The conformations and basal conformational dynamics of translocation factor SecDF vary with translocon SecYEG interaction.

The general secretory, or Sec, system is a primary protein export pathway from the cytosol of Escherichia coli and all eubacteria. Integral membrane protein complex SecDF is a translocation factor that enhances polypeptide secretion, which is driven by the Sec translocase, consisting of translocon SecYEG and ATPase SecA. SecDF is thought to utilize a proton gradient to effectively pull precursor proteins from the cytoplasm into the periplasm. Working models have been developed to describe the structure and function of SecDF, but important mechanistic questions remain unanswered. Atomic force microscopy (AFM) is a powerful technique for studying the dynamics of single-molecule systems including membrane proteins in near-native conditions. The sharp tip of the AFM provides direct access to membrane-external protein conformations. Here, we acquired AFM images and kymographs (∼100 ms resolution) to visualize SecDF protrusions in near-native supported lipid bilayers and compared the experimental data to simulated AFM images based on static structures. When studied in isolation, SecDF exhibited a stable and compact conformation close to the lipid bilayer surface, indicative of a resting state. Interestingly, upon SecYEG introduction, we observed changes in both SecDF conformation and conformational dynamics. The population of periplasmic protrusions corresponding to an intermediate form of SecDF, which is thought to be active in precursor protein handling, increased more than ninefold. In conjunction, our dynamics measurements revealed an enhancement in the transition rate between distinct SecDF conformations when the translocon was present. Together, this work provides a novel vista of basal-level SecDF conformational dynamics in near-native conditions.

Amygdala DCX and blood Cdk14 are implicated as cross-species indicators of individual differences in fear, extinction, and resilience to trauma exposure.

Doublecortin (DCX) has long been implicated in, and employed as a marker for, neurogenesis, yet little is known about its function in non-neurogenic brain regions, including the amygdala. This study sought first to explore, in rodents, whether fear learning and extinction modulate amygdala DCX expression and, second, to assess the utility of peripheral DCX correlates as predictive biomarkers of trauma response in rodents and humans. Pavlovian conditioning was found to alter DCX protein levels in mice 24 h later, resulting in higher DCX expression associated with enhanced learning in paradigms examining both the acquisition and extinction of fear (p < 0.001). This, in turn, is associated with differences in freezing on subsequent fear expression tests, and the same relationship between DCX and fear extinction was replicated in rats (p < 0.001), with higher amygdala DCX levels associated with more rapid extinction of fear. RNAseq of amygdala and blood from mice identified 388 amygdala genes that correlated with DCX (q < 0.001) and which gene ontology analyses revealed were significantly over-represented for neurodevelopmental processes. In blood, DCX-correlated genes included the Wnt signaling molecule Cdk14 which was found to predict freezing during both fear acquisition (p < 0.05) and brief extinction protocols (p < 0.001). High Cdk14 measured in blood immediately after testing was also associated with less freezing during fear expression testing (p < 0.01). Finally, in humans, Cdk14 expression in blood taken shortly after trauma was found to predict resilience in males for up to a year post-trauma (p < 0.0001). These data implicate amygdala DCX in fear learning and suggest that Cdk14 may serve as a predictive biomarker of trauma response.

Atomic force microscopy for quantitative understanding of peptide-induced lipid bilayer remodeling.

A number of peptides are known to bind lipid bilayer membranes and cause these natural barriers to leak in an uncontrolled manner. Though membrane permeabilizing peptides play critical roles in cellular activity and may have promising future applications in the therapeutic arena, significant questions remain about their mechanisms of action. The atomic force microscope (AFM) is a single molecule imaging tool capable of addressing lipid bilayers in near-native fluid conditions. The apparatus complements traditional assays by providing local topographic maps of bilayer remodeling induced by membrane permeabilizing peptides. The information garnered from the AFM includes direct visualization and statistical analyses of distinct bilayer remodeling modes such as highly localized pore-like voids in the bilayer and dispersed thinned membrane regions. Colocalization of distinct remodeling modes can be studied. Here we examine recent work in the field and outline methods used to achieve precise AFM image data. Experimental challenges and common pitfalls are discussed as well as techniques for unbiased analysis including the Hessian blob detection algorithm, bootstrapping, and the Bayesian information criterion. When coupled with robust statistical analyses, high precision AFM data is poised to advance understanding of an important family of peptides that cause poration of membrane bilayers.

