Search

BackgroundAscertaining preferences for SARS-CoV-2 testing and incorporating findings into the design and implementation of strategies for delivering testing services may enhance testing uptake and engagement, a prerequisite to reducing onward transmission. ObjectiveThis study aims to determine important drivers of decisions to obtain a SARS-CoV-2 test in the context of increasing community transmission. MethodsWe used a discrete choice experiment to assess preferences for SARS-CoV-2 test type, specimen type, testing venue, and results turnaround time. Participants (n=4793) from the US national longitudinal Communities, Households and SARS-CoV-2 Epidemiology (CHASING) COVID Cohort Study completed our online survey from July 30 to September 8, 2020. We estimated the relative importance of testing method attributes and part-worth utilities of attribute levels, and simulated the uptake of an optimized testing scenario relative to the current typical testing scenario of polymerase chain reaction (PCR) via nasopharyngeal swab in a provider’s office or urgent care clinic with results in >5 days. ResultsTest result turnaround time had the highest relative importance (30.4%), followed by test type (28.3%), specimen type (26.2%), and venue (15.0%). In simulations, immediate or same-day test results, both PCR and serology, or oral specimens substantially increased testing uptake over the current typical testing option. Simulated uptake of a hypothetical testing scenario of PCR and serology via a saliva sample at a pharmacy with same-day results was 97.7%, compared to 0.6% for the current typical testing scenario, with 1.8% opting for no test. ConclusionsTesting strategies that offer both PCR and serology with noninvasive methods and rapid turnaround time would likely have the most uptake and engagement among residents in communities with increasing community transmission of SARS-CoV-2.

BACKGROUND: Oropharyngeal colonization with pathogenic organisms contributes to the development of ventilator-associated pneumonia in intensive care units. Although considered basic and potentially nonessential nursing care, oral hygiene has been proposed as a key intervention for reducing ventilator-associated pneumonia. Nevertheless, evidence from randomized controlled trials that could inform best practice is limited. OBJECTIVE: To appraise the peer-reviewed literature to determine the best available evidence for providing oral care to intensive care patients receiving mechanical ventilation and to document a research agenda for this important activity in optimizing patients' outcomes. METHODS: Articles published from 1985 to 2006 in English and indexed in the CINAHL, MEDLINE, Joanna Briggs Institute, Cochrane Library, EMBASE, and DARE databases were searched by using the key terms oral hygiene, oral hygiene practices, oral care, mouth care, mouth hygiene, intubated, mechanically ventilated, intensive care, and critical care. Reference lists of retrieved journal articles were searched for publications missed during the primary search. Finally, the Google search engine was used to do a comprehensive search of the World Wide Web to ensure completeness of the search. The search strategy was verified by a health librarian. RESULTS: The search yielded 55 articles: 11 prospective controlled trials, 20 observational studies, and 24 descriptive reports. Methodological issues and the heterogeneity of samples precluded meta-analysis. CONCLUSIONS: Despite the importance of providing oral hygiene to intensive care patients receiving mechanical ventilation, high-level evidence from rigorous randomized controlled trials or high-quality systematic reviews that could inform clinical practice is scarce. [ABSTRACT FROM AUTHOR]

OBJECTIVE: Two recent retrospective studies independently reported typically pathogenic bacteria in normally sterile sites of infants succumbing to sudden unexpected death in infancy (SUDI). These findings suggested a proportion of unexplained SUDI might be triggered by bacteraemia. The objective was to assess these observations in the context of the pathology and epidemiology of sudden infant death syndrome (SIDS) in relation to the role of infection and inflammation as triggers of these deaths. DESIGN: A review of the literature to identify potential risk factors for unexplained infant deaths and proposal of a theoretical model for SUDI. RESULTS: Pathologic and epidemiological evidence suggests a hypothesis based on three factors: bacterial translocation, pathogen pattern recognition insufficiency and prenatal exposure to infection. CONCLUSION: We propose that sterile site infections in which common toxigenic bacteria are identified indicate a brief bacteraemic episode prior to death. This might reflect an ineffective innate response to invasive pathogens that results in reduced clearance of the bacteria. Thymomegaly observed consistently among infants diagnosed under the category of SIDS might have its origins in prenatal life, perhaps generated via in utero infection or exposure to microbial antigens which results in thymocyte priming. There is consistent evidence for an infectious aetiology in many unexplained SUDI. Future directions for research are suggested. [ABSTRACT FROM AUTHOR]

Whole genome sequencing has been an effective tool in the discovery of variants that cause rare diseases. In this study, we determined the suitability of a novel avidity sequencing approach for rare disease applications. We built a sample to results workflow, combining this sequencing technology with standard library preparation kits, analysis workflows, and interpretation tools. We applied the workflow to ten pedigrees with inherited retinal degeneration (IRD) phenotype. Candidate variants of interest identified through whole genome sequencing were further evaluated using segregation analysis in the additional family members. Potentially causal variants in known IRD genes were detected in five of the ten cases. These high confidence variants were found in ABCA4, CERKL, MAK, PEX6 and RDH12 genes associated with retinal degeneration, that could be sufficient to cause pathology. Pending confirmatory clinical evaluation, we observed a 50% diagnostic yield, consistent with previously reported outcomes of IRD patient analysis. The study confirms that avidity sequencing is effective in detection of causal variants when used for whole genome sequencing in rare disease applications., Competing Interests: Authors BJK, JM, JZ, BRL, and SK are current or former employees of Element Biosciences, which has commercialized the sequencing technology described in the paper. They may own stock options in the company. This does not alter our adherence to PLOS ONE policies on sharing data and materials. Author Contributions PB and RA: study design and manuscript writing. AV, AMB, DL: study design and procuring the DNA and sample information. BJK and JM: preparing libraries and performing sequencing. JZ: study design and library preparation. BRJ and SK: manuscript preparation and analysis., (Copyright: © 2024 Biswas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Genome analysis of individuals affected by retinitis pigmentosa (RP) identified two rare nucleotide substitutions at the same genomic location on chromosome 11 (g.61392563 [GRCh38]), 69 base pairs upstream of the start codon of the ciliopathy gene TMEM216 (c.-69G>A, c.-69G>T [GenBank: NM_001173991.3]), in individuals of South Asian and African ancestry, respectively. Genotypes included 71 homozygotes and 3 mixed heterozygotes in trans with a predicted loss-of-function allele. Haplotype analysis showed single-nucleotide variants (SNVs) common across families, suggesting ancestral alleles within the two distinct ethnic populations. Clinical phenotype analysis of 62 available individuals from 49 families indicated a similar clinical presentation with night blindness in the first decade and progressive peripheral field loss thereafter. No evident systemic ciliopathy features were noted. Functional characterization of these variants by luciferase reporter gene assay showed reduced promotor activity. Nanopore sequencing confirmed the lower transcription of the TMEM216 c.-69G>T allele in blood-derived RNA from a heterozygous carrier, and reduced expression was further recapitulated by qPCR, using both leukocytes-derived RNA of c.-69G>T homozygotes and total RNA from genome-edited hTERT-RPE1 cells carrying homozygous TMEM216 c.-69G>A. In conclusion, these variants explain a significant proportion of unsolved cases, specifically in individuals of African ancestry, suggesting that reduced TMEM216 expression might lead to abnormal ciliogenesis and photoreceptor degeneration., Competing Interests: Declaration of interests All the authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodule-specific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Exposure of eukaryotic cells to ionizing radiation or clastogenic chemicals leads to formation of DNA double-strand breaks (DSBs). These lesions are also generated internally by chemicals and enzymes, in the absence of exogenous agents, though the sources and consequences of such endogenously generated DSBs remain poorly understood. In the current study, we have investigated the impact of reduced recombinational repair of endogenous DSBs on stress responses, cell morphology and other physical properties of S. cerevisiae (budding yeast) cells. Use of phase contrast and DAPI-based fluorescence microscopy combined with FACS analysis confirmed that recombination-deficient rad52 cell cultures exhibit chronically high levels of G 2 phase cells. Cell cycle phase transit times during G 1 , S and M were similar in WT and rad52 cells, but the length of G 2 phase was increased by three-fold in the mutants. rad52 cells were larger than WT in all phases of the cycle and displayed other quantifiable changes in physical characteristics. The high G 2 cell phenotype was abolished when DNA damage checkpoint genes, but not spindle assembly checkpoint genes, were co-inactivated with RAD52. Several other RAD52 group mutants (rad51, rad54, rad55, rad57 and rad59) also exhibited the high G 2 cell phenotype. The results indicate that recombination deficiency leads to accumulation of unrepaired DSBs during normal mitotic growth that activate a major stress response and produce distinct changes in cellular physiology and morphology., Competing Interests: Declaration of competing interest None., (Copyright © 2023 Elsevier Inc. All rights reserved.)

