Nuclear small-subunit ribosomal RNA gene-based characterization, molecular phylogeny and PCR detection of the Neoparamoeba from western Long Island Sound lobster

Author Posting. © National Shellfisheries Association, 2005. This article is posted here by permission of National Shellfisheries Association for personal use, not for redistribution. The definitive version was published in Journal of Shellfish Research 24 (2005): 719-731, doi:10.2983/0730-8000(2005)24[719:NSRRGC]2.0.CO;2.Western Long Island Sound (LIS) lobsters collected by trawl surveys, lobstermen and coastal residents during 2000 to 2002 were identified histologically as infected with a parasome-containing amoeba. Primers to conserved SSU rRNA sequences of parasome-containing amoebae and their nonparasome-containing relatives were used to amplify overlapping SSU rRNA fragments of the presumptive parasite from gill, antenna, antennal gland and ventral nerve cord of infected lobsters. The consensus sequence constructed from these fragments had 98% or greater nucleotide sequence identity with SSU rRNA gene sequences of strains of Neoparamoeba pemaquidensis and associated with high confidence in distance- and parsimony-based phylogenetic analyses with strains of Neoparamoeba pemaquidensis and not members of the family Paramoebidae, e.g., Paramoeba eilhardi. Primers designed to SSU rRNA sequences of the lobster amoeba and other paramoebid/vexilliferid amoebae were used in a nested polymerase chain reaction (PCR) protocol to test DNA extracted from formalin-fixed paraffin-embedded tissues of lobsters collected during the 1999 die-off, when this amoeba initially was identified by light and electron microscopy and reported to be a paramoeba of the genera Paramoeba or Neoparamoeba (Mullen et al. 2004). All sequences amplified from 1999 lobsters, with the exception of one, had 98% to 99% identity to each other, and the 1999 PCR product consensus had 98% identity to Neoparamoeba pemaquidensis strains CCAP 1560/4 (AF371969.1) and 1560/5 (AF371970.1). Molecular characterization of the amoeba from western LIS lobsters by direct amplification circumvents a collective inability to culture the organism in vitro, provides insight into the molecular epidemiology of neoparamoebiasis in American lobster, and allows for PCR-based detection of infected lobsters for future research and diagnostics.Funding for this work was provided by the Connecticut Department of Environmental Protection under Long Island Sound Research Fund Grant No. CWF 333-R to S. Frasca; and by the Connecticut Sea Grant College Program, Grants No. LR/LR-4 to R. Gast and No. LR/LR-5 to P. Gillevet and C. O’Kelly, through the US Department of Commerce, National Oceanic and Atmospheric Administration (NOAA), Award NA16RG1364

Advancements in high-resolution imaging of the iridocorneal angle

High-resolution imaging methods of the iridocorneal angle (ICA) will lead to enhanced understanding of aqueous humor outflow mechanisms and a characterization of the trabecular meshwork (TM) morphology at the cellular level will help to better understand glaucoma mechanics (e.g., cellular level biomechanics of the particulate glaucomas). This information will translate into immense clinical value, leading to more informed and customized treatment selection, and improved monitoring of procedural interventions that lower intraocular pressure (IOP). Given ICA anatomy, imaging modalities that yield intrinsic optical sectioning or 3D imaging capability will be useful to aid in the visualization of TM layers. This minireview examines advancements in imaging the ICA in high-resolution

Spectroscopic characterization of reaction centers of the (M)Y210W mutant of the photosynthetic bacterium Rhodobacter sphaeroides

The tyrosine-(M)210 of the reaction center of Rhodobacter sphaeroides 2.4.1 has been changed to a tryptophan using site-directed mutagenesis. The reaction center of this mutant has been characterized by low-temperature absorption and fluorescence spectroscopy, time-resolved sub-picosecond spectroscopy, and magnetic resonance spectroscopy. The charge separation process showed bi-exponential kinetics at room temperature, with a main time constant of 36 ps and an additional fast time constant of 5.1 ps. Temperature dependent fluorescence measurements predict that the lifetime of P* becomes 4–5 times slower at cryogenic temperatures. From EPR and absorbance-detected magnetic resonance (ADMR, LD-ADMR) we conclude that the dimeric structure of P is not significantly changed upon mutation. In contrast, the interaction of the accessory bacteriochlorophyll BA with its environment appears to be altered, possibly because of a change in its position