Outcome of neoadjuvant treatment for pancreatic cancer in elderly patients: comparative, observational cohort study.

BACKGROUND: Use of neoadjuvant therapy for elderly patients with pancreatic cancer has been debatable. With FOLFIRINOX (folinic acid, 5-fluorouracil, irinotecan, oxaliplatin) or gemcitabine plus nab-paclitaxel (GnP) showing tremendous effects in improving the overall survival of patients with borderline resectable and locally advanced pancreatic cancer, there is no definitive consensus regarding the use of this regimen in the elderly. METHODS: This study evaluated the eligibility of elderly patients with borderline resectable or locally advanced pancreatic cancer for neoadjuvant therapy. Patients registered in the database of pancreatic cancer at the University of Colorado Cancer Center, who underwent neoadjuvant treatment between January 2011 and March 2019, were separated into three age groups (less than 70, 70-74, 75 or more years) and respective treatment outcomes were compared. RESULTS: The study included 246 patients with pancreatic cancer who underwent neoadjuvant treatment, of whom 154 and 71 received chemotherapy with FOLFIRINOX and GnP respectively. Among these 225 patients, 155 were younger than 70 years, 36 were aged 70-74 years, and 34 were aged 75 years or older. Patients under 70 years old received FOLFIRINOX most frequently (124 of 155 versus 18 of 36 aged 70-74 years, and 12 of 34 aged 75 years or more; P < 0.001). Resectability was similar among the three groups (60.0, 58.3, and 55.9 per cent respectively; P = 0.919). Trends towards shorter survival were observed in the elderly (median overall survival time 23.6, 18.0, and 17.6 months for patients aged less than 70, 70-74, and 75 or more years respectively; P = 0.090). After adjusting for co-variables, age was not a significant predictive factor. CONCLUSION: The safety and efficacy of multiagent chemotherapy in patients aged 75 years or over were similar to those in younger patients. Modern multiagent regimens could be a safe and viable treatment option for clinically fit patients aged at least 75 years.

The need for physiological phenotyping to develop new drugs for airways disease.

Asthma and COPD make up the majority of obstructive airways diseases (OADs), which affects ∼11 % of the population. The main drugs used to treat OADs have not changed in the past five decades, with advancements mainly comprising variations on existing treatments. The recent biologics are beneficial to only specific subsets of patients. Part of this may lie in our inability to adequately characterise the tremendous heterogeneity in every aspect of OAD. The field is currently moving towards the concept of personalised medicine, based on a focus on treatable traits that are objective, measurable and modifiable. We propose extending this concept via the use of emerging clinical tools for comprehensive physiological phenotyping. We describe, based on published data, the evidence for the use of functional imaging, gas washout techniques and oscillometry, as well as potential future applications, to more comprehensively assess and predict treatment response in OADs. In this way, we hope to demonstrate how physiological phenotyping tools will improve the way in which drugs are prescribed, but most importantly, will facilitate development of new drugs for OADs.

Halobacterium bonnevillei sp. nov., Halobaculum saliterrae sp. nov. and Halovenus carboxidivorans sp. nov., three novel carbon monoxide-oxidizing Halobacteria from saline crusts and soils.