SOX7 is a transcription factor-encoding gene located in a region on chromosome 8p23.1 that is recurrently deleted in individuals with ventricular septal defects (VSDs). We have previously shown that Sox7-/- embryos die of heart failure around E11.5. Here, we demonstrate that these embryos have hypocellular endocardial cushions with severely reduced numbers of mesenchymal cells. Ablation of Sox7 in the endocardium also resulted in hypocellular endocardial cushions, and we observed VSDs in rare E15.5 Sox7flox/-;Tie2-Cre and Sox7flox/flox;Tie2-Cre embryos that survived to E15.5. In atrioventricular explant studies, we showed that SOX7 deficiency leads to a severe reduction in endocardial-to-mesenchymal transition (EndMT). RNA-seq studies performed on E9.5 Sox7-/- heart tubes revealed severely reduced Wnt4 transcript levels. Wnt4 is expressed in the endocardium and promotes EndMT by acting in a paracrine manner to increase the expression of Bmp2 in the myocardium. Both WNT4 and BMP2 have been previously implicated in the development of VSDs in individuals with 46,XX sex reversal with dysgenesis of kidney, adrenals and lungs (SERKAL) syndrome and in individuals with short stature, facial dysmorphism and skeletal anomalies with or without cardiac anomalies 1 (SSFSC1) syndrome, respectively. We now show that Sox7 and Wnt4 interact genetically in the development of VSDs through their additive effects on endocardial cushion development with Sox7+/-;Wnt4+/- double heterozygous embryos having hypocellular endocardial cushions and perimembranous and muscular VSDs not seen in their Sox7+/- and Wnt4+/- littermates. These results provide additional evidence that SOX7, WNT4 and BMP2 function in the same pathway during mammalian septal development and that their deficiency can contribute to the development of VSDs in humans., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Importance: Latent tuberculosis infection (LTBI) can progress to active tuberculosis disease, causing morbidity and mortality., Objective: To review the evidence on benefits and harms of screening for and treatment of LTBI in adults to inform the US Preventive Services Task Force (USPSTF)., Data Sources: PubMed/MEDLINE, Cochrane Library, and trial registries through December 3, 2021; references; experts; literature surveillance through January 20, 2023., Study Selection: English-language studies of LTBI screening, LTBI treatment, or accuracy of the tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). Studies of LTBI screening and treatment for public health surveillance or disease management were excluded., Data Extraction and Synthesis: Dual review of abstracts, full-text articles, and study quality; qualitative synthesis of findings; meta-analyses conducted when a sufficient number of similar studies were available., Main Outcomes and Measures: Screening test accuracy; development of active tuberculosis disease, transmission, quality of life, mortality, and harms., Results: A total of 113 publications were included (112 studies; N = 69 009). No studies directly evaluated the benefits and harms of screening. Pooled estimates for sensitivity of the TST were 0.80 (95% CI, 0.74-0.87) at the 5-mm induration threshold, 0.81 (95% CI, 0.76-0.87) at the 10-mm threshold, and 0.60 (95% CI, 0.46-0.74) at the 15-mm threshold. Pooled estimates for sensitivity of IGRA tests ranged from 0.81 (95% CI, 0.79-0.84) to 0.90 (95% CI, 0.87-0.92). Pooled estimates for specificity of screening tests ranged from 0.95 to 0.99. For treatment of LTBI, a large (n = 27 830), good-quality randomized clinical trial found a relative risk (RR) for progression to active tuberculosis at 5 years of 0.35 (95% CI, 0.24-0.52) for 24 weeks of isoniazid compared with placebo (number needed to treat, 112) and an increase in hepatotoxicity (RR, 4.59 [95% CI, 2.03-10.39]; number needed to harm, 279). A previously published meta-analysis reported that multiple regimens were efficacious compared with placebo or no treatment. Meta-analysis found greater risk for hepatotoxicity with isoniazid than with rifampin (pooled RR, 4.22 [95% CI, 2.21-8.06]; n = 7339)., Conclusions and Relevance: No studies directly evaluated the benefits and harms of screening for LTBI compared with no screening. TST and IGRAs were moderately sensitive and highly specific. Treatment of LTBI with recommended regimens reduced the risk of progression to active tuberculosis. Isoniazid was associated with higher rates of hepatotoxicity than placebo or rifampin.

Congenital diaphragmatic hernia (CDH) can occur in isolation or in conjunction with other birth defects (CDH+). A molecular etiology can only be identified in a subset of CDH cases. This is due, in part, to an incomplete understanding of the genes that contribute to diaphragm development. Here, we used clinical and molecular data from 36 individuals with CDH+ who are cataloged in the DECIPHER database to identify genes that may play a role in diaphragm development and to discover new phenotypic expansions. Among this group, we identified individuals who carried putatively deleterious sequence or copy number variants affecting CREBBP, SMARCA4, UBA2, and USP9X. The role of these genes in diaphragm development was supported by their expression in the developing mouse diaphragm, their similarity to known CDH genes using data from a previously published and validated machine learning algorithm, and/or the presence of CDH in other individuals with their associated genetic disorders. Our results demonstrate how data from DECIPHER, and other public databases, can be used to identify new phenotypic expansions and suggest that CREBBP, SMARCA4, UBA2, and USP9X play a role in diaphragm development., (© 2022 Wiley Periodicals LLC.)

Aggression is a major challenge on child/adolescent inpatient psychiatric units. A screening instrument to accurately identify risk is urgently needed. To determine the predictive validity of the Brief Rating of Aggression by Children and Adolescents (BRACHA). Prospective cohort study. BRACHA is administered by clinical staff in the emergency department (ED) prior to inpatient psychiatric admission. A consecutive sample of 10,054 admitted patients from 2010-2021. No patients refused screening nor were excluded. BRACHA administered to patients in the ED prior to admission at Cincinnati Children's Hospital Medical Center (CCHMC). Patient behavioral outcomes measured by Overt Aggression Scale (OAS), categorizing aggression as verbal or physical, then as towards self, others, or objects. Female patients comprised 53.6% (n = 5,386) of the sample. Most patients were white (n = 6,556, 65.2%). Patients ranged in age from 4 to 18 years, with a mean age of 13.6 ± 3.1 years. A single biological parent (n = 5,317, 52.9%) was the predominant living arrangement among patients. The Area Under the Curve (AUC), as an assessment of predictive validity across all possible cut-offs of BRACHA scores ranged from 0.640 (aggression to self) to 0.758 (physical aggression towards others). Our findings support the BRACHA as a useful predictive instrument for aggression in inpatient psychiatric admissions from ED regardless of length of stay. Treating staff are then able to immediately classify risk level and inform care plans for all lengths of hospitalization. Applies to potential risk for aggression, except for self-aggression. Future data analyses will evaluate demographic factors to determine which improve predictive power of the BRACHA and can be used to create a BRACHA calculator. To our knowledge, this naturalistic outcomes study is one of the largest in psychiatry. The BRACHA will continue to be studied to evaluate risk for aggression on inpatient units and aim to assist in keeping unit staff and patients safe., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Rates of suicide have increased among Black Americans. Suicide is now the 3 rd leading cause of death for Black Americans between the ages of 1-19 and the 4 th leading cause of death for Black Americans aged 20-44. Due to the increasing need in the community, a marked increase in literature focusing on suicide in the Black community has been published since 2018. To build a better understanding of the current state of the literature on suicidality among Black Americans and to offer suggestions for further areas of research, a systematic review was conducted. Spirituality and religious beliefs are often an important cultural focus in the Black community. Some religious beliefs pose potential unintended regarding the sanctity of life among Black Americans. The focus of this systematic review was religiosity's effect on suicidality among Black Americans. Religiosity was found to have a protective effect against suicidality among Black Americans while discouraging formal mental health services utilization. This systematic review also reveals a dearth of research on the relationship between religiosity and suicide related stigma. Areas for further research are mentioned, and religious institutions as mental health intervention centers are encouraged., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

