The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium.

BACKGROUND: The rapid identification of lineage remains a challenge in the genotyping of clinical isolates of recombinogenic pathogens. The chromosome of Mycobacterium avium subsp. hominissuis (MAH), an agent of Mycobacterium avium complex (MAC) lung disease, is often mosaic and is composed of chromosomal segments originating from different lineages. This makes it difficult to infer the MAH lineage in a simple experimental set-up. To overcome this difficulty, we sought to identify chromosomal marker genes containing lineage-specific alleles by genome data mining. RESULTS: We conducted genetic population structure analysis, phylogenetic analysis, and a survey of historical recombination using data from 125 global MAH isolates. Six MAH lineages (EA1, EA2, SC1, SC2, SC3, and SC4) were identified in the current dataset. One P-450 gene (locus_tag MAH_0788/MAV_0940) in the recombination-cold region was found to have multiple alleles that could discriminate five lineages. By combining the information about allele type from one additional gene, the six MAH lineages as well as other M. avium subspecies were distinguishable. A recombination-cold region of 116 kb contains an insertion hotspot and is flanked by a mammalian cell-entry protein operon where allelic variants have previously been reported to occur. Hence, we speculate that the acquisition of lineage- or strain-specific insertions has introduced homology breaks in the chromosome, thereby reducing the chance of interlineage recombination. CONCLUSIONS: The allele types of the newly identified marker genes can be used to predict major lineages of M. avium. The single nucleotide polymorphism typing approach targeting multiallelic loci in recombination-cold regions will facilitate the epidemiological study of MAC, and may also be useful for equivalent studies of other nontuberculous mycobacteria potentially carrying mosaic genomes.

High-density extracellular probes reveal dendritic backpropagation and facilitate neuron classification.

Different neuron types serve distinct roles in neural processing. Extracellular electrical recordings are extensively used to study brain function but are typically blind to cell identity. Morphoelectrical properties of neurons measured on spatially dense electrode arrays have the potential to distinguish neuron types. We used high-density silicon probes to record from cortical and subcortical regions of the mouse brain. Extracellular waveforms of each neuron were detected across many channels and showed distinct spatiotemporal profiles among brain regions. Classification of neurons by brain region was improved with multichannel compared with single-channel waveforms. In visual cortex, unsupervised clustering identified the canonical regular-spiking (RS) and fast-spiking (FS) classes but also indicated a subclass of RS units with unidirectional backpropagating action potentials (BAPs). Moreover, BAPs were observed in many hippocampal RS cells. Overall, waveform analysis of spikes from high-density probes aids neuron identification and can reveal dendritic backpropagation. NEW & NOTEWORTHY It is challenging to identify neuron types with extracellular electrophysiology in vivo. We show that spatiotemporal action potentials measured on high-density electrode arrays can capture cell type-specific morphoelectrical properties, allowing classification of neurons across brain structures and within the cortex. Moreover, backpropagating action potentials are reliably detected in vivo from subpopulations of cortical and hippocampal neurons. Together, these results enhance the utility of dense extracellular electrophysiology for cell-type interrogation of brain network function.

Some strains that have converged to infect Prunus spp. trees are members of distinct Pseudomonas syringae genomospecies and ecotypes as revealed by in silico genomic comparison.

A complementary taxonomic and population genetic study was performed to delineate genetically and ecologically distinct species within the Pseudomonas syringae complex by assessing 16 strains including pathovar strains that have converged to infect Prunus spp. trees, and two outgroups. Both average nucleotide identity and genome-to-genome distance comparison methods revealed the occurrence of distinct genomospecies, namely 1, 2, 3 and 8 (sensu Gardan et al.), with the latter two being closely related. Strains classified as P. s. pv. morsprunorum clustered into two distinct genomospecies, namely 2 and 8. Both the AdaptML and hierarchical Bayesian analysis of population structure methods highlighted the presence of three ecotypes, and the taxonomically related genomospecies 3 and 8 strains were members of the same ecotype. The distribution of pathogenic and virulence-associated genetic traits among Pseudomonas strains did not reveal any distinct type III secretion system effector or phytotoxin distribution pattern that characterized single genomospecies and strains that infect Prunus spp. The complete WHOP (Woody HOst and Pseudomonas spp.) genomic region and the entire ß-ketoadipate gene cluster, including the catBCA operon, were found only in the members of genomospecies 2 and in the two P. s. pv. morsprunorum strains of genomospecies 8. A reduced gene flow between the three ecotypes suggested that point mutations played a larger role during the evolution of the strains than recombination. Our data support the idea that Prunus trees can be infected by different strains of distinct Pseudomonas genomospecies/ecotypes through diverse mechanisms of host colonization and infection. Such strains may represent particular lineages that emerged from environments other than that of the infected plant upon acquiring genetic traits that gave them the ability to cause plant diseases. The complementary assessment of bacterial strains using both taxonomic approaches and methods that reveal ecologically homogeneous populations has proven useful in confirming the cohesion of bacterial clusters.

