Corynebacterium genus, six species that can produce diphtheria toxin  form a clade referred to as the C. diphtheria complex. These species have been found in humans and other animals, causing diphtheria or other diseases. Here we show the results of a genome scale analysis to identify positive selection in protein-coding genes that may have resulted in the adaptations of these species to their ecological niches and suggest drug and vaccine targets.Within the pathogenic bacterial species Corynebacterium. Ten phylogenetic groups were tested for positive selection using the PosiGene pipeline, including species and biovars from the C. diphtheria complex. The detected genes were tested for recombination and had their sequences alignments and homology manually examined. The final genes were investigated for their function and a probable role as vaccine or drug targets.Forty genomes were sampled to represent species, subspecies or biovars of C. diphtheriae (two), C. pseudotuberculosis (10), C. rouxii (one), and C. ulcerans (six). Those were found to be involved in defense, translation, energy production, and transport and in the metabolism of carbohydrates, amino acids, nucleotides, and coenzymes. Fourteen were identified as essential genes, and six as virulence factors. Thirteen from the 19 genes were identified as potential drug targets and four as potential vaccine candidates. These genes could be important in the prevention and treatment of the diseases caused by these bacteria.Nineteen genes were detected in the species  Corynebacterium are gram-positive bacteria of biotechnological, medical, and veterinary importance   . These w(PATRIC)  and down(PATRIC) .The taxonomy of the samples was verified using TYGS . TYGS deCorynebacterium genomes. Ten foreground genomes were tested , two subclades represent C. pseudotuberculosis (biovars equi and ovis), and two subclades representing C. ulcerans lineages (lineage 1 and 2).A genome-scale positive selection analysis was performed using the PosiGene pipeline  on the Ce tested  represenC. diphtheriae NCTC 11397T was selected as both the reference and anchor genome. In the first step, orthologous gene sequences were aligned to the anchor genome sequences using CLUSTALW  as the non-pathogenic reference. The islands were predicted by genes with C+G content and codon usage deviation, presence of transposases, presence of specific genes, non-conservation in comparison to reference genome, and flanking tRNA genes. The islands were classified according to the proportion of specific genes as pathogenicity islands, metabolic islands, resistance islands and symbiotic islands. Finally, prophages were predicted using PHASTER (GIPSy v1.1.2  was used PHASTER .Virulence genes and drug targets were predicted using the Pipeline Builder for Identification of Targets (PBIT) . PBIT prVaccine targets were predicted from the transmembrane, putative surface exposed and secreted proteins predicted using SurfG+ and Vaxign  with preC. casei LMG S-19264 was discarded due to its being identified as Brevibacterium linens based on the TYGS pipeline  depending upon the 10 foregrounds that were used  showed recombination in two out of four genes when Cd was the foreground, and one out of nine genes when Cp was used , wiwas used . Manual was used . SurfG+ was used . Thirty-C 11397T  and S17.C. diphtheriae, 10 in C. pseudotuberculosis, one in C. rouxii, and six in C. ulcerans , we identified two genes encoding proteins predicted to be essential and involved in translation, amino acid transport and metabolism , is a 30S ribosomal subunit that binds to the initiator Met-tRNA (ansB) and translation efficiency (rpsC). rpsC was suggested as a drug target but has homology to a protein in the human gut microbiota proteome, requiring compounds that can selectively inhibit it.In tabolism . The genia cells . This geia cells . The secMet-tRNA . PossiblC. pseudotuberculosis was the foreground (Cp), eight positively selected genes were identified. Five of the genes were tagged as essential, and three as virulence factors. They are involved in translation, coenzyme transport and metabolism, inorganic ion transport, defense from foreign DNA, nucleotide transport and metabolism and adhesion (mntC) plays a role in the transport of Mn2+ and Zn2+ (folP2) is nonfunctional according to PATRIC annotation but functional genes with this annotation are essential for the de novo synthesis of folate (prfA) recognizes the stop codons UAA and UAG, promoting the end of translation (pgmB) is capable of interconverting 2- and 3-phosphoglycerate in glycolysis  are not characterized as essential, so may not be suitable drug targets. Adenosine deaminase (add) catalyzes the hydrolytic deamination of adenosine into inosine , tissue adhesion on a new host range (spaE), improved efficiency for defense against foreign DNA (HNH endonuclease), translation (prfA), and metabolism of nucleotides (add) and carbohydrates (pgmB).Why would these particular genes be under positive selection? One could hypothesize that there would be more efficient manganese uptake (mntC and spaE) were indicated due to either their membrane location, their predicted epitopes, and that they might have surface exposed sites that are under positive selection. There were four drug targets , two genes were identified as being under positive selection, and were also characterized as essential. These two genes (mapB and tyrS) are both involved in translation (mapB) cleaves the initiator methionine from newly synthesized polypeptides (tyrS) attaches the amino acid tyrosine to the appropriate tRNA  was identified when C. rouxii was used as the foreground (Cr). It had no predicted domains, but it could be a vaccine target candidate  was identified when C. ulcerans was used as the foreground (Cul). glyA encodes a serine hydroxymethyltransferase enzyme . Two of them were essential, involved in carbohydrate transport and metabolism (dhaK) gene is in GI34. This enzyme phosphorylates ketones and short chain aldoses using adenosine triphosphate (ATP) (citE) and is probably one of the catalytic subunits of citrate lyase, the enzyme that catalyzes the cleavage of citrate to acetate and oxaloacetate during citrate fermentation (ERS451417_00635) with no predicted domain or cellular localization.Three genes were identified when the tabolism . The Phote (ATP) . The secentation . Both prdhaK and citE) appear to be related to metabolism inside the host. In Listeria monocytogenes, Phosphoenolpyruvate-dihydroxyacetone phosphotransferase (DhaK and other subunits) is required to utilize carbon sources for amino acid synthesis inside murine macrophages  were less pathogenic for the model Galleria mellonella . The DNA polymerase III epsilon subunit (dnaQ) has a domain with 3′–5′ exonuclease proofreading activity  biosynthesis pathway (dnaQ) and biosynthesis of the essential cofactor cobalamin (cobK). Neither of these genes had any predictable druggability.Two essential genes  were ideactivity . The oth pathway . The mutC. pseudotuberculosis, where the pilin SpaE could have enhanced adhesion to different host species tissues. Although the specific adaptations are not clear, an amino acid fixed by positive selection is an attractive target for a therapeutic molecule, as a non-synonymous mutation that could avoid interaction would decrease fitness. These genes could be used for reverse vaccinology and in silico drug targeting methods.It is reported that most of the genes identified as being under positive selection are exposed on the surface and are involved in host colonization, and resistance to phage and antibiotics . Those uC. diphtheriae, C. pseudotuberculosis, C. rouxii and C. ulcerans. Based on our pipeline and literature data, 13 genes are candidate drug targets and four are potential vaccine targets, but their effectiveness would require experimental validation.In this analysis, we predicted 19 genes with non-synonymous mutations that are probably involved in adaptations found in the pathogens 10.7717/peerj.12662/supp-1Supplemental Information 1Click here for additional data file.10.7717/peerj.12662/supp-2Supplemental Information 2Click here for additional data file.10.7717/peerj.12662/supp-3Supplemental Information 3Click here for additional data file.10.7717/peerj.12662/supp-4Supplemental Information 4Click here for additional data file.10.7717/peerj.12662/supp-5Supplemental Information 5Click here for additional data file.10.7717/peerj.12662/supp-6Supplemental Information 6Click here for additional data file.10.7717/peerj.12662/supp-7Supplemental Information 7Click here for additional data file.10.7717/peerj.12662/supp-8Supplemental Information 8Click here for additional data file.10.7717/peerj.12662/supp-9Supplemental Information 9Click here for additional data file.10.7717/peerj.12662/supp-10Supplemental Information 10Click here for additional data file.10.7717/peerj.12662/supp-11Supplemental Information 11Click here for additional data file.10.7717/peerj.12662/supp-12Supplemental Information 12Click here for additional data file.10.7717/peerj.12662/supp-13Supplemental Information 13Click here for additional data file.10.7717/peerj.12662/supp-14Supplemental Information 14Click here for additional data file.10.7717/peerj.12662/supp-15Supplemental Information 15Click here for additional data file.10.7717/peerj.12662/supp-16Supplemental Information 16Click here for additional data file.10.7717/peerj.12662/supp-17Supplemental Information 17Click here for additional data file.10.7717/peerj.12662/supp-18Supplemental Information 18Click here for additional data file.