We previously identified a homozygous G178R mutation in human ASRGL1 ( hASRGL1 ) through whole-exome analysis responsible for early onset retinal degeneration (RD) in patients with cone-rod dystrophy. The mutant G178R ASRGL1 expressed in Cos-7 cells showed altered localization, while the mutant ASRGL1 in E. coli lacked the autocatalytic activity needed to generate the active protein. To evaluate the effect of impaired ASRGL1 function on the retina in vivo, we generated a mouse model with c.578_579insAGAAA (NM_001083926.2) mutation ( Asrgl1 mut/mut ) through the CRISPR/Cas9 methodology. The expression of ASGRL1 and its asparaginase activity were undetectable in the retina of Asrgl1 mut/mut mice. The ophthalmic evaluation of Asrgl1 mut/mut mice showed a significant and progressive decrease in scotopic electroretinographic (ERG) response observed at an early age of 3 months followed by a decrease in photopic response around 5 months compared with age-matched wildtype mice. Immunostaining and RT-PCR analyses with rod and cone cell markers revealed a loss of cone outer segments and a significant decrease in the expression of Rhodopsin , Opn1sw , and Opn1mw at 3 months in Asrgl1 mut/mut mice compared with age-matched wildtype mice. Importantly, the retinal phenotype of Asrgl1 mut/mut mice is consistent with the phenotype observed in patients harboring the G178R mutation in ASRGL1 confirming a critical role of ASRGL1 in the retina and the contribution of ASRGL1 mutations in retinal degeneration.

PAX5 is a transcription factor associated with abnormal posterior midbrain and cerebellum development in mice. PAX5 is highly loss-of-function intolerant and missense constrained, and has been identified as a candidate gene for autism spectrum disorder (ASD). We describe 16 individuals from 12 families who carry deletions involving PAX5 and surrounding genes, de novo frameshift variants that are likely to trigger nonsense-mediated mRNA decay, a rare stop-gain variant, or missense variants that affect conserved amino acid residues. Four of these individuals were published previously but without detailed clinical descriptions. All these individuals have been diagnosed with one or more neurodevelopmental phenotypes including delayed developmental milestones (DD), intellectual disability (ID), and/or ASD. Seizures were documented in four individuals. No recurrent patterns of brain magnetic resonance imaging (MRI) findings, structural birth defects, or dysmorphic features were observed. Our findings suggest that PAX5 haploinsufficiency causes a neurodevelopmental disorder whose cardinal features include DD, variable ID, and/or ASD., (© 2022 Wiley Periodicals LLC.)

Congenital diaphragmatic hernia (CDH) is often detectable prenatally. Advances in genetic testing have made it possible to obtain a molecular diagnosis in many fetuses with CDH. Here, we review the aneuploidies, copy number variants (CNVs), and single genes that have been clearly associated with CDH. We suggest that array-based CNV analysis, with or without a chromosome analysis, is the optimal test for identifying chromosomal abnormalities and CNVs in fetuses with CDH. To identify causative sequence variants, whole exome sequencing (WES) is the most comprehensive strategy currently available. Whole genome sequencing (WGS) with CNV analysis has the potential to become the most efficient and effective means of identifying an underlying diagnosis but is not yet routinely available for prenatal diagnosis. We describe how to overcome and address the diagnostic and clinical uncertainty that may remain after genetic testing, and review how a molecular diagnosis may impact recurrence risk estimations, mortality rates, and the availability and outcomes of fetal therapy. We conclude that after the prenatal detection of CDH, patients should be counseled about the possible genetic causes of the CDH, and the genetic testing modalities available to them, in accordance with generally accepted guidelines for pretest counseling in the prenatal setting., (© 2022 John Wiley & Sons Ltd.)

We report the genome sequence of Frankia sp. strain ArI3, recovered as a single contig from one run of the Oxford Nanopore Technologies (ONT) MinION instrument. The genome has a G+C content of 72%, is 7,541,222 bp long, and contains 5,427 predicted protein-coding genes.

Genus Frankia is comprised primarily of nitrogen-fixing actinobacteria that form root nodule symbioses with a group of hosts known as the actinorhizal plants. These plants are evolutionarily closely related to the legumes that are nodulated by the rhizobia. Both host groups utilize homologs of nodulation genes for root-nodule symbiosis, derived from common plant ancestors. The corresponding endosymbionts, Frankia and the rhizobia, however, are distantly related groups of bacteria, leading to questions about their symbiotic mechanisms and evolutionary history. To date, a stable system of electrotransformation has been lacking in Frankia despite numerous attempts by research groups worldwide. We have identified type IV methyl-directed restriction systems, highly-expressed in a range of actinobacteria, as a likely barrier to Frankia transformation. Here we report the successful electrotransformation of the model strain F. alni ACN14a with an unmethylated, broad host-range replicating plasmid, expressing chloramphenicol-resistance for selection and GFP as a marker of gene expression. This system circumvented the type IV restriction barrier and allowed the stable maintenance of the plasmid. During nitrogen limitation, Frankia differentiates into two cell types: the vegetative hyphae and nitrogen-fixing vesicles. When the expression of egfp under the control of the nif gene cluster promoter was localized using fluorescence imaging, the expression of nitrogen fixation in nitrogen-limited culture was localized in Frankia vesicles but not in hyphae. The ability to separate gene expression patterns between Frankia hyphae and vesicles will enable deeper comparisons of molecular signaling and metabolic exchange between Frankia -actinorhizal and rhizobia-legume symbioses to be made, and may broaden potential applications in agriculture. Further downstream applications are possible, including gene knock-outs and complementation, to open up a range of experiments in Frankia and its symbioses. Additionally, in the transcriptome of F. alni ACN14a, type IV restriction enzymes were highly expressed in nitrogen-replete culture but their expression strongly decreased during symbiosis. The down-regulation of type IV restriction enzymes in symbiosis suggests that horizontal gene transfer may occur more frequently inside the nodule, with possible new implications for the evolution of Frankia., (Copyright © 2019 Gifford, Vance, Nguyen and Berry.)

Background: Intake of large neutral amino acids (LNAA) may inhibit phenylalanine (PHE) transport across the blood brain barrier and assist with blood PHE control in patients with phenylketonuria (PKU). We evaluated the interrelationship between LNAA in plasma and diet on Phe:Tyr (P:T) ratio in patients with PKU and the influence of dietary factors on plasma LNAA markers., Methods: Plasma amino acid values and 3-day food record analysis from two studies (34 male/30 female; age 4.6-47 years) were examined. For pediatrics (<18 years) and adults (≥18 years) the relationship between P:T ratio, plasma LNAA, and dietary intake patterns were investigated., Results: Dietary factors influencing P:T ratio included intake of total protein (g/kg), medical food (MF) protein (g/kg, % below Rx), and LNAA (g) in the full cohort ( P  < .05). Associations were found between plasma valine and other dietary and plasma LNAA in pediatrics ( P  < .05) and plasma LNAA with dietary LNAA intake in adults ( P = .019). Plasma P:T ratio was inversely associated with plasma LNAA concentrations in both age groups ( P  < .05). Aside from histidine in pediatrics ( P = .024), plasma LNAA did not differ by having plasma PHE levels within or above the therapeutic range (120-360 μmol/L). Plasma LNAA in both age groups was similar to reported healthy control values., Conclusion: P:T ratio is significantly tied to dietary LNAA, adherence to MF Rx, and plasma LNAA concentrations. Additionally, P:T ratio and valine may be effective clinical proxies for determining LNAA metabolic balance and LNAA quality of the diet in patients with PKU., Competing Interests: The authors have no relevant financial relationships or conflicts of interest to disclose., (© 2019 The Authors. Journal of Inherited Metabolic Disease published by John Wiley & Sons Ltd on behalf of SSIEM.)

