The diversity of Class II transposable elements in mammalian genomes has arisen from ancestral phylogenetic splits during ancient waves of proliferation through the genome

DNA transposons make up three percent of the human genome, roughly the same percentage as genes. However, due to their inactivity, they are often ignored in favour of the more abundant, active, retroelements. Despite this relative ignominy, there are a number of interesting questions to be asked of these transposon families. One particular question relates to the timing of proliferation and inactivation of elements in a family. Does an ongoing process of turnover occur, or is the process more akin to a life cycle for the family, with elements proliferating rapidly before deactivation at a later date? We answer this question by tracing back to the most recent common ancestor of each modern transposon family, using two different methods. The first method identifies the most recent common ancestor of the species in which a family of transposon fossils can still be found, which we assume will have existed soon after the true origin date of the transposon family. The second method uses molecular dating techniques to predict the age of the most recent common ancestor element from which all elements found in a modern genome are descended. Independent data from five pairs of species are used in the molecular dating analysis: Human- Chimpanzee, Human-Orangutan, Dog-Panda, Dog-Cat and Cow-Pig. Orthologous pairs of elements from host species pairs are included, and the divergence dates of these species are used to constrain the analysis. We discover that, in general, the times to element common ancestry, for a given family, are the same for the different species pairs, suggesting that there has been no order-specific process of turnover. Furthermore, for most families, the ages of the common ancestor of the host species and of that of the elements are similar, suggesting a life cycle model for the proliferation of transposons. Where these two ages differ, in families found only in Primates and Rodentia, for example, we find that the host species date is later than that of the common ancestor of the elements, implying that there may be large deletions of elements from host species, examples of which were found in their ancestors

An Electronic Analog of Synthetic Genetic Networks

An electronic analog of a synthetic genetic network known as the repressilator is proposed. The repressilator is a synthetic biological clock consisting of a cyclic inhibitory network of three negative regulatory genes which produces oscillations in the expressed protein concentrations. Compared to previous circuit analogs of the repressilator, the circuit here takes into account more accurately the kinetics of gene expression, inhibition, and protein degradation. A good agreement between circuit measurements and numerical prediction is observed. The circuit allows for easy control of the kinetic parameters thereby aiding investigations of large varieties of potential dynamics

Elucidating the present-day chemical composition, seasonality and source regions of climate-relevant aerosols across the Arctic land surface

The Arctic is warming two to three times faster than the global average, and the role of aerosols is not well constrained. Aerosol number concentrations can be very low in remote environments, rendering local cloud radiative properties highly sensitive to available aerosol. The composition and sources of the climate-relevant aerosols, affecting Arctic cloud formation and altering their microphysics, remain largely elusive due to a lack of harmonized concurrent multi-component, multi-site, and multi-season observations. Here, we present a dataset on the overall chemical composition and seasonal variability of the Arctic total particulate matter (with a size cut at 10 mu m, PM10, or without any size cut) at eight observatories representing all Arctic sectors. Our holistic observational approach includes the Russian Arctic, a significant emission source area with less dedicated aerosol monitoring, and extends beyond the more traditionally studied summer period and black carbon/sulfate or fine-mode pollutants. The major airborne Arctic PM components in terms of dry mass are sea salt, secondary (non-sea-salt, nss) sulfate, and organic aerosol (OA), with minor contributions from elemental carbon (EC) and ammonium. We observe substantial spatiotemporal variability in component ratios, such as EC/OA, ammonium/nss-sulfate and OA/nss-sulfate, and fractional contributions to PM. When combined with component-specific back-trajectory analysis to identify marine or terrestrial origins, as well as the companion study by Moschos et al 2022 Nat. Geosci. focusing on OA, the composition analysis provides policy-guiding observational insights into sector-based differences in natural and anthropogenic Arctic aerosol sources. In this regard, we first reveal major source regions of inner-Arctic sea salt, biogenic sulfate, and natural organics, and highlight an underappreciated wintertime source of primary carbonaceous aerosols (EC and OA) in West Siberia, potentially associated with the oil and gas sector. The presented dataset can assist in reducing uncertainties in modelling pan-Arctic aerosol-climate interactions, as the major contributors to yearly aerosol mass can be constrained. These models can then be used to predict the future evolution of individual inner-Arctic atmospheric PM components in light of current and emerging pollution mitigation measures and improved region-specific emission inventories.Peer reviewe

Predicting cleavability of peptide sequences by HIV protease via correlation-angle approach

In designing HIV protease inhibitors as potential drugs for AIDS therapy, knowledge about what peptide sequences in polyproteins are cleavable by HIV proteases is very useful. In this article, based on the formulation that any octapeptide can be uniquely expressed as a 160-dimensional vector and the principle that the similarity of any two such vectors is associated with their correlation angle, a new method is proposed to predict the cleavability of a peptide sequence by HIV-1 and HIV-2 proteases. The average predicted accuracy the new method for the 105 peptide sequences whose cleavability by HIV-1 protease is known is 96/105=9.14%, which is about 8% higher than that by the existing method for the same set of data. A considerably high rate of correct prediction was also obtained when the new method was used to predict the HIV-2 protease-cleaved sites in some proteins.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45081/1/10930_2005_Article_BF01028191.pd

Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana

Background: CRISPR-Cas is a recent and powerful addition to the molecular toolbox which allows programmable genome editing. It has been used to modify genes in a wide variety of organisms, but only two alga to date. Here we present a methodology to edit the genome of Thalassiosira pseudonana, a model centric diatom with both ecological significance and high biotechnological potential, using CRISPR-Cas. Results