CD14 and ALPK1 Affect Expression of Tight Junction Components and Proinflammatory Mediators upon Bacterial Stimulation in a Colonic 3D Organoid Model

Cd14 and Alpk1 both encode pathogen recognition receptors and are known candidate genes for affecting severity in inflammatory bowel diseases. CD14 acts as a coreceptor for bacterial lipopolysaccharide (LPS), while ALPK1 senses ADP-D-glycero-beta-D-manno-heptose, a metabolic intermediate of LPS biosynthesis. Intestinal barrier integrity can be influenced by CD14, whereas to date, the role of ALPK1 in maintaining barrier function remains unknown. We used colon-derived 3D organoids, first characterised for growth, proliferation, stem cell markers, and expression of tight junction (TJ) components using qPCR and immunohistochemistry. They showed characteristic crypt stem cells, apical shedding of dead cells, and TJ formation. Afterwards, organoids of different genotypes (WT, Il10-/-, Cd14-/-, and Alpk1-/-) were then stimulated with either LPS or Escherichia coli Nissle 1917 (EcN). Gene expression and protein levels of cytokines and TJ components were analysed. WT organoids increased expression of Tnfα and tight junction components. Cd14-/- organoids expressed significantly less Tnfα and Ocln after LPS stimulation than WT organoids but reacted similarly to WT organoids after EcN stimulation. In contrast, compared to WT, Alpk1-/- organoids showed decreased expression of different TJ and cytokine genes in response to EcN but not LPS. However, Western blotting revealed an effect of ALPK1 on TJ protein levels. These findings demonstrate that Cd14, but not Alpk1, alters the response to LPS stimulation in colonic epithelial cells, whereas Alpk1 is involved in the response upon bacterial challenge. © 2020 Pascal Brooks et al

Measuring endogenous corticosterone in laboratory mice - a mapping review, meta-analysis, and open source database

Evaluating stress in laboratory animals is a key principle in animal welfare. Measuring corticosterone is a common method to assess stress in laboratory mice. There are, however, numerous methods to measure glucocorticoids with differences in sample matrix (e.g., plasma, urine) and quantification techniques (e.g., enzyme immunoassay or radioimmunoassay). Here, the authors present a mapping review and a searchable database, giving a complete overview of all studies mea­suring endogenous corticosterone in mice up to February 2018. For each study, information was recorded regarding mouse strain and sex; corticosterone sample matrix and quantification technique; and whether the study covered the research theme animal welfare, neuroscience, stress, inflammation, or pain (the themes of specific interest in our con­sortium). Using all database entries for the year 2012, an exploratory meta-regression was performed to determine the effect of predictors on basal corticosterone concentrations. Seventy-five studies were included using the predictors sex, time-since-lights-on, sample matrix, quantification technique, age of the mice, and type of control. Sex, time-since-lights-on, and type of control significantly affected basal corticosterone concentrations. The resulting database can be used, inter alia, for preventing unnecessary duplication of experiments, identifying knowledge gaps, and standardizing or heterogenizing methodologies. These results will help plan more efficient and valid experiments in the future and can answer new questions in silico using meta-analyses

Measuring Endogenous Corticosterone in Laboratory Mice - a Mapping Review, Meta-Analysis, and Open Source Database

Evaluating stress in laboratory animals is a key principle in animal welfare. Measuring corticosterone is a common method to assess stress in laboratory mice. There are, however, numerous methods to measure glucocorticoids with differences in sample matrix (e.g., plasma, urine) and quantification techniques (e.g., enzyme immunoassay or radioimmunoassay). Here, the authors present a mapping review and a searchable database, giving a complete overview of all studies measuring endogenous corticosterone in mice up to February 2018. For each study, information was recorded regarding mouse strain and sex; corticosterone sample matrix and quantification technique; and whether the study covered the research theme animal welfare, neuroscience, stress, inflammation, or pain (the themes of specific interest in our consortium). Using all database entries for the year 2012, an exploratory meta-regression was performed to determine the effect of predictors on basal corticosterone concentrations. Seventy-five studies were included using the predictors sex, time-since-lights-on, sample matrix, quantification technique, age of the mice, and type of control. Sex, time-since-lights-on, and type of control significantly affected basal corticosterone concentrations. The resulting database can be used, inter alia, for preventing unnecessary duplication of experiments, identifying knowledge gaps, and standardizing or heterogenizing methodologies. These results will help plan more efficient and valid experiments in the future and can answer new questions in silico using meta-analyses