The early Frankia-Alnus symbiotic molecular exchanges were analyzed in detail by protein and RNA omics. For this, Frankia cells were placed in the presence of Alnus roots but separated by a dialysis membrane for 64 h. The bacterial cells were then harvested and analyzed by high-throughput proteomics and transcriptomics (RNA-seq). The most upregulated gene clusters were found to be the potassium transporter operon kdp and an ABC transporter operon of uncharacterized function. The most upregulated proteins were found to be acyl dehydrogenases and the potassium transporter Kdp. These suggest a preadaptation to the impending stresses linked to the penetration into isotonic host tissues and a possible rearrangement of the membrane. Another cluster among the 60 most upregulated ones that comprised two cellulases and a cellulose synthase was conserved among the Frankia and other actinobacteria such as Streptomyces. Cellulase activity was detected on CMC all along the length of the root but not away from it. Frankia alni ACN14a was found to be unable to respire or grow on glucose as sole carbon source. The cellulose synthase was found active at the tip of hyphae in response to Alnus root exudates, resulting in a calcofluor stained tip., (© 2019 Society for Applied Microbiology and John Wiley & Sons Ltd.)

Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show that cluster-2 inocula represent groups of strains, and that strains not represented in symbiotic structures, that is, unable to perform symbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that North American strains contain more transposase genes than Eurasian strains. An analysis of the evolution and distribution of the host plants indicated that bursts of transposition may have coincided with niche competition with other cluster-2 Frankia strains. The first genome of an inoculum from the Southern Hemisphere, obtained from nodules of Coriaria papuana in Papua New Guinea, represents a novel species, postulated as Candidatus Frankia meridionalis. All Frankia-enriched metagenomes obtained in this study contained homologs of the canonical nod genes nodABC; the North American genomes also contained the sulfotransferase gene nodH, while the genome from the Southern Hemisphere only contained nodC and a truncated copy of nodB., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Neuroblastoma is the most common childhood solid tumor, yet the prognosis for high-risk disease remains poor. We demonstrate here that arginase 2 (ARG2) drives neuroblastoma cell proliferation via regulation of arginine metabolism. Targeting arginine metabolism, either by blocking cationic amino acid transporter 1 (CAT-1)-dependent arginine uptake in vitro or therapeutic depletion of arginine by pegylated recombinant arginase BCT-100, significantly delayed tumor development and prolonged murine survival. Tumor cells polarized infiltrating monocytes to an M1-macrophage phenotype, which released IL1β and TNFα in a RAC-alpha serine/threonine-protein kinase (AKT)-dependent manner. IL1β and TNFα established a feedback loop to upregulate ARG2 expression via p38 and extracellular regulated kinases 1/2 (ERK1/2) signaling in neuroblastoma and neural crest-derived cells. Proteomic analysis revealed that enrichment of IL1β and TNFα in stage IV human tumor microenvironments was associated with a worse prognosis. These data thus describe an immune-metabolic regulatory loop between tumor cells and infiltrating myeloid cells regulating ARG2, which can be clinically exploited. SIGNIFICANCE: These findings illustrate that cross-talk between myeloid cells and tumor cells creates a metabolic regulatory loop that promotes neuroblastoma progression., (©2018 American Association for Cancer Research.)

Two types of nitrogen-fixing root nodule symbioses are known, rhizobial and actinorhizal symbioses. The latter involve plants of three orders, Fagales, Rosales, and Cucurbitales. To understand the diversity of plant symbiotic adaptation, we compared the nodule transcriptomes of Datisca glomerata (Datiscaceae, Cucurbitales) and Ceanothus thyrsiflorus (Rhamnaceae, Rosales); both species are nodulated by members of the uncultured Frankia clade, cluster II. The analysis focused on various features. In both species, the expression of orthologs of legume Nod factor receptor genes was elevated in nodules compared to roots. Since arginine has been postulated as export form of fixed nitrogen from symbiotic Frankia in nodules of D. glomerata , the question was whether the nitrogen metabolism was similar in nodules of C. thyrsiflorus . Analysis of the expression levels of key genes encoding enzymes involved in arginine metabolism revealed up-regulation of arginine catabolism, but no up-regulation of arginine biosynthesis, in nodules compared to roots of D. glomerata , while arginine degradation was not upregulated in nodules of C. thyrsiflorus . This new information corroborated an arginine-based metabolic exchange between host and microsymbiont for D. glomerata , but not for C. thyrsiflorus. Oxygen protection systems for nitrogenase differ dramatically between both species. Analysis of the antioxidant system suggested that the system in the nodules of D. glomerata leads to greater oxidative stress than the one in the nodules of C. thyrsiflorus , while no differences were found for the defense against nitrosative stress. However, induction of nitrite reductase in nodules of C. thyrsiflorus indicated that here, nitrite produced from nitric oxide had to be detoxified. Additional shared features were identified: genes encoding enzymes involved in thiamine biosynthesis were found to be upregulated in the nodules of both species. Orthologous nodule-specific subtilisin-like proteases that have been linked to the infection process in actinorhizal Fagales, were also upregulated in the nodules of D. glomerata and C. thyrsiflorus . Nodule-specific defensin genes known from actinorhizal Fagales and Cucurbitales, were also found in C. thyrsiflorus. In summary, the results underline the variability of nodule metabolism in different groups of symbiotic plants while pointing at conserved features involved in the infection process.

Plants within the Nitrogen-fixing Clade (NFC) of Angiosperms form root nodule symbioses with nitrogen-fixing bacteria. Actinorhizal plants (in Cucurbitales, Fagales, Rosales) form symbioses with the actinobacteria Frankia while legumes (Fabales) form symbioses with proteobacterial rhizobia. Flavonoids, secondary metabolites of the phenylpropanoid pathway, have been shown to play major roles in legume root nodule symbioses: as signal molecules that in turn trigger rhizobial nodulation initiation signals and acting as polar auxin transport inhibitors, enabling a key step in nodule organogenesis. To explore a potentially broader role for flavonoids in root nodule symbioses across the NFC, we combined metabolomic and transcriptomic analyses of roots and nodules of the actinorhizal host Datisca glomerata and legumes of the genus Medicago. Patterns of biosynthetic pathways were inferred from flavonoid metabolite profiles and phenylpropanoid gene expression patterns in the two hosts to identify similarities and differences. Similar classes of flavonoids were represented in both hosts, and an increase in flavonoids generally in the nodules was observed, with differences in flavonoids prominent in each host. While both hosts produced derivatives of naringenin, the metabolite profile in D. glomerata indicated an emphasis on the pinocembrin biosynthetic pathway, and an abundance of flavonols with potential roles in symbiosis. Additionally, the gene expression profile indicated a decrease in expression in the lignin/monolignol pathway. In Medicago sativa , by contrast, isoflavonoids were highly abundant featuring more diverse and derived isoflavonoids than D. glomerata. Gene expression patterns supported these differences in metabolic pathways, especially evident in a difference in expression of cinnamic acid 4-hydroxylase (C4H), which was expressed at substantially lower levels in D. glomerata than in a Medicago truncatula transcriptome where it was highly expressed. C4H is a major rate-limiting step in phenylpropanoid biosynthesis that separates the pinocembrin pathway from the lignin/monolignol and naringenin-based flavonoid branches. Shikimate O -hydroxycinnamoyltransferase, the link between flavonoid biosynthesis and the lignin/monolignol pathway, was also expressed at much lower levels in D. glomerata than in M. truncatula . Our results indicate (a) a likely major role for flavonoids in actinorhizal nodules, and (b) differences in metabolic flux in flavonoid and phenylpropanoid biosynthesis between the different hosts in symbiosis.

