Editorial: Microbial Taxonomy, Phylogeny and Biodiversity

The great diversity of microbial life is the remaining majorreservoir of unknown biologicaldiversity on Earth. To understand this vast, but largely unperceived diversity with its untappedgenetic, enzymatic and industrial potential, microbial systematics is undergoing a revolutionarychange in its approach to describe novel taxa based on genomic/envirogenomic information(Rosselló-Móra and Whitman, 2019)S

From the Gene Sequence to the Phylogeography through the Population Structure: The Cases of Yersinia ruckeri and Vibrio tapetis

Multilocus sequence analysis (MLSA) and multilocus sequence typing (MLST) are nowadays considered as gold standards in the study of microbial systematic, being both techniques based on the interpretation of the sequences of several housekeeping genes. In this context, the sequences can be analyzed from different points of view. On the one hand, the phylogeny of the bacterial species can be estimated using the MLSA approach and on the other hand, the structure of the population can be inferred by means of MLST. Moreover, most species display some degree of population structure that can be interpreted in geographic and chronological contexts, that is, phylogeographic studies. In this review, the phylogeny and population structure of two important fish and shellfish pathogens, Yersinia ruckeri and Vibrio tapetis, exhibiting very different evolutive patterns will be analyzed. In both cases, the species form robust and monophyletic groups from a phylogenetic point of view. Regarding to the population structure, very different results were found. While Y. ruckeri follows an epidemic model of clonal expansion with well‐adapted clones that explode to be widely distributed, V. tapetis appears to have a mixed structure in where the paradox of clonality and high level of variability coexist. Furthermore, phylogeographical studies provided the evolutionary and geographical context for the species, allowing the determination of historical and spatial influences on the diversification of both species

The Stokes-Einstein Relation at Moderate Schmidt Number

The Stokes-Einstein relation for the self-diffusion coefficient of a spherical particle suspended in an incompressible fluid is an asymptotic result in the limit of large Schmidt number, that is, when momentum diffuses much faster than the particle. When the Schmidt number is moderate, which happens in most particle methods for hydrodynamics, deviations from the Stokes-Einstein prediction are expected. We study these corrections computationally using a recently-developed minimally-resolved method for coupling particles to an incompressible fluctuating fluid in both two and three dimensions. We find that for moderate Schmidt numbers the diffusion coefficient is reduced relative to the Stokes-Einstein prediction by an amount inversely proportional to the Schmidt number in both two and three dimensions. We find, however, that the Einstein formula is obeyed at all Schmidt numbers, consistent with linear response theory. The numerical data is in good agreement with an approximate self-consistent theory, which can be used to estimate finite-Schmidt number corrections in a variety of methods. Our results indicate that the corrections to the Stokes-Einstein formula come primarily from the fact that the particle itself diffuses together with the momentum. Our study separates effects coming from corrections to no-slip hydrodynamics from those of finite separation of time scales, allowing for a better understanding of widely observed deviations from the Stokes-Einstein prediction in particle methods such as molecular dynamics.Comment: Submitte

Two-dimensional proteome reference map of Vibrio tapetis, the aetiological agent of brown ring disease in clams

Aims: Vibrio tapetis is the etiological agent of brown ring disease (BRD) in clams, one of the most threatening diseases affecting this commercially important bivalve. In this study we have constructed a proteome reference map of the V. tapetis type strain CECT 4600T. Methods and Results: Eighty-two proteins, consistently present in all 2D-gels, were identified by mass spectrometry or by de novo sequencing. The majority of the proteins identified (66%) belonged to four COG categories: 'Carbohydrate transport and metabolism', 'Post-translational modification, protein turnover and chaperones', 'Energy production', and 'Amino acid transport and metabolism'. Glyceraldehyde-3-phosphate dehydrogenase, enolase, fructose-bisphosphate aldolase, phosphoglycerate kinase. molecular chaperones Dnak and GroEL, alkyl hydroperoxide reductase, peptidyl-prolyl cis-trans isomerase B and factor Tu, were identified among the 20 most abundant proteins. A comparison of this reference map with that obtained for the V. tapetis strain GR0202RD, with different origin and pathophysiological characteristics, was performed. Conclusions: Under the culture conditions employed in this study, glucose degradation is one of the major pathways for energy production in Vibrio tapetis. In addition, the two strains studied, although with remarkable differences at genetic and pathophysiological levels, showed a high similarity under laboratory conditions. Significance and Impact of the Study: The results obtained here can be considered as a first step to gather valuable information on protein expression, related not only to diverse cellular functions and regulation but also to pathogenesis and bacterium-host interactions in the disease process

Magnetic Fields in Evolved Stars: Imaging the Polarized Emission of High-Frequency SiO Masers