Mycobacterium caprae was diagnosed in a 65-year-old goat breeder from northern Greece. This case represents a documented occupational transmission of M. caprae and highlights the importance of enhanced laboratory screening and increased surveillance for zoonotic tuberculosis control.Pulmonary tuberculosis caused by  Mycobacterium caprae, a member of Mycobacterium tuberculosis complex (MTBC), causes caprine tuberculosis (TB)  and an erythrocyte sedimentation rate of 112 mm/h. Chest radiograph and computed tomography scans revealed upper lobe cavities and infiltrations, predominantly on the left side (https://www.tosoh.com). We determined drug sensitivity on a strain grown on sodium pyruvate-LJ medium by Genotype MTBDRplus  and on solid media. We documented sensitivity to first-line anti-TB drugs and pyrazinamide. Because of the patient’s occupation, laboratory investigation included zoonotic species. GenoType MTBC differentiated the isolate as M. bovis subspecies caprae.In August 2019, a 65-year-old male goat breeder from northern Greece was admitted to the Aristotle University Pulmonology Department at G. Papanikolaou Hospital  for weight loss, productive cough, and fever <38.5https://www.genoscreen.fr) on crude DNA, using 6 quadruplex PCR and fluorescent primers with capillary electrophoresis. Identification was performed with the MIRU-VNTRplus database  Typing Kit (Genoscreen, rs 30–33  Figure.The patient received a standard anti-TB regimen for 9 months and responded favorably. Cultures and acid-fast bacilli turned negative 10 days after treatment and were negative 2.5 months after treatment. Erythrocyte sedimentation rate dropped to 25 mm/h, and the patient gained 17 kg. Chest radiograph and computed tomography scans showed remarkable improvement (M. caprae disease is further underestimated because of differences in laboratory capacity and lack of routine surveillance data. Zoonotic TB is a public health hazard, resulting in serious economic losses and having a substantial effect on poor and marginalized communities (Zoonotic TB causes an estimated 147,000 new human cases and 12,500 deaths annually worldwide (M. tuberculosis infection. Since 2019, enhanced laboratory screening and surveillance for high-risk patients related to animal breeding have been used in Greece. Timely application of bacteriologic and genotyping techniques, less frequently used in routine laboratory investigation until recently, highlighted the role of M. caprae as a human pathogen. MIRU-VNTR revealed a unique isolate similar to patterns reported in animals in Eastern Europe and the Balkans (M. caprae zoonotic TB in Greece are limited. A dairy goat farm outbreak in northern Greece was the first documented in 2005; M. caprae caused pneumonia among animals, and the mortality rate reached 92% (M. bovis isolate identified as M. bovis subsp. caprae in a GenoType MTBC assay evaluation study.Contaminated food and airborne transmission pose considerable risks to persons in contact with infected animals or animal products (M. caprae, a recently identified separate MTBC species, should be carefully addressed nationally and internationally. Key risk populations in countries not officially TB-free and with sizeable goat populations must be identified, occupational history sought, testing capacity extended, and monitoring and reporting improved. A One Health approach that highlights interdependence of human and animal health sectors is needed to curb the spread of this pathogen.Mycobacterium caprae, northern Greece, 2019. Additional information about occupational exposure to zoonotic tuberculosis caused by


Baetis rutilocylindratus and Cloeon dipterum (Baetidae), and Habrophlebiodes zijinensis (Leptophlebiidae). All mtgenomes had a complete set of 13 protein-coding genes and a conserved orientation except for two inverted tRNAs in H. zijinensis. Phylogenetic reconstructions using 21 mayfly mtgenomes and representatives of seven additional orders recovered both Baetidae and Leptophlebiidae as well supported monophyletic clades, with Ephemeroptera as the sister-taxon to all other winged insects (i.e. Odonata and Neoptera).Mayflies (Ephemeroptera) are a semi-aquatic insect order with comparatively few genomic data available despite their phylogenetic position at the root of the winged-insects and possession of ancestral traits. Here, we provide three mitochondrial genomes (mtgenomes) from representatives of the two most species-rich families,  The number of published molecular markers and genomes of the semi-aquatic insect order Ephemeroptera (mayflies) is low compared to the evolutionary diversity that the order represents . Their DNA was extracted using the DNeasy® Blood & Tissue  kit. Initially, four fragments of the mtgenome were amplified via standard PCR using universal primers . All purified amplification products were sequenced successively in both directions using a 3130 xl  capillary sequencer. The mtgenome of C. dipterum was obtained from DNA of laboratory-reared subimago specimens (full siblings). The laboratory-founder individual was collected in the United States of America . Analysis of nuclear and mitochondrial markers established the species as one of six putative species of C. dipterum s.l. with a geographical distribution in North America and Europe  of the two most diverse Ephemeroptera families: n et al. . In orden et al.  using aln et al. , using tn et al. . All mtgn et al.  and tRNAn et al. .B. rutilocylindratus), 15,407 bp (C. dipterum), and 14,355 bp (H. zijinensis) long, whereby the one of B. rutilocylindratus was complete (i.e. circular). All three contained the entire set of 13 protein-coding genes (PCGs), two rRNAs, and 22 (B. rutilocylindratus and C. dipterum) or 19 tRNAs (H. zijinensis). Gene order was conserved with the exception of two inverted tRNAs  in H. zijinensis.The sequences are deposited in GenBank with the accession numbers GU936204, MW149047, and GU936203. They were 14,883 bp (https://github.com/brettc/partitionfinder). Petrobius brevistylis  was specified as outgroup. The recovered phylogeny (Bayesian phylogenetic trees were reconstructed based on the nucleotide dataset of the 13 PCGs using MrBayes v.3.2.7 (Ronquist et al. hylogeny  was highClick here for additional data file.


Fragaria orientalis Lozinsk. is valuable germplasm material for cross breeding in Fragaria. In this study, we assembled the complete mitochondrial genome of F. orientalis using a combination of Illumina data and Nanopore data. The mitochondrial genome was 275,143 bp in length, including 29 protein-coding genes, 20 tRNA genes, and three rRNA genes, with a total GC content 45.23%. Seven protein-coding genes contained introns, and three were trans-spliced. Phylogenetic analysis indicated that F. orientalis is making a sister clade to the Amygdaloideae species. The complete mitochondrial genome of F. orientalis reported in this study will improve our understanding of Fragaria evolution. Fragaria orientalis is a wild tetraploid strawberry, that is distributed mainly in Heilongjiang, Jilin and Liaoning Provinces of Northeast China  under the voucher number DF2020-23. Mitochondrial DNA was extracted from fresh leaves using a plant mitochondrial extraction kit  and then sequenced on Illumina NovaSeq 6000 platform and Nanopore platform, respectively. Approximately 4.8 Gb of raw data were generated with insert-size 450 bp paired-end read lengths on the Illumina sequencing platform. A total of 59 Mb long-reads data comprising 23,812 reads were generated on the Nanopore sequencing platform. The mitochondrial genome was de novo assembled using the Illumina data by GetOrganelle v1.64  . The specimen and DNA were deposited at the Beijing Academy of Forestry and Pomology Sciences  contained introns, and three genes  were trans-spliced. Three genes  used ACG as the start codon, whereas nad1 and mttB used GTG and TTG, respectively. As the stop codon, fifteen genes ended with TAA, seven genes  with TGA, and seven genes  with TAG. Sequences of 12 common protein-coding genes  were aligned with homologous genes from 10 species. Phylogenetic analysis showed that F. orientalis is making an isolated clade, which is a sister to the clade making by species from Amygdaloideae (F. orientalis reported in this study will improve our understanding of Fragaria evolution.The aloideae . The com


Collected data give low-to-average quality evidence for beneficial effects of ADSC-related interventions in scar treatment. Some studies suggest that these interventions are noninferior to PRP or fractional CO2 laser.In recent years, lipofilling became a popular scar treatment method. Its beneficial outcomes have been partly attributed to the regenerative capacity of adipose-derived stem cells (ADSCs), suspended in an extracellular matrix—the stromal vascular fraction (SVF). The aim of this review was to verify if existing data support the clinical use of ADSC-related interventions in scar treatment. A systematic search of the literature was performed in July 2020 in five databases . Articles written in English, except for reviews, letters and editorials, were identified and screened for eligibility. We looked for reports of any outcomes in scars treated with ADSCs or SVF. Data from selected articles were extracted and the quality of each study was assessed. Five hundred and fourteen studies were identified in the primary search, of which nineteen were eventually included in the systematic review. Extracted data pointed to beneficial microscopic, functional and aesthetic outcomes in a total of 665 patients. Six studies included comparative interventions—platelet-rich plasma or CO We. We15]. We searched using electronic databases: MEDLINE, Cochrane Control Trials Register, EMBASE, Web of Science and Scopus. To identify all relevant articles, we used prespecified search engines for each database . AdditioEach relevant publication was categorized using the PICO model. Articles were included based on predefined selection criteria: appropriate PICO (using ADSCs or SVF in scar treatment), reporting of the outcomes and a defined isolation protocol. Exclusion criteria were animal