A Population-Based Cohort Study on Diagnosis and Early Management of Anorectal Malformation in the UK and Ireland.

BACKGROUND: This study describes the presentation and initial management of anorectal malformation (ARM); evaluating the frequency, causes and consequences of late diagnosis. METHODS: A prospective, population cohort study was undertaken for newly diagnosed ARMs in the UK and Ireland from 01/10/2015 and 30/09/2016. Follow-up was completed at one year. Data are presented as n (%), appropriate statistical methods used. Factors associated with late diagnosis; defined as: detection of ARM either following discharge or more than 72 h after birth were assessed with univariable logistic regression. RESULTS: Twenty six centres reported on 174 cases, 158 of which were classified according to the type of malformation and 154 had completed surgical data. Overall, perineal fistula was the most commonly detected anomaly 43/158 (27%); of the 41 of these children undergoing surgery, 15 (37%) had a stoma formed. 21/154 (14%, CI95{9-20}) patients undergoing surgery experienced post-operative complications. Thirty-nine (22%) were diagnosed late and 12 (7%) were detected >30 days after birth. Factors associated with late diagnosis included female sex (OR 2.06; 1.0-4.26), having a visible perineal opening (OR 2.63; 1.21-5.67) and anomalies leading to visible meconium on the perineum (OR 18.74; 2.47-141.73). 56/174 (32%) had a diagnosis of VACTERL association (vertebral, anorectal, cardiac, tracheal, oesophageal, renal and limb); however, not all infants were investigated for commonly associated anomalies. 51/140 (36%) had a cardiac anomaly detected on echocardiogram. CONCLUSION: There is room for improvement within the care for infants born with ARM in the UK and Ireland. Upskilling those performing neonatal examination to allow timely diagnosis, instruction of universal screening for associated anomalies and further analysis of the factors leading to clinically unnecessary stoma formation are warranted. LEVEL OF EVIDENCE: II (Prospective Cohort Study <80% follow-up).

Application of experimental design as a statistical approach to recover bioactive peptides from different food sources.

Bioactive peptides (BAPs) derived from samples of animals and plants have been widely recommended and consumed for their beneficial properties to human health and to control several diseases. This work presents the applications of experimental designs (DoE) used to perform factor screening and/or optimization focused on finding the ideal hydrolysis condition to obtain BAPs with specific biological activities. The collection and discussion of articles revealed that Box Behnken Desing and Central Composite Design were the most used. The main parameters evaluated were pH, time, temperature and enzyme/substrate ratio. Among vegetable protein sources, soy was the most used in the generation of BAPs, and among animal proteins, milk and shrimp stood out as the most explored sources. The degree of hydrolysis and antioxidant activity were the most investigated responses in obtaining BAPs. This review brings new information that helps researchers apply these DoE to obtain high-quality BAPs with the desired biological activities.

Indirect estimates of natal dispersal distance from genetic data in a stream-dwelling fish (Mogurnda adspersa).