The Single-Case Reporting Guideline In BEhavioural Interventions (SCRIBE) 2016 statement

We developed a reporting guideline to provide authors with guidance about what should be reported when writing a paper for publication in a scientific journal using a particular type of research design: the single-case experimental design. This report describes the methods used to develop the Single-Case Reporting guideline In BEhavioural interventions (SCRIBE) 2016. As a result of 2 online surveys and a 2-day meeting of experts, the SCRIBE 2016 checklist was developed, which is a set of 26 items that authors need to address when writing about single-case research. This article complements the more detailed SCRIBE 2016 Explanation and Elaboration article (Tate et al., 2016) that provides a rationale for each of the items and examples of adequate reporting from the literature. Both these resources will assist authors to prepare reports of single-case research with clarity, completeness, accuracy, and transparency. They will also provide journal reviewers and editors with a practical checklist against which such reports may be critically evaluated. We recommend that the SCRIBE 2016 is used by authors preparing manuscripts describing single-case research for publication, as well as journal reviewers and editors who are evaluating such manuscripts.Funding for the SCRIBE project was provided by the Lifetime Care and Support Authority of New South Wales, Australia. The funding body was not involved in the conduct, interpretation or writing of this work. We acknowledge the contribution of the responders to the Delphi surveys, as well as administrative assistance provided by Kali Godbee and Donna Wakim at the SCRIBE consensus meeting. Lyndsey Nickels was funded by an Australian Research Council Future Fellowship (FT120100102) and Australian Research Council Centre of Excellence in Cognition and Its Disorders (CE110001021). For further discussion on this topic, please visit the Archives of Scientific Psychology online public forum at http://arcblog.apa.org. (Lifetime Care and Support Authority of New South Wales, Australia; FT120100102 - Australian Research Council Future Fellowship; CE110001021 - Australian Research Council Centre of Excellence in Cognition and Its Disorders)Published versio

Imaging Glaucomatous Damage Across the Temporal Raphe

PURPOSE. To image and analyze anatomical differences at the temporal raphe between normal and glaucomatous eyes using adaptive optics scanning laser ophthalmoscopy (AOSLO) and optical coherence tomography (OCT), and to relate these differences to visual field measurements. METHODS. Nine glaucomatous eyes of 9 patients (age 54-78 years, mean deviation of visual field [MD] À5.03 to À0.20 dB) and 10 normal eyes of 10 controls (age 54-81, MD À1.13 to þ1.39 dB) were enrolled. All the participants were imaged in a region that was centered approximately 98 temporal to the fovea. The size of imaging region was at least 108 vertically by 48 horizontally. The raphe gap, defined as the distance between the superior and inferior retinal nerve fiber layer (RNFL) bundles, was measured. A bundle index was computed to quantify the relative reflectivity and density of the nerve fiber bundles. We also measured thickness of the ganglion cell complex (GCC) and RNFL. RESULTS. The raphe gap was larger in glaucomatous eyes than control eyes. Specifically, eight glaucomatous eyes with local averaged field loss no worse than À3.5 dB had larger raphe gaps than all control eyes. The bundle index, GCC thickness, and RNFL thickness were on average reduced in glaucomatous eyes, with the first two showing statistically significant differences between the two groups. CONCLUSIONS. Structural changes in the temporal raphe were observed and quantified even when local functional loss was mild. These techniques open the possibility of using the raphe as a site for glaucoma research and clinical assessment

Cervical dysplasia and cancer and the use of hormonal contraceptives in Jamaican women

