Transfer Genes Research Articles

Unraveling diverse survival strategies of microorganisms to vanadium stress in aquatic environments

Worldwide vanadium contamination is posing serious risks to ecosystems. Although abilities of microbial communities to cope with vanadium stress using specific survival strategies have been reported, little is known regarding their relative importance and the underlying detoxification/tolerance mechanisms. Herein, we investigated the potential survival strategies of microbial communities and associated pathways in aquatic environments based on geochemistry and molecular biology. High vanadium content was observed for both water (12.6 ± 1.15 mg/L) and sediment (1.18 × 103 ± 10.4 mg/kg) in the investigated polluted stream. Co-occurrence network investigation implied that microbial communities showed cooperative interactions to adapt to the vanadium-polluted condition. Vanadium was also characterized as one of the vital factors shaping the community structure via redundancy analysis and structural equation models. Based on the metagenomic technology, three survival strategies including denitrification pathway, electron transfer, and metal resistance in innate microbes under the vanadium stress were revealed, with comprehensively summarized vanadium detoxification/tolerance genes. Remarkable role of electron transfer genes and the prevalent existence of resistance genes during detoxifying vanadium were highlighted. Overall, these findings provide novel insights into survival strategies under the vanadium contamination in aquatic environments, which can be of great significance for the identification, isolation, and application of vanadium reducing bacteria in vanadium bioremediation.

Fabrication and Characterization of pcDNA3.1(+) Location within Chitosan/Nanoparticles Complexes for Enhanced Gene Delivery.

Chitosan nanoparticles (CSNP) are becoming a popular alternative for delivering nucleic acids to tissues for gene transfer (gene therapy). The size and morphology of these biodegradable nano-carriers are adjustable, and their positive charge allows them to interact strongly with negatively charged nucleic acids. This study aimed to fabricate and characterize pcDNA3.1 (+) plasmid (pDNA) and CSNP complexes and determine the plasmid location in these vehicles. The characteristics of the pDNA/CSNP complex after production were investigated by SEM, XRD, DLS, TGA, and FTIR. The capacity of CSNP to form complexes with pDNA was investigated by labeling free plasmids with the fluorescent intercalating dye OliGreen. The stability of pDNA/CSNP in the presence of chitosanase was evaluated. Surface-Enhanced Raman Spectroscopy (SERS) for pDNA localization was performed, and absorption rate in BALB/c mice was assessed by real-time PCR. The optimum pDNA/CSNP ratio for plasmid complex formation was established to be 1:2 (w.w) by measuring spectroscopy. At these optimum complex formation ratios, spectroscopy, and gel digest experiments, SERS indicated that a part of the pDNA was present on the complex outer surface. The findings of plasmid absorption in mouse thigh tissue by real-time PCR revealed that the rate of gene uptake was significantly greater at a dose of 1:2 (w.w) of pDNA/CSNP than in other groups (P< 0.001). The findings of this study reveal exactly pDNA fits into polymer nanostructured delivery systems, allowing the formulation to be adjusted for selective distribution. This understanding will aid future research into the system's functioning in vitro and in vivo.

Genetic editing of multi-resistance plasmids in Escherichia coli isolated from meat during transfer

Resistance plasmids mediate the rapid spread of antimicrobial resistance, which poses a threat to veterinary and human healthcare. This study addresses the question whether resistance plasmids from Escherichia coli isolated from foodstuffs always transfer unchanged to recipient E. coli cells, or that genetic editing can occur. Strains containing between one and five different plasmids were co-incubated with a standard recipient strain. Plasmids isolated from transconjugant strains were sequenced using short and long read technologies and compared to the original plasmids from the donor strains. After one hour of co-incubation only a single plasmid was transferred from donor to recipient strains. If the donor possessed several plasmids, longer co-incubation resulted in multiple plasmids being transferred. Transferred plasmids showed mutations, mostly in mobile genetic elements, in the conjugative transfer gene pilV and in genes involved in plasmid maintenance. In one transconjugant, a resistance cluster encoding tetracycline resistance was acquired by the IncI1 plasmid from the IncX1 plasmid that was also present in the donor strain, but that was not transferred. A single plasmid transferred twelve times back and forth between E. coli strains resulted in a fully conserved plasmid with no mutations, apart from repetitive rearrangements of pilV from and back to its original conformation in the donor strain. The overall outcome suggests that some genetic mutations and rearrangements can occur during plasmid transfer. The possibility of such mutations should be taken into consideration in epidemiological research aimed at attribution of resistance to specific sources.