Recent work has highlighted the need to account for hierarchical patterns of genetic structure when estimating evolutionary and ecological parameters of interest. This caution is particularly relevant to studies of riverine organisms, where hierarchical structure appears to be commonplace. Here, we indirectly estimate dispersal distance in a hierarchically structured freshwater fish, Mogurnda adspersa. Microsatellite and mitochondrial DNA (mtDNA) data were obtained for 443 individuals across 27 sites separated by an average of 1.3 km within creeks of southeastern Queensland, Australia. Significant genetic structure was found among sites (mtDNA Φ(ST) = 0.508; microsatellite F(ST) = 0.225, F'(ST) = 0.340). Various clustering methods produced congruent patterns of hierarchical structure reflecting stream architecture. Partial mantel tests identified contiguous sets of sample sites where isolation by distance (IBD) explained F(ST) variation without significant contribution of hierarchical structure. Analysis of mean natal dispersal distance (σ) within sets of IBD-linked sample sites suggested most dispersal occurs over less than 1 km, and the average effective density (D(e)) was estimated at 11.5 individuals km(-1); indicating sedentary behavior and small effective population size are responsible for the remarkable patterns of genetic structure observed. Our results demonstrate that Rousset's regression-based method is applicable to estimating the scale of dispersal in riverine organisms and that identifying contiguous populations that satisfy the assumptions of this model is achievable with genetic clustering methods and partial correlations.

Treatment of rheumatoid arthritis with curcumin analog 3,5-bis(arylidene)-4-piperidone.

Rheumatoid arthritis (RA) is an inflammatory disease. Curcumin can inhibit NF-κB and reduce the expression of inflammation-related genes. Aim: To evaluate the potential development of 6d in the clinical treatment of inflammatory diseases such as RA. Methods: Using a skeleton fusion strategy to synthesize curcumin analogues for 6d. This work evaluates anti-inflammatory activity by conducting anti-arthritis experiments (adjuvant-induced RA models) on rats. Western blot and ELISA were used to detect the expression of inflammatory-related proteins and cytokines. Molecular docking analysis confirmed the binding effect of 6d with active sites. Conclusion: 6d inhibits NF-κB has a protective effect on arthritis caused by RA.

Phytochemicals and Their Correlation with Molecular Data in Micromeria and Clinopodium (Lamiaceae) Taxa.

A study of the phytochemical and molecular characteristics of ten Micromeria and six Clinopodium taxa (family Lamiaceae) distributed in the Balkan Peninsula was carried out. The phytochemicals detected in essential oils by gas chromatography, mass spectrometry, and molecular data amplified fragment length polymorphism were used to study the taxonomic relationships among the taxa and the correlations between phytochemical and molecular data. STRUCTURE analysis revealed three genetic groups, while Bayesian Analysis of Population Structure grouped the studied taxa into 11 clusters nested in the groups obtained by STRUCTURE. Principal components analysis performed with the 21 most represented compounds in the essential oils yielded results that were partly consistent with those obtained by STRUCTURE and neighbour-joining analyses. However, their geographic distributions did not support the genetic grouping of the studied taxa and populations. The Mantel test showed a significant correlation between the phytochemical and genetic data (r = 0.421, p < 0.001). Genetic distance explained 17.8% of the phytochemical distance between populations. The current taxonomic position of several of the studied taxa is yet to be satisfactorily resolved, and further studies are needed. Such future research should include nuclear and plastid DNA sequences from a larger sample of populations and individuals.

Commentary on early management of meconium ileus in infants with cystic fibrosis: A prospective population cohort study.

This is a commentary on the manuscript titled "Early Management of Meconium Ileus in Infants with Cystic Fibrosis: A Prospective Population Cohort Study" by Long A-M, et al.

Early management of meconium ileus in infants with cystic fibrosis: A prospective population cohort study.

BACKGROUND: Contemporary early outcome data of meconium Ileus (MI) in cystic fibrosis (CF) are lacking on a population level. We describe these and explore factors associated with successful non-operative management. METHODS: A prospective population-cohort study using an established surveillance system (BAPS-CASS) was conducted October 2012-September 2014. Live-born infants with bowel-obstruction from inspissated meconium in the terminal ileum and CF were reported. Data are described as median (interquartile range, IQR). RESULTS: 56 infants were identified. 14/56(25%) had primary laparotomy (13/23 complicated MI, 1/33 simple), the remainder underwent contrast enema. Twelve, (12/33 (36%) with simple MI) achieved decompression. 8/12 (67%) who decompressed had >1 enema vs 3/20 (15%) with simple MI who had laparotomy after enema. The number of enemas per infant (1-4), contrast agents and their concentration, were highly variable. Enterostomy was formed at 24/44(55%) of laparotomies. In infants with simple MI, time to full enteral feeds was 6 (2-10) days in those decompressing with enema vs 15 (9-19) days with laparotomy after enema. Case fatality was 4% (95% CI 0.4-12%). Two infants, both preterm died, both in the second month after birth. CONCLUSIONS: Infants with simple MI achieving successful enema decompression were more likely to have had repeat enemas than those who proceeded to laparotomy. Successful non-operative management was associated with a shorter time to full feeds. The early management of infants with MI is highly variable and not standardised across the UK and Ireland.