Root nodule symbiosis (RNS) is a symbiotic interaction established between angiosperm hosts and nitrogen-fixing soil bacteria in specialized organs called root nodules. The host plants provide photosynthate and the microsymbionts supply fixed nitrogen. The origin of RNS represents a major evolutionary event in the angiosperms, and understanding the genetic underpinnings of this event is of major economic and agricultural importance. Plants that engage in RNS are restricted to a single angiosperm clade known as the nitrogen-fixing clade (NFC), yet occur in multiple lineages scattered within the NFC. It has been postulated that RNS evolved in two steps: a gain-of-predisposition event occurring at the base of the NFC, followed by a gain-of-function event in each host plant lineage. Here, we first explore the premise that RNS has evolved from a single common background, and then we explore whether a two-step process better explains the evolutionary origin of RNS than either a single-step process, or multiple origins. We assembled the transcriptomes of root and nodule of two actinorhizal plants, Ceanothus thyrsiflorus and Datisca glomerata . Together with the corresponding published transcriptomes of the model legume Medicago truncatula , the gene expression patterns in roots and nodules were compared across the three lineages. We found that orthologs of many genes essential for RNS in the model legumes are expressed in all three lineages, and that the overall nodule gene expression patterns were more similar to each other than expected by random chance, a finding that supports a common evolutionary background for RNS shared by the three lineages. Moreover, phylogenetic analyses suggested that a substantial portion of the genes experiencing selection pressure changes at the base of the NFC also experienced additional changes at the base of each host plant lineage. Our results (1) support the occurrence of an event that led to RNS at the base of the NFC, and (2) suggest a subsequent change in each lineage, most consistent with a two-step origin of RNS. Among several conserved functions identified, strigolactone-related genes were down-regulated in nodules of all three species, suggesting a shared function similar to that shown for arbuscular mycorrhizal symbioses.

Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe region of Oaxaca, Mexico. This landrace is characterized by the extensive development of aerial roots that secrete a carbohydrate-rich mucilage. Analysis of the mucilage microbiota indicated that it was enriched in taxa for which many known species are diazotrophic, was enriched for homologs of genes encoding nitrogenase subunits, and harbored active nitrogenase activity as assessed by acetylene reduction and 15N2 incorporation assays. Field experiments in Sierra Mixe using 15N natural abundance or 15N-enrichment assessments over 5 years indicated that atmospheric nitrogen fixation contributed 29%-82% of the nitrogen nutrition of Sierra Mixe maize., Competing Interests: Howard-Yana Shapiro is affiliated with Mars, Incorporated, one of the research sponsors. Author Cristobal Heitmann was unable to confirm authorship or contributions himself, and this was carried out collectively by the other co-authors.

The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

The genus Frankia comprises a group of nitrogen-fixing actinobacteria that form root-nodule symbioses with perennial dicotyledonous plants in the nitrogen-fixing clade. These bacteria have been characterized phylogenetically and grouped into four clusters (clusters 1-4). Cluster 2 contains mostly uncultured strains that induce nodules on species of the genera Datisca (Datiscaceae), Coriaria (Coriariaceae), Ceanothus (Rhamnaceae) and several genera in the family Rosaceae (Cercocarpus, Chamaebatia, Dryas, Purshia), all of which except members of the genus Coriaria are present within the California Floristic Province (CFP) or neighbouring areas of western North America. Those strains occurring in western North America are genetically very closely related to one another, and genetically distinct from strains characterized from other locales. We hereby propose to create a 'Candidatus Frankia californiensis' species for those cluster 2 strains of the genus Frankia with both high genetic similarity and a geographical distribution in or near the CFP.

Background: Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multiple species. At the same time, in silico orthology prediction tools often require large computational resources only available on computing clusters. Here we present OrthoReD, an open-source orthology prediction tool with accuracy comparable to published tools that requires only a desktop computer. The low computational resource requirement of OrthoReD is achieved by repeating orthology searches on one gene of interest at a time, thereby generating a reduced dataset to limit the scope of orthology search for each gene of interest., Results: The output of OrthoReD was highly similar to the outputs of two other published orthology prediction tools, OrthologID and/or OrthoDB, for the three dataset tested, which represented three phyla with different ranges of species diversity and different number of genomes included. Median CPU time for ortholog prediction per gene by OrthoReD executed on a desktop computer was <15 min even for the largest dataset tested, which included all coding sequences of 100 bacterial species., Conclusions: With high-throughput sequencing, unprecedented numbers of genes from non-model organisms are available with increasing need for clear information about their orthologies and/or functional equivalents in model organisms. OrthoReD is not only fast and accurate as an orthology prediction tool, but also gives researchers flexibility in the number of genes analyzed at a time, without requiring a high-performance computing cluster.

The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia, cluster I, II, and III strains are capable of forming effective nitrogen-fixing symbiotic associations, while cluster IV strains generally do not. Cluster II Frankia strains have rarely been detected in soil devoid of host plants, unlike cluster I or III strains, suggesting a stronger association with their host. To investigate the degree of host influence, we characterized the cluster II Frankia strain distribution in rhizosphere soil in three locations in northern California. The presence/absence of cluster II Frankia strains at a given site correlated significantly with the presence/absence of host plants on the site, as determined by glutamine synthetase (glnA) gene sequence analysis, and by microbiome analysis (16S rRNA gene) of a subset of host/nonhost rhizosphere soils. However, the distribution of cluster II Frankia strains was not significantly affected by other potential determinants such as host-plant species, geographical location, climate, soil pH, or soil type. Rhizosphere soil microbiome analysis showed that cluster II Frankia strains occupied only a minute fraction of the microbiome even in the host-plant-present site and further revealed no statistically significant difference in the α-diversity or in the microbiome composition between the host-plant-present or -absent sites. Taken together, these data suggest that host plants provide a factor that is specific for cluster II Frankia strains, not a general growth-promoting factor. Further, the factor accumulates or is transported at the site level, i.e., beyond the host rhizosphere., Importance: Biological nitrogen fixation is a bacterial process that accounts for a major fraction of net new nitrogen input in terrestrial ecosystems. Transfer of fixed nitrogen to plant biomass is especially efficient via root nodule symbioses, which represent evolutionarily and ecologically specialized mutualistic associations. Frankia spp. (Actinobacteria), especially cluster II Frankia spp., have an extremely broad host range, yet comparatively little is known about the soil ecology of these organisms in relation to the host plants and their rhizosphere microbiomes. This study reveals a strong influence of the host plant on soil distribution of cluster II Frankia spp., (Copyright © 2016 American Society for Microbiology.)

Background: The ability to establish root nodule symbioses is restricted to four different plant orders. Soil actinobacteria of the genus Frankia can establish a symbiotic relationship with a diverse group of plants within eight different families from three different orders, the Cucurbitales, Fagales and Rosales. Phylogenetically, Frankia strains can be divided into four clusters, three of which (I, II, III) contain symbiotic strains. Members of Cluster II nodulate the broadest range of host plants with species from four families from two different orders, growing on six continents. Two Cluster II genomes were sequenced thus far, both from Asia., Results: In this paper we present the first Frankia cluster II genome from North America (California), Dg2, which represents a metagenome of two major and one minor strains. A phylogenetic analysis of the core genomes of 16 Frankia strains shows that Cluster II the ancestral group in the genus, also ancestral to the non-symbiotic Cluster IV. Dg2 contains the canonical nod genes nodABC for the production of lipochitooligosaccharide Nod factors, but also two copies of the sulfotransferase gene nodH. In rhizobial systems, sulfation of Nod factors affects their host specificity and their stability., Conclusions: A comparison with the nod gene region of the previously sequenced Dg1 genome from a Cluster II strain from Pakistan shows that the common ancestor of both strains should have contained nodABC and nodH. Phylogenetically, Dg2 NodH proteins are sister to rhizobial NodH proteins. A glnA-based phylogenetic analysis of all Cluster II strains sampled thus far supports the hypothesis that Cluster II Frankia strains came to North America with Datisca glomerata following the Madrean-Tethyan pattern.