Effect of sulfamethazine on the horizontal transfer of plasmid-mediated antibiotic resistance genes and its mechanism of action

As a new type of environmental pollutant, antibiotic resistance genes (ARGs) pose a huge challenge to global health. Horizontal gene transfer (HGT) represents an important route for the spread of ARGs. The widespread use of sulfamethazine (SM2) as a broad-spectrum bacteriostatic agent leads to high residual levels in the environment, thereby increasing the spread of ARGs. Therefore, we chose to study the effect of SM2 on the HGT of ARGs mediated by plasmid RP4 from Escherichia coli (E. coli) HB101 to E. coli NK5449 as well as its mechanism of action. The results showed that compared with the control group, SM2 at concentrations of 10 mg/L and 200 mg/L promoted the HGT of ARGs, but transfer frequency decreased at concentrations of 100 mg/L and 500 mg/L. The transfer frequency at 200 mg/L was 3.04 × 10−5, which was 1.34-fold of the control group. The mechanism of SM2 improving conjugation transfer is via enhancement of the mRNA expression of conjugation genes (trbBP, trfAP) and oxidative stress genes, inhibition of the mRNA expression of vertical transfer genes, up regulation of the outer membrane protein genes (ompC, ompA), promotion of the formation of cell pores, and improvement of the permeability of cell membrane to promote the conjugation transfer of plasmid RP4. The results of this study provide theoretical support for studying the spread of ARGs in the environment.

Betaine Promotes Fat Accumulation and Reduces Injury in Landes Goose Hepatocytes by Regulating Multiple Lipid Metabolism Pathways.

Simple SummaryBetaine is a safe, effective, naturally occurring trimethylglycine, which is widely used as a nutritional supplement in animal husbandry. Early research showed betaine redistributes body fat by regulating systemic fatty acid metabolism. We previously found that betaine reduces sebum thickness and abdominal fat, and increases liver weight and triglyceride content, in Landes geese fed with high-energy carbohydrates. However, the mechanism underlying these effects remained unclear. Here, we present an in vitro Landes goose fatty liver model, which was developed using primary hepatocytes and a high-glucose medium simulating the conditions of high-energy carbohydrate feeding in vivo. We used this model to investigate the effects of betaine supplementation. Our results suggest that betaine increases lipid deposition, reduces lipid droplet size, and restores mitochondrial membrane potential (β-oxidation) and the expression of genes involved in lipid hydrolysis transfer genes. By contrast, the expression of fatty acid synthesis genes was down-regulated. The comprehensive effect led to an increase in total triglyceride in the liver, but a healthier steatosis phenotype. Overall, these results show that betaine could improve the quality of foie-gras while decreasing the injury to geese that results from overfeeding.Betaine is a well-established supplement used in livestock feeding. In our previous study, betaine was shown to result in the redistribution of body fat, a healthier steatosis phenotype, and an increased liver weight and triglyceride storage of the Landes goose liver, which is used for foie-gras production. However, these effects are not found in other species and strains, and the underlying mechanism is unclear. Here, we studied the underpinning molecular mechanisms by developing an in vitro fatty liver cell model using primary Landes goose hepatocytes and a high-glucose culture medium. Oil red-O staining, a mitochondrial membrane potential assay, and a qRT-PCR were used to quantify lipid droplet characteristics, mitochondrial β-oxidation, and fatty acid metabolism-related gene expression, respectively. Our in vitro model successfully simulated steatosis caused by overfeeding. Betaine supplementation resulted in small, well-distributed lipid droplets, consistent with previous experiments in vivo. In addition, mitochondrial membrane potential was restored, and gene expression of fatty acid synthesis genes (e.g., sterol regulatory-element binding protein, diacylglycerol acyltransferase 1 and 2) was lower after betaine supplementation. By contrast, the expression of lipid hydrolysis transfer genes (mitochondrial transfer protein and lipoprotein lipase) was higher. Overall, the results provide a scientific basis and theoretical support for the use of betaine in animal production.

WAT3R: recovery of T-cell receptor variable regions from 3' single-cell RNA-sequencing.