We present Submillimeter Array observations of high frequency SiO masers around the supergiant VX Sgr and the semi-regular variable star W Hya. The J=5-4, v=1 28SiO and v=0 29SiO masers of VX Sgr are shown to be highly linearly polarized with a polarization from ~5-60%. Assuming the continuum emission peaks at the stellar position, the masers are found within ~60 mas of the star, corresponding to ~100 AU at a distance of 1.57 kpc. The linear polarization vectors are consistent with a large scale magnetic field, with position and inclination angles similar to that of the dipole magnetic field inferred in the H2O and OH maser regions at much larger distances from the star. We thus show for the first time that the magnetic field structure in a circumstellar envelope can remain stable from a few stellar radii out to ~1400 AU. This provides further evidence supporting the existence of large scale and dynamically important magnetic fields around evolved stars. Due to a lack of parallactic angle coverage, the linear polarization of masers around W Hya could not be determined. For both stars we observed the 28SiO and 29SiO isotopologues and find that they have a markedly different distribution and that they appear to avoid each other. Additionally, emission from the SO 5_5-4_4 line was imaged for both sources. Around W Hya we find a clear offset between the red- and blue-shifted SO emission. This indicates that W Hya is likely host to a slow bipolar outflow or a rotating disk-like structure.Comment: 8 pages, 7 figures, accepted for publication in ApJ. Online table will be available with published versio

Primary physical education, coaches and continuing professional development

This is an Author's Accepted Manuscript of an article published in Sport, Education and Society, 16(4), 485 - 505, 2011, copyright @ Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/13573322.2011.589645.Physical education (PE) in primary schools has traditionally been taught by qualified primary teachers. More recently, some teaching of PE in primary schools has been undertaken by coaches (mostly football coaches). These coaches hold national governing body awards but do not hold teaching qualifications. Thus, coaches may not be adequately prepared to teach PE in curriculum time. The purpose of this study was to evaluate the perceptions of a group of community-based football coaches working in primary schools for the impact of a Continuing Professional Development (CPD) programme on their ability to undertake ‘specified work’ to cover PE in primary schools. The programme focused on four areas identified as important to enable coaches to cover specified work: short- and medium-term planning, pedagogy, knowledge of the curriculum and reflection. Results showed that for the majority of coaches the CPD programme had made them more aware of the importance of these four areas and had helped to develop their knowledge and ability to put this into practice in covering planning, preparation and assessment time. However, further input is still required to develop coaches’ knowledge and understanding in all four areas, but especially their curriculum knowledge, as well as their ability to put these into practice consistently. These findings are discussed in relation to the implications of employing coaches to cover the teaching of PE in primary schools and, if employed, what CPD coaches need to develop the necessary knowledge, skill and understanding for covering specified work in schools

Correlation between Infrared Colors and Intensity Ratios of SiO Maser Lines

We present the results of SiO millimeter-line observations of a sample of known SiO maser sources covering a wide dust-temperature range. A cold part of the sample was selected from the SiO maser sources found in our recent SiO maser survey of cold dusty objects. The aim of the present research is to investigate the causes of the correlation between infrared colors and SiO maser intensity ratios among different transition lines. In particular, the correlation between infrared colors and SiO maser intensity ratio among the J=1-0 v=1, 2, and 3 lines are mainly concerned in this paper. We observed in total 75 SiO maser sources with the Nobeyama 45m telescope quasi-simultaneously in the SiO J=1-0 v=0, 1, 2, 3, 4 and J=2-1 v=1, 2 lines. We also observed the sample in the 29SiO J=1-0 v=0 and J=2-1 v=0, and 30SiO J=1-0 v=0 lines, and the H2O 6(1,6)-5(2,3) line. As reported in previous papers, we confirmed that the intensity ratios of the SiO J=1-0 v=2 to v=1 lines clearly correlate with infrared colors. In addition, we found possible correlation between infrared colors and the intensity ratios of the SiO J=1-0 v=3 to v=1&2 lines. Two overlap lines of H2O (i.e., 11(6,6) nu_2=1 -> 12(7,5) nu_2=0 and 5(0,5) nu_2=2 -> 6(3,4) nu_2=1) might explain these correlation if these overlap lines become stronger with increase of infrared colors, although the phenomena also might be explained by more fundamental ways if we take into account the variation of opacity from object to object.Comment: 49 pages, 7 figures, 3 tables, accepted for publication in ApJ. Full resolution version available at http://www.asiaa.sinica.edu.tw/~junichi/paper

Late HIV Diagnosis but Earlier Antiretroviral Treatment Initiation in Northwest Spain: Impact of Current Treatment Guidelines.

BACKGROUND: Current HIV treatment guidelines recommend antiretroviral treatment (ART) initiation for all HIV-infected individuals regardless of CD4 count. This study evaluates the immunological and virological status and the clinical characteristics of patients who have started ART in the last 8 years in the Northwest of Spain. METHODS: All HIV-infected patients who have started ART between January 2009 and December 2016 at a reference hospital in the Northwest of Spain were included in this retrospective observational study. Epidemiological, clinical, and immunovirological features and antiretroviral drugs used for initiation were recorded. A statistical analysis was performed using SPSS version 19 software. Categorical and continuous variables were compared by the specific statistical tests, and a logistic regression model was used to identify time associated with Center for Disease Control and Prevention (CDC) categories change. RESULTS: A high proportion of HIV-infected patients (66.7%) had initiated ART with CD4 counts <350 cells/mm(3) in the last 8 years. From these, most of them (68.3%) had <350 CD4 counts at first contact with HIV specialist medical team, 12.2% had no indications for ART initiation in the last clinic visit before ART initiation according to the national guidelines at that moment, 11.0% were lost to follow-up because of lack of compliance with scheduled visits and 8.5% of patients refused treatment. A logistic regression model showed that a delay of one month since the first contact with HIV specialist medical team to ART initiation involves a risk of worsening in the CDC clinical category (odds ratio: 1.02 [95% confidence interval: 1.012-1.029]; P < .001). A trend towards an earlier start of ART was observed during 2015 and 2016, likely influenced by the last treatment guidelines recommendations. CONCLUSION: High proportion of HIV-infected patients (66.7%) had initiated ART with CD4 counts <350 cells/mm(3) in the last 8 years. The main reasons for this problem were analyzed and an important rate of late diagnosis was identified. However, a trend towards an earlier start of ART was observed during 2015 and 2016, likely influenced by the last treatment guidelines recommendations. These findings highlight the need to promote and facilitate HIV testing to reduce the late diagnosis as well as counseling on HIV prevention, treatment, and linkage care

White privilege, empathy and alterity in higher education : Teaching about race and racism in the sociology of PE and sport

In this chapter we provide a reflexive account on personal experiences teaching in HE in order to consider the extent to which our status as white HE practitioners reinforces and/or undermines white privilege in HE. As lecturers teaching within the discipline of sociology in physical education (PE) and sport contexts, we question whether our delivery of lectures on race and racism effectively challenges racialised discourses and encourages social action within our field. Despite the fact that the undergraduate programmes we work on incorporate lectures on race and ethnicity as a crucial part of the curriculum, these sessions have rarely been delivered by black and minority ethnic (BME) academics. We therefore consider whether our practice can provide a critical pedagogic voice, or if it simply provides a platform for white academics to unconsciously reinforce the institutional whiteness of HE. In particular, we reflect upon the possibility for white academics to empathise with the racialised social experiences of BME students in our cohorts, and the potential risk that our practice simply offers tokenistic discussion of race which reinforce the current forms of inequality and white privilege, whilst violating the alterity of our students

Relationship between time from symptom''s onset to diagnosis and prognosis in patients with symptomatic colorectal cancer

BACKGROUND: Controversy exists regarding the relationship of the outcome of patients with colorectal cancer (CRC) with the time from symptom onset to diagnosis. The aim of this study is to investigate this association, with the assumption that this relationship was nonlinear and with adjustment for multiple confounders, such as tumor grade, symptoms, or admission to an emergency department. METHODS: This multicenter study with prospective follow-up was performed in five regions of Spain from 2010 to 2012. Symptomatic cases of incident CRC from a previous study were examined. At the time of diagnosis, each patient was interviewed, and the associated hospital and clinical records were reviewed. During follow-up, the clinical records were reviewed again to assess survival. Cox survival analysis with a restricted cubic spline was used to model overall and CRC-specific survival, with adjustment for variables related to the patient, health service, and tumor. RESULTS: A total of 795 patients had symptomatic CRC and 769 of them had complete data on diagnostic delay and survival. Univariate analysis indicated a lower HR for death in patients who had diagnostic intervals less than 4.2 months. However, after adjustment for variables related to the patient, tumor, and utilized health service, there was no relationship of the diagnostic delay with survival of patients with colon and rectal cancer, colon cancer alone, or rectal cancer alone. Cubic spline analysis indicated an inverse association of the diagnostic delay with 5-year survival. However, this association was not statistically significant. CONCLUSIONS: Our results indicated that the duration of diagnostic delay had no significant effect on the outcome of patients with CRC. We suggest that the most important determinant of the duration of diagnostic delay is the biological profile of the tumor. However, it remains the responsibility of community health centers and authorities to minimize diagnostic delays in patients with CRC and to implement initiatives that improve early diagnosis and provide better outcomes. © 2022. The Author(s)