Wharton's jelly mesenchymal stem cells (WJMSCs) are being increasingly recognized for their ectodermal differentiation potential. Previously, we demonstrated that when WJMSC were seeded onto an acellular matrix material derived from Wharton's jelly and cultured in osteogenic induction media, generated CK19 positive cells and hair-like structures indicative of ectodermal differentiation of WJMSCs. In this manuscript, we examine the underlying mechanism behind this observation using a variety of microscopy and molecular biology techniques such as western blotting and qPCR. We demonstrate that these hair-like structures are associated with live cells that are positive for epithelial and mesenchymal markers such as cytokeratin-19 and α-smooth muscle actin, respectively. We also show that up-regulation of β-catenin and noggin, along with the expression of TGF-β and SMAD and inhibition of BMP4 could be the mechanism behind this ectodermal differentiation and hair-like structure formation., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of D. glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common symbiotic pathway also used by arbuscular mycorrhizal fungi. However, so far, no molecules resembling rhizobial Nod factors could be isolated from Frankia cultures. Alone among Frankia genomes available to date, the genome of Dg1 contains the canonical nod genes nodA, nodB and nodC known from rhizobia, and these genes are arranged in two operons which are expressed in D. glomerata nodules. Furthermore, Frankia Dg1 nodC was able to partially complement a Rhizobium leguminosarum A34 nodC::Tn5 mutant. Phylogenetic analysis showed that Dg1 Nod proteins are positioned at the root of both α- and β-rhizobial NodABC proteins. NodA-like acyl transferases were found across the phylum Actinobacteria, but among Proteobacteria only in nodulators. Taken together, our evidence indicates an Actinobacterial origin of rhizobial Nod factors.

The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of the class Actinobacteria and evaluated eight different hypotheses for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S and 23S rRNA gene sequences or their concatenation, and a tree based on the concatenation of MLSA genes (encoding AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenated tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenation of 54 proteins. In that tree, the orders Bifidobacteriales, Coriobacteriales, 'Corynebacteriales', 'Micromonosporales', 'Propionibacteriales', 'Pseudonocardiales', Streptomycetales and 'Streptosporangiales' were recovered while the orders 'Frankiales' and Micrococcales were not. It is thus proposed that the order 'Frankiales', which has an effectively but not validly published name, be split into Frankiales ord. nov. (type family Frankiaceae), Geodermatophilales ord. nov. (Geodermatophilaceae), Acidothermales ord. nov. (Acidothermaceae) and Nakamurellales ord. nov. (Nakamurellaceae). The order Micrococcales should also be split into Micrococcales (genera Kocuria, Rothia, Micrococcus, Arthrobacter, Tropheryma, Microbacterium, Leifsonia and Clavibacter), Cellulomonales (Beutenbergia, Cellulomonas, Xylanimonas, Jonesia and Sanguibacter) and Brachybacteriales (Brachybacterium) but the formal proposal for this will have to wait until more genomes become available for a significant proportion of strains in this order., (© 2014 CNRS.)

The role of bacteria in the causation of sudden infant death syndrome (SIDS) is gaining acceptance. Mainstream research favouring respiratory compromise has failed to provide a plausible pathogenetic mechanism despite many years of investigation and thousands of research papers. Bacterial colonisation of the colon of the human infant is influenced by many factors including age, mode of delivery, diet, environment, and antibiotic exposure. The gut microbiome influences development of the immune system. The gut microflora could be important in protection against the bacteria and/or their toxins purportedly involved in SIDS pathogenesis. The aim was to perform a preliminary investigation of the gut microflora in sudden infant death syndrome (SIDS) compared with live comparison babies. The intestinal contents from 52 SIDS, and 102 faecal samples from age-matched live comparison infants were screened by PCR to target 16s RNA genes of Clostridium innocuum, Cl. Perfringens, Cl. difficile, Bacteroides thetaiotaomicron and Staphylococcus aureus. Gut colonisation of the babies with these bacteria was analysed in relation to age, gender and type of feeding; and for SIDS babies sleeping position. Cl. difficile, Cl. innocuum and B. thetaiotaomicron were significantly associated with SIDS with 25%, 46% and 30% of cases PCR positive for these respective bacteria compared with only 6%, 23% and 8.8% respectively in the comparison group. SIDS babies had dual colonisation by both Cl. perfringens and Cl. difficile significantly more often than comparison babies and also with triple colonisation by Cl. perfringens, Cl. difficile and Cl. innocuum. SIDS babies were more often colonised by S. aureus than comparison babies. In addition, SIDS babies found prone were significantly more likely to be colonised by S. aureus than for other positions recorded (OR = ∞; CI = 2·04 - ∞). No significant differences between breast and bottle-fed SIDS babies was observed in regard to each clostridial bacterium, or S. aureus, however Cl. innocuum was found to be significantly associated with formula feeding in the comparison cohort. Comparison of breast and formula feeding of SIDS babies with live comparison babies revealed significant differences with regards to some of the clostridial bacteria. Age-specific differences in gut bacterial microbiome were observed in both SIDS and comparison healthy babies. This study gives an insight into differences in the gut bacterial microbiome of SIDS babies compared with healthy babies. These differences could be important in contributing to a baby's susceptibility to infection and therefore to SIDS. The association of S. aureus colonisation with prone sleep position supports the hypothesis that prone sleep position could increase the risk of ingestion/inhalation of bacteria contaminating the sleeping surface and could account for the increased risk of SIDS in babies who are put to sleep prone. The study provides impetus for broader studies into the gut microbiome of babies and could lead to effective approaches to SIDS prevention., (Crown Copyright © 2014. Published by Elsevier GmbH. All rights reserved.)

Background: Effective oral hygiene has been proposed as a key factor in the reduction of dental plaque colonisation and subsequent development of ventilator associated pneumonia (VAP). Listerine(®) oral rinse, while used extensively in dental practice has rarely been tested in mechanically ventilated patients. Sodium bicarbonate as an oral rinse has been more commonly utilised in oral hygiene regimens in intensive care patients., Aim: To test the efficacies of the essential oil mouth rinse, Listerine(®) (Pfizer) and sodium bicarbonate in the reduction of dental plaque colonisation with respiratory pathogens and the subsequent development of VAP., Methods: The study design was a prospective, single blind randomised comparative study of adult patients mechanically ventilated for at least 4 days. Patients were randomised to Listerine(®) (Pfizer) oral rinse twice daily, sodium bicarbonate oral rinse 2/24 or sterile water 2/24 (control group). All groups received tooth brushing 3 times a day. Dental plaque colonisation (primary outcome) and incidence of ventilator associated pneumonia (secondary outcome) were studied., Results: Three hundred and ninety-eight patients were randomised to either the Listerine group (127), sodium bicarbonate group (133) or the control group (138). Baseline characteristics were similar for all groups. There were no significant differences between the control and study groups in colonisation of dental plaque at Day 4 (p=0.243). Ventilator associated pneumonia was diagnosed in 18 patients. The incidence was, Listerine(®) group 4.7%, sodium bicarbonate group 4.5% and control 4.3% [OR, 0.99; 95% CI, 0.31 to 3.16; p=0.92]., Conclusions: Compared to the control group, Listerine(®) or sodium bicarbonate oral rinses were not more effective in the reduction of colonisation of dental plaque or the incidence of VAP. Given the low incidence of VAP, the common factor of a small, soft toothbrush as part of an oral hygiene regimen suggests possible benefit in mechanically ventilated patients., (Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.)