Three novel carbon monoxide-oxidizing Halobacteria were isolated from Bonneville Salt Flats (Utah, USA) salt crusts and nearby saline soils. Phylogenetic analysis of 16S rRNA gene sequences revealed that strains PCN9T, WSA2T and WSH3T belong to the genera Halobacterium, Halobaculum and Halovenus, respectively. Strains PCN9T, WSA2T and WSH3T grew optimally at 40 °C (PCN9T) or 50 °C (WSA2T, WSH3T). NaCl optima were 3 M (PCN9T, WSA2T) or 4 M NaCl (WSH3T). Carbon monoxide was oxidized by all isolates, each of which contained a molybdenum-dependent CO dehydrogenase. G+C contents for the three respective isolates were 66.75, 67.62, and 63.97 mol% as derived from genome analyses. The closest phylogenetic relatives for PCN9T, WSA2T and WSH3T were Halobacterium noricense A1T, Halobaculum roseum D90T and Halovenus aranensis EB27T with 98.71, 98.19 and 95.95 % 16S rRNA gene sequence similarities, respectively. Genome comparisons of PCN9T with Halobacterium noricense A1T yielded an average nucleotide identity (ANI) of 82.0% and a digital DNA-DNA hybridization (dDDH) value of 25.7 %; comparisons of WSA2T with Halobaculum roseum D90T yielded ANI and dDDH values of 86.34 and 31.1 %, respectively. The ANI value for a comparison of WSH3T with Halovenus aranensis EB27T was 75.2 %. Physiological, biochemical, genetic and genomic characteristics of PCN9T, WSA2T and WSH3T differentiated them from their closest phylogenetic neighbours and indicated that they represent novel species for which the names Halobaculum bonnevillei, Halobaculum saliterrae and Halovenus carboxidivorans are proposed, respectively. The type strains are PCN9T (=JCM 32472=LMG 31022=ATCC TSD-126), WSA2T (=JCM 32473=ATCC TSD-127) and WSH3T (=JCM 32474=ATCC TSD-128).

Direct Comparison between Bayesian and Frequentist Uncertainty Quantification for Nuclear Reactions.

Until recently, uncertainty quantification in low energy nuclear theory was typically performed using frequentist approaches. However in the last few years, the field has shifted toward Bayesian statistics for evaluating confidence intervals. Although there are statistical arguments to prefer the Bayesian approach, no direct comparison is available. In this work, we compare, directly and systematically, the frequentist and Bayesian approaches to quantifying uncertainties in direct nuclear reactions. Starting from identical initial assumptions, we determine confidence intervals associated with the elastic and the transfer process for both methods, which are evaluated against data via a comparison of the empirical coverage probabilities. Expectedly, the frequentist approach is not as flexible as the Bayesian approach in exploring parameter space and often ends up in a different minimum. We also show that the two methods produce significantly different correlations. In the end, the frequentist approach produces significantly narrower uncertainties on the considered observables than the Bayesian. Our study demonstrates that the uncertainties on the reaction observables considered here within the Bayesian approach represent reality more accurately than the much narrower uncertainties obtained using the standard frequentist approach.

Steroid insensitive fixed airflow obstruction is not related to airway inflammation in older non-smokers with asthma.

There is limited evidence linking airway inflammation and lung function impairment in older non-smoking asthmatics with fixed airflow obstruction (FAO), which can develop despite treatment with inhaled corticosteroids (ICS). We assessed lung function (spirometry, forced oscillation technique (FOT)), lung elastic recoil and airway inflammation using bronchoalveolar lavage (BAL) in non-smoking adult asthmatics with FAO, following 2 months treatment with high-dose ICS/long-acting beta-agonist. Subjects demonstrated moderate FAO, abnormal FOT indices and loss of lung elastic recoil. This cross-sectional study showed a lack of a relationship between BAL neutrophils, eosinophils, inflammatory cytokines and lung function impairment. Other inflammatory pathways or the effect of inflammation on lung function over time may explain FAO development.

Probable pulmonary embolism with repeat administration of prothrombin complex concentrate in a factor Xa inhibitor patient.