studies, review letters and editorials, inadequate PICO, use of artificial materials  for delivery of ADSCs or SVF, and a substantial lack of methodology.Study eligibility was assessed by screening titles and if necessary, abstracts. Later, full texts were assessed for inclusion and exclusion criteria. All disagreements were resolved by a consensus between the two reviewers .The following information was extracted from each study by AS: study design, isolation procedure, population, intervention, microscopic and clinical outcomes. WP assessed the data extraction procedure and implemented necessary corrections. Risk of bias was assessed for randomized controlled trials using Cochrane’s Risk of Bias 2 Tool . StrengtWe did not perform quantitative statistical analysis of selected studies because of methodological and clinical heterogeneity. A systematic review of the methodology and outcomes was undertaken instead.The primary search yielded 514 scientific papers . After dWu et al.  reportedCarstens et al.  treated Pallua et al.  presenteThe first two cases presented innovative uses of SVF in scar treatment, both incorporating ultrasound examination as an objective measurement tool. Pallua et al. used lipoconcentrate—not an entirely new approach since similar methods have been described earlier. All these studies lacked a statistical analysis .p < 0.05), apart from height, which was not reported. Fat resorption occurred in six cases. Seventy-six percent of patients assessed the results as excellent or good. This study showed significant aesthetic improvement in atrophic scars after nanofat injection.Ghareeb et al.  treated p < 0.05) in terms of pigmentation , flexibility (100%), thickness , pruritus (94%), pain (100%) and vascularity (33%). It is the second study that showed significant improvement in manual functionality after SVF injection in post-burn hand scarring.In his second study, Carstens et al.  reportedp < 0.05), apart from the scar surface area. Of patients with a scar history of <5 years, 92.6% had good aesthetic results, whereas only 14.3% of patients with older scars shared this outcome (p = 0.001). In this study, significant aesthetic improvement in mostly hypertrophic scars was shown after nanofat injection.Bhooshan et al.  used nanp = 0.01), but no changes in elastic fibers. Previously undetectable sebaceous and sweat glands were visualized by immunostaining 6 months after treatment. Here, nanofat rendered significant aesthetic improvement in atrophic facial scars.Gu et al.  studied p < 0.01). Vascularity, pigmentation, hardness, flexibility and pliability improved in particular (p < 0.01). In this study, scar aesthetics improved after SVF injection, though various assessment methods provided ambiguous results.Lee et al.  reportedUyulmaz et al.  treated p < 0.001). In the observer’s opinion, the overall score was better, but only pliability and pigmentation improved significantly (p < 0.001). Here, nanofat injections rendered significant aesthetic improvement in post-burn facial scars.Jan et al.  reportedn = 48), analysing it prospectively . MRI and ultrasound examination showed lower fat reabsorption in the SVF and PRP groups in treated facial scars. In this study, authors showed that SVF- or PRP-enriched fat grafting significantly improved graft survival, thus improving the aesthetic outcome.Gentile et al.  studied p < 0.05). Height (p = 0.04) for the SBSES and pliability (p = 0.04) in the VSS were significantly better in the SVF-treated group vs. control. Here, aesthetics of scars significantly improved after SVF injection compared to no SVF supplementation.The second study by Lee et al.  comparedAuthors of the first study incorporated objective imaging techniques with an adequate follow-up, however, they failed to report some of the outcomes. This was the first study to compare PRP with SVF-enriched fat in scar treatment. Lee et al. used objective scar assessment scales and masked the analyst, but collected a small and heterogenous sample of patients. Both studies lacked a statistical analysis of patients’ baseline characteristics .2 fractional laser were used in monthly intervals on one side of the face. DMEM was applied to the control side. One month after the third treatment, patients’ satisfaction with the ADSC-CM-treated side was significantly higher vs. the control side (2.35 ± 0.69 vs. 2.08 ± 0.76). The result was corroborated by objective assessment with the ECCA  score (26.15 ± 19.16 vs. 32.7 ± 18.1), performed by two blinded evaluators. In the ADSC-CM group, the melanin index and transepidermal water loss were significantly lower at the end of the study, whereas biophysical examination showed improved elasticity and hydration. Cheek biopsies showed a more ample improvement in collagen (49.98% vs. 36.09%) and elastin (37.61% vs. 26.13%) density vs. control. In this work, ADSC-conditioned medium rendered aesthetic, biophysical and histological improvement in patients with atrophic acne scars, compared to placebo.Zhou et al.  performe2 fractional laser in the treatment of post-acne scars in 10 patients. Three months after treatment, scar severity decreased in both groups , as measured by the Goodman and Baron scale, with no differences between the cohorts (p = 0.183). Scar area percentage was reduced after 2 and 3 months—similarly in both groups (p < 0.001). TEWL improved quicker in the SVF-treated group (p = 0.004); however, the final TEWL and hydration outcomes were similar on both sides after 3 months (p = 0.279). No difference in patients’ satisfaction was noted (p = 0.234). The authors showed that there were no significant differences in biophysical and aesthetic outcomes, when comparing SVF with fractional CO2 laser in post-acne scars.Abou Eitta et al.  conducteShalaby et al.  comparedDespite smaller populations, the first two studies utilized more adequate methods than the last one. Their major advantages were an innate control group (split-face), scar homogeneity and a blinded outcome assessment. Baseline differences between the groups and the etiology of various scars hinder interpretation of Shalaby’s study .p = 0.218). However, after 3 months, a higher reduction percentage was shown in the PRP group (80.2%) vs. the SVF group (66.5%) (p = 0.023). Authors used an image analyzer to perform a quantitative histological assessment. Epidermal thickness  and collagen content  improved significantly (p < 0.05) with no differences between both groups. Elastin was more intensively produced after the PRP treatment . In this study, an advantage of PRP over SVF was shown in terms of long-term scar surface reduction and elastin concentration, but not patients’ satisfaction, nor other histological measurements.Elkahky et al.  comparedp < 0.05). SVF yields were measured and compared between the groups. Authors associated the SVF cell number with clinical improvement. Here, nanofat enhanced aesthetics in patients with post-burn or post-traumatic scars, with improvement proportional to the degree of nanofat condensation.Gentile et al.  compared2 fractional laser addition to nanofat + PRP treatment in a group of 30 patients with chronic acne scars. All patients underwent two courses of either treatment (with or without laser) 6 months apart. Three months after the second treatment, skin thickness improved in the laser-treated group (p = 0.007), but not in control (p = 0.12), compared with the preoperative values. The calculated change in thickness between the pre- and post-op period, however, did not differ between groups (0.67 cm in A and 0.63 cm in B). Baseline skin thickness differed between groups (0.532 cm in A and 0.737 cm in B). Measurements were taken with ultrasound. The postoperative patients’ quality of life was similar in both groups, evaluated with the FACE-Q module. Results of this study are not easy to interpret due to significant baseline imbalances between the groups. It seems fractional CO2 laser addition to nanofat + PRP may improve skin thickness, but the credibility of this finding is questionable.Tenna et al.  studied p < 0 05), similarly in both groups. Compared to baseline, postoperative MRI scans showed increased fat accumulation over the stump in the SVF-treated groups, but not in the control. The authors showed that SVF supplementation prolongs the fat graft survival, though it does not improve aesthetic outcomes compared to fat grafting alone.Malik et al.  treated The above-mentioned RCTs were of poor quality, bearing a considerable or high risk of bias . Only MaAuthors of selected articles used a variety of isolation techniques. The majority of them are illustrated in a simplified form in Protocols of enzymatic SVF isolation varied between studies. Most commonly (six studies) they included tissue digestion with collagenase and subsequent centrifugation  are case reports or case series. Among randomized controlled trials, the overall risks of bias were assessed as considerable or high. Nevertheless, authors present corroborating results, suggesting beneficial effects of ADSCs/SVF in scar treatment.Internationally accepted scar quality measuring tools like VSS, POSAS or VAS enable simple and objective outcome evaluation  and were2 laser in the treatment of post-acne scars but found no significant differences [Few studies compared nanofat/SVF with alternative treatments. Results suggest that aesthetic outcomes and patients’ satisfaction do not differ significantly in comparison with classic fat grafting. Fat accumulation and reabsorption, however, improves in nanofat/SVF-treated groups ,65. Threferences .Quantitative and semiquantitative histological analyses undertaken in selected studies showed increased elastin and collagen production, coupled with increased dermal thickness and neovascularization ,55,56,61The abundance of SVF/ADSC isolation methods and multiple nanofat processing protocols pose a challenge to interpreting collected results. They also reflect great heterogeneity of clinical practices. Some authors altered the original nanofat production procedure by additional centrifugations before and/or after the homogenization step ,61,67,68This review is limited by English language preference and the exclusion of animal studies (possibly including human subjects) from the search engine. We are awaiting reports of randomized trials studying preventive SVF use, keloid treatment, SVF comparison with PRP and isolated ADSC administration ,46,47,482 laser in terms of clinical outcomes. Many poor-quality papers were published and high-quality data are needed to support the use of ADSCs/SVF in clinical practice. Adequate randomized controlled trials are required to compare ADSC-related interventions with other methods, as well as different ADSC/SVF isolation methods with each other. Hopefully, this review will pave the way for conducting future research and will be helpful in navigating through methodological discrepancies.Collected data give limited low-to-average quality evidence for beneficial effects of ADSC-related interventions in scar treatment. Some evidence suggests that SVF/nanofat is noninferior to common approaches, such as PRP or fractional CO