The possibility of quantifying the superimposed signal of glutamate and glutamine (Glx) and its components by ¹H magnetic resonance spectroscopy (MRS) in the spinal cord is an exciting challenge with important clinical applications in neurological conditions. The spinal cord is a particularly difficult region of interest due to its small volume, magnetic field inhomogeneities and physiological motion. In this study, we investigated for the first time the feasibility of obtaining quantitative measurements of Glx in healthy cervical spinal cord by ¹H MRS at 3 T. The aim of this study was to compare two commercially available MRS sequences by spectral simulations and in vivo. A short echo time (TE) point resolved spectroscopy (PRESS) with TE = 30 ms and a stimulated echo acquisition mode (STEAM) with TE = 11 ms and mixing time (TM) = 17 ms were compared for reliability of Glx fit. Data allowed us to determine sample size estimates for future clinical studies for the first time. Results showed that PRESS provided a reliable fit for Glx in all cases (Cramér Rao lower bounds < 20%) whereas no reliable Glx fits were achieved using STEAM. Neither protocol provided reliable Glu quantification. The power calculations showed that a minimum sample size of 17 subjects per group was needed to detect Glx changes of > 20% using the PRESS sequence. This study proposed a clinically feasible MRS method for Glx detection in the human cervical cord in vivo including sample sizes needed for conclusive clinical studies., (Copyright © 2012 John Wiley & Sons, Ltd.)

Members of the noncultured clade of Frankia enter into root nodule symbioses with actinorhizal species from the orders Cucurbitales and Rosales. We report the genome sequence of a member of this clade originally from Pakistan but obtained from root nodules of the American plant Datisca glomerata without isolation in culture.

In recent years, our understanding of the plant side of actinorhizal symbioses has evolved rapidly. No homologues of the common nod genes from rhizobia were found in the three Frankia genomes published so far, which suggested that Nod factor-like molecules would not be used in the infection of actinorhizal plants by Frankia. However, work on chimeric transgenic plants indicated that Frankia Nod factor equivalents signal via the same transduction pathway as rhizobial Nod factors. The role of auxin in actinorhizal nodule formation differs from that in legume nodulation. Great progress has been made in the analysis of pathogenesis-related and stress-related gene expression in nodules. Research on nodule physiology has shown the structural and metabolic diversity of actinorhizal nodules from different phylogenetic branches. The onset of large-scale nodule transcriptome analysis in different actinorhizal systems will provide access to more information on the symbiosis and its evolution.

Nitrogen-fixing root nodules are plant organs specialised for symbiotic transfer of nitrogen and carbon between microsymbiont and host. The organisation of nitrogen assimilation, storage and transport processes is partitioned at the subcellular and tissue levels, in distinctive patterns depending on the symbiotic partners. In this review, recent advances in understanding of actinorhizal nodule nitrogen assimilation are presented. New findings indicate that Frankia within nodules of Datisca glomerata (Presl.) Baill. carries out both primary nitrogen assimilation and biosynthesis of arginine, rather than exporting ammonium. Arginine is a typical storage form of nitrogen in plant tissues, but is a novel nitrogen carrier molecule in root nodule symbioses. Thus Frankia within D. glomerata nodules exhibits considerable metabolic independence. Furthermore, nitrogen reassimilation is likely to take place in the host in the uninfected nodule cortical cells of this root nodule symbiosis, before amino acid export to host sink tissues via the xylem. The role of an augmented pericycle in carbon and nitrogen exchange in root nodules deserves further attention in actinorhizal symbiosis, and further highlights the importance of a comprehensive, structure-function approach to understanding function in root nodules. Moreover, the multiple patterns of compartmentalisation in relation to nitrogen flux within root nodules demonstrate the diversity of possible functional interactions between host and microsymbiont that have evolved in the nitrogen-fixing clade.

Actinorhizal plants are a group of taxonomically diverse angiosperms with remarkable economic and ecological significance. Most actinorhizal plants are able to thrive under extreme adverse environmental conditions as well as to fix atmospheric nitrogen due to their capacity to establish root nodule symbioses with Frankia bacteria. This special issue of Functional Plant Biology is dedicated to actinorhizal plant research, covering part of the work presented at the 16th International Meeting onFrankia and Actinorhizal Plants, held on 5-8 September 2010, in Oporto, Portugal. The papers (4 reviews and 10 original articles) give an overall picture of the status of actinorhizal plant research and the imposed challenges, covering several aspects of the symbiosis, ecology and molecular tools.

Objectives: Oropharyngeal colonisation has been identified as a factor contributing to ventilator associated pneumonia (VAP) in the Intensive Care Unit (ICU). We sought to develop a clinical practice guideline for providing oral hygiene in the critically ill., Research Methodology: Following a systematic literature review a prospectively derived consensus development conference was convened and sponsored by a clinical governance unit., Results: The consensus development conference generated 12 recommendations for tools and solutions; frequency and duration of cleaning; oral assessment tools and oral hygiene protocols. These recommendations underwent a validation process., Conclusions: In light of sparse high level evidence to inform guidelines, further research is needed inform clinical practice. Oral hygiene is a critical element of nursing care and a standardised approach has the potential to improve clinical outcomes., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Background: Ventilator associated pneumonia remains an important concern in the intensive care unit (ICU). An increasing body of evidence shows that mortality and morbidity can be reduced by implementing a range of preventive strategies, including optimizing oral hygiene., Aim: The aim of this feasibility study was to test two oral hygiene strategies on the effects of microbial colonization of dental plaque with respiratory pathogens (primary outcome) and incidence of ventilator associated pneumonia (secondary outcome)., Methods: A single blind randomised comparative study was conducted in a 20-bed adult intensive care unit in a university hospital. Patients with an expected duration of mechanical ventilation more than 48 h were eligible. Patients were randomised to one of three study regimens (Group A control, second hourly oral rinse with sterile water, Group B sodium bicarbonate mouth wash second hourly, and Group C twice daily irrigations with chlorhexidine 0.2% aqueous oral rinse and second hourly irrigations with sterile water). All study options included cleaning with a toothbrush and non foaming toothpaste., Results: Data from a total of 109 patients were analyzed. Group A 43, Group B 33 and Group C 33 (mean age: 58 ± 17 years, simplified acute physiology score II: 44 ± 14 points). On admission no significant differences were found between groups for all clinical data. While Group B showed a greater trend to reduction in bacterial colonization no significant differences could be demonstrated at Day 4 of admission (p=0.302). The incidence of ventilator associated pneumonia was evenly spread between Groups B and C (5%) while Group A was only 1%., Conclusions: While a number of studies have advocated the use of various mouth rinses in reducing colonization of dental plaque a standardized oral hygiene protocol which includes the use of mechanical cleaning with a toothbrush may be a factor in the reduction of colonization of dental plaque with respiratory pathogens. This feasibility study provides data to inform future adequately powered studies., (Copyright © 2010 Elsevier Ltd. All rights reserved.)