WHAT IS KNOWN AND OBJECTIVE: Prothrombin complex concentrate (PCC) is a plasma-derived concentrate used to replenish clotting factors. There are limited recommendations for treating coagulopathy induced by direct oral anticoagulants (DOAC). Data are limited regarding both total dose and repeated dosing with this population. CASE SUMMARY: We describe a case of an adult patient anticoagulated with apixaban who received two 35 unit/kg doses of PCC resulting in suspected pulmonary embolism. WHAT IS NEW AND CONCLUSION: Treatment of DOAC-induced bleeding remains an "off-label" indication for PCC. Additional doses should be given with caution if given at all and patients monitored closely.

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement.

BACKGROUND: Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. RESULTS: We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps. CONCLUSIONS: These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.

Insecticidal activity of a recombinant knottin peptide from Loxosceles intermedia venom and recognition of these peptides as a conserved family in the genus.

Loxosceles intermedia venom comprises a complex mixture of proteins, glycoproteins and low molecular mass peptides that act synergistically to immobilize envenomed prey. Analysis of a venom-gland transcriptome from L. intermedia revealed that knottins, also known as inhibitor cystine knot peptides, are the most abundant class of toxins expressed in this species. Knottin peptides contain a particular arrangement of intramolecular disulphide bonds, and these peptides typically act upon ion channels or receptors in the insect nervous system, triggering paralysis or other lethal effects. Herein, we focused on a knottin peptide with 53 amino acid residues from L. intermedia venom. The recombinant peptide, named U2 -sicaritoxin-Li1b (Li1b), was obtained by expression in the periplasm of Escherichia coli. The recombinant peptide induced irreversible flaccid paralysis in sheep blowflies. We screened for knottin-encoding sequences in total RNA extracts from two other Loxosceles species, Loxosceles gaucho and Loxosceles laeta, which revealed that knottin peptides constitute a conserved family of toxins in the Loxosceles genus. The insecticidal activity of U2 -SCTX-Li1b, together with the large number of knottin peptides encoded in Loxosceles venom glands, suggests that studies of these venoms might facilitate future biotechnological applications of these toxins.

The microtubular cytoskeleton of olfactory neurons derived from patients with schizophrenia or with bipolar disorder: Implications for biomarker characterization, neuronal physiology and pharmacological screening.

Schizophrenia (SZ) and Bipolar Disorder (BD) are highly inheritable chronic mental disorders with a worldwide prevalence of around 1%. Despite that many efforts had been made to characterize biomarkers in order to allow for biological testing for their diagnoses, these disorders are currently detected and classified only by clinical appraisal based on the Diagnostic and Statistical Manual of Mental Disorders. Olfactory neuroepithelium-derived neuronal precursors have been recently proposed as a model for biomarker characterization. Because of their peripheral localization, they are amenable to collection and suitable for being cultured and propagated in vitro. Olfactory neuroepithelial cells can be obtained by a non-invasive brush-exfoliation technique from neuropsychiatric patients and healthy subjects. Neuronal precursors isolated from these samples undergo in vitro the cytoskeletal reorganization inherent to the neurodevelopment process which has been described as one important feature in the etiology of both diseases. In this paper, we will review the current knowledge on microtubular organization in olfactory neurons of patients with SZ and with BD that may constitute specific cytoskeletal endophenotypes and their relation with alterations in L-type voltage-activated Ca(2+) currents. Finally, the potential usefulness of neuronal precursors for pharmacological screening will be discussed.

Family-oriented services in pediatric rehabilitation: a scoping review and framework to promote parent and family wellness.