Rhizosphere-resident fungi that are helpful to plants are generally termed as ‘plant growth promoting fungi’ (PGPF). These fungi are one of the chief sources of the biotic inducers known to give their host plants numerous advantages, and they play a vital role in sustainable agriculture. Today’s biggest challenge is to satisfy the rising demand for crop protection and crop yield without harming the natural ecosystem. Nowadays, PGPF has become an eco-friendly way to improve crop yield by enhancing seed germination, shoot and root growth, chlorophyll production, and fruit yield, etc., either directly or indirectly. The mode of action of these PGPF includes the solubilization and mineralization of the essential micro- and macronutrients needed by plants to regulate the balance for various plant processes. PGPF produce defense-related enzymes, defensive/volatile compounds, and phytohormones that control pathogenic microbes’ growth, thereby assisting the plants in facing various biotic and abiotic stresses. Therefore, this review presents a holistic view of PGPF as efficient natural biofertilizers to improve crop plants’ growth and resistance. Trichoderma, Talaromyces, Fusarium, Phytophthora, Penicillium, Rhizoctonia, Gliocladium, Phoma, etc.) have been reported to date to boost plants’ growth, and to enhance their innate immunity and other important secondary metabolites in plants  fungus have been shown to maximize the PPO activity in cucumber plants upon treatment  and nonsporulating [GU21-2] fungus increased the chitinase activity in cucumber upon inoculation with Colletotrichum orbiculare [Trichoderma elicited a high level of β-1,3 glucanase and chitinase enzyme activities, which induced resistance in Capsicum and French bean plants [Phoma sp.) and non-sporulating fungus GU21-2 treatment caused high glucanase activity in cucumber [Penicillium sp. have induced increased chitinase activity in the case of pearl millet upon pathogen inoculation [Trichoderma atroviride treatment on cucumber plants increased PPO enzyme activity upon challenge inoculation with Rhizoctonia solani [Nicotiana benthamiana, and reduced P. nicotianae and TMV infection [PGPF, like l millet , and rooucanases . A signichrymans . A rise operties . T. harzFusarium . Phoma sbiculare . Trichodn plants . PGPF  promoted cucumber plants’ growth under salt stress [Penicillium sp., isolated from the rhizosphere soil of peanut, improved the saline tolerance ability in sesame plants [Trichoderma spp. elicited abiotic stress tolerance ability against biotic pressure imposed by phytopathogens [T. atroviride treatment improved the drought tolerance ability of maize plants with increased antioxidant enzyme machinery [T. hamatum treatment triggered growth and the drought tolerant capacity in Theobroma cacao. T. harzianum treatment mitigated the salt (NaCl) tolerance capacity in Indian mustard plants with maximized antioxidant enzyme defense machinery [Crop plants encounter different abiotic stress challenges—including excessive temperature, drought, salinity, floods, and heavy metal accumulation—which exclusively affect crop plant growth and yield ,202. Mosressures . Trichodt stress . Penicile plants . Trichodathogens . T. atroachinery . T. hamaachinery .Microsphaeropsis, Mucor, Steganosporium, Phoma, Aspergillus, Alternaria and Peyronellaea were—have been reported to protect Arabidopsis plants from heavy metal accumulation [T. harzianum improved salt, osmotic, heat and oxidative stress conditions in A. thaliana plants with an increase in heat shock protein, and APX and SOS transcript activities [T. virens improved the cadmium tolerance ability in N. tabacum plants with a reduction in lipid peroxidation and increased antioxidant enzyme activity [T. harzianum treatment increased the drought tolerance ability in N. tabacum plants with an increase in their relative water content, along with a decline in their transpiration rate [Penicillium and Aspergillus spp., and this PGPF resilience to adverse environment pressures is due to the production of osmotic substances [Different groups of PGPF—such as mulation . T. harztivities . T. vireactivity . T. harzion rate . Furtherion rate . PGPF stion rate . During ion rate . Lignin ion rate . Saline ion rate ,221. PGPion rate . PGPF inion rate . Differeion rate . A sodiubstances .C. protuberata in Dichanthelium lanuginosum, but both the fungus and the plant showed no survival ability above 38 °C [Penicillium sp. were reported to boost plant immunity in sesame plants upon Fusarium infection under salt stress conditions [Penicillium resedanum induced GA production, which promoted chilli plants’ growth under abiotic pressures [Trichoderma sp. has been reported to possess a tolerance ability toward heavy metals, chiefly zinc, copper, lead, cadmium, and so on [T. harzianum elicited ROS production via ISR activation by Thph 1 and 2 proteins in the case of maize [4 and α-keto- butyrate upon root colonization in plants [Trichoderma spp. produced ACC-deaminase, which regulates the endogenous ACC level, thereby eliciting root elongation and improving plants’ inherent resistance capacity against abiotic pressures [T. longibrachiatum (T6) enhanced wheat plant growth and increased the capacity level to tolerate NaCl pressure by increasing ACC-deaminase enzyme activity (lowering ethylene) and IAA gene expression. This alleviated the effect caused Na+ damage and enhanced Na+ or H+ (antiporter gene) in wheat plants [Heat tolerance ability has been imparted by ve 38 °C . Differenditions . Heavy tnditions . Penicilressures . Trichodnd so on ,229. Thend so on . PGPF alnd so on ,211. A cnd so on . T. harzof maize . Therefoof maize ,211. Proof maize . PGPF trn plants . Differeressures . Accordit plants . The tolThe disease is not the only outcome of plant-microbe interactions. Plants do have defense mechanisms that they utilize themselves, both locally and systemically. Several mutually beneficial relationships between plants and microbes affect agricultural productivity and plants’ health in general. These systems have also been the foci of intensive studies. In symbiotic relationships, the microbe assists the plant with nutrient absorption, or contributes biochemical and molecular activities that the plant lacks . The plaPresently, most of the research studies are focused on combating plant diseases through chemical insecticides or pesticides and fungicides, which are lethal to beneficial soil microflora and are also not safe for human consumption. Moreover, many chemical fertilizers, chiefly N, P, and K, have been applied to improve various crop plants’ growth, which causes soil pollution . TherefoPGPF applications are highly efficient in enhancing crop yield, crop quality, and the sustainable management of plant diseases. The treatment with PGPF will reduce the cost and pollution effect caused by chemical fertilizers. PGPF can be used as a substitute to reduce the use of agrochemicals in plant disease management. The use of PGPF improves plant performance and crop yield in agricultural fields. Information about PGPF and host plant interactions with the pathogen infection helps us understand the signaling mechanism involved in plant growth and resistance. The induction of resistance mediated by PGPF is linked with the production of phytohormones, defense-related enzymes, antibiotics and other signaling hormones, which play a crucial role in offering long-time protection and resistance during biotic and abiotic pressures. Thus, the treatment of PGPF increased crop yield production and reduced the disease-causing effect of pathogens in agricultural crop fields.


Candida auris is an emerging human pathogen associated with multidrug resistance and nosocomial outbreaks. We report the draft genome sequences of 19 C. auris isolates that were associated with a cluster of cases in a hospital in Hong Kong. Candida auris is an emerging human pathogen associated with multidrug resistance and nosocomial outbreaks. We report the draft genome sequences of 19 C. auris isolates that were associated with a cluster of cases in a hospital in Hong Kong. Candida auris was first described in Japan in 2009  and B11245 (GenBank accession no. GCA_008275145.1) . C. auris strain B8411 (GenBank accession no. GCA_002759435.2) was selected as the reference genome, and the raw reads of sequenced C. auris isolates from each of the four established clades, including strains B11215 (GenBank accession no. SRR3883446 [clade I/South Asia]), B11220 (GenBank accession no. SRR3883452 [clade II/East Asia]), B11223 (GenBank accession no. SRR3883455 [clade III/South Africa]), and B11244 (GenBank accession no. SRR3883465 [clade IV/South America]), were added to the analysis (Single nucleotide polymorphism (SNP) analysis was performed using Snippy v4.41 . The. Thehttpanalysis . Our resanalysis .ERG11 mutation, were observed (Gene mutations associated with antifungal resistance, including a reported observed , 11. ThePRJEB34199. The accession numbers for the assembly and raw reads for individual isolates are provided in The whole-genome sequencing project has been deposited in DDBJ/ENA/GenBank under the accession no.