Early population-based outcomes of infants born with congenital diaphragmatic hernia.

PURPOSE: This study aims to describe short-term outcomes of live-born infants with congenital diaphragmatic hernia (CDH) and to identify prognostic factors associated with early mortality. DESIGN: A prospective population cohort study was undertaken between April 2009 and September 2010, collecting data on live-born infants with CDH from all 28 paediatric surgical centres in the UK and Ireland using an established surgical surveillance system. Management and outcomes are described. Prognostic factors associated with death before surgery are explored. RESULTS: Two hundred and nineteen live-born infants with CDH were reported within the data collection period. There were 1.5 times more boys than girls (n=133, 61%). Thirty-five infants (16%) died without an operation. This adverse outcome was associated with female sex (adjusted OR (aOR) 3.96, 95% CI 1.66 to 9.47), prenatal diagnosis (aOR 4.99, 95% CI 1.31 to 18.98), and the need for physiological support in the form of inotropes (aOR 9.96, 95% CI 1.19 to 83.25) or pulmonary vasodilators (aOR 4.09, 95% CI 1.53 to 10.93). Significant variation in practice existed among centres, and some therapies potentially detrimental to infant outcomes were used, including pulmonary surfactant in 45 antenatally diagnosed infants (34%). Utilisation of extracorporeal membrane oxygenation was very low compared with published international studies (n=9/219, 4%). Postoperative 30-day survival was 98% for 182 infants with CDH who were adequately physiologically stabilised and underwent surgery. CONCLUSION: This is the first British Isles population-based study reporting outcome metrics for infants born with CDH. 16% of babies did not survive to undergo surgery. Factors associated with poor outcome included female sex and prenatal diagnosis. Early postoperative survival in those who underwent surgical repair was excellent.

Production of biogenic manganese oxides coupled with methane oxidation in a bioreactor for removing metals from wastewater.

Biogenic manganese oxide (BioMnOx) can efficiently adsorb various minor metals. The production of BioMnOx in reactors to remove metals during wastewater treatment processes is a promising biotechnological method. However, it is difficult to preferentially enrich manganese-oxidizing bacteria (MnOB) to produce BioMnOx during wastewater treatment processes. A unique method of cultivating MnOB using methane-oxidizing bacteria (MOB) to produce soluble microbial products is proposed here. MnOB were successfully enriched in a methane-fed reactor containing MOB. BioMnOx production during the wastewater treatment process was confirmed. Long-term continual operation of the reactor allowed simultaneous removal of Mn(II), Co(II), and Ni(II). The Co(II)/Mn(II) and Ni(II)/Mn(II) removal ratios were 53% and 19%, respectively. The degree to which Mn(II) was removed indicated that the enriched MnOB used utilization-associated products and/or biomass-associated products. Microbial community analysis revealed that methanol-oxidizing bacteria belonging to the Hyphomicrobiaceae family played important roles in the oxidation of Mn(II) by using utilization-associated products. Methane-oxidizing bacteria were found to be inhibited by MnO2, but the maximum Mn(II) removal rate was 0.49 kg m-3 d-1.

Distribution of antimicrobial resistance determinants, virulence-associated factors and clustered regularly interspaced palindromic repeats loci in isolates of Enterococcus faecalis from various settings and genetic lineages.