Diversity of the T-cell receptor (TCR) repertoire is central to adaptive immunity. The TCR is composed of α and β chains, encoded by the TRA and TRB genes, of which the variable regions determine antigen specificity. To generate novel biological insights into the complex functioning of immune cells, combined capture of variable regions and single-cell transcriptomes provides a compelling approach. Recent developments enable the enrichment of TRA and TRB variable regions from widely used technologies for 3'-based single-cell RNA-sequencing (scRNA-seq). However, a comprehensive computational pipeline to process TCR-enriched data from 3' scRNA-seq is not available. Here, we present an analysis pipeline to process TCR variable regions enriched from 3' scRNA-seq cDNA. The tool reports TRA and TRB nucleotide and amino acid sequences linked to cell barcodes, enabling the reconstruction of T-cell clonotypes with associated transcriptomes. We demonstrate the software using peripheral blood mononuclear cells from a healthy donor and detect TCR sequences in a high proportion of single T cells. Detection of TCR sequences is low in non-T-cell populations, demonstrating specificity. Finally, we show that TCR clones are larger in CD8 Memory T cells than in other T-cell types, indicating an association between T-cell clonotypes and differentiation states. The Workflow for Association of T-cell receptors from 3' single-cell RNA-seq (WAT3R), including test data, is available on GitHub (https://github.com/mainciburu/WAT3R), Docker Hub (https://hub.docker.com/r/mainciburu/wat3r) and a workflow on the Terra platform (https://app.terra.bio). The test dataset is available on GEO (accession number GSE195956). Supplementary data are available at Bioinformatics online.

A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods.

Despite significant public health concerns regarding infectious diseases in air environments, potentially harmful microbiological indicators, such as antibiotic resistance genes (ARGs) in bioaerosols, have not received significant attention. Traditionally, bioaerosol studies have focused on the characterization of microbial communities; however, a more serious problem has recently arisen due to the presence of ARGs in bioaerosols, leading to an increased prevalence of horizontal gene transfer (HGT). This constitutes a process by which bacteria transfer genes to other environmental media and consequently cause infectious disease. Antibiotic resistance in water and soil environments has been extensively investigated in the past few years by applying advanced molecular and biotechnological methods. However, ARGs in bioaerosols have not received much attention. In addition, ARG and HGT profiling in air environments is greatly limited in field studies due to the absence of suitable methodological approaches. Therefore, this study comprehensively describes recent findings from published studies and some of the appropriate molecular and biotechnological methods for monitoring antibiotic resistance in bioaerosols. In addition, this review discusses the main knowledge gaps regarding current methodological issues and future research directions.

Betaine Alleviates High-Fat Diet-Induced Disruptionof Hepatic Lipid and Iron Homeostasis in Mice.

Non-alcoholic fatty liver disease (NAFLD) is characterized by excessive fat deposition in the liver, which is often associated with disrupted iron homeostasis. Betaine has been reported to be hepatoprotective, yet whether and how betaine ameliorates high-fat diet-induced disruption of hepatic lipid and iron homeostasis remains elusive. In this study, mice were fed either standard (CON) or high-fat diet (HFD) for 9 weeks to establish a NAFLD model. Mice raised on HF diet were then assigned randomly to HF and HFB groups, HFB group being supplemented with 1% (w/v) of betaine in the drinking water for 13 weeks. Betaine supplementation significantly alleviated excessive hepatic lipid deposition and restored hepatic iron content. Betaine partly yet significantly reversed HFD-induced dysregulation of lipogenic genes such as PRARγ and CD36, as well as the iron-metabolic genes including FPN and HAMP that encodes hepcidin. Similar mitigation effects of betaine were observed for BMP2 and BMP6, the up-stream regulators of hepcidin expression. Betaine significantly rectified disrupted expression of methyl transfer gene, including BHMT, GNMT and DNMT1. Moreover, HFD-modified CpG methylation on the promoter of PRARγ and HAMP genes was significantly reversed by betaine supplementation. These results indicate that betaine alleviates HFD-induced disruption of hepatic lipid and iron metabolism, which is associated with modification of CpG methylation on promoter of lipogenic and iron-metabolic genes.

Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes

Animals display a fascinating diversity of body plans. Correspondingly, genomic analyses have revealed dynamic evolution of gene gains and losses among animal lineages. Here we sequence six new myriapod genomes (three millipedes, three centipedes) at key phylogenetic positions within this major but understudied arthropod lineage. We combine these with existing genomic resources to conduct a comparative analysis across all available myriapod genomes. We find that millipedes generally have considerably smaller genomes than centipedes, with the repeatome being a major contributor to genome size, driven by independent large gains of transposons in three centipede species. In contrast to millipedes, centipedes gained a large number of gene families after the subphyla diverged, with gains contributing to sensory and locomotory adaptations that facilitated their ecological shift to predation. We identify distinct horizontal gene transfer (HGT) events from bacteria to millipedes and centipedes, with no identifiable HGTs shared among all myriapods. Loss of juvenile hormone O-methyltransferase, a key enzyme in catalysing sesquiterpenoid hormone production in arthropods, was also revealed in all millipede lineages. Our findings suggest that the rapid evolution of distinct genomic pathways in centipede and millipede lineages following their divergence from the myriapod ancestor, was shaped by differing ecological pressures.

Genetic Diversity and Streptomycin Sensitivity in Xanthomonas axonopodis pv. punicae Causing Oily Spot Disease in Pomegranates

Xanthomonas axonopodis pv. punicae (Xap) causes bacterial blight disease in pomegranates, often leading to 60–80% economic loss. In absence of a suitable Xap-resistant variety, the near-monoculture of the susceptible variety, Bhagwa, has aggravated the problem further. In recent times, Xap has spread to different geographical regions, indicating the wide adaptability of the pathogen. Moreover, lower sensitivity of Xap towards streptocycline containing streptomycin sulphate and tetracycline sulphate (9:1) under field conditions is frequently reported. Therefore, the current study was undertaken to assess the genetic variability of Xap isolates using SSR markers, their in vitro sensitivity towards streptomycin was evaluated, and the probable molecular basis of acquired resistance was studied. Two highly diverse isolates showed extreme differences in their pathogenicity, indicating the highly evolving nature of the pathogen. Moreover, all the isolates showed less than 50% growth inhibition on media containing 1500 µg/mL streptomycin, indicating a lower level of antibiotic sensitivity. On the molecular level, 90% of the isolates showed the presence of strA-strB genes involved in streptomycin metabolism. Additionally, G to A transitions were observed in the rpsL gene in some of the isolates. The molecular data suggest that horizontal gene transfer (strAB) and/or spontaneous gene mutation (in rpsL) could be responsible for the observed lower sensitivity of Xap towards streptomycin.

3D pore-matched PANI@CNT bioanode for efficient electron extraction from toluene

Microbial fuel cell (MFC) can harvest chemical energy stored in volatile organic compounds (VOCs) and consequently are of great potential for waste gas treatment and energy recovery. However, the inadequate connection between active cells and bioanode substrate hinders the extracellular electron transfer, especially in the upper layer of biofilm, resulting in restricted degradation capacity and power output. Herein, we propose a pore matching strategy to establish electron transfer nanowires around individual cells by embedding them separately inside a pore-matched sponge (core-shell polyaniline @ carbon nanotube, PANI@CNT). The resulting MFC for toluene degradation presents 4.41 times increase in power density (279.91 mW m−2), 2.64 times increase in coulombic efficiency (18.13%), and 2.02 times increase in toluene degradation activity (0.77 h−1), which also possesses considerable advantages over literature results. Furthermore, metagenomic analysis indicates that the genes for transmembrane and extracellular electron transfer are down-regulated, validating the effectiveness of the PANI@CNT nanowires linking individual cells with bioanode substrate. These findings reveal the feasibility of the pore matching strategy to boost toluene degradation and power extraction in MFC, and give an in-depth insight into transmembrane and extracellular electron transfer mechanisms.

Current Trends and Perspectives in the Immune Therapy for Substance Use Disorders.