Phaeocystis globosa is a well-known species for its pivotal role in global carbon and sulfur cycles and for its capability of forming harmful algal blooms (HABs) with serious ecological consequences. Its mitochondrial genome (mtDNA) sequence has been reported in 2014 but it remains incomplete due to its long repeat sequences. In this study, we constructed the first full-length mtDNA of P. globosa, which was a circular genome with a size of 43,585 bp by applying the PacBio single molecular sequencing method. The mtDNA of this P. globosa strain (CNS00066), which was isolated from the Beibu Gulf, China, encoded 19 protein-coding genes (PCGs), 25 tRNA genes, and two rRNA genes. It contained two large repeat regions of 6.7 kb and ∼14.0 kb in length, respectively. The combined length of these two repeat regions, which were missing from the previous mtDNA assembly, accounted for almost half of the entire mtDNA and represented the longest repeat region among all sequenced haptophyte mtDNAs. In this study, we tested the hypothesis that repeat unit amplification is a driving force for different mtDNA sizes. Comparative analysis of mtDNAs of five additional P. globosa strains  revealed that all six mtDNAs shared identical numbers of genes but with dramatically different repeat regions. A homologous repeat unit was identified but with hugely different numbers of copies in all P. globosa strains. Thus, repeat amplification may represent an important driving force of mtDNA evolution in P. globosa.The haptophyte  Phaeocystis globosa is a cosmopolitan phytoplankton that plays a pivotal role in global carbon and sulfur cycles by releasing substantial quantities of dimethylsulfide propionate (DMSP)  . It is ae (DMSP) . P. glob threats .P. globosa has high level of genetic diversity. Various physiological and ecological characteristics were observed among different P. globosa strains. For example, P. globosa strains collected in different ocean regions  have different acute toxic effects to Artemia sinica  have been applied to distinguish P. globosa strains with limited success  of the first n length . One mol globosa . Comparaiversity .P. globosa  were characterized. Although most members within an element family are identical, some are not  described herein were isolated from samples collected in 2019 from P. globosa bloom waters of the Beibu Gulf, China and Vietnam sea area (2SiO3) (–1 m–2 of cool white fluorescent illumination.The five sea area . Single- (2SiO3) . CultureP. globosa as reference sequences. The assembled sequences were further validated by aligning sequencing reads against the assembled result using BWA  were used for morphological observation. 18S rDNA was assembled basing Illumina reads with GetOrganelle , with pusing BWA  and SAMtsing BWA  and visusing BWA . For physing BWA . The ambsing BWA . There wsing BWA . The sup BioEdit .Cultures at the exponential growth phase were harvested and concentrated by centrifugation. Two sequencing methods were used for the genomes in this study. All five strains obtained in this study were sequenced using Illumina sequencing, while the strain CNS00066 was also sequenced using PacBio Sequel II sequencing technology.P. globosa strains were prepared for whole genome sequencing. DNA degradation and contamination were monitored on 1% agarose gels. DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer . Sequencing libraries were generated using NEBNext® DNA Library Prep Kit following manufacturer’s recommendations and indices were added to each sample. The genomic DNA was randomly fragmented to a size of 350 bp by shearing, then DNA fragments were end polished, A-tailed, and ligated with the NEBNext adapter for Illumina sequencing, and further PCR enriched by generic adapter P5 and P7 oligos. The PCR products were purified (AMPure XP system) and resulted in libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer system and quantified using real-time PCR. Qualified libraries were sequenced on an Illumina platform according to effective concentration and data volume at Novogene . Sequencing was done using NovaSeq PE150 .For Illumina sequencing, total nucleic acids were extracted using the OMEGA HP Plant DNA Mini Kit  and quantified using a NanoDrop One spectrophotometer . DNA samples of five For strain CNS00066, the long-read DNA sequencing technology PacBio Sequel II was used for constructed the complete mitochondrion genome. For PacBio Sequel II sequencing, high quality genomic DNA was extracted using a modified CTAB method. RNase A was used to remove RNA contaminants. The quality of the DNA was checked by agarose gel electrophoresis. One long insert library (15 kb) was prepared, which was sequenced using the PacBio Sequel II platform . We generated 6.44 Gb HiFi reads.For Illumina sequencing data, methods of quality control and assembly were similar with P. globosa strain Pg-G(A) (NC_021637) (The resulting assembly scaffolds from the mtDNA were determined using BLAST  of the c_021637) . One mtD_021637)  and SAMt_021637)  and visu_021637) . We succ_021637)  and SAMt_021637)  and visu_021637) .P. globosa mtDNA (KC967226) with minimap2 (version 2.5)   using thion 2.5)  to obtaiion 2.5)  and SAMtion 2.5)  and visuion 2.5) .cox1.In order to facilitate comparative analysis, the starting sites of mtDNAs were all adjusted to 1 homology searches. Transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs) were identified using tRNAscan-SE 2.0  obtained in this study were identified based on comparative analysis of 18S rDNA sequences. The five P. globosa strains were nested within P. globosa monophyletic clade with robust support . V4 region of 18S rDNA was also analyzed, and the numbers of nucleotide differences between P. globosa strains were 0-6 nucleotides, which were much smaller than that of other congeneric species (11-20 nucleotides). 18 of 25 Phaeocystis 18S rDNA sequences have complete V9 region, and we analyzed the V9 region of these 18 strains. The number of V9 region nucleotide differences between P. globosa strains were 0-2 nucleotides, which was indistinguishable from other congeneric species (0-20 nucleotides). This indicated that V9 region does not provide enough resolution for species identification in Phaeocystis.Five  support . The numP. globosa strains, CNS00066 was a solitary-celled  clustered with P. globosa (KC967226) with moderate support. The mtDNAs of four strains CNS00069 (MW435863), CNS00087 (MW435865), CNS00262 (MW435861), and CNS00266 (MW435862), which were isolated from the Beibu Gulf in China and Vietnam sea area, clustered together in a different clade. The species in Coccolithophyceae, Pavlovophyceae, and Rappephyceae all formed well supported branches, and Rappephyceae was sister to the Pavlovophyceae. The phylogenetic relationship was generally agreed with the 18S rDNA-based phylogenetic relationship in this study and previous results basing mitochondrial and plastid dataset (To explore the evolutionary relationship between  members . The mtD dataset  with minP. globosa (five obtained in this study and KC967226) shared an identical number (19) of PCGs , which encode subunits of the ATP synthase complex, were identified. Seven genes encoding NADH dehydrogenase subunits, nad1-6 and nad4L, were detected. Three genes encoding complex IV (cytochrome c oxidase subunits), cox1, cox2 and cox3 were identified. Four genes encoding ribosomal proteins, rpl16, rps12, rps14 and rps3 were detected. One gene encoding complex III (cytochrome c reductase) cob was identified. A total of 25 tRNA genes and two rRNA genes (rrnL and rrnS) are present in the P. globosa mtDNA. 5S rRNA gene was not detected. None of the genes contained intron except rrnL (23S rRNA) gene in mtDNA of P. globosa strain Pg-G(A), which contained a single intron.The six mtDNAs of  of PCGs . Four ofPhaeocystis. Comparison of genome organization and gene order were shown in Phaeocystis. Within P. globosa strains, two gene arrangement events were discovered. The first was mtDNAs of strain CNS00066 and strain Pg-G(A), which showed identical gene orders (blocks a-b-c-d-e), and the second were mtDNAs of strains CNS00069, CNS00087, CNS00262, and CNS00266, which showed another identical gene order, and blocks order was a-b-d-e-c. Compared with the first genome organization, the block b was inverted and reversed, and the block c and the blocks d-e were reciprocally translocated in the second genome organization. A high degree of syntenic conservation was identified between P. globosa strains CNS00066, Pg-G(A) and P. antarctica, except that block e (nad5) was inverted and reversed in P. antarctica. Compared to P. globosa, another additional tRNA gene trnE-UUC was found in P. antarctica.We performed a comparative analysis of seven mtDNAs of the genus , two rRNAs (rnl and rns), and 20 tRNAs genes . These mtDNAs also showed important differences. For example, rpl14 and rps19 were found only in Pavlovales (Pavlovophyceae). The rps14 was absent from Chrysochromulina sp. NIES-1333  and Pavlomulina ranunculiformis NIES-3900, the rps3 was absent from Chrysochromulina sp. NIES-1333 , Pavlovales, Haptophyta sp. isolate H2 and P. ranunculiformis NIES-3900. The nad9 was found only in P. ranunculiformis NIES-3900. The atp8 gene was absent only in Isochrysidales, while the dam was found only in the Emiliania huxleyi . The dam gene, which encodes a DNA adenine methyltransferase, is common in bacterial genomes. Using tblastn search, we found that dam gene was also present in a closely related species Gephyrocapsa oceanica  and distantly related Aureococcus anophagefferens (Ochrophyta) mtDNAs, but absent from other studied mtDNAs. It may be gained via horizontal gene transfer. Further investigation is needed to test this possibility. Compared with mtDNAs of other Haptophyte species, the Chrysochromulina sp. NIES-1333 mtDNA encoded three extra trnM-CAU genes and one extra trnS-ACU gene, leading to a total of six trnM-CAU genes and three trnS genes. The six trnM-CAU genes were dispersed in genome, with sequence identities ranging from 36.4% to 100%. In contrast, no obvious similarity was found among three trnS genes. The rps8 gene was only found in Isochrysidales and Prymnesiales. P. antarctica  had an extra trnE-UUC gene. The 5S rRNA gene was found only in Pavlovales (Pavlovophyceae). The trnG-UCC, trnP-UGG and trnS-UGA genes were only absent in Haptophyta sp. isolate H2. The trnW gene contained UCA anticodon in Coccolithophyceae and CCA anticodon in Pavlovophyceae and Rappephyceae. The trnR gene contained ACG anticodon in Coccolithophyceae and Pavlovophyceae, a UCG anticodon in Rappephyceae.Comparison of 18 mtDNAs of species in the phylum Haptophyta  revealed interesting features in gene content . They shPhaeocysits. In addition, GUG may serve as the translation initiation codon for atp4, rps8 in E. huxleyi, atp9, nad4, and rpl14 in D. viridis, atp4 in Haptophyta sp. isolate H2, atp9, rpl14, and rps14 in Pavlova. The UUG may serve as the translation initiation codon for atp6, atp9, nad4, nad4L, nad9 in P. ranunculiformis