Family-oriented services are not as common as one would expect, given the widespread endorsement of family-centred care, the role of parents in supporting optimal child outcomes, and legislation and literature indicating that parent outcomes are important in their own right. There are no published service delivery frameworks describing the scope of services that could be delivered to promote parent and family wellness. A scoping review was conducted to identify types of family-oriented services for parents of children with physical disabilities and/or intellectual impairments. This information was then synthesized into a conceptual framework of services to inform service selection and design. A scoping review of the recent literature was performed to capture descriptions of services targeting parents/families of children with physical disabilities and/or intellectual impairments, published in a six-year period (2009 to 2014). Six databases were searched and 557 retrieved articles were screened using inclusion and exclusion criteria. Thirty six relevant articles were identified. Based on descriptions of services in these articles, along with seminal articles describing the nature of desirable services, we propose a needs-based and capacity-enhancing framework outlining a continuum of family-oriented services for parents of children with disabilities. The framework includes six types of services to meet parent/family needs, organized as a continuum from fundamental information/education services, to those supporting parents to deliver services to meet their child's needs, to a variety of services addressing parents' own needs (support groups, psychosocial services and service coordination). The framework provides pediatric rehabilitation service organizations with a way to consider different possible family-oriented services. Implications include the particular importance of providing information resources, support groups and psychosocial services to meet parents' needs, enhance capacity and promote family wellness. There is also an opportunity to provide composite parent-child services to address the needs of both parents and children.

Identification of environmentally stable QTL for resistance against Leptosphaeria maculans in oilseed rape (Brassica napus).

KEY MESSAGE: Six stable QTL for resistance against L. maculans (phoma stem canker) have been identified by QTL × environment interaction analysis using data from five winter oilseed rape field experiments. Phoma stem canker, caused by Leptosphaeria maculans, is a disease of worldwide importance on oilseed rape (Brassica napus). Quantitative trait loci (QTL)-mediated resistance against L. maculans in B. napus is considered to be race non-specific and potentially durable. Identification and evaluation of QTL for resistance to L. maculans is important for breeding oilseed rape cultivars with durable resistance. An oilseed rape mapping population was used to detect QTL for resistance against L. maculans in five winter oilseed rape field experiments under different environments. A total of 17 QTL involved in 'field' quantitative resistance against L. maculans were detected and collectively explained 51% of the phenotypic variation. The number of QTL detected in each experiment ranged from two to nine and individual QTL explained 2-25% of the phenotypic variation. QTL × environment interaction analysis suggested that six of these QTL were less sensitive to environmental factors, so they were considered to be stable QTL. Markers linked to these stable QTL will be valuable for selection to breed for effective resistance against L. maculans in different environments, which will contribute to sustainable management of the disease.

Isolation and characterization of Acidobacterium ailaaui sp. nov., a novel member of Acidobacteria subdivision 1, from a geothermally heated Hawaiian microbial mat.

A novel member of Acidobacteria was isolated from a microbial mat growing on a geothermally heated dead tree trunk in Hawai'i Volcanoes National Park (HI, USA). The rod-shaped, Gram-negative capsulated cells of strain PMMR2T were non-motile and catalase and oxidase negative. Growth occurred aerobically from 15 to 55 °C (optimum, 40 °C) and at pH values from 4.5 to 7.0 (optimum, 6.5). A limited range of sugars and organic acids supported growth. However, results of a genomic analysis suggested that various polysaccharides might be hydrolysed as carbon sources, and evidence for pectin degradation was observed in liquid cultures. A genomic analysis also revealed genes for a Group 1f uptake hydrogenase; assays with liquid cultures confirmed hydrogen consumption, including uptake at sub-atmospheric concentrations. Nitrate was not dissimilated to nitrite. Major membrane fatty acids included iso-C15 : 0 and iso-C17 : 0. The G+C content was 57.2mol%. A comparative genome analysis revealed an average nucleotide identity of 72.2 % between PMMR2T and its nearest cultured phylogenetic neighbour, Acidobacterium capsulatum ATCC 51196T (=JCM 7670T); analysis of the 16S rRNA gene revealed a 96.8 % sequence identity with Acidobacterium capsulatum ATCC 51196T. These results and other phenotypic differences indicated that strain PMMR2T represents a novel species in the genus Acidobacterium, for which the name Acidobacterium ailaaui sp. nov. is proposed. The type strain, PMMR2T (=DSM 27394T=LMG 28340T), is the second formal addition to the genus Acidobacterium.

A randomised comparison between ultrasound and nerve stimulation for infraclavicular catheter placement.

