Streams of data from drops of water: 21st century molecular microbial ecology

Microorganisms are ubiquitous and represent a taxonomically and functionally diverse component of freshwater environments of significant ecological importance. The bacteria, archaea, and microbial eukarya in freshwater systems support a range of ecosystem processes and functions, including mediating all major biogeochemical cycles, and therefore regulate the flow of multiple ecosystem services. Yet relative to conspicuous higher taxa, microbial ecology remains poorly understood. As the anthropocene progresses, the demand for freshwater–ecosystem services is both increasing with growing human population density, and by association, increasingly threatened from multiple and often interacting stressors, such as climate change, eutrophication, and chemical pollution. Thus, it is imperative to understand the ecology of microorganisms and their functional role in freshwater ecosystems if we are to manage the future of these environments effectively. To do this, researchers have developed a vast array of molecular tools that can illuminate the diversity, composition, and activity of microbial communities. Within this primer, we discuss the history of molecular approaches in microbial ecology, and highlight the scope of questions that these methods enable researchers to address. Using some recent case studies, we describe some exemplar research into the microbial ecology of freshwater systems, and emphasize how molecular methods can provide novel ecological insights. Finally, we detail some promising developments within this research field, and how these might shape the future research landscape of freshwater microbial ecology

The Cow: Discovery of a Luminous, Hot, and Rapidly Evolving Transient

We present the ATLAS discovery and initial analysis of the first 18 days of the unusual transient event, ATLAS18qqn/AT2018cow. It is characterized by a high peak luminosity (~1.7 × 1044 erg s−1), rapidly evolving light curves (>5 mag rise to peak in ~3.5 days), and hot blackbody spectra, peaking at ~27,000 K that are relatively featureless and unchanging over the first two weeks. The bolometric light curve cannot be powered by radioactive decay under realistic assumptions. The detection of high-energy emission may suggest a central engine as the powering source. Using a magnetar model, we estimated an ejected mass of 0.1–0.4 M ${}_{\odot }$, which lies between that of low-energy core-collapse events and the kilonova, AT2017gfo. The spectra cooled rapidly from 27,000 to 15,000 K in just over two weeks but remained smooth and featureless. Broad and shallow emission lines appear after about 20 days, and we tentatively identify them as He i although they would be redshifted from their rest wavelengths. We rule out that there are any features in the spectra due to intermediate mass elements up to and including the Fe group. The presence of r-process elements cannot be ruled out. If these lines are due to He, then we suggest a low-mass star with residual He as a potential progenitor. Alternatively, models of magnetars formed in neutron star mergers, or accretion onto a central compact object, give plausible matches to the data

Relationship between early development of spelling and reading

The research reported in this thesis examined the relationship between beginning spelling and reading. More specifically, it focussed on the relationship between the development of early reading and spelling in a context where the approach to early reading instruction includes systematic phonological awareness and decoding instruction. A critical assumption made by proponents of developmental early literacy models is that transfer of skills and knowledge from reading to spelling will occur spontaneously and without formal instruction (Frith, 1980). By contrast instruction-centred approaches make the assumption that there are critical pre-requisite skills that can and should be taught explicitly (Carnine, Silbert & Kameenui, 1997). The difference between these approaches is highlighted in the treatment of invented spelling, a popular activity in Western Australian junior primary classes. A series of studies was undertaken to examine the effect on invented and standard spelling performance of teaching Year 1 children phonological awareness and the strategy of sounding out words. Data were gathered from a range of settings using different research tools. The relationship between phonological awareness and beginning reading and spelling performance was explored initially through a single case study. A post-hoc study was then undertaken with a cohort of students who had received systematic decoding instruction to examine whether proficiency in the decoding of nonwords was related to spelling performance. This permitted an analysis of common sub-skills of decoding and encoding. In the main study the effect on different aspects of reading and spelling performance of using Let\u27s Decode, an approach that includes explicit phonological awareness and systematic decoding instruction, was investigated. In addition, an analysis was made of whether students who received explicit instruction in skills known to contribute to beginning reading and spelling produced superior invented spelling samples. A qualitative analysis was made of the. pre and post invented spelling tests of two pairs of students from the control and intervention groups matched on invented spelling and phonological awareness skills at the beginning of the year, and re tested at the end of Year 1. The final research question involved a single-subject research design to examine the effect of explicit instruction in isolating phonemes in words and prompts to \u27listen for sounds\u27 prior to, and during, the process of spelling words. The single case study revealed a child who was regarded as a competent speller and reader but who could only read words in a familiar context and who had developed a strategy for spelling words based on copying an adult model. This was interpreted as evidence supporting the need for phonological awareness instruction as a pre-requisite for spelling. The post-hoc analysis of a class of students who had received systematic decoding instruction showed that no student classified as a \u27good decoder\u27 could also be classified as a \u27poor speller\u27. This result was considered evidence of a strong link between the phonological knowledge that is required to decode and the role of alphabetic knowledge in spelling. The main study revealed phonological awareness and systematic decoding instruction was associated with superior invented and conventional spelling and reading performance on all reading and spelling measures. Of particular importance was the finding that students who commenced the study with very weak phonological awareness and who subsequently received systematic phonological and decoding instruction showed greater gains in invented spelling than matched students in the control condition. The single subject design showed the effectiveness of phonological awareness individualised instruction on invented spelling for weak students from both intervention and control conditions. It was concluded that the ability to invent spelling is improved when students receive explicit instruction in phonological awareness and systematic decoding but that some students, namely those with persistent weakness in phonological awareness, also require explicit prompts to apply their alphabetic knowledge to spelling words. The implications for instruction of these findings are discussed