NIES-3900, atp9, cox1, cox2, cox3, cob, nad1, nad4, rpl16, and rps3 in Chrysochromulina sp. NIES-1333, cox3 in C. tobinii CCMP291, cox2 and nad2 in Haptophyta sp. isolate H2, and rps14 in genus Pavlova.Alernative start codons were used in different haptophyte mtDNAs. AUG was the primary start codon in haptophyte mtDNAs and only known start codon in mtDNAs of Ancoracysta twista, Rhodomonas salina (Cryptophyceae), Aureococcus anophagefferens , Phaeodactylum tricornutum , Lotharella oceanica  , cob gene encoded encoding complex III (cytochrome c reductase), nad1, nad2, nad3, nad4L, nad4, nad5 and nad6 genes encoded NADH dehydrogenase subunits. rps3, rps12, and rps14 genes encoded ribosomal proteins. These genes are probably the most essentially important core genes and perform basic functions. Interestingly, P globosa mtDNA contained the lowest number (19) of PCGs, compared to other five mtDNAs.We also compared PCGs in mtDNAs of Haptophyte species with that of phyceae) . These sP. globosa mtDNA diversity in evolution, we constructed mtDNAs of four additional P. globosa strains . The mtDNAs of these strains were still incomplete, suggesting the presence of complex repeat sequences that remain to be resolved. Nevertheless, all genes were successfully identified in these sequences, suggesting that the missing sequences were repeat regions most likely without containing any genes. Aside from the repeat regions, mtDNAs were also relatively compact which was similar to that of strain CNS00066. AT contents of these strains were 66.7-67.2%, which were a little lower than the complete mtDNA of CNS00066.To test our hypothesis that plasticity of repeat regions may be an important driver of P. globosa strains contained two noticeable repeat regions with varying lengths in different strains: repeat 1 and repeat 2 , and two unfinished repeat regions were located at the ends of two transcription units. The current known repeats length of Phaeocystis strains was substantially shorter than the corresponding repeat in strain CNS00066.The mtDNAs of all repeat 2 . The lenPhaeocystis may have occurred through repeat-mediated recombination.The locations of the repeat regions were also variable among different strains. Within the strains CNS00066 and Pg-G(A), two repeat regions were located between block c and block d, block e and block a, respectively. Within strains , two repeats were between block a and block b, block e and block c, respectively. Gene structure rearrangement was close to repeat regions, such as the block b in strains  was inverted compared with that of CNS00066. This suggested that rearrangement in mtDNA of Two complex repeat regions were observed in mtDNA of strain CNS00066 . Six repRepeat region 1 can be divided into two segments repeat 1a and repeat 1b. A large inverted repeat p1  encompassing 573 bp spanning repeat 1a and repeat 1b. Repeat 1 was composed of repeat units A, B, D and E in various arrangements, mainly including B-D-E-A (∼260 bp) repeat units, D-E-A (∼210 bp) repeat units, and B-D-A (∼248 bp) repeat units.Repeat 2 also consisted of two segments, repeat 2a and repeat 2b, and a large inverted repeat p2  spanning repeat 2a and repeat 2b. Repeat 2 featured repeat units B, C and F. Maximal 106 consecutive tandem copies of repeat unit B were within repeat 2a. Repeat units B and C showed various arrangements with B-C (114 bp) repeat units being the common arrangement.The palindromic sequences p1 and p2 which were adjacent to inversion points, exhibiting a strong potential to form stable stem–loop structures . The repPhaeocystis species, we hypothesized that the repeat units identified in different mtDNAs share homology. To test this hypothesis, we analyzed the repeats of mtDNAs of five P. globosa strains obtained in this study, in addition to the P. globosa strain Pg-G(A) and the P. antarctica strain. Results showed that homologous repeat unit A could be identified in all P. globosa mtDNAs  and tandem duplication mutations in non-coding regions in the larger mtDNA  has two small intergenic repeats of 1624 bp and 1630 bp, and missing a large, complex repeated sequence array.Among the known 18 mtDNAs of haptophyte species, nine were reported as complete sequences, and other nine were reported as partial sequences. Nine full-length mtDNAs all contain repeat regions of various lengths ranging from 1.9 to 20.7 kb . The mtDPavlova lutheri CCMP 1325 and all Phaeocystis strains. No obvious repeat regions were found in Chrysochromulina parva UW 1161, Haptophyta sp. isolate H2 and P. ranunculiformis NIES-3900, and their mtDNAs are partial sequences and have not been successfully assembled. Homologous sequences of the repeat region of P. globosa have not been discovered in other haptophyte species. Length of repeat region of different P. globosa strains was variable. The repeat length polymorphism maybe used as molecular marker for specific strains.Seven of nine partial mtDNAs were obviously truncated in the repeat regions, including those of Phylogenetic analysis using mtDNAs revealed that Rappephyceae was sister to the Pavlovophyceae, while Prymnesiophyceae split from their common ancestor earlier. However, the support was only moderate , suggestP. globosa for the first time. It was a circular genome with a size of 43,585 bp, encoding 19 PCGs, 25 tRNA genes and two rRNA genes. Surprisingly it was found to contain two large-sized repeat regions of 6.7 kb and ∼14.0 kb in length, respectively. The combined length of these two repeat regions accounted for almost half of the entire mtDNA. The length and the repetitive nature of these two repeat regions made it challenging to construct the complete length of full-length mtDNA of P. globosa. Further analysis revealed that the repeat regions consisted of combinations of several of repeat units. To explore the nature of repeat sequences in other P. globosa strains, we have also constructed mtDNAs of four additional P. globosa strains . Comparative analysis revealed that corresponding repeat regions were readily identified in all strains but with different lengths. A homologous repeat unit A was found to be prevalent among all P. globosa strains, but with different numbers of copies and length. In addition to differences in repeats, these mtDNAs also differed in gene structure rearrangement. Another surprising result identified in this project was the plasticity of the repeat regions of the mtDNAs of different P. globosa strains. Thus, repeats may be an important driving force of mtDNA evolution. In addition, the mtDNAs of different P. globosa strains showed variations, suggesting that the mtDNAs can be used as a super molecular marker for distinguishing different strains.In this study, we successfully constructed the full-length mtDNA of https://www.ncbi.nlm.nih.gov/nuccore/MW435860,MW435863, MW435865,MW435861,MW435862; https://www.ncbi.nlm.nih. gov/nuccore/MN927483,MN927485,MN927500,MW575291,MW 575290, https://dataview.ncbi.nlm.nih.gov/object/SRR14711855, and http://www.ncbi.nlm.nih.gov/bioproject/732653.The original contributions presented in the study are publicly available. This data can be found here: NC conceived of the project. HS and YC organized the strain selection, cultivation, DNA preparation, and genome sequencing. HS organized the assembly, annotation, quality control, and analyzed the data with suggestions from others. HS and NC wrote the manuscript with inputs from others. FL revised the manuscript. All authors read and approved the final version of the manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Puccinellia tenuiflora and glycophytic Gramineae plants, and compared their transcriptional and physiological responses to salinity stress. Under salinity stress, the K+ concentration in the root was slightly enhanced in P. tenuiflora, but it was greatly reduced in the glycophytic Gramineae plants, which provided a physiological explanation for differences in salinity tolerance between P. tenuiflora and these glycophytes. Interestingly, several K+ uptake gene families from P. tenuiflora experienced family expansion and positive selection during evolutionary history. This gene family expansion and the elevated expression of K+ uptake genes accelerated K+ accumulation and decreased Na+ toxicity in P. tenuiflora roots under salinity stress. Positively selected P. tenuiflora K+ uptake genes may have evolved new functions that contributed to development of P. tenuiflora salinity tolerance. In addition, the expansion of the gene families involved in pentose phosphate pathway, sucrose biosynthesis, and flavonoid biosynthesis assisted the adaptation of P. tenuiflora to survival under high salinity conditions.Halophytes and glycophytes exhibit clear differences in their tolerance to high levels of salinity. The genetic mechanisms underlying this differentiation, however, remain unclear. To unveil these mechanisms, we surveyed the evolution of salinity-tolerant gene families through comparative genomic analyses between the model halophyte  Salt-affected soils may contain NaCl alone, NaCl and Na2SO4, or NaCl and Na2CO3. Plant growth under saline conditions is influenced by multiple stress factors, including direct ion injury and osmotic stress inflicted by Na+ and Cl– and indirect nutrient stresses caused by competition from Na+ and Cl–  is a forage grass with high nutritional value and strong tolerance for salinity and alkaline stresses . P. tenuiflora was bred as a grass variety and is not an endangered or protected species, so no specific permissions were required for its application in this study. The reference genome of P. tenuiflora used in this study was reported in our previous publication  and physiological measurements. The P. tenuiflora seeds were provided by Jilin Academy of Agricultural Sciences, Changchun, China.The taxonomy characteristics of lication . The gen2  were obtained from NCBI, Ensembl, and http://marinegenomics.oist.jp/gallery/. To exclude putative fragmented genes, the genes encoding protein sequences shorter than 50 amino acids were filtered   . Three cP-values of each branch using the Viterbi method with a randomly generated likelihood distribution. The exact P-values for transitions between the parent and child family sizes were estimated using this method for all branches of the phylogenetic tree  method.Genes from different species were clustered into gene families using OrthoMCL software (see Text Footnote 3) with a 1.5 inflation index . The gentic tree . Positivtauschii  and Gblotauschii . Positivtauschii  of PAML tauschii  by settiNucleotide variations at the 5′ and 3′ ends of intact LTR retrotransposons and DNA substitution rates were calculated . The nuc+ transporter (AKT), Na+/H+ exchanger (NHX), and high-affinity K+ transporter (HKT) proteins among O. sativa, H. vulgare, A. tauschii, P. tenuiflora, and D. glomerata using MEME Suite 5.2 .We carried out a motif analysis of the low affinity Kuite 5.2 . The ortSeeds of P. tenuiflora (variety Baicheng), O. sativa (variety JIJING88), H. vulgare (variety Zhu4300), D. glomerata (variety Sparta), and Triticum aestivum (variety