Substance use disorders (SUDs) are an extremely challenging category of disorders because of the high rate of relapse, lower life expectancy, important rate of psychiatric and somatic co-morbidity, lack of patients' insight during most of the disease duration, healthcare costs, etc. One of the reasons to consider these disorders very difficult for physicians and the healthcare system is the lack of adequate pharmacological agents with long-term proven efficacy. So far, there are no Food and Drug Administration (FDA) or European Medicines Agency (EMA)-approved treatments for most of the SUDs, except for alcohol use disorder, nicotine use disorder, and opioid use disorder. Immunotherapy has been considered a possible solution to SUDs because it may selectively target a certain drug of abuse, it may have a long-lasting effect (several weeks or months), and it ensures an adequate therapeutic adherence. The objective of this paper was to establish the current stage of research in the field of SUDs vaccines, based on a brief literature review. Vaccines for cocaine and nicotine dependence have reached phase III trials, while other researchers are focusing on passive immunization therapy for methamphetamine use disorder. New generations of vaccines are currently explored, and they are based on superior technologies compared to the first generation of immune therapy (e.g., viral transfer genes, more immunogenic adjuvants, or higher specificity haptens). Therefore, finding immune therapies for substance use disorders SUDs remains a matter of interest, and this approach may be useful for the management of an extremely dangerous and versatile psychiatric pathology.

Overview of Salmonella Genomic Island 1-Related Elements Among Gamma-Proteobacteria Reveals Their Wide Distribution Among Environmental Species.

The aim of this study was to perform an in silico analysis of the available whole-genome sequencing data to detect syntenic genomic islands (GIs) having homology to Salmonella genomic island 1 (SGI1), analyze the genetic variations of their backbone, and determine their relatedness. Eighty-nine non-redundant SGI1-related elements (SGI1-REs) were identified among gamma-proteobacteria. With the inclusion of the thirty-seven backbones characterized to date, seven clusters were identified based on integrase homology: SGI1, PGI1, PGI2, AGI1 clusters, and clusters 5, 6, and 7 composed of GIs mainly harbored by waterborne or marine bacteria, such as Vibrio, Shewanella, Halomonas, Idiomarina, Marinobacter, and Pseudohongiella. The integrase genes and the backbones of SGI1-REs from clusters 6 and 7, and from PGI1, PGI2, and AGI1 clusters differed significantly from those of the SGI1 cluster, suggesting a different ancestor. All backbones consisted of two parts: the part from attL to the origin of transfer (oriT) harbored the DNA recombination, transfer, and mobilization genes, and the part from oriT to attR differed among the clusters. The diversity of SGI1-REs resulted from the recombination events between GIs of the same or other families. The oriT appeared to be a high recombination site. The multi-drug resistant (MDR) region was located upstream of the resolvase gene. However, most SGI1-REs in Vibrio, Shewanella, and marine bacteria did not harbor any MDR region. These strains could constitute a reservoir of SGI1-REs that could be potential ancestors of SGI1-REs encountered in pathogenic bacteria. Furthermore, four SGI1-REs did not harbor a resolvase gene and therefore could not acquire an integron. The presence of mobilization genes and AcaCD binding sites indicated that their conjugative transfer could occur with helper plasmids. The plasticity of SGI1-REs contributes to bacterial adaptation and evolution. We propose a more relevant classification to categorize SGI1-REs into different clusters based on their integrase gene similarity.

Optimization of Agrobacterium-mediated transformation procedure for an indica rice variety-Khang Dan 18

In addition to traditional methods, advanced biotechnologies, especially CRISPR/Cas9-mediated genome editing, have emerged as effective tools for improving important agronomic traits in rice. However, the critical step for utilizing these systems is to develope an effective system for rice transformation and regeneration. This study was performed to establish procedures for Agrobacterium-mediated transformation and regeneration of rice cultivar Khang Dan 18 (KD18) – a popular indica variety in the North of Vietnam. The tissue cultures procedure with optimized medium compositions showed high frequencies of callus induction and shoot regeneration, at 94.7% and 45.3% respectively. We found that 30 mg/L of hygromycin was an effective concentration for transgenic KD18 selection. Light-yellow friable calli were used as the starting material for transformation mediated by A. tumefaciens strain AGL1 harbouring pHUE411 vector containing gus intron and hygromycin resistance gene (hptII). Important factors related to transformation procedure had been optimized in this study. The high transformation frequency (12.8%) was achieved by using the optimized procedure for KD18 cultivar. In which, bacterial density (OD600), infection time and co-cultivation period were performed at 0.1, 20 minutes and 3 days, respectively. PCR analysis using specific primers and the histological GUS staining demonstrated the presence of hptII and gus genes in transgenic rice lines. This result provides a potential protocol to transfer genes of interest into KD18 as well as other indica rice cultivars.