Previous studies on biological pretreatment of switchgrass by solid-state fermentation with Acidothermus cellulolyticus 11B have shown that inhibitory compounds prevent growth on untreated switchgrass. A. cellulolyticus was grown in liquid medium containing cellobiose with phenolic monomers added to determine if the phenolic compounds are one possible source of inhibition. Cinnamic acid derivatives (trans-p-coumaric, trans-ferulic, and hydrocinnamic acids), hydroxybenzoic acids (p-hydroxybenzoic, syringic, and vanillic acids), benzaldehydes (vanillin and p-hydroxybenzaldehyde), and condensed tannin monomers (catechin and epicatechin) were tested at levels up to 20 mM. All compounds exhibited a dose-response relationship and strongly inhibited growth at 20 mM. trans-p-Coumaric acid was found to be the strongest inhibitor of A. cellulolyticus growth, with a specific growth rate of 0.004 h(-1) at 1 mM (0.18 h(-1) without phenolic monomer). GC-MS and HPLC methods were used to confirm the presence of these phenolic compounds in switchgrass and measure the amounts extracted using different conditions. The amounts of phenolic compounds measured were found to be higher than the threshold for growth inhibition. Leaching with water at 55°C was inefficient at removing bound phenolics, whereas NaOH treatment improved efficiency. Phenolic compounds spiked into alkaline pretreated switchgrass were also found to inhibit growth of A. cellulolyticus in solid-state fermentation. However, addition of insoluble polyvinylpolypyrrolidone (PVPP) to switchgrass improved growth of A. cellulolyticus in liquid cultures, providing a possible approach for alleviating microbial inhibition due to phenolic compounds in lignocellulose., (Copyright © 2010 American Institute of Chemical Engineers (AIChE).)

We cloned and purified the major family 10 xylanase (Xyn10A) from Acidothermus cellulolyticus 11B. Xyn10A was active on oat spelt and birchwood xylans between 60°C and 100°C and between pH 4 and pH 8. The optimal activity was at 90°C and pH 6; specific activity and K(m) for oat spelt xylan were 350 μmol xylose produced min⁻¹ mg of protein⁻¹ and 0.53 mg ml⁻¹, respectively. Based on xylan cleavage patterns, Xyn10A is an endoxylanase, and its half-life at 90°C was approximately 1.5 h in the presence of xylan.

Purpose: To investigate the three-dimensional (3D) fast-recovery fast spin-echo accelerated (FRFSE-XL) sequence as a new application for measuring the intraorbital optic nerve (ION) mean cross-sectional area in vivo and to determine its value within a commonly used high resolution imaging protocol., Materials and Methods: The entire ION was scanned in nine healthy volunteers (mean age 32 +/- 4 years) using the 3D FRFSE-XL sequence and a commonly used high resolution short-echo fast fluid-attenuated inversion-recovery (sTE fFLAIR) sequence with identical slice locations at 1.5T. The mean cross-sectional area from both sequences was measured on a slice-by-slice basis from 3 mm behind the globe to the orbital apex. The reproducibility of both techniques was assessed from repeated scans (scan-rescan) and repeated image analysis (intraobserver)., Results: Measurement of the mean cross-sectional area of the anterior 9 mm segment of the ION was only possible using the 3D FRFSE-XL sequence with a mean area of 11.6 +/- 2.2 mm(2) (scan rescan COV = 3.3 +/- 1.5, intraobserver COV = 2.4 +/- 0.02) whereas the remainder segment of the ION (i.e., 9 mm behind the globe to the orbital apex) could only be measured with the use of the sTE fFLAIR with a mean area of 8.5 +/- 1.7 mm(2) (scan rescan COV = 4.9 +/- 2.5 and intraobserver COV = 3.70 +/- 0.03)., Conclusion: The 3D FRFSE-XL allows fast and reproducible measurement of the cross-sectional area of the anterior 9 mm segment of the ION, which is not possible using commonly used imaging sequences due to image degradation from motion, and is of complementary value to the existing imaging protocol for ION atrophy quantification.

Growth of Acidothermus cellulolyticus in solid-state fermentation and its required growth conditions were investigated in this study. Extraction of switchgrass was required for growth. Under the experimental conditions, extraction ratio had the most significant effect on the growth of A. cellulolyticus. Heat treatment (in the form of autoclaving) of switchgrass did not have a significant effect on the growth rate; however, longer heat treatment times had a negative effect on the total growth. Moisture content adjustment had no effect on the release of inhibitors into extracts. Our results showed that leaching at a minimum 40:1 (gram water: gram dry biomass) removed inhibitory compound(s) from switchgrass. Upon extraction A. cellulolyticus colonized switchgrass in solid fermentation without exogenous addition of carbon and nitrogen sources. It is the first demonstration of growth of A. cellulolyticus in solid fermentation., (Copyright 2009 American Institute of Chemical Engineers)

Objective: To review differences between primary retroperitoneal lymph node dissection (P-RPLND) and RPLND after chemotherapy (PC-RPLND) in a contemporary series of patients with testicular cancer, to validate the proposed low morbidity., Patients and Methods: Patients who had undergone RPLND at our institution in 2001-2008 were identified and their clinical charts reviewed; in all, 190 were identified and perioperative data obtained., Results: Of the 190 patients who had RPLND, 98 (52%) and 92 (48%) had P- and PC-RPLND, respectively. Histology of the orchidectomy specimen consisted of embryonal carcinoma in 146 (76%) patients, also including lymphovascular invasion in 83 (44%). The mean (range) operative duration was 206 (110-475) min and the mean blood loss was 294 (50-7000) mL. The median hospital stay was 4 days. Mean blood loss, operative duration and hospital stay were significantly less for the P-RPLND than for PC-RPLND groups (P < 0.05). There were 18 (9%) perioperative complications in all. There were no deaths in either group., Conclusions: The short-term morbidity of open RPLND is acceptable, and open RPLND is safe and effective at select tertiary centres. When compared with historical data, the present contemporary series shows that the operative duration, blood loss and hospital stay have improved, with few complications. These contemporary data should be considered when comparing laparoscopic with open RPLND.

Aims: This investigation was designed to explore the role of IL-1RN genotype in unexplained infant deaths (including sudden infant death syndrome (SIDS)), non-infectious infant deaths, and infectious infant deaths, and to investigate whether IL-1RN genotype is related to the finding of organisms in normally sterile sites in infant deaths., Methods: IL-1RN 89bp variable number of tandem repeat polymorphism genotype was determined using polymerase chain reaction for 49 cases of unexplained sudden unexpected death in infancy (uSUDI), 13 cases of infectious sudden unexpected death in infancy, 10 cases of non-infectious sudden unexpected death in infancy, and 103 live control infants. IL-1RN genotype was then compared with the presence of bacteria in normally sterile sites in infant deaths., Results: An association was found between the homozygous A2 allele and uSUDI (P = 0.007; 95% confidence interval 1.41-17.67) where carriage of the 2/2 genotype was 4.85 times more likely to increase risk of uSUDI compared with the predominant 1/1 genotype., Conclusions: The role of infection in uSUDI and SIDS may be via an immune response pathway where IL-1RN A2 affects interleukin (IL)-1 regulation. These results are consistent with previous research where polymorphic genotypes conferring more severe proinflammatory responses are found more frequently in uSUDI/SIDS infants than in controls.

We present here the complete 2.4-Mb genome of the cellulolytic actinobacterial thermophile Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in the genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized and elevating the industrial value of this organism. A sizable fraction of these hydrolytic enzymes break down plant cell walls, and the remaining either degrade components in fungal cell walls or metabolize storage carbohydrates such as glycogen and trehalose, implicating the relative importance of these different carbon sources. Several of the A. cellulolyticus secreted cellulolytic and xylanolytic enzymes are fused to multiple tandemly arranged carbohydrate binding modules (CBM), from families 2 and 3. For the most part, thermophilic patterns in the genome and proteome of A. cellulolyticus were weak, which may be reflective of the recent evolutionary history of A. cellulolyticus since its divergence from its closest phylogenetic neighbor Frankia, a mesophilic plant endosymbiont and soil dweller. However, ribosomal proteins and noncoding RNAs (rRNA and tRNAs) in A. cellulolyticus showed thermophilic traits suggesting the importance of adaptation of cellular translational machinery to environmental temperature. Elevated occurrence of IVYWREL amino acids in A. cellulolyticus orthologs compared to mesophiles and inverse preferences for G and A at the first and third codon positions also point to its ongoing thermoadaptation. Additional interesting features in the genome of this cellulolytic, hot-springs-dwelling prokaryote include a low occurrence of pseudogenes or mobile genetic elements, an unexpected complement of flagellar genes, and the presence of three laterally acquired genomic islands of likely ecophysiological value.