Chinese Spring) were planted in plastic pots containing washed sand under greenhouse conditions (24–26°C day and 18–21°C night under 16-h light). The rice and wheat seeds were provided by Dr. Bao Liu , and the H. vulgare seeds and D. glomerata seeds were provided by the Chinese Academy of Agricultural Sciences . The pots (15 plants per pot) were cultured for 15 days with half-strength Hoagland nutrient solution. We stressed 15-day-old seedlings (at about the three leaves stage) through daily exposure to half-strength Hoagland nutrient solution containing 300 mM NaCl. Control plants were watered with half-strength Hoagland nutrient solution. We used a randomized complete block design. After 12 and 48 h of exposure to salinity stress, we collected physiological measurement samples from all of the five species and RNA samples from P. tenuiflora and D. glomerata. There were three biological replicates of each treatment and tissue, and each biological replicate comprised a pool of 5–20 plants. A total of 2 μg RNA per sample was used as the input material for the RNA sample preparations. Sequencing libraries were generated using a NEBNext UltraTM RNA Library Prep Kit for Illumina  following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. All downstream analyses were performed with high quality clean data. About 6 Gb of clean data for each sample were used to perform the transcriptional analysis. Statistically significant differentially expressed genes (DEGs) were discovered using the DESeq2 R package, and DEG was defined by the adjusted P-value (FDR) <0.05 and Fold Change ≥2. The DEGs were subjected to gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses with a GOseq R package . Quantitative real-time PCR (qRT-PCR) was employed to validate the results of the transcriptome analysis. RNA samples from the P. tenuiflora roots taken at 48 h after the onset of salt treatment were treated with DNaseI (Invitrogen), reverse-transcribed using SuperScriptTM RNase HReverse Transcriptase (Invitrogen), and then subjected to qRT-PCR analysis. Amplification of the target genes was monitored by SYBR Green. Actin and GAPDH were used as internal control genes. The gene expression data were analyzed using the ΔΔCt method . The statistical analysis (t-test) of the qRT-PCR and physiological measurements was performed using SPSS 16.0 . package  and KOBA package , respectt method . Dried sP. tenuiflora and D. glomerata was about 12.8 million years ago , including 580 Mb of LTR retrotransposons (52.43%) , phenylalanine metabolism, flavone and flavonol biosynthesis, flavonoid biosynthesis, and biosynthesis of amino acids  . We estistachyon . The LTRlomerata . The fre process . The KEGno acids . We wereexpanded .P. tenuiflora genes were positively selected over time  gene (ID: PtO_2103.26) and HKT1:3 gene (ID: PtO_1129.21) were upregulated at 48 h, and two voltage-gated potassium channel genes (IDs: PtO_1129.2 and PtF_428.24) were upregulated at both 12 and 48 h (NHX (Na+/H+ exchanger) genes and a V-H+- ATPase gene were upregulated in the roots of P. tenuiflora at 12 h or 48 h but not in the leaves (LEA genes and 12 dehydrin genes were upregulated in the roots or leaves of P. tenuiflora (Glucose-6-phosphate dehydrogenase (G6PDH) is the rate-controlling gene for the PPP, sucrose synthase genes are central to sucrose biosynthesis, and flavonoid 3′,5′-hydroxylase genes are critical to flavonoid biosynthesis. Two flavonoid 3′,5′-hydroxylase genes (IDs: PtF_517.39 and PtO_820.20) were upregulated in the leaves of P. tenuiflora at 12 h, and G6PDH (PtO_647.1) was upregulated in the roots of P. tenuiflora at 12 h  were upregulated in the roots or leaves of P. tenuiflora. Five abscisic acid (ABA) responsive element binding factor (ABF) genes, which are core ABA signaling genes and two 9-cis-epoxycarotenoid dioxygenase (NCED) genes, which are critical to ABA biosynthesis, were upregulated in the roots or leaves of P. tenuiflora. Some superoxide dismutase genes and glutathione S-transferase genes were also upregulated in P. tenuiflora. The qRT-PCR experiment was carried out using gene-specific primers to validate the results of the RNAseq experiment  and y = log2 (fold change of the D. glomerata ortholog) for each gene; the fold change was the ratio of stress to control of the expression level (P. tenuiflora ortholog (PtO) and D. glomerata ortholog (DgO) displayed similar responses to salinity stress , V-H+-ATPase gene, and NHX gene were upregulated in the roots of P. tenuiflora at both 12 and 48 h but not in roots of D. glomerata. In summary, PtO and DgO exhibit similar expression responses to salinity stress in the ABA pathway, dehydrin, and LEA genes, but they displayed different expression responses in HKT1;3, V-H+-ATPase, NHX, and G6PDH.To compare the gene expression response of on level . About 6y stress . We alsoy stress . For sev at 12 h . The PtO at 12 h . HKT1;3  at 48 h . The potP. tenuiflora occurred later than that of its close species, H. vulgare and D. glomerata. The LTR insertion events in P. tenuiflora occurred mostly during the Pleistocene Epoch, which lasted from approximately 2.6 million years to 11,700 years ago, including at least five documented major ice ages. Repeated ice ages  can result in frequent change in sea-level due to the exchange of water between ice and ocean . Interestingly, the number of SMP, LEA1, and LEA4 subfamilies in P. tenuiflora was much lower than that in D. glomerata   . Indeed,y stress . Interes history . We prop drought . The evoPuccinellia tenuiflora exhibited an extremely low Na+ concentration in the salinity-stressed shoots  may be a candidate Na+ excretion gene, which should be investigated in the future.d shoots . When the plants . This recophytes . Our rescophytes . Althouglomerata . HKT1;3 lomerata . The HKTnd wheat . TherefoP. tenuiflora may have inhabited saline environments for several millions of years and so may have evolved unique metabolic traits in response to its long-term exposure to severe soil salinity and drought. Our comparative genomics analysis revealed that the P. tenuiflora genes that were positively selected during evolutionary history were enriched in response to abiotic stimuli and response to stress , two flavonoid 3′,5′-hydroxylase genes , and three sucrose synthase genes were upregulated in the roots or leaves of P. tenuiflora under salinity stress  . It is oo stress . The sele plants . In addiynthesis . Accordiy stress . The PPPy stress . The enhnuiflora . Flavononuiflora , and sucnuiflora . Therefoy stress . In addinuiflora , which mP. tenuiflora was linked to its K+ uptake characteristics and strong capacity to control Na+ influx into shoots, and some P. tenuiflora K+ uptake gene families experienced expansion and positive selection during evolutionary history. During the adaptation of P. tenuiflora to high soil salinity, expanded salinity-tolerant genes have exerted dosage effects, and positively-selected salinity-tolerant genes may have been involved in the construction of new salinity tolerance pathways. This was the genomic basis for salinity tolerance differentiation between P. tenuiflora and glycophytic Gramineae plants . The genome sequence of P. tenuiflora is available from NCBI (https://www. ncbi.nlm.nih.gov/genome/?term=QRDG00000000.1) (accession number QRDG00000000.1).The original contributions generated for this study are publicly available. This data can be found here: All raw data of transcriptional analysis are available at NCBI (accession number CY and RG: experiment design. RG, LZ, KZ, HL, NB, and CY: performance of experiments. RG, CY, LZ, and KZ: data analysis. CY, RG, LZ, and KZ: manuscript writing. All authors read and approved the final manuscript.KZ was employed by Beijing Novogene Bioinformatics Technology Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Staphylococcus aureus (S.aureus) which can produce exfoliative toxins. The generalized SSSS is recommended to be admitted and treated with intravenous antibiotics. However, there were limited reports on whether personal and clinical factors can have impacts on the duration of intravenous antibiotic application for pediatric patients with generalized SSSS.Staphylococcal Scalded Skin Syndrome (SSSS) is caused by a special type of S.aureus in different samples and the antibiotic-resistant profile were investigated.We performed a study to assess the factors affecting intravenous antibiotic treatment course of SSSS patients. Additionally, the positive culture rates of S.aureus in different sample sources were calculated and the drug sensitivity results were statistically compared by pairwise Chi square test.Two hundred nineteen patients with generalized SSSS were included. Gender, age, area, season, maximum axillary temperature, white blood cell (WBC) count, C-reactive protein (CRP) level, types of intravenous antibiotics, and types of external antibiotics were recorded as the baseline. Simple linear regression was applied in the univariate analysis to determine the variables with statistical significance and then these variables were further examined in multivariate linear regression model. The positive culture rates of p < 0.05) and external application of fusidic acid  were associated with shorter treatment course, elevated leukocytes  and CRP level  were associated with longer treatment course. The positive culture rates of periorificial swabs, throat swabs, and blood samples were 54.55, 30.77, and 5.97% respectively. The resistant rates of levofloxacin (8.33%), gentamycin (8.33%), tetracycline (25%), oxacillin (8.33%), vancomycin (0%) were significantly lower than the ones of erythromycin (100%), trimethoprim-sulfamethoxazole (TMP/SMX) (83.33%), clindamycin (91.67%), penicillin G(100%) (p < 0.001).According to the multiple linear regression, older ages (β = − 0.01, S.aureus in periorificial and throat swabs were higher. Oxacillin and vancomycin resistance was rare and clindamycin resistance was common. Clindamycin monotherapy for SSSS should be avoided.Elevated leukocytes and CRP level indicated prolonged intravenous antibiotic treatment course. Older ages and external application of fusidic acid helped to reduce the treatment course. Compared with blood samples, the culture positive rates of  There are two forms of SSSS including the generalized SSSS and the localized one which is also called bullous impetigo. Erythematous blisters and honey-colored crusts especially in the diaper area were found in bullous impetigo. Most of the body surface is involved in generalized SSSS, which may lead to critical condition of the patients , ammation . Some repulation , 33. Furpulation , 35. BasS.aureus, which has been confirmed by some previous studies [S.aureus [S.aureus to fusidic acid than to mupirocin in China. Some Chinese experts have already compared the resistance rate of mupirocin with the one of fusidic acid. Liu YC et.al observed that only 1.7% of the methicillin-sensitive S. aureus strains were resistant to fusidic acid and 3.0% of the MRSA strains were resistant to fusidic acid [. Liu QZ et al. performed an observational study and found that among the 53 high-level mupirocin-resistant MRSA strains, none was resistant to fusidic acid [In our study, the external application of fusidic acid other than mupirocin helped to reduce the intravenous antibiotic treatment course. The reason may be that the fusidic acid were favorable in eliminating the colonization of  studies , 37. Wha studies . Liu Y eS.aureus . Of notedic acid . Liu QZ dic acid . Similardic acid , they foS. aureus and toxins responsible for SSSS to further confirm the culprit pathogen and diagnosis. Secondly, we did not perform the antimicrobial sensitivity tests of fusidic acid and mupirocin among the S.aureus strains. Multicenter prospective research with further laboratory investigations of S.aureus is necessary for the future.There were some limitations in our study. Firstly, we did not have data on phage types of the isolated S.aureus in periorificial and throat swabs were higher. Clindamycin-resistant isolates were much more common than oxacillin-resistant and vancomycin-resistant ones, suggesting clindamycin monotherapy for SSSS should be avoided. Oxacillin resistance was rare and amoxicillin-clavulanic acid, cefazolin, and cefuroxime were still effective in treating SSSS.It can be concluded that younger age, elevated WBC and CRP levels indicated longer length of intravenous antibiotic application, external application of fusidic acid other than mupirocin helped to reduce the intravenous antibiotic treatment course. Compared with blood samples, the culture positive rates of