We conducted this study to determine if placement of infraclavicular catheters guided by ultrasound is quicker than placement guided by nerve stimulation. Infraclavicular brachial plexus catheters were inserted in 210 randomly allocated patients who were scheduled for elective hand or elbow surgery. Needle and catheter placement was guided by ultrasound (n = 105) or by nerve stimulation (n = 105). The primary outcome was time to sensory block success. Success rate was similar between the two techniques (83.2% vs 81.4%, p = 0.738). However, placement of ultrasound-guided catheters took less time (7.2 [2.5] vs 9.6 [3.6] min, p < 0 .001). Pain and satisfaction scores, and incidence of nerve deficit, were also similar with both techniques.

Greater parallel heterogeneity of airway narrowing and airway closure in asthma measured by high-resolution CT.

BACKGROUND: Heterogeneous airway narrowing and closure are characteristics of asthma. However, they have never been quantified by direct measurements of parallel sister airways obtained from image data, and the anatomical basis of these processes remains unknown. METHODS: Seven normal and nine asthmatic subjects underwent high-resolution CT, before and after methacholine challenge. Mean lumen areas of the entire airways were measured in 28 and 24 parallel sister airway pairs (a pair of airways arising from the same bifurcation) respectively (range 1.0-8.7 mm diameter). Heterogeneous narrowing was defined as the median difference in percentage narrowing between parallel sister airways. Forced oscillatory respiratory resistance (Rrs) and spirometry were measured before and after methacholine challenge conducted while supine. RESULTS: The airways of asthmatics were smaller at baseline, and following bronchoconstriction there were similar decreases in FEV1, increases in Rrs and mean narrowing of airways for asthmatic and non-asthmatic groups. Non-asthmatics required higher doses of methacholine than asthmatics to achieve the same changes. However, parallel heterogeneity (median (IQR) 33% (27-53%) vs 11% (9-18%), p<0.001) and airway closure (24.1% and 7.7%, p=0.001, χ(2)) were greater in asthmatics versus non-asthmatics. CONCLUSION: We found clear evidence of differences in airway behaviour in the asthmatic group. Asthmatic airways were narrower at baseline and responded to inhaled methacholine by more heterogeneous narrowing of parallel sister airways and greater airway closure.

A retrospective study of past graduates of a residential life skills program for youth with physical disabilities.

BACKGROUND: Young people with physical disabilities experience issues regarding employment, schooling, independent living and establishing meaningful personal relationships. A lack of life skills has been recognized as an important factor contributing to this lag. The Independence Program (TIP) is a short-term residential life skills program that aims to equip youth with the foundational life skills required to assume adult roles. This study retrospectively examined the achievements, skills acquired and program attributions of youth and young adults who took part in this three-week immersive teen independence program over a 20-year period. METHODS: A total of 162 past graduates were invited to take part, with 78 doing so (a 48% response rate). These past graduates completed an online survey assessing objective outcomes such as employment and independent living; subjective outcomes such as feeling in control and living meaningful lives; and reflections on skills acquired, opportunities experienced and attributions to TIP. RESULTS: The majority of respondents were female (71%), had a diagnosis of cerebral palsy (55%) and ranged from 20 to 35 years of age (92%). Despite a range of outcomes related to the achievement of adult roles, high levels of life satisfaction and overall quality of life were reported. Nearly every respondent reported using the skills they learned at the program in their lives afterwards and a high percentage attributed the acquisition and consolidation of core life skills to participating in this intensive immersive program. CONCLUSIONS: Although causality cannot be assumed, respondents reflected very positively on the opportunities provided by TIP to develop their independent living and life skills, extend their social networks and understand their strengths and weaknesses. Such findings validate the importance of targeted skill development to assist young people with physical disabilities in attaining their life goals and encourage focused investigations of key features in program design.

Thermomicrobium carboxidum sp. nov., and Thermorudis peleae gen. nov., sp. nov., carbon monoxide-oxidizing bacteria isolated from geothermally heated biofilms.