Exile Vol. XLIII No. 2

41st Year Title Page i Epigraphy by Ezra Pound ii Table of Contents iii / Contributors\u27 Notes 70-71 Editorial Board 72-73 ART Untitled by Kari Hernquist \u2799 4 Talking Out my Window by Heather Trabert \u2797 13 Renamed I by Ben Blake \u2797 18 photo paint by alex e. blazer \u2797 23 Butterfly by Mary Donnelley \u2797 32 unabridged by alex e. blazer \u2797 37 Holding Me In by Heather Trabert \u2797 43 Untitled by Kari Hernquist \u2797 55 Untitled by Camille Gammon-Hittelman \u2799 61 Stars by Mary Donnelley \u2797 69 POETRY Victrola by erin c. malone \u2799 1 All by Kellam Ayres \u2797 2-3 curtailed sun in the net by alex e. blazer \u2797 5 the weaker sex by Bekah Taylor \u2700 6 A poem concerning a silent manifesto by Colin Bossen \u2798 14 Father by Alison Stine \u2700 15 Vacant by Sean Boyle \u2700 16 Ecstasy by Amy spears \u2798 17 Seven Haikus by Jen Suster \u2797 21 Pages from a Diary by Trish Klei \u2797 22 Watching an Ageless Woman and an Ancient Trade by Heather Trabert \u2797 24-25 Still Waters by Jay Brandeis \u2799 26 just shy of freedom by Sean Boyle \u2700 36 [Touch the mothers you never knew] by Heather Trabert \u2797 38 Fishing for Meaning by Bekah Taylor \u2700 39 the novel by Sara Brown \u2799 40-41 annihilation by erin c. malone \u2799 42 Upon Enlistment by Trish Klei \u2797 44 the expatriate by erin c. malone \u2799 47 Rockettes by Trish Klei \u2797 48-49 Abstraction by Colin Bossen \u2798 54 always kinesis by alex e. blazer \u2797 56-57 Lily by Alison Stine \u2700 58-59 Falling In by Bekah Taylor \u2700 60 this bird has flown by paul durica \u2700 62-63 exfoliating some sun by alex e. blazer \u2797 64 Liberation: May 8, 1945 by Jen suster \u2797 65 PROSE Journal: 12 December 1996 through 15 January 1997 by Lynn Tramonte \u2798 7-12 Ash by paul durica \u2700 19-20 Birdhouse by Tyler Smith \u2797 27-35 Party in December by paul durica \u2700 45-46 Smoke Circles by Alison Stine \u2700 50-53 Seal by Lynn Tramonte \u2798 66-68 All submissions are reviewed on an anonymous basis, and all editorial decisions are shared equally among the members of the Editorial Board. -72 Cover art Toy Child by Ben Blake \u2797 -7

A review of patients who suddenly deteriorate in the presence of paramedics

<p>Abstract</p> <p>Background</p> <p>The report of the Ministerial Review of Trauma and Emergency Services in Victoria, Australia, recommended that paramedics be permitted to divert to the closest hospital in incidences of life threatening situations prior to and during transport. An audit of patients that suddenly deteriorated in paramedic care was recommended by the Ministerial Review. The objective of the study was to identify the number and outcome of patients who suddenly deteriorated in the presence of paramedics.</p> <p>Methods</p> <p>A retrospective cohort study of trauma patients who suddenly deteriorated in the presence of paramedics during 2002. As there was no standard definition, sudden deterioration was defined using a predetermined set of physiological criteria. Patient care record data of patients who suddenly deteriorated were compared with the State Trauma Registry to determine those who sustained hospital defined major trauma. Patient care records where hospital bypass was undertaken were identified and analysed. Ethics committee approval was obtained.</p> <p>Results</p> <p>There were 2,893 patients that suddenly deteriorated according to predefined criteria. 2,687 (5.1% of the total trauma patients for 2002) were suitable for further analysis. The majority of patients had a sudden decrease in BP (n = 2,463) with 4.3% having hospital defined major trauma. For patients with a sudden decrease in conscious state or a total GCS score of less than 13 (n = 77), 37.7% had hospital defined major trauma; and a sudden increase/decrease in pulse rate and sudden decrease in BP (n = 65), 26.2% had hospital defined major trauma. Only 28 documented incidents of hospital bypass were identified.</p> <p>Conclusion</p> <p>This study suggests that the incidents of patients suddenly deteriorating in the presence of paramedics are low and the incidence of hospital bypass is not well documented.</p

Salmonella Phage ST64B Encodes a Member of the SseK/NleB Effector Family

Salmonella enterica is a species of bacteria that is a major cause of enteritis across the globe, while certain serovars cause typhoid, a more serious disease associated with a significant mortality rate. Type III secreted effectors are major contributors to the pathogenesis of Salmonella infections. Genes encoding effectors are acquired via horizontal gene transfer, and a subset are encoded within active phage lysogens. Because the acquisition of effectors is in flux, the complement of effectors possessed by various Salmonella strains frequently differs. By comparing the genome sequences of S. enterica serovar Typhimurium strain SL1344 with LT2, we identified a gene with significant similarity to SseK/NleB type III secreted effector proteins within a phage ST64B lysogen that is absent from LT2. We have named this gene sseK3. SseK3 was co-regulated with the SPI-2 type III secretion system in vitro and inside host cells, and was also injected into infected host cells. While no role for SseK3 in virulence could be identified, a role for the other family members in murine typhoid was found. SseK3 and other phage-encoded effectors were found to have a significant but sparse distribution in the available Salmonella genome sequences, indicating the potential for more uncharacterised effectors to be present in less studied serovars. These phage-encoded effectors may be principle subjects of contemporary selective processes shaping Salmonella-host interactions

