanisms underlying pyrethrin production.

Correlation Between Antimicrobial Resistance, Virulence Determinants and Biofilm Formation Ability Among Extraintestinal Pathogenic Escherichia coli Strains Isolated in Catalonia, Spain

Escherichia coli is a well-characterized bacterium highly prevalent in the human intestinal tract and the cause of many important infections. The aim of this study was to characterize 376 extraintestinal pathogenic E. coli strains collected from four hospitals in Catalonia (Spain) between 2016 and 2017 in terms of antimicrobial resistance, siderophore production, phylogroup classification, and the presence of selected virulence and antimicrobial resistance genes. In addition, the association between these characteristics and the ability to form biofilms was also analyzed. The strains studied were classified into four groups according to their biofilm formation ability: non-biofilm formers (15.7%), weak (23.1%), moderate (35.6%), and strong biofilm formers (25.6%). The strains were highly resistant to ciprofloxacin (48.7%), trimethoprim-sulfamethoxazole (47.9%), and ampicillin (38%), showing a correlation between higher resistance to ciprofloxacin and lower biofilm production. Seventy-three strains (19.4%) were ESBL-producers. However, no relationship between the presence of ESBL and biofilm formation was found. The virulence factor genes fimH (92%), pgaA (84.6%), and irp1 (77.1%) were the most prevalent in all the studied strains. A statistically significant correlation was found between biofilm formation and the presence of iroN, papA, fimH, sfa, cnf, hlyA, iutA, and colibactin-encoding genes clbA, clbB, clbN, and clbQ. Interestingly, a high prevalence of colibactin-encoding genes (19.9%) was observed. Colibactin is a virulence factor, which interferes with the eukaryotic cell cycle and has been associated with colorectal cancer in humans. Most colibactin-encoding E. coli isolates belonged to phylogroup B2, exhibited low antimicrobial resistance but moderate or high biofilm-forming ability, and were significantly associated with most of the virulence factor genes tested. Additionally, the analysis of their clonal relatedness by PFGE showed 48 different clusters, indicating a high clonal diversity among the colibactin-positive strains. Several studies have correlated the pathogenicity of E. coli and the presence of virulence factor genes; however, colibactin and its relationship to biofilm formation have been scarcely investigated. The increasing prevalence of colibactin in E. coli and other Enterobacteriaceae and the recently described correlation with biofilm formation, makes colibactin a promising therapeutic target to prevent biofilm formation and its associated adverse effects.

Characterization and Complete Genome Analysis of a Novel Escherichia Phage, vB_EcoM-RPN242

The novel Escherichia phage vB_EcoM-RPN242 was isolated using a strain of Escherichia coli host originated from a diarrheal piglet. The phage was able to form plaques on the E. coli lawn at 15−45ºC. Moreover, it was stable over a wide pH (4−10) and temperature (4−70ºC) range. The vB_EcoM-RPN242 genome was found to be a linear, double-stranded DNA consisting of 154,840 base pairs. There were 195 protein-encoding genes and 2 tRNAs detected in the genome, however no unfavorable gene was found. According to the overall nucleotide sequence comparison, the vB_EcoM-RPN242 possibly represents a new phage species in the genus Agtrevirus.

Evaluation of biomarkers in the studies of keloid tissue after laser therapy

In this paper, we discuss what biomarkers to choose if there is a need to describe the results of laser therapy targeting keloid skin. We elevate the known cytomarkers (Krt14, Lgals7, Krt5, Dcn, Lum, Igfbp5, Cd31, Vwf, Stambpl1, Uqcrb, Cd3 and Acta2), biomarkers of the inflammatory response (Cd45/Ptprc, Adgre1, Ly6g, Il1b, Il4, Il13, Il22, Cxcl2 и Ccl17), as well as the proteins of extracellular matrix (type I and III collagens; precursors of COL5A1 and COLA1A; FTL, COL3A1, PGLS, CNN2, ANXA2, TPSAB1, COL12A1, precursors of APCS and ALB), and their encoding genes (FGF7, BAX, CCND1, MMP3, MMP9, CXCL1, -2, -5, -6 and -12; IL8, S100A7 and IL1A), those expression and co-location may potentially change the appearance and internal structure of damaged skin. We also describe how to choose biomarkers using the results genomic studies and their limitations. Moreover, we provide examples of how different groups of gene and protein biomarkers are used in experimental biology and clinical practice. According to the previously published data, well-known biomarkers verified on animal models, depend on their biological effects, let to characterize structural changes and changes in the composition of cells represented at the site of damage before and after the treatment. In addition, the published experimental and clinical data provide an opportunity to analyze the efficiency of new experimental approaches and compare them to each other.