Enterococcus faecalis represents an important factor of hospital-associated infections (HAIs). The knowledge on its evolution from a commensal to an opportunistic pathogen is still limited; thus, we performed a study to characterise distribution of factors that may contribute to this adaptation. Using a collection obtained from various settings (hospitalised patients, community carriers, animals, fresh food, sewage, water), we investigated differences in antimicrobial susceptibility, distribution of antimicrobial resistance genes, virulence-associated determinants and phenotypes, and CRISPR loci in the context of the clonal relatedness of isolates. Bayesian Analysis of Population Structure revealed the presence of three major groups; two subgroups comprised almost exclusively HAI isolates, belonging to previously proposed enterococcal high-risk clonal complexes (HiRECCs) 6 and 28. Isolates of these two subgroups were significantly enriched in antimicrobial resistance genes, presumably produced a polysaccharide capsule and often carried the aggregation substance asa1; distribution of other virulence-associated genes, such as esp and cyl, formation of a biofilm and gelatinase production were more variable. Moreover, both subgroups showed a low prevalence of CRISPR-Cas 1 and 3 and presence of small CRISPR2 variants. Our study confirms the importance of HiRECCs in the population of E. faecalis and their confinement to the hospital settings.

Oesophageal atresia with no distal tracheoesophageal fistula: Management and outcomes from a population-based cohort.

PURPOSE: To describe the incidence and outcomes to one-year in infants born with oesophageal atresia (OA) with no distal tracheoesophageal fistula within a population cohort. METHODS: A subgroup analysis of a prospective multicentre population cohort study was undertaken describing the outcomes of infants with OA and no tracheoesophageal fistula, (type A) and those with only an upper pouch fistula, (type B). MAIN RESULTS: Twenty-one of 151 infants in the whole cohort were diagnosed with type A or B oesophageal atresia (14%). Fifteen were type A (71%) and six type B (29%). Infants with type B had a shorter gap length than those with type A: 2.5 vertebral bodies (2-3) vs. 5 (4-6) (p=0.008). All infants with type B OA underwent oesophageal anastomosis, 83% (n=5) as the primary procedure. All infants with type A, underwent staged management. Six (40%) had delayed primary anastomosis and eight required oesophageal replacement (53%). One infant died prior to reconstruction. The median time to delayed primary anastomosis in infants with type A or B OA was 82days (75-89days) (n=7). The median time to oesophageal replacement was 94days (89-147days) (n=8). Median length of stay for infants with type A or B OA from first operation to first discharge was 101days (31-123days). CONCLUSIONS: Infants with type B OA had a shorter gap length and all were managed with oesophageal anastomosis. OA with no distal tracheoesophageal fistula is uncommon at a population level and frequently has a complex course. LEVEL OF EVIDENCE: Rating: II.

Diversity of Cryphonectria parasitica populations from the Carpathian Basin.

The ascomycetous fungus Cryphonectria parasitica (Murr.) is one of the most important fungal pathogens of chestnut (Castanea sativa Mill.), causing chestnut blight. It is originated from Eastern Asia and was introduced into North America, and later into Europe. Almost 100 C. parasitica isolates were collected mainly from the Carpathian Basin to study their diversity and phylogenetic relationships. Three nuclear molecular markers were tested: (i) internal transcribed spacers (ITS), (ii) translation elongation factor 1 subunit alpha (tef1), and (iii) six microsatellite loci. The ITS region proved to be highly polymorphic but this kind of variability did not reflect the geographical regions of the isolates, while the tef1 sequences were identical in all isolates. Microsatellite haplotype diversity was relatively high (0.923-0.984) calculated for the fungal populations of the Carpathian Basin. This may have resulted from the multiple introductions from diverse origins of the populations, close to the first site of observation in Northern Italy. The BAPS analysis of the microsatellite markers occasionally grouped together samples from remote geographical origin, suggesting human assistance in the introduction of new C. parasitica haplotypes from distinct areas.

Accuracy and efficiency of algorithms for the demarcation of bacterial ecotypes from DNA sequence data.

Identification of closely related, ecologically distinct populations of bacteria would benefit microbiologists working in many fields including systematics, epidemiology and biotechnology. Several laboratories have recently developed algorithms aimed at demarcating such 'ecotypes'. We examine the ability of four of these algorithms to correctly identify ecotypes from sequence data. We tested the algorithms on synthetic sequences, with known history and habitat associations, generated under the stable ecotype model and on data from Bacillus strains isolated from Death Valley where previous work has confirmed the existence of multiple ecotypes. We found that one of the algorithms (ecotype simulation) performs significantly better than the others (AdaptML, GMYC, BAPS) in both instances. Unfortunately, it was also shown to be the least efficient of the four. While ecotype simulation is the most accurate, it is by a large margin the slowest of the algorithms tested. Attempts at improving its efficiency are underway.