Probiotic supplementation of preterm infants may prevent serious morbidities associated with prematurity.To investigate the impact of probiotic supplementation on the gut microbiota and determine factors associated with detection of probiotic species in the infant gut.Probiotic supplementation increases the long-term colonization of probiotic species in the gut of preterm infants.Bifidobacterium longum subsp. infantis BB-02, Bifidobacterium animalis subsp. lactis BB-12 and Streptococcus thermophilus TH-4) for prevention of late-onset sepsis. The presence of B. longum subsp. infantis, B. animalis subsp. lactis and S. thermophilus was determined for up to 23 months after supplementation ended using real-time PCR. Logistic regression was used to investigate the impact of probiotic supplementation on the presence of each species.Longitudinal stool samples were collected from a cohort of very preterm infants participating in a blinded randomized controlled trial investigating the impact of probiotic supplementation (containing B. longum subsp. infantis lactis, B. animalis subsp.   and S. thermophilus  was increased during the supplementation period in infants receiving probiotic supplementation. Post-supplementation, probiotic-supplemented infants had increased detection of B. longum subsp. infantis  and B. animalis subsp. lactis . Commencing probiotic supplementation before 5 days from birth was associated with increased detection of the probiotic species over the study period .Detection of B. longum subsp. infantis BB-02, B. animalis subsp. lactis BB-12 and S. thermophilus TH-4 enhances the presence of probiotic species in the gut microbiota of very preterm infants during and after supplementation. Commencing probiotic supplementation shortly after birth may be important for improving the long-term colonization of probiotic species.Probiotic supplementation with  Bifidobacterium species and Lactobacillus species, and higher numbers of potentially pathogenic Enterobacteriaceae and Clostridium difficile  or placebo . Infants commenced the assigned intervention when they were tolerating at least 1 ml of milk feeds every 4 h. Infants continued to receive the intervention until discharge home or term-corrected age, whichever came first. Stool swabs were collected from Victorian infants as close to the following time points as possible: prior to commencement of the study powder, after 1, 4 and 8 weeks of study powder, and at 6 and 12 months of age corrected for prematurity. An anal swab was collected if the infant had not yet passed a stool, and a swab of the first meconium was collected where available.The lsewhere . BrieflyB. longum subsp. infantis, B. animalis subsp. lactis, S. thermophilus  were collected from infants. Participant characteristics are summarized in A total of 683 infants were recruited to the B. animalis subsp. lactis , with the majority of post-supplementation specimens collected 6–12 months after the last dose of powder . Post-supplementation, infants who received probiotic had increased detection of B. longum subsp. infantis  and B. animalis subsp. lactis , but no difference in detection of S. thermophilus .A total of 679 specimens were collected prior to starting supplementation . There was no significant difference in the detection of o groups . A totalB. longum subsp. infantis, B. animalis subsp. lactis and S. thermophilus between randomization groups prior to supplementation . During the supplementation period, the Cq value of the three probiotic species was lower (indicating higher abundance) in infants receiving probiotic compared to placebo infants . Post-supplementation we observed lower Cq values of B. longum subsp. infantis in probiotic-supplemented infants , but no difference in the Cq values of B. animalis subsp. lactis or S. thermophilus. While the Cq values of B. longum subsp. infantis and B. animalis subsp. lactis were lowest during the supplementation period, the Cq values of S. thermophilus were lowest post-supplementation.We observed no difference in the Cq value of B. animalis subsp. lactis , B. longum subsp. infantis  and S. thermophilus . Receiving 65 days or more of probiotic was associated with increased detection of B. animalis subsp. lactis , but not the other two species. Gestational age ≤ 28 weeks was associated with decreased detection of S. thermophilus , and low birth weight (< 1000 g) was associated with decreased detection of both S. thermophilus  and B. longum subsp. infantis . Infants exposed to antibiotics were less likely to have detection of the three probiotic species, but this was only statistically significant for S. thermophilus . Breastmilk feeding rates in this cohort were high (97 %) [Using logistic regression, we examined the association between key variables  and the detection of the probiotic species over the whole study period in only those infants who received the probiotic (Table S3). Commencing probiotic supplementation within 5 days after birth was associated with increased detection of weight < 00 g was Bifidobacterium  and three control infants found, using qPCR assays, that B. bifidium was increased in probiotic-supplemented infants during and after supplementation [L. acidophilus was rarely detected in either probiotic or control infants [n=1310 preterm infants) of the probiotic B. breve BBG-001, found that 84 % of probiotic-supplemented infants were colonized with B. breve BBG-001 by strain-specific qPCR at 2 weeks of age compared to 35 % of control infants [B. breve was detected in the stool of 84 % of probiotic infants compared to 49 % of placebo infants at 36 weeks of postmenstrual age [et al. [B. breve was detected in 91 % (n=67/74) of infants supplemented with B. breve M-16V vs. 38 % (n=25/66) of control infants 3 weeks after supplementation.Our findings are consistent with previous studies that report increased detection of probiotic strains in probiotic-supplemented infants compared to controls. A small longitudinal study investigating the gut microbiota of only seven infants supplemented with Infloran  and previous studies [B. longum subsp. infantis had a relatively lower Cq post-supplementation compared to B. animalis subsp. lactis, suggesting that B. longum subsp. infantis may be more effective at colonizing the gut. This is supported by a two-part study of 17 infants that reported increased faecal Bifidobacterium (by 16S rRNA gene sequencing) in infants supplemented with B. longum subsp. infantis compared to infants supplemented with B. animalis subsp. lactis [The presence of the probiotic species during supplementation is not necessarily confirmation that colonization of these species has occurred: rather it may simply represent detection of ingested probiotic that has passed through the gastrointestinal tract. Infants in our study provided specimens for up to 23 months post-supplementation, with the majority of specimens collected 6–12 months after ending supplementation (Table S1). Increased detection of probiotic species post-supplementation as demonstrated in our study . In addition, we found that early gestational age (<28 weeks), low birth weight (<1000 g) and antibiotic use were each associated with decreased detection of one or more of the probiotic species. Consistent with this, the PiPs study reported that in infants randomized to probiotic, increasing gestational age was associated with increased colonization and antibiotic use was associated with decreased colonization . Early g infants . Thus itS. thermophilus was the most prevalent species detected post-supplementation and no difference in detection was observed between probiotic and placebo-supplemented infants (S. thermophilus is commonly used in the production of yoghurt and some cheeses [S. thermophilus post-supplementation in both allocation groups may suggest it was acquired through diet. infants . Most sp cheeses , so the B. longum subsp. infantis, B. animalis subsp. lactis and S. thermophilus detected were the probiotic strains. However, the increased detection of probiotic species in probiotic-supplemented infants compared to controls during the supplementation period suggests that the probiotic strains were present in these infants. Second, the PCR primers used for detection of S. thermophilus also detect S. salivarius [B. longum subsp. infantis, B. lactis and S. thermophilus exist between probiotic and control infants. Finally, the detection of the probiotic species in samples collected prior to supplementation could indicate some cross-colonization took place while the infants were in the neonatal unit, which has previously been reported [There are limitations to this study. First, the qPCR assays used were not strain-specific. As a result, we cannot be certain that the ivarius . A wholereported .B. longum subsp. infantis BB-02, S. thermophilus TH-4 and B. animalis subsp. lactis BB-12 enhances the presence of B. longum subsp. infantislactis, B. animalis subsp.  and S. thermophilus in the gut microbiota of preterm infants during supplementation. We followed infants for up to 23 months post-supplementation and found increased detection of both Bifidobacterium probiotic species in infants randomized to probiotic compared to placebo infants, which suggests that probiotic use may result in long-term colonization. Importantly, we report that commencing probiotic supplementation shortly after birth may be important for improved long-term colonization of probiotic species.We report that probiotic supplementation with Click here for additional data file.