Diabetic Foot Ulcer Infections and Pseudomonas aeruginosa Biofilm Production During the COVID-19 Pandemic

During the different waves of the coronavirus (COVID-19) pandemic, there has been an increased incidence of diabetes mellitus and diabetic foot infections. Among gram-negative bacteria, Pseudomonas aeruginosa is the predominant causative agent for diabetic foot ulcer infections in low-resource countries. P. aeruginosa possesses a variety of virulence factors, including biofilm formation. Biofilm formation is an important benchmark characteristic in the pathophysiology of diabetic foot ulceration. The main objective of the current study was to identify the most commonly isolated organisms and their antibiotic susceptibility patterns in diabetic foot patients during the COVID-19 pandemic. We also determined the genes associated with bacterial persistence and biofilm formation in the predominantly isolated organism. Accordingly, 100 wound swab samples were collected from diabetic foot patients from different hospitals in Alexandria, Egypt. Through phenotypic detection of biofilm formation, 93% (40) of the 43 P. aeruginosa isolates examined were categorized as biofilm producers. Molecular detection of the biofilm-encoding genes among the 43 P. aeruginosa isolates was as follows: algD (100%), pelF (88%) and pslD (49.7%), and this highlights a need for biofilm formation inhibitors to prevent the persistence of bacterial pathogens, and thus achieve better clinical outcomes in diabetic foot ulcer infections.

Thylakoid grana stacking revealed by multiplex genome editing of LHCII encoding genes

Land plant chloroplasts differ from algal ones for their thylakoid membranes being organized in grana: piles of vesicles paired by their stromal surface, forming domains including Photosystem (PS) II and its antenna while excluding PS I and ATPase to stroma membranes, connecting grana stacks. The molecular basis of grana stacking remain unclear. We obtained genotypes lacking the trimeric antenna complex (Lhcb1-2-3), the monomeric Lhcb4-5-6, or both. Full deletion caused loss of grana, while either monomers or trimers support 50% stacking. The expression of Lhcb5 alone restored stacking at 50%, while Lhcb2 alone produced huge grana which broke down upon light exposure. Cyclic electron transport was maintained in the lack of stacking, while excitation energy balance between photosystems and the repair efficiency of damaged Photosystem II were affected. We conclude that grana evolved for need of regulating energy balance between photosystems under terrestrial canopy involving rapid changes in photon spectral distribution.

Transcriptome Analysis Unveils the Effects of Proline on Gene Expression in the Yeast Komagataella phaffii

Komagataella phaffii yeast is one of the most important biocompounds producing microorganisms in modern biotechnology. Optimization of media recipes and cultivation strategies is key to successful synthesis of recombinant proteins. The complex effects of proline on gene expression in the yeast K. phaffii was analyzed on the transcriptome level in this work. Our analysis revealed drastic changes in gene expression when K. phaffii was grown in proline-containing media in comparison to ammonium sulphate-containing media. Around 18.9% of all protein-encoding genes were differentially expressed in the experimental conditions. Proline is catabolized by K. phaffii even in the presence of other nitrogen, carbon and energy sources. This results in the repression of genes involved in the utilization of other element sources, namely methanol. We also found that the repression of AOX1 gene promoter with proline can be partially reversed by the deletion of the KpPUT4.2 gene.

Activity of imipenem/relebactam on Klebsiella pneumoniae with different mechanisms of imipenem non-susceptibility

Background and Objectives: Imipenem/relebactam (IMP/R) is a newly FDA approved β-lactam/β-lactamase inhibitor combination. Relebactam ability to restore IMP activity could differ according to the cause of imipenem non-susceptibility. Therefore, we investigated the in-vitro activity of IMP/R against Klebsiella pneumoniae with different mechanisms of imi- penem non-susceptibility. Materials and Methods: Imipenem-nonsusceptible (IMP-NS) K. pneumoniae isolates were collected and characterized for β-lactamase encoding genes by multiplex PCR. For IMP-NS carbapenemase-negative isolates, study of Ompk35 & Ompk36 gene expression was performed by reverse transcription-PCR while efflux pump activity was studied by minimum inhibitory concentration (MIC) reduction assay using efflux pump inhibitor. Susceptibility testing of K. pneumoniae to IMP and IMP/R were achieved by broth microdilution (BMD) method. Results: During the study period, 140 isolates of IMP-NS K. pneumoniae were collected. BMD method showed that relebac- tam restored IMP susceptibility in 100%, 60% and 49% of isolates that only harbor AmpC, extended spectrum beta lactamase (ESBL) and carbapenemases, respectively. IMP/R was most potent against all bla KPC and 50% of bla _producing isolates. No demonstrable activity of IMP/R against K. pneumoniae harboring metallo-β-lactamases (MBLs). Out of 18 isolates with IMP non-suceptibility due to porins loss with overproduction of ESBL and/or AmpC, 14 (77.7%) isolates were IMP/R sus- ceptible. IMP/R showed no activity against isolates with only efflux pump hyperactivity. Conclusion: Relebactam could restore IPM activity in KPC or AmpC-producing IMP/NS K. pneumoniae but with no ac- tivity against MBL- producing isolates. Relebactam activity against isolates harbouring-bla OXA-48 or with altered Ompk35 & Ompk36 gene expression and efflux pump hyperactivity need further studies. Therefore, using IMP/R antibiotic in the treat- ment of infections caused by IMP/NS K. pneumoniae should be based on its molecular profile of IMP resistance to optimize the utility of IMP/R.