Not Perfect, but Better: Primary Care Providers’ Experiences with Electronic Referrals in a Safety Net Health System

BackgroundElectronic referrals can improve access to subspecialty care in safety net settings. In January 2007, San Francisco General Hospital (SFGH) launched an electronic referral portal that incorporated subspecialist triage, iterative communication with referring providers, and existing electronic health record data to improve access to subspecialty care.ObjectiveWe surveyed primary care providers (PCPs) to assess the impact of electronic referrals on workflow and clinical care.DesignWe administered an 18-item, web-based questionnaire to all 368 PCPs who had the option of referring to SFGH.MeasurementsWe asked participants to rate time spent submitting a referral, guidance of workup, wait times, and change in overall clinical care compared to prior referral methods using 5-point Likert scales. We used multivariate logistic regression to identify variables associated with perceived improvement in overall clinical care.ResultsTwo hundred ninety-eight PCPs (81.0%) from 24 clinics participated. Over half (55.4%) worked at hospital-based clinics, 27.9% at county-funded community clinics, and 17.1% at non-county-funded community clinics. Most (71.9%) reported that electronic referrals had improved overall clinical care. Providers from non-county-funded clinics (AOR 0.40, 95% CI 0.14-0.79) and those who spent > or =6 min submitting an electronic referral (AOR 0.33, 95%CI 0.18-0.61) were significantly less likely than other participants to report that electronic referrals had improved clinical care.ConclusionsPCPs felt electronic referrals improved health-care access and quality; those who reported a negative impact on workflow were less likely to agree. While electronic referrals hold promise as a tool to improve clinical care, their impact on workflow should be considered

Diseases of the rich? The social patterning of hypertension in six low- and middle-income countries

This paper identifies a general perception among development policymakers that health conditions such as hypertension and other non-communicable diseases (NCDs) disproportionately affect privileged socioeconomic groups. The paper argues that this framing of the issue is derived more from established discourses and institutional dynamics than from evidence. The paper then assesses the validity of this view, with reference to the social patterning of hypertension in China, Ghana, India, Mexico, the Russian Federation and South Africa. Using data for adults aged 50+ from the WHO Survey of Ageing and Adult Health, it finds the social patterning of hypertension prevalence varies markedly between the study countries, but that hypertension awareness and control rates are generally lower for less-advantaged groups. This reveals a need to challenge misleading representations of NCD pandemics and for interventions that specifically target the poor

Assembly PCR synthesis of optimally designed, compact, multi-responsive promoters suited to gene therapy application

MRC-DTA studentship award British Pharmacological Society Integrative Awar

Unravelling the effects of age, period and cohort on metabolic syndrome components in a Taiwanese population using partial least squares regression

<p>Abstract</p> <p>Background</p> <p>We investigate whether the changing environment caused by rapid economic growth yielded differential effects for successive Taiwanese generations on 8 components of metabolic syndrome (MetS): body mass index (BMI), systolic blood pressure (SBP), diastolic blood pressure (DBP), fasting plasma glucose (FPG), triglycerides (TG), high-density lipoprotein (HDL), Low-density lipoproteins (LDL) and uric acid (UA).</p> <p>Methods</p> <p>To assess the impact of age, birth year and year of examination on MetS components, we used partial least squares regression to analyze data collected by Mei-Jaw clinics in Taiwan in years 1996 and 2006. Confounders, such as the number of years in formal education, alcohol intake, smoking history status, and betel-nut chewing were adjusted for.</p> <p>Results</p> <p>As the age of individuals increased, the values of components generally increased except for UA. Men born after 1970 had lower FPG, lower BMI, lower DBP, lower TG, Lower LDL and greater HDL; women born after 1970 had lower BMI, lower DBP, lower TG, Lower LDL and greater HDL and UA. There is a similar pattern between the trend in levels of metabolic syndrome components against birth year of birth and economic growth in Taiwan.</p> <p>Conclusions</p> <p>We found cohort effects in some MetS components, suggesting associations between the changing environment and health outcomes in later life. This ecological association is worthy of further investigation.</p

Saturated Fatty Acids and Risk of Coronary Heart Disease: Modulation by Replacement Nutrients

Despite the well-established observation that substitution of saturated fats for carbohydrates or unsaturated fats increases low-density lipoprotein (LDL) cholesterol in humans and animal models, the relationship of saturated fat intake to risk for atherosclerotic cardiovascular disease in humans remains controversial. A critical question is what macronutrient should be used to replace saturated fat. Substituting polyunsaturated fat for saturated fat reduces LDL cholesterol and the total cholesterol to high-density lipoprotein cholesterol ratio. However, replacement of saturated fat by carbohydrates, particularly refined carbohydrates and added sugars, increases levels of triglyceride and small LDL particles and reduces high-density lipoprotein cholesterol, effects that are of particular concern in the context of the increased prevalence of obesity and insulin resistance. Epidemiologic studies and randomized clinical trials have provided consistent evidence that replacing saturated fat with polyunsaturated fat, but not carbohydrates, is beneficial for coronary heart disease. Therefore, dietary recommendations should emphasize substitution of polyunsaturated fat and minimally processed grains for saturated fat

Dietary intake of fish, omega-3, omega-6 polyunsaturated fatty acids and vitamin D and the prevalence of psychotic-like symptoms in a cohort of 33 000 women from the general population

<p>Abstract</p> <p>Background</p> <p>Low intake of fish, polyunsaturated fatty acids (PUFA) and vitamin D deficiency has been suggested to play a role in the development of schizophrenia. Our aim was to evaluate the association between the intake of different fish species, PUFA and vitamin D and the prevalence of psychotic-like symptoms in a population-based study among Swedish women.</p> <p>Methods</p> <p>Dietary intake was estimated using a food frequency questionnaire among 33 623 women aged 30-49 years at enrolment (1991/92). Information on psychotic-like symptoms was derived from a follow-up questionnaire in the years 2002/03. Participants were classified into three predefined levels: low, middle and high frequency of symptoms. The association between diet and psychotic-like symptoms was summarized in terms of relative risks (RR) and corresponding 95% confidence intervals and was evaluated by energy-adjusted multinomial logistic regression.</p> <p>Results</p> <p>18 411 women were classified as having a low level of psychotic-like symptoms, 14 395 as middle and 817 as having a high level. The risk of high level symptoms was 53% (95% CI, 30-69%) lower among women who ate fish 3-4 times per week compared to women who never ate fish. The risk was also lower for women with a high intake of omega-3 and omega-6 PUFA compared to women with a lower intake of these fatty acids. The effect was most pronounced for omega-6 PUFAs. The RR comparing the highest to the lowest quartile of omega-6 PUFAs intake was 0.78 (95% CI, 0.64-0.97). The associations were J-shaped with the strongest reduced risk for an intermediate intake of fish or PUFA. For fatty fish (herring/mackerel, salmon-type fish), the strongest inverse association was found for an intermediate intake (RR: 0.81, 95% CI, 0.66-0.98), whereas a high intake of fatty fish was associated with an increased risk of psychotic-like symptoms (RR: 1.90, 95% CI, 1.34-2.70). Women in the highest compared with the lowest quartile of vitamin D consumption experienced a 37% (95% CI, 22-50%) lower risk of psychotic-like symptoms.</p> <p>Conclusion</p> <p>Our findings raise a possibility that adult women with a high intake of fish, omega-3 or omega-6 PUFA and vitamin D have a lower rate of psychotic-like symptoms.</p