Isolation of Unknown Genes from Human Bone Marrow by Differental Screening and Single-Pass cDNA Sequences Determination

A cDNA sequencing project was initiated to characterize gene expression in human bone marrow and develop strategies to isolate novel genes. Forty-eight random cDNAs from total human bone marrow were subjected to single-pass DNA sequence analysis to determine a limited complexity of mRNAs expressed in the bone marrow. Overall, 8 cDNAs (17%) showed no similarity to known sequences. Information from DNA sequence analysis was used to develop a differential prescreen to subtract unwanted cDNAs and to enrich for unknown cDNAs. Forty-eight cDNAs that were negative with a complex probe were subject to single-pass DNA sequence determination. Of these prescreened cDNAs, the number of unknown sequences increased to 23 (48%). Unknown cDNAs were also characterized by RNA expression analysis using 25 different human leukemic cell lines. Of 13 unknown cDNAs tested, 10 were expressed in all cell types tested and 3 revealed a hematopoietic lineage-restricted expression pattern. Interestingly, while a total of only 96 bone marrow cDNAs were sequenced, 31 of these cDNAs represent sequences from unknown genes and 12 showed significant similarities to sequences in the data bases. One cDNA revealed a significant similarity to a serine/threonine-protein kinase at the amino acid level (56% identity for 123 amino acids) and may represent a previously unknown kinase. Differential screening techniques coupled with single-pass cDNA sequence analysis may prove to be a powerful and simple technique to examine developmental gene expression

Aquilegia, Vol. 18 No. 1, January- February 1994: Newsletter of the Colorado Native Plant Society

https://epublications.regis.edu/aquilegia/1069/thumbnail.jp

Late-Holocene climate dynamics recorded in the peat bogs of Tierra del Fuego, South America

The ombrotrophic peat bogs of Tierra del Fuego are located within the southern westerly wind belt (SWWB), which dominates climate variability in this region. We have reconstructed late-Holocene water-table depths from three peat bogs and aimed to relate these records to shifts in regional climate. Water-table depths were quantified by the analysis of testate amoeba assemblages, and a regional transfer function was used to infer past water-table depths. During the last 2000 years, testate amoeba assemblages have been relatively stable, with a dominance of Difflugia pulex and Difflugia pristis type, and an increase in Assulina muscorum and other Euglyphida at the top of each section. Multivariate analyses show that water-table depth remained the main environmental variable explaining assemblages along the TiA12 core, but reconstructions were not significant for the two other cores. In line with the low variability in assemblages, water tables were relatively stable during the last 2000 years. Slightly wetter conditions were found between ~1400 and 900 cal. BP and a pronounced recent dry shift was reconstructed in all of the three peat profiles. Considering the regional climatic context, this recent shift may have been forced by a decrease in precipitation and warmer conditions linked to an increase in the importance of the SWWB. Nevertheless, we cannot exclude the influence of higher UV-B radiation resulting from the local degradation of the ozone layer since the late 1970s, which may have had an additional effect on the relative presence of A. muscorum in the southern Patagonian region

Climate warming, marine protected areas and the ocean-scale integrity of coral reef ecosystems

Coral reefs have emerged as one of the ecosystems most vulnerable to climate variation and change. While the contribution of a warming climate to the loss of live coral cover has been well documented across large spatial and temporal scales, the associated effects on fish have not. Here, we respond to recent and repeated calls to assess the importance of local management in conserving coral reefs in the context of global climate change. Such information is important, as coral reef fish assemblages are the most species dense vertebrate communities on earth, contributing critical ecosystem functions and providing crucial ecosystem services to human societies in tropical countries. Our assessment of the impacts of the 1998 mass bleaching event on coral cover, reef structural complexity, and reef associated fishes spans 7 countries, 66 sites and 26 degrees of latitude in the Indian Ocean. Using Bayesian meta-analysis we show that changes in the size structure, diversity and trophic composition of the reef fish community have followed coral declines. Although the ocean scale integrity of these coral reef ecosystems has been lost, it is positive to see the effects are spatially variable at multiple scales, with impacts and vulnerability affected by geography but not management regime. Existing no-take marine protected areas still support high biomass of fish, however they had no positive affect on the ecosystem response to large-scale disturbance. This suggests a need for future conservation and management efforts to identify and protect regional refugia, which should be integrated into existing management frameworks and combined with policies to improve system-wide resilience to climate variation and change

Exploring the impact of selection bias in observational studies of COVID-19: a simulation study

BACKGROUND: Non-random selection of analytic subsamples could introduce selection bias in observational studies. We explored the potential presence and impact of selection in studies of SARS-CoV-2 infection and COVID-19 prognosis. METHODS: We tested the association of a broad range of characteristics with selection into COVID-19 analytic subsamples in the Avon Longitudinal Study of Parents and Children (ALSPAC) and UK Biobank (UKB). We then conducted empirical analyses and simulations to explore the potential presence, direction and magnitude of bias due to this selection (relative to our defined UK-based adult target populations) when estimating the association of body mass index (BMI) with SARS-CoV-2 infection and death-with-COVID-19. RESULTS: In both cohorts, a broad range of characteristics was related to selection, sometimes in opposite directions (e.g. more-educated people were more likely to have data on SARS-CoV-2 infection in ALSPAC, but less likely in UKB). Higher BMI was associated with higher odds of SARS-CoV-2 infection and death-with-COVID-19. We found non-negligible bias in many simulated scenarios. CONCLUSIONS: Analyses using COVID-19 self-reported or national registry data may be biased due to selection. The magnitude and direction of this bias depend on the outcome definition, the true effect of the risk factor and the assumed selection mechanism; these are likely to differ between studies with different target populations. Bias due to sample selection is a key concern in COVID-19 research based on national registry data, especially as countries end free mass testing. The framework we have used can be applied by other researchers assessing the extent to which their results may be biased for their research question of interest