Synergistic effect of sulfidated nanoscale zerovalent iron in donor and recipient bacterial inactivation and gene conjugative transfer inhibition

Antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) are widespread in urban wastewater treatment plants (UWTPs). In this research, a horizontal transfer model of recipient (Pseudomonas. HLS-6) and donor (Escherichia coli DH5α carries RP4 plasmid) was constructed to explore the effect of sulfidated nanoscale zerovalent iron (S-nZVI) on the efficiency of plasmid-mediated horizontal transfer. When the S/Fe was 0.1, the inactivation efficiency of 1120 mg/L S-nZVI on the donor and recipient bacteria were 2.36 ± 0.03 log and 3.50 ± 0.17 log after 30 min, respectively (initial ARB concentration ≈ 5 ×107 CFU/mL). Effects of treatment time, S/Fe molar ratio, S-nZVI dosage and initial bacterial concentration were systemically studied. S-nZVI treatment could increase the extracellular alkaline phosphatase and malondialdehyde content of the ARB, cause oxidative stress in the bacteria, destroy the cell structure and damage the intracellular DNA. This study provided evidence and insights into possible underlying mechanisms for reducing conjugative transfer, such as hindering cell membrane repair, inducing the overproduction of reactive oxygen species, inhibiting the SOS response, reducing the expression of ARGs and related transfer genes. S-nZVI could inhibit the gene conjugative transfer while inactivating the ARB. The findings provided an alternative method for controlling antibiotic resistance.

Improving bulk RNA-seq classification by transferring gene signature from single cells in acute myeloid leukemia.

The advances in single-cell RNA sequencing (scRNA-seq) technologies enable the characterization of transcriptomic profiles at the cellular level and demonstrate great promise in bulk sample analysis thereby offering opportunities to transfer gene signature from scRNA-seq to bulk data. However, the gene expression signatures identified from single cells are typically inapplicable to bulk RNA-seq data due to the profiling differences of distinct sequencing technologies. Here, we propose single-cell pair-wise gene expression (scPAGE), a novel method to develop single-cell gene pair signatures (scGPSs) that were beneficial to bulk RNA-seq classification to transfer knowledge across platforms. PAGE was adopted to tackle the challenge of profiling differences. We applied the method to acute myeloid leukemia (AML) and identified the scGPS from mouse scRNA-seq that allowed discriminating between AML and control cells. The scGPS was validated in bulk RNA-seq datasets and demonstrated better performance (average area under the curve [AUC] = 0.96) than the conventional gene expression strategies (average AUC$\le$0.88) suggesting its potential in disclosing the molecular mechanism of AML. The scGPS also outperformed its bulk counterpart, which highlighted the benefit of gene signature transfer. Furthermore, we confirmed the utility of scPAGE in sepsis as an example of other disease scenarios. scPAGE leveraged the advantages of single-cell profiles to enhance the analysis of bulk samples revealing great potential of transferring knowledge from single-cell to bulk transcriptome studies.

The Ancient Origins of Death Domains Support the 'Original Sin' Hypothesis for the Evolution of Programmed Cell Death.

The discovery of caspase homologs in bacteria highlighted the relationship between programmed cell death (PCD) evolution and eukaryogenesis. However, the origin of PCD genes in prokaryotes themselves (bacteria and archaea) is poorly understood and a source of controversy. Whether archaea also contain C14 peptidase enzymes and other death domains is largely unknown because of a historical dearth of genomic data. Archaeal genomic databases have grown significantly in the last decade, which allowed us to perform a detailed comparative study of the evolutionary histories of PCD-related death domains in major archaeal phyla, including the deepest branching phyla of Candidatus Aenigmarchaeota, Candidatus Woesearchaeota, and Euryarchaeota. We identified death domains associated with executioners of PCD, like the caspase homologs of the C14 peptidase family, in 321 archaea sequences. Of these, 15.58% were metacaspase type I orthologues and 84.42% were orthocaspases. Maximum likelihood phylogenetic analyses revealed a scattered distribution of orthocaspases and metacaspases in deep-branching bacteria and archaea. The tree topology was incongruent with the prokaryote 16S phylogeny suggesting a common ancestry of PCD genes in prokaryotes and subsequent massive horizontal gene transfer coinciding with the divergence of archaea and bacteria. Previous arguments for the origin of PCD were philosophical in nature with two popular propositions being the "addiction" and 'original sin' hypotheses. Our data support the 'original sin' hypothesis, which argues for a pleiotropic origin of the PCD toolkit with pro-life and pro-death functions tracing back to the emergence of cellular life-the Last Universal Common Ancestor State.