Two thermophilic, Gram-stain-positive, rod-shaped, non-spore-forming bacteria (strains KI3(T) and KI4(T)) were isolated from geothermally heated biofilms growing on a tumulus in the Kilauea Iki pit crater on the flank of Kilauea Volcano (Hawai'i, USA). Strain KI3(T) grew over an examined temperature range of 50-70 °C (no growth at 80 °C) and a pH range of 6.0-9.0, with optimum growth at 70 °C and pH 7.0. Strain KI4(T) grew at temperatures of 55-70 °C and a pH range of 5.8-8.0, with optimum growth at 65 °C and pH 6.7-7.1. The DNA G+C contents of strains KI3(T) and KI4(T) were 66.0 and 60.7 mol%, respectively. The major fatty acid for both strains was 12-methyl C(18 : 0). Polar lipids in strain KI3(T) were dominated by glycolipids and phosphatidylinositol, while phosphatidylinositol and phosphoglycolipids dominated in strain KI4(T). Strain KI3(T) oxidized carbon monoxide [6.7±0.8 nmol CO h(-1) (mg protein)(-1)], but strain KI4(T) did not. 16S rRNA gene sequence analyses determined that the strains belong to the class Thermomicrobia, and that strains KI3(T) and KI4(T) are related most closely to Thermomicrobium roseum DSM 5159(T) (96.5 and 91.1% similarity, respectively). 16S rRNA gene sequence similarity between strain KI3(T) and strain KI4(T) was 91.4%. Phenotypic features and phylogenetic analyses supported the affiliation of strain KI3(T) to the genus Thermomicrobium, while results of chemotaxonomic, physiological and biochemical assays differentiated strains KI3(T) and KI4(T) from Thermomicrobium roseum. Strain KI3(T) ( = DSM 27067(T) = ATCC BAA-2535(T)) is thus considered to be the type strain of a novel species, for which the name Thermomicrobium carboxidum sp. nov. is proposed. Additionally, the characterization and phylogenetic position of strain KI4(T) showed that it represents a novel species of a new genus, for which the name Thermorudis peleae gen. nov., sp. nov. is proposed. The type strain of Thermorudis peleae is KI4(T) ( = DSM 27169(T) = ATCC BAA-2536(T)).

Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria.

A thermophilic, aerobic, Gram-stain-positive bacterium (strain PM5(T)), which formed mycelia of irregularly branched filaments and produced multiple exospores per cell, was isolated from a geothermally heated biofilm. Strain PM5(T) grew at 40-65 °C and pH 4.1-8.0, with optimal growth at 55 °C and pH 6.0. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain PM5(T) belonged to the class Ktedonobacteria, and was related most closely to Thermogemmatispora onikobensis ONI-1(T) (97.7 % similarity) and Thermogemmatispora foliorum ONI-5(T) (96.1 %). Morphological features and fatty acid profiles (major fatty acids: iso-C17 : 0, iso-C19 : 0 and 12,17-dimethyl C18 : 0) supported the affiliation of strain PM5(T) to the genus Thermogemmatispora. Strain PM5(T) oxidized carbon monoxide [CO; 10±1 nmol h(-1) (mg protein)(-1)], but did not grow with CO as a sole carbon and energy source. Results from analyses of related strains indicated that the capacity for CO uptake occurred commonly among the members of the class Ktedonobacteria; 13 of 14 strains tested consumed CO or harboured coxL genes that potentially enabled CO oxidation. The results of DNA-DNA hybridization and physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain PM5(T) from the two recognized species of the genus Thermogemmatispora. Strain PM5(T) differed from Thermogemmatispora onikobensis ONI-1(T) in its production of orange pigment, lower temperature optimum, hydrolysis of casein and starch, inability to grow with mannitol, xylose or rhamnose as sole carbon sources, and utilization of organic acids and amino acids. Strain PM5(T) is therefore considered to represent a novel species, for which the name Thermogemmatispora carboxidivorans sp. nov. is proposed. The type strain is PM5(T) ( = DSM 45816(T) = ATCC BAA-2534(T)).