<p>Abstract</p> <p>Background</p> <p>This study was conducted to determine whether use of hormonal contraceptives is associated with cervical dysplasia and cancer in a population where there is widespread use of hormonal contraception and the rates of cervical cancer remain high at 27.5/100,000.</p> <p>Methods</p> <p>A case-control study was conducted among women visiting the colposcopy and gynaelogical clinics at a tertiary referral hospital. Two hundred and thirty six cases CIN I (72), II (59), III (54), cancer (51) and 102 controls, consented and were interviewed on use of contraceptives using a structured questionnaire. Logistic regression was used to determine odds ratios (ORs) and 95% confidence intervals (CIs) associated with use of hormonal contraception in cases and controls and in low and high risk cases. Recruitment was carried out from 2001–2002.</p> <p>Results</p> <p>Contraceptives used were: oral contraceptives – 35%, injections (depot medroxy progesterone acetate (Depo-provera) – 10%, Intrauterine devices – 2%, combinations of these and tubal ligation – 30%. 23% reported use of 'other' methods, barrier contraceptives or no form of contraception. Barrier contraceptive use was not significantly different between cases and controls. Current and/or past exposure to hormonal contraceptives (HC) by use of the pill or injection, alone or in combination with other methods was significantly higher in the cases. In multivariate analysis with age and number of sexual partners as co-variates, use of hormonal contraception was associated both with disease, [OR, 1.92 (CI 1.11, 3.34; p = 0.02] and severity of the disease [OR, 2.22 (CI 1.05, 4.66) p = 0.036]. When parity and alcohol consumption were added to the model, hormonal contraception was no longer significant. The significant association with high risk disease was retained when the model was controlled for age and number of sexual partners. Depo-provera use (with age and number of sexual partners as covariates) was also associated with disease [OR, 2.43 (CI 1.39, 4.57), p = 0.006] and severity of disease [OR 2.51 (1.11, 5.64) p = 0.027]. With parity and alcohol added to this model, depo-provera use retained significance. Exposure to HC > 4 years conferred more risk for disease and severity of disease.</p> <p>Conclusion</p> <p>Hormonal contraception did confer some risk of dysplasia and women using HC should therefore be encouraged to do regular Pap smear screening.</p

Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention

© 2016 International Society for Microbial Ecology All rights reserved. Pulmonary symptoms in cystic fibrosis (CF) begin in early life with chronic lung infections and concomitant airway inflammation leading to progressive loss of lung function. Gradual pulmonary function decline is interspersed with periods of acute worsening of respiratory symptoms known as CF pulmonary exacerbations (CFPEs). Cumulatively, CFPEs are associated with more rapid disease progression. In this study multiple sputum samples were collected from adult CF patients over the course of CFPEs to better understand how changes in microbiota are associated with CFPE onset and management. Data were divided into five clinical periods: pre-CFPE baseline, CFPE, antibiotic treatment, recovery, and post-CFPE baseline. Samples were treated with propidium monoazide prior to DNA extraction, to remove the impact of bacterial cell death artefacts following antibiotic treatment, and then characterised by 16S rRNA gene-targeted high-throughput sequencing. Partitioning CF microbiota into core and rare groups revealed compositional resistance to CFPE and resilience to antibiotics interventions. Mixed effects modelling of core microbiota members revealed no significant negative impact on the relative abundance of Pseudomonas aeruginosa across the exacerbation cycle. Our findings have implications for current CFPE management strategies, supporting reassessment of existing antimicrobial treatment regimens, as antimicrobial resistance by pathogens and other members of the microbiota may be significant contributing factors

Salmonella Strains Isolated from Galápagos Iguanas Show Spatial Structuring of Serovar and Genomic Diversity

It is thought that dispersal limitation primarily structures host-associated bacterial populations because host distributions inherently limit transmission opportunities. However, enteric bacteria may disperse great distances during food-borne outbreaks. It is unclear if such rapid long-distance dispersal events happen regularly in natural systems or if these events represent an anthropogenic exception. We characterized Salmonella enterica isolates from the feces of free-living Galápagos land and marine iguanas from five sites on four islands using serotyping and genomic fingerprinting. Each site hosted unique and nearly exclusive serovar assemblages. Genomic fingerprint analysis offered a more complex model of S. enterica biogeography, with evidence of both unique strain pools and of spatial population structuring along a geographic gradient. These findings suggest that even relatively generalist enteric bacteria may be strongly dispersal limited in a natural system with strong barriers, such as oceanic divides. Yet, these differing results seen on two typing methods also suggests that genomic variation is less dispersal limited, allowing for different ecological processes to shape biogeographical patterns of the core and flexible portions of this bacterial species' genome