Carriage of distinct blaKPC-2 and blaOXA-48 plasmids in a single ST11 hypervirulent Klebsiella pneumoniae isolate in Egypt

BackgroundCarbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) causes serious infections with significant morbidity and mortality. However, the epidemiology and transmission mechanisms of CR-hvKP and the corresponding carbapenem-resistant plasmids require further investigation. Herein, we have characterized an ST11 K. pneumoniae strain EBSI041 from the blood sample encoding both hypervirulence and carbapenem resistance phenotypes from a patient in Egypt.ResultsK. pneumoniae strain EBSI041 showed multidrug-resistance phenotypes, where it was highly resistant to almost all tested antibiotics including carbapenems. And hypervirulence phenotypes of EBSI041 was confirmed by the model of Galleria mellonella infection. Whole-genome sequencing analysis showed that the hybrid plasmid pEBSI041-1 carried a set of virulence factors rmpA, rmpA2, iucABCD and iutA, and six resistance genes aph(3′)-VI, armA, msr(E), mph(E), qnrS, and sul2. Besides, blaOXA-48 and blaSHV-12 were harboured in a novel conjugative IncL-type plasmid pEBSI041-2. The blaKPC-2-carrying plasmid pEBSI041-3, a non-conjugative plasmid lacking the conjugative transfer genes, could be transferred with the help of pEBSI041-2, and the two plasmids could fuse into a new plasmid during co-transfer. Moreover, the emergence of the p16HN-263_KPC-like plasmids is likely due to the integration of pEBSI041-3 and pEBSI041-4 via IS26-mediated rearrangement.ConclusionTo the best of our knowledge, this is the first report on the complete genome sequence of KPC-2- and OXA-48-coproducing hypervirulent K. pneumoniae from Egypt. These results give new insights into the adaptation and evolution of K. pneumoniae during nosocomial infections.

Complete mitochondrial genome of the Korean endemic springtail Homidia koreana Lee & Lee, 1981 (Collembola: Entomobryidae)

The Korean endemic springtail Homidia koreana Lee & Lee, 1981 is popular in the leaf litter of various forests of South Korea, probably widely distributed throughout the Korean Peninsula. The complete mitochondrial genome of H. koreana was sequenced, assembled, and annotated. The mitochondrial genome of H. koreana consists of a circular DNA molecule of 14,846 bp, with 68.4% AT content. It comprises 13 protein-coding genes (PCGs), 22 transfer (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. The molecular phylogenetic relationships estimated using MrBayes 3.2 revealed that H. koreana was closely related to Homidia socia Denis, 1929, both of which belong to the genus Homidia.

DO PROBIOTICS HAVE A FUTURE IN NEONATOLOGY? (ANALYSIS OF THE LATEST DATA. PART 3)

The issue of feasibility and effectiveness of probiotics use in newborns is still discussable. A position letter of the Committee on nutrition of the European Society for Pediatric NutritionGastroenterology, Hepatology, and(ESPGHAN) and the Working group of the ESPGHAN on probiotics and prebiotics issues was published in May 2020 in “Pediatric Gastroenterology and Nutrition” magazine as for the use of probiotics in premature newborns. The third part of the literature continues with the position paper and the results of many randomized controlled clinical trials of probiotics. The article considers the answers to 6 clinical questions posed by the working group of the Committee to assess the feasibility of use, routes of administration, dosage and duration of use, as well as the effectiveness and quality of probiotic drugs. It was proved that probiotics, in general, could decrease the level of necrotising enterocolitis, sepsis, and mortality. On the other hand, an increasing number of commercial products containing probiotics of non optimal quality are available. In addition, a large number of departments in the world regularly suggest probiotic supplements as a treatment standard despite the absence of any solid evidence. Moreover, the emphasis was placed on issues of safety of probiotic supplements for premature newborns. Guarantee of quality of probiotic product is deliverance of probiotic strains by transfer genes of resistance to antibiotics, the ability to regularly detect sepsis while using probiotics.