Observations and Theoretical Implications of the Large Separation Lensed Quasar SDSS J1004+4112

We study the recently discovered gravitational lens SDSS J1004+4112, the first quasar lensed by a cluster of galaxies. It consists of four images with a maximum separation of 14.62''. The system has been confirmed as a lensed quasar at z=1.734 on the basis of deep imaging and spectroscopic follow-up observations. We present color-magnitude relations for galaxies near the lens plus spectroscopy of three central cluster members, which unambiguously confirm that a cluster at z=0.68 is responsible for the large image separation. We find a wide range of lens models consistent with the data, but they suggest four general conclusions: (1) the brightest cluster galaxy and the center of the cluster potential well appear to be offset by several kpc; (2) the cluster mass distribution must be elongated in the North--South direction, which is consistent with the observed distribution of cluster galaxies; (3) the inference of a large tidal shear (~0.2) suggests significant substructure in the cluster; and (4) enormous uncertainty in the predicted time delays between the images means that measuring the delays would greatly improve constraints on the models. We also compute the probability of such large separation lensing in the SDSS quasar sample, on the basis of the CDM model. The lack of large separation lenses in previous surveys and the discovery of one in SDSS together imply a mass fluctuation normalization \sigma_8=1.0^{+0.4}_{-0.2} (95% CL), if cluster dark matter halos have an inner slope -1.5. Shallower profiles would require higher values of \sigma_8. Although the statistical conclusion might be somewhat dependent on the degree of the complexity of the lens potential, the discovery is consistent with the predictions of the abundance of cluster-scale halos in the CDM scenario. (Abridged)Comment: 21 pages, 24 figures, 5 tables, accepted for publication in Ap

PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution

Mosaicism is increasingly recognized as a cause of developmental disorders with the advent of next-generation sequencing (NGS). Mosaic mutations of PIK3CA have been associated with the widest spectrum of phenotypes associated with overgrowth and vascular malformations. We performed targeted NGS using 2 independent deep-coverage methods that utilize molecular inversion probes and amplicon sequencing in a cohort of 241 samples from 181 individuals with brain and/or body overgrowth. We identified PIK3CA mutations in 60 individuals. Several other individuals (n = 12) were identified separately to have mutations in PIK3CA by clinical targetedpanel testing (n = 6), whole-exome sequencing (n = 5), or Sanger sequencing (n = 1). Based on the clinical and molecular features, this cohort segregated into three distinct groups: (a) severe focal overgrowth due to low-level but highly activating (hotspot) mutations, (b) predominantly brain overgrowth and less severe somatic overgrowth due to less-activating mutations, and (c) intermediate phenotypes (capillary malformations with overgrowth) with intermediately activating mutations. Sixteen of 29 PIK3CA mutations were novel. We also identified constitutional PIK3CA mutations in 10 patients. Our molecular data, combined with review of the literature, show that PIK3CA-related overgrowth disorders comprise a discontinuous spectrum of disorders that correlate with the severity and distribution of mutations

Reliability and validity of two fitness tracker devices in the laboratory and home environment for older community-dwelling people

© 2018 The Author(s). Background: Two-thirds of older Australians are sedentary. Fitness trackers have been popular with younger people and may encourage older adults to become more active. Older adults may have different gait patterns and as such it is important to establish whether fitness trackers are valid and reliable for this population. The aim of the study was to test the reliability and validity of two fitness trackers (Fitbit Flex and ChargeHR) by step count when worn by older adults. Reliability and validity were tested in two conditions: 1) in the laboratory using a two-minute-walk-test (2MWT) and 2) in a free-living environment. Methods: Two 2MWTs were completed while wearing the fitness trackers. Participants were videoed during each test. Participants were then given one fitness tracker and a GENEactiv accelerometer to wear at home for 14-days. Results: Thirty-one participants completed two 2MWTs and 30 completed the free-living procedure. Intra Class Correlation's of the fitness trackers with direct observation of steps (criterion validity) was high (ICC:0.86,95%CI:0.76,0.93). However, both fitness trackers underestimated steps. Excellent test-retest reliability (ICC = 0.75) was found between the two 2MWTs for each device, particularly the ChargeHR devices. Good strength of agreement was found for total distance and steps (fitness tracker) and moderate-to-vigorous physical activity (GENEactiv) for the free-living environment (Spearman Rho's 0.78 and 0.74 respectively). Conclusion: Reliability and validity of the Flex and ChargeHR when worn by older adults is good, however both devices underestimated step count within the laboratory environment. These fitness trackers appear suitable for consumer use and promoting physical activity for older adults

Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies’ publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010’s top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century [1]. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question [1–12] in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in undergraduate education leads to increased undergraduate and post-graduate retention in the sciences [13–16]. Toward this end, many undergraduate teaching organizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [ www.pkal.org])