What do people with aphasia want to be able to say? A content analysis of words identified as personally relevant by people with aphasia

Background Word finding is a common difficulty for people with aphasia. Targeting words that are relevant to the individual could maximise the usefulness and impact of word finding therapy. Aims To provide insights into words that people with aphasia perceive to be personally relevant. Methods and procedures 100 people with aphasia were each asked to identify 100 words that would be particularly important for them to be able to say. Two speech and language therapist researchers conducted a quantitative content analysis of the words selected. The words were coded into a framework of topics and subtopics. The frequency with which different words and topics were selected was then calculated. Outcomes and results 100 participants representing 20 areas of the United Kingdom ranged in age from 23 to 85 years. Word finding difficulties ranged from mild to severe. The sample of 9999 words selected for practice included 3095 different words in 27 topics. The majority of words selected (79.4%) were from the topics ‘food and drink’ (30.6%), ‘nature and gardening’ (10.3%), ‘entertainment’ (9.4%), ‘places’ (7.3%), ‘people’ (6.7%), ‘house’ (6.5%), ‘clothes’ (5.2%) and ‘travel’ (3.5%). The 100 words types chosen with the greatest frequency were identified. These account for 27 percent of the 9999 words chosen by the participants. Discussion Personally relevant vocabulary is unique to each individual and is likely to contain specific or specialist words for which material needs to be individually prepared. However there is some commonality in the words chosen by people with aphasia. This could inform pre-prepared materials for use in word finding therapy from which personally relevant words could be selected for practice

Protocol for the Smoking, Nicotine and Pregnancy (SNAP) trial: double-blind, placebo-randomised, controlled trial of nicotine replacement therapy in pregnancy

Background: Smoking in pregnancy remains a public health challenge. Nicotine replacement therapy (NRT) is effective for smoking cessation in non-pregnant people, but because women metabolise nicotine and cotinine much faster in pregnancy, it is unclear whether this will be effective for smoking cessation in pregnancy. The NHS Health Technology Assessment Programme (HTA)-funded smoking, nicotine and pregnancy ( SNAP) trial will investigate whether or not nicotine replacement therapy ( NRT) is effective, cost-effective and safe when used for smoking cessation by pregnant women. Methods/Design: Over two years, in 5 trial centres, 1050 pregnant women who are between 12 and 24 weeks pregnant will be randomised as they attend hospital for ante-natal ultrasound scans. Women will receive either nicotine or placebo transdermal patches with behavioural support. The primary outcome measure is biochemically-validated, self-reported, prolonged and total abstinence from smoking between a quit date ( defined before randomisation and set within two weeks of this) and delivery. At six months after childbirth self-reported maternal smoking status will be ascertained and two years after childbirth, self-reported maternal smoking status and the behaviour, cognitive development and respiratory symptoms of children born in the trial will be compared in both groups. Discussion: This trial is designed to ascertain whether or not standard doses of NRT ( as transdermal patches) are effective and safe when used for smoking cessation during pregnancy

Alternative pre-analytic sample handling techniques for glucose measurement in the absence of fluoride tubes in low resource settings.

INTRODUCTION: Sodium fluoride (NaF) tubes are the recommended tubes for glucose measurements, but these are expensive, have limited number of uses, and are not always available in low resource settings. Alternative sample handling techniques are thus needed. We compared glucose stability in samples collected in various tubes exposed to different pre-analytical conditions in Uganda. METHODS: Random (non-fasted) blood samples were drawn from nine healthy participants into NaF, Ethylenediaminetetraacetic acid (EDTA), and plain serum tubes. The samples were kept un-centrifuged or centrifuged with plasma or serum pipetted into aliquots, placed in cool box with ice or at room temperature and were stored in a permanent freezer after 0, 2, 6, 12 and 24 hours post blood draw before glucose analysis. RESULTS: Rapid decline in glucose concentrations was observed when compared to baseline in serum (declined to 64%) and EDTA-plasma (declined to 77%) after 6 hours when samples were un-centrifuged at room temperature whilst NaF-plasma was stable after 24 hours in the same condition. Un-centrifuged EDTA-plasma kept on ice was stable for up to 6 hours but serum was not stable (degraded to 92%) in the same conditions. Early centrifugation prevented glucose decline even at room temperature regardless of the primary tube used with serum, EDTA-plasma and NaF-plasma after 24 hours. CONCLUSION: In low resource settings we recommend use of EDTA tubes placed in cool box with ice and analysed within 6 hours as an alternative to NaF tubes. Alternatively, immediate separation of blood with manual hand centrifuges will allow any tube to be used even in remote settings with no electricity