Correction: A target enrichment approach for enhanced recovery of Synchytrium endobioticum nuclear genome sequences.

[This corrects the article DOI: 10.1371/journal.pone.0296842.].

Production of Ochratoxin A and Citrinin and the Expression of Their Biosynthetic Genes from Penicillium verrucosum in Liquid Culture.

Penicillium verrucosum is a fungal pathogen capable of producing two mycotoxins of concern, ochratoxin A (OTA) and citrinin (CIT). The production profile of these two mycotoxins is not well understood but could help mitigate co-contamination in the food supply. As such, the production of OTA and CIT from P. verrucosum DAOMC 242724 was investigated under different growing conditions in liquid culture. We found that among the different liquid media chosen, liquid YES (yeast extract sucrose) medium induced the highest production of both OTA and CIT, when P. verrucosum DAOMC 242724 was cultured in stationary mode. Shake culture significantly reduced the amounts of OTA and CIT produced. Among all culture conditions tested, far greater amounts of CIT were produced compared to OTA. Consequently, upon transcriptomic data analysis, a statistically significant increase in the expression of CIT biosynthetic genes was easier to detect than the expression of OTA biosynthetic genes. Our study also revealed that the putative biosynthetic gene clusters of OTA and CIT in P. verrusocum DAOMC 242724 are likely distinct from each other. It appears that despite sharing a highly similar structure, the isocoumarin rings of OTA and CIT are each assembled by a specialized polyketide synthase enzyme. Our data identified a putative nonreducing polyketide synthase responsible for assembling the carbo-skeleton of CIT. In contrast, a highly reducing polyketide synthase appears to be involved in the biosynthesis of OTA.

A prospective cohort study with serum anti-mullerian hormone levels change in patients undergoing uterine preservation after gestational trophoblastic neoplasia treatment with a methotrexate regimen.

Objectives: To monitor changes in serum anti-Mullerian hormone (AMH) levels of the patients with gestational trophoblastic neoplasia (GTN) who have undergone uterine preservation during treatment with a Methotrexate (MTX) regimen and associations with AMH variations. Methods: This observational prospective cohort study included 35 patients with low-risk GTN with uterine preservation during single-agent MTX chemotherapy at Hanoi Obstetrics and Gynecology Hospital from August 2021 to August 2022. Serum AMH levels were measured before initiation of chemotherapy and after the 1st, 2nd, and 3rd chemotherapy cycles. AMH evolution and its associations with some factors were analyzed. Results: The median basal AMH level before chemotherapy was 2.87 ng/mL (0.96 - 7.9 ng/mL) and negatively correlated with age. The serum AMH levels decreased significantly after each chemotherapy cycle (2.87 vs. 1.16, 0.91, 0.41 ng/mL). The median magnitude of the AMH levels decline after 1st, 2nd, and 3rd chemotherapy cycles were 51.2%, 69.4%, and 84.6% (p<0.001), respectively. AMH variation was associated with the basal AMH level, but not with age, ßhCG at diagnosis and menstrual status. Conclusion: Our study has shown that the serum AMH levels declined rapidly and steadily in all patients during chemotherapy for GTN. Although AMH cannot be used to monitor fertility potential lonely, these new studies improve our knowledge of ovarian toxicity and ovarian reserve during chemotherapy and strongly support the use of fertility preservation strategies.

A target enrichment approach for enhanced recovery of Synchytrium endobioticum nuclear genome sequences.

Potato wart disease is caused by the obligate fungal pathogen Synchytrium endobioticum. DNA extraction from compost, purified spores and crude wart tissue derived from tuber galls of infected potatoes often results in low S. endobioticum DNA concentration or highly contaminated with DNA coming from other microorganisms and the potato host. Therefore, Illumina sequencing of these samples generally results in suboptimal recovery of the nuclear genome sequences of S. endobioticum. A hybridization-based target enrichment protocol was developed to strongly enhance the recovery of S. endobioticum DNA while off-target organisms DNA remains uncaptured. The design strategy involved creating a set of 180,000 molecular baits targeting both gene and non-gene regions of S. endobioticum. The baits were applied to whole genome amplified DNA samples of various S. endobioticum pathotypes (races) in compost, from purified spores and crude wart tissue samples. This was followed by Illumina sequencing and bioinformatic analyses. Compared to non-enriched samples, target enriched samples: 1) showed a significant increase in the proportion of sequenced bases mapped to the S. endobioticum nuclear genome, especially for crude wart tissue samples; 2) yielded sequencing data with higher and better nuclear genome coverage; 3) biased genome assembly towards S. endobioticum sequences, yielding smaller assembly sizes but higher representation of putative S. endobioticum contigs; 4) showed an increase in the number of S. endobioticum genes detected in the genome assemblies. Our hybridization-based target enrichment protocol offers a valuable tool for enhancing genome sequencing and NGS-based molecular detection of S. endobioticum, especially in difficult samples.

[Neuroanatomical and neuropsychological correlates of shopping addiction behaviour. A systematic review]. / Correlatos neuroanatómicos y neuropsicológicos del comportamiento de adicción a las compras. Una revisión sistemática.

INTRODUCTION: The incidence of compulsive buying has increased over the last two decades and it has a substantial negative impact on consumers' overall functioning. However, despite its clinical relevance, the neuropsychological mechanisms and neural correlates underlying this phenomenon are still unknown. Also, compulsive buying behaviour remains unrecognised as a diagnostic category belonging to addictive disorders. AIM: The aim of the study is to systematically analyse the available empirical evidence on compulsive buying in order to identify the underlying neuropsychological variables and neural correlates. MATERIALS AND METHODS: PubMed, Scopus and ScienceDirect were searched for the mechanisms behind this phenomenon. RESULTS: The results show only 11 recent studies that investigate these mechanisms. In addition, the protocol of this systematic review was pre-registered in the international PROSPERO register (registration number CRD42023427497). CONCLUSIONS: The studies reviewed refer to impaired executive functions, decision-making and sensitivity to rewards, and a tendency to reactivity to purchase-related cues. This pattern of behaviour appears to involve a loss of behavioural control linked to dysregulation of structures such as the striatum and frontal regions. The results obtained are examined and similarities with the mechanisms underlying other addictions are discussed.

TITLE: Correlatos neuroanatómicos y neuropsicológicos del comportamiento de adicción a las compras. Una revisión sistemática.Introducción. La incidencia de la compra compulsiva ha aumentado en las últimas dos décadas y supone un impacto negativo sustancial en el funcionamiento general de los consumidores. No obstante, a pesar de su relevancia clínica, todavía se desconocen los mecanismos neuropsicológicos y los correlatos neurales subyacentes a este fenómeno. Asimismo, el comportamiento de compra compulsiva continúa sin reconocerse como una categoría diagnóstica perteneciente a los trastornos adictivos. Objetivo. El objetivo del estudio es analizar de forma sistemática la evidencia empírica disponible sobre la compra compulsiva con la finalidad de identificar las variables neuropsicológicas y los correlatos neurales subyacentes. Materiales y métodos. Se realizó una búsqueda en PubMed, Scopus y ScienceDirect sobre los mecanismos subyacentes a este fenómeno. Resultados. Los resultados muestran únicamente 11 estudios recientes que indagan sobre estos mecanismos. Además, se realizó un registro previo del protocolo de esta revisión sistemática en el registro internacional PROSPERO (número de registro CRD42023427497). Conclusiones. Los estudios analizados aluden a una alteración en la función ejecutiva, en la toma de decisiones y en la sensibilidad a la recompensa, y una tendencia a la reactividad de señales relacionadas con las compras. Este patrón conductual parece implicar una pérdida del control del comportamiento vinculado a la desregulación de estructuras como el estriado y las regiones frontales. Se examinan los resultados obtenidos y se analizan las similitudes existentes con los mecanismos subyacentes a otras adicciones.

Kinetics of photocatalytic degradation of organic compounds: a mini-review and new approach.

Organic compounds are widespread pollutants in wastewater, causing significant risks for living organisms. In terms of advanced oxidation processes, photocatalysis is known as an effective technology for the oxidation and mineralization of numerous non-biodegradable organic contaminants. The underlying mechanisms of photocatalytic degradation can be explored through kinetic studies. In previous works, Langmuir-Hinshelwood and pseudo-first-order models were commonly applied to fit batch-mode experimental data, revealing critical kinetic parameters. However, the application or combination conditions of these models were inconsistent or ignored. This paper briefly reviews kinetic models and various factors influencing the kinetics of photocatalytic degradation. In this review, kinetic models are also systemized by a new approach to establish a general concept of a kinetic model for the photocatalytic degradation of organic compounds in an aqueous solution.

Cytospora paraplurivora sp. nov. isolated from orchards with fruit tree decline syndrome in Ontario, Canada.

A new species of Cytospora was isolated from cankered wood of Prunus spp. during a survey of orchards exhibiting symptoms of fruit tree decline syndrome in southern Ontario, Canada. We found isolates that are morphologically similar to species in the Cytosporaceae family, which is characterized by single or labyrinthine locules, filamentous conidiophores or clavate to elongate obovoid asci and allantoid, hyaline conidia. Multi-gene phylogenetic analysis of ITS, LSU, act and tef1- α showed that the isolates form a distinct clade, sister to Cytospora plurivora. Morphologically, our isolates showed differences in the length of conidia and culture characteristics compared to C. plurivora, suggesting the establishment of a new species. The species is described as Cytospora paraplurivora sp. nov. and placed in the family Cytosporaceae of Diaporthales. Additionally, we sequenced, assembled and characterized the genome of the representative isolate for this new species. The phylogenomic analysis confirms the species order and family level classification. C. paraplurivora sp. nov. has the potential to severely affect stone fruits production, causing cankers and dieback in stressed trees, and eventually leads to tree decline. Pathogenicity tests show that the species is pathogenic to Prunus persica var. persica.

Automated and Clinically Optimal Treatment Planning for Cancer Radiotherapy.

Each year, approximately 18 million new cancer cases are diagnosed worldwide, and about half must be treated with radiotherapy. A successful treatment requires treatment planning with the customization of penetrating radiation beams to sterilize cancerous cells without harming nearby normal organs and tissues. This process currently involves extensive manual tuning of parameters by an expert planner, making it a time-consuming and labor-intensive process, with quality and immediacy of critical care dependent on the planner's expertise. To improve the speed, quality, and availability of this highly specialized care, Memorial Sloan Kettering Cancer Center developed and applied advanced optimization tools to this problem (e.g., using hierarchical constrained optimization, convex approximations, and Lagrangian methods). This resulted in both a greatly improved radiotherapy treatment planning process and the generation of reliable and consistent high-quality plans that reflect clinical priorities. These improved techniques have been the foundation of high-quality treatments and have positively impacted over 4,000 patients to date, including numerous patients in severe pain and in urgent need of treatment who might have otherwise required longer hospital stays or undergone unnecessary surgery to control the progression of their disease. We expect that the wide distribution of the system we developed will ultimately impact patient care more broadly, including in resource-constrained countries.

Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium.

The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1-D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.

Genome Characterization and Development of Real-Time PCR Assays for Ditylenchus Dipsaci and D. Weischeri.

The stem and bulb nematode Ditylenchus dipsaci is a destructive nematode pest on many crops and is internationally quarantined in many countries, whereas Ditylenchus weischeri, only known to infect a weed plant (Cirsium arvense), is an unregulated nematode species with no known economic importance. In this study, we used comparative genomics to identify multiple gene regions and developed novel real-time PCR assays for the detection of D. dipsaci and D. weischeri. We sequenced the genomes of two mixed-stage nematode populations of D. dipsaci and two mixed-stage nematode populations of D. weischeri. The assembled genomes of D. dipsaci were 228.2 Mb and 239.5 Mb, and the genomes of D. weischeri were 177.0 Mb and 196.3 Mb. Depending on the species, 21,403-27,365 gene models were predicted. Using orthologous group analysis, single-copy and species-specific genes were identified. Primers and probes were designed targeting two species-specific genes in each species. The assays detected as low as 12 pg of DNA from the target species, or as few as five nematodes, with a Cq of 31 cycles or less. Our study provides genome data for two additional D. dipsaci isolates and two D. weischeri isolates, and four new and validated molecular assays to be used for rapid detection and identification of the two species.

Apicidin biosynthesis is linked to accessory chromosomes in Fusarium poae isolates.

BACKGROUND: Fusarium head blight is a disease of global concern that reduces crop yields and renders grains unfit for consumption due to mycotoxin contamination. Fusarium poae is frequently associated with cereal crops showing symptoms of Fusarium head blight. While previous studies have shown F. poae isolates produce a range of known mycotoxins, including type A and B trichothecenes, fusarins and beauvericin, genomic analysis suggests that this species may have lineage-specific accessory chromosomes with secondary metabolite biosynthetic gene clusters awaiting description. METHODS: We examined the biosynthetic potential of 38 F. poae isolates from Eastern Canada using a combination of long-read and short-read genome sequencing and untargeted, high resolution mass spectrometry metabolome analysis of extracts from isolates cultured in multiple media conditions. RESULTS: A high-quality assembly of isolate DAOMC 252244 (Fp157) contained four core chromosomes as well as seven additional contigs with traits associated with accessory chromosomes. One of the predicted accessory contigs harbours a functional biosynthetic gene cluster containing homologs of all genes associated with the production of apicidins. Metabolomic and genomic analyses confirm apicidins are produced in 4 of the 38 isolates investigated and genomic PCR screening detected the apicidin synthetase gene APS1 in approximately 7% of Eastern Canadian isolates surveyed. CONCLUSIONS: Apicidin biosynthesis is linked to isolate-specific putative accessory chromosomes in F. poae. The data produced here are an important resource for furthering our understanding of accessory chromosome evolution and the biosynthetic potential of F. poae.

Development and evaluation of a target enrichment bait set for phylogenetic analysis of oomycetes.

Target enrichment is a term that encompasses multiple related approaches where desired genomic regions are captured by molecular baits, leaving behind redundant or non-target regions in the genome, followed by amplification and next-generation sequencing of those captured regions. A molecular bait set was developed based on 426 single-copy, oomycete-specific orthologs and 3 barcoding genes. The bait set was tested on 27 oomycete samples (belonging to the Saprolegniales, Albuginales, and Peronosporales) derived from live and herbarium specimens, as well as control samples of true fungi and plants. Results show that (i) our method greatly enriches for the targeted orthologs on oomycete samples, but insignificantly on fungal and plant samples; (ii) an average of 263 out of 429 orthologs (61%) were recovered from oomycete live and herbarium specimens; (iii) sequencing roughly 100 000 read pairs per sample is sufficient for optimal ortholog recovery while maintaining low sequencing costs; and (iv) the expected relationships were recovered by phylogenetic analysis from the data generated. This is the first report of an oomycete-specific target enrichment method with broad potential applications for evolutionary and taxonomic studies. A key benefit of our target enrichment method is that it allows researchers to easily unlock the vast and unexplored oomycete genomic diversity stored in natural history collections.

Inhibitory effect of different chicken-derived lactic acid bacteria isolates on drug resistant Salmonella SE47 isolated from eggs.

Lactic Acid Bacteria (LAB) regulate and maintain the stability of healthy microbial flora, inhibit the adhesion of pathogenic bacteria and promote the colonization of beneficial micro-organisms. The drug resistance and pathogenicity of Salmonella enteritis SE47 isolated from retail eggs were investigated. Meanwhile, Enterococcus faecalis L76 and Lactobacillus salivarius LAB35 were isolated from intestine of chicken. With SE47 as indicator bacteria, the diameters of L76 and LAB35 inhibition zones were 12 mm and 8·5 mm, respectively, by agar inhibition circle method, which indicated that both of them had inhibitory effect on Salmonella, and L76 had better antibacterial effect; two chicken-derived lactic acid bacteria isolates and Salmonella SE47 were incubated with Caco-2. The adhesion index of L76 was 17·5%, which was much higher than that of LAB35 (10·21%) and SE47 (4·89%), this experiment shows that the higher the bacteriostatic effect of potential probiotics, the stronger the adhesion ability; then Caco-2 cells were incubated with different bacteria, and the survival of Caco-2 cells was observed by flow cytometry. Compared with Salmonella SE47, the results showed that lactic acid bacteria isolates could effectively protect Caco-2 cells; finally, after different bacteria incubated Caco-2 cells, according to the cytokine detection kit, the RNA of Caco-2 cells was extracted and transcribed into cDNA, then detected by fluorescence quantitative PCR, the results showed that L76 could protect Caco-2 cells from the invasion of Salmonella SE47, with less cell membrane rupture and lower expression of MIF and TNF genes. Therefore, the lactic acid bacteria isolates can effectively inhibit the adhesion of Salmonella and protect the integrity of intestinal barrier.

Comparison of Two Methods for Presurgical Volumetric Evaluation of Alveolar Cleft Bone Defects Using Computer-Aided Engineering.

ABSTRACT: Precise volumetric evaluation of the alveolar cleft facilitates accurate preparation of bone substitutes and reduces donor site morbidity. This study investigates 2 advanced presurgical volumetric assessment methods that use computer-aided engineering (CAE) software. Preoperative computed tomography (CT) scans from 20 unilateral alveolar cleft patients undergoing secondary alveolar bone grafting (SABG) were analyzed by CAE software. Cleft defect volumes were calculated using the mirror-reversed technique and the subtraction method. The mirror-reversed technique determines defect volume by reversing the noncleft side to the cleft side. The subtraction method determines defect volume by subtracting a mask of the preoperative cleft from a mask generated after simulated cleft filling. The mean defect volumes and calculation times of the mirror-reversed technique (1.27 ±â€Š0.35 cm3; 11.80 ±â€Š1.79 seconds) and the subtractive method (1.23 ±â€Š0.32 cm3; 9.43 ±â€Š1.35 seconds) did not differ significantly. In Bland-Altman analysis the 2 methods were equivalent for alveolar cleft defect assessment. Both methods exhibited acceptable interobserver reliability, high precision, clinical convenience, time efficiency, and high reproducibility, and can serve as valuable tools for the planning and execution of SABG. The subtraction method has broader potential applicability and can simulate intraoperative bone grafting more effectively.

Determinants of Risk Factors for Renal Impairment among HIV-Infected Patients Treated with Tenofovir Disoproxil Fumarate-Based Antiretroviral Regimen in Southern Vietnam.

BACKGROUND: The situation of renal impairment among HIV-infected patients treated with TDF-based antiretroviral (ARV) regimen greater than 3 years is little known when TDF use has been promptly increasing in Vietnam. METHODS: We analyse demographic and clinical data from a cross-sectional survey of 400 HIV-infected patients aged ≥18 years, who were treatment-naive or switched TDF regimen within over 3 years between November 2018 and March 2019. Serological tests for serum creatinine, ALT, and AST were performed. Renal impairment was defined as an estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2. Multivariate regression analyses were used to explore the risk factors associated with renal impairment. RESULTS: At the baseline, 7.8% of respondents had estimated glomerular filtration rate (eGFR) of 30-59 mL/min/1.73 m2 and 0.8% had eGFR of 15-29 mL/min/1.73 m2, out of 34 (8.5%) of participants who had renal impairment. Multivariate analysis showed that participants who had preexposure to isoniazid (adjusted PR [aPR] = 0.35 Cl: 0.14-0.91) compared with nonexposure to isoniazid who had a BMI from 18.5 up to 25 kg/m2 (aPR = 0.31 Cl: 0.15-0.62) compared with BMI below 18.5 kg/m2 were less likely to suffer from renal impairment. Patients aged greater than 60 years (aPR = 26.75, 95% Cl: 3.38-211.62) compared with those aged 20-29 years were more likely to have increased risk of renal impairment. CONCLUSION: Our findings underscore the need for longitudinal studies to assess the influence of TDF on maintaining the low prevalence of renal impairment among HIV-infected patients in Vietnam.

Description and complete genome sequences of Bradyrhizobium symbiodeficiens sp. nov., a non-symbiotic bacterium associated with legumes native to Canada.

Four bacterial strains isolated from root nodules of soybean plants that had been inoculated with root-zone soil of either Amphicarpaea bracteata (Hog Peanut) or Desmodium canadense (Showy Tick Trefoil) growing in Canada, were previously characterized and placed in a novel lineage within the genus Bradyrhizobium. The taxonomic status of the novel strains was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated housekeeping gene sequences (atp D, gln II, rec A, gyr B and rpo B) placed all novel strains in a highly supported lineage distinct from named Bradyrhizobium species. Data for sequence similarities of concatenated housekeeping genes of novel strains relative to type strains of named species were consistent with the phylogenetic data. Average nucleotide identity values of genome sequences (84.5-93.7 %) were below the threshold value of 95-96 % for bacterial species circumscription. Close relatives to the novel strains are Bradyrhizobium amphicarpaeae, Bradyrhizobium ottawaense and Bradyrhizobium shewense. The complete genomes of strains 85S1MBT and 65S1MB consist of single chromosomes of size 7.04 and 7.13 Mbp, respectively. The genomes of both strains have a G+C content of 64.3 mol%. These strains lack a symbiosis island as well as key nodulation, nitrogen-fixation and photosystem genes. Data from various phenotypic tests including growth characteristics and carbon source utilization supported the sequence-based analyses. Based on the data presented here, the four strains represent a novel species for which the name B radyrhizobium symbiodeficiens sp. nov., is proposed, with 85S1MBT (=LMG 29937T=HAMBI 3684T) as the type strain.

Emergence of New Delhi Metallo-Beta-Lactamase (NDM) and Klebsiella pneumoniae Carbapenemase (KPC) Production by Escherichia coli and Klebsiella pneumoniae in Southern Vietnam and Appropriate Methods of Detection: A Cross-Sectional Study.

Carbapenemase-producing Enterobacteriaceae (CPE) are well known to cause many serious infections resulting in increasing mortality rate, treatment cost, and prolonged hospitalization. Among the widely recognized types of carbapenemases, New Delhi ß-lactamase (NDM) and Klebsiella pneumoniae carbapenemase (KPC) are the most important enzymes. However, in Vietnam, there are only scattered reports of CPE due to the lack of simple and affordable methods that are suitable to laboratory conditions. This study aims to survey the characteristics of carbapenem-resistant E. coli and K. pneumoniae (CR-E/K) at two hospitals in Southern Vietnam and perform some simple methods to detect the two enzymes. A total of 100 CR-E/K strains were collected from clinical isolates of Gia Dinh People's Hospital and Dong Nai General Hospital, Vietnam, from November 2017 to May 2018. The patient-related information was also included in the analysis. We conducted real-time polymerase chain reaction (PCR), Modified Hodge Test (MHT), and combined disk test (CDT) on all isolates. Carbapenemase-encoding genes were detected in 47 isolates (36 NDM, 10 KPC, and one isolate harboring both genes). The E. coli strain carrying simultaneously these two genes was the first case reported here. Most of isolates were collected from patients in ICU, Infectious Disease Department, and Department of Urologic Surgery. Urine and sputum were two common specimens. The true positive rate (sensitivity, TPR) and specificity (SPC) of the imipenem-EDTA (ethylen diamine tetra acetic acid) for NDM detection and the imipenem-PBA (phenylboronic acid) for KPC detection on E. coli were 93.8%, 97.1% and 66.7%, 95.7%, respectively. Meanwhile, the imipenem-EDTA for NDM detection and the imipenem-PBA for KPC detection among K. pneumonia achieved 90.5%, 100% and 100%, 92.9% TPR and SPC, respectively. However, MHT showed low sensitivity and specificity. Our findings showed that CP-E/K were detected with high prevalence in the two hospitals. We suggest that CDT can be used as a low-priced and accurate method of detection.

Description and complete genome sequence of Bradyrhizobium amphicarpaeae sp. nov., harbouring photosystem and nitrogen-fixation genes.

A bacterial strain, designated 39S1MBT, isolated from a root nodule of a soybean plant that had been inoculated with root-zone soil of Amphicarpaea bracteata (hog peanut) growing in Canada, was previously characterized and placed in a novel lineage within the genus Bradyrhizobium. The taxonomic status of strain 39S1MBT was verified by genomic and phenotypic analyses. Phylogenetic analyses of individual and concatenated protein-encoding gene sequences (atpD, glnII, recA, gyrB and rpoB) placed 39S1MBT in a lineage distinct from named species. Data for sequence similarities of concatenated genes relative to type strains of named species supported the phylogenetic data. Average nucleotide identity values of genome sequences (84.5-91.7 %) were well below the threshold value for bacterial species circumscription. Based on these data, Bradyrhizobium ottawaense OO99T and Bradyrhizobium shewense ERR11T are close relatives of 39S1MBT. The complete genome of 39S1MBT consists of a single 7.04 Mbp chromosome without a symbiosis island; G+C content is 64.7 mol%. Present in the genome are key photosystem and nitrogen-fixation genes, but not nodulation and type III secretion system genes. Sequence analysis of the nitrogen fixation gene, nifH, placed 39S1MBT in a novel lineage distinct from named Bradyrhizobium species. Data for phenotypic tests including growth characteristics and carbon source utilization supported the sequence-based analyses. Based on the data presented here, a novel species with the name Bradyrhizobium amphicarpaeae sp. nov. is proposed with 39S1MBT (=LMG 29934T=HAMBI 3680T) as the type strain.

Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum.

Synchytrium endobioticum is an obligate biotrophic soilborne Chytridiomycota (chytrid) species that causes potato wart disease, and represents the most basal lineage among the fungal plant pathogens. We have chosen a functional genomics approach exploiting knowledge acquired from other fungal taxa and compared this to several saprobic and pathogenic chytrid species. Observations linked to obligate biotrophy, genome plasticity and pathogenicity are reported. Essential purine pathway genes were found uniquely absent in S. endobioticum, suggesting that it relies on scavenging guanine from its host for survival. The small gene-dense and intron-rich chytrid genomes were not protected for genome duplications by repeat-induced point mutation. Both pathogenic chytrids Batrachochytrium dendrobatidis and S. endobioticum contained the largest amounts of repeats, and we identified S. endobioticum specific candidate effectors that are associated with repeat-rich regions. These candidate effectors share a highly conserved motif, and show isolate specific duplications. A reduced set of cell wall degrading enzymes, and LysM protein expansions were found in S. endobioticum, which may prevent triggering plant defense responses. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, reflects characteristic biological differences between the phyla, and shows commonalities in genomic features among pathogenic fungi.

"Three Subunit" Classification of Lesser-Form Cleft Lip and Muscle Analysis and Reconstruction of These Subunits Based on the Microanatomic Structures of Muscles in the Normal Upper Lip.

BACKGROUND: The main phenotypic features of lesser-form cleft lip include nasal, philtrum, and vermilion deformities. The manifestations of lesser-form cleft lip vary greatly, and it is difficult to rebuild these subunits during the operation. METHODS: "Three subunits" classification of lesser-form cleft lip was identified as nasal deformity (N), philtrum deformity (P), or vermilion deformity (V); and slight deformity (0) or obvious deformity (1). A total of 200 patients with lesser-form cleft lip were classified into one of the following 8 types: N1P1V1, N1P1V0, N0P1V1, N1P0V1, N0P0V1, N1P0V0, N0P1V0, or N0P0V0. Then the authors discussed the deformities of the lesser-form cleft lip and the reconstruction of the muscles in these subunits based on the microanatomic structure of the nasolabial muscle. RESULTS: This retrospective review included 200 patients with a lesser-form cleft lip, who were seen at our center from 2015 to 2017. There were 149 (74.5%) N1P1V1, 11 (5.5%) N1P1V0, 13 (6.5%) N0P1V1, 4 (2.0%) N1P0V1, 8 (4.0%) N0P0V1, 10 (5.0%) N1P0V0, 1 (0.5%) N0P1V0, and 4 (2%) N0P0V0 clefts. The various deformities of nasal floor, philtrum ridge, and vermilion may suggest that the muscle bundles in these subunits are abnormal and the operation should be performed to simulate the running directions and tension lines of these local muscles. CONCLUSIONS: The microanatomic structure and the tension lines of the nasolabial muscles can provide new perspectives for better understanding and repairing the lesser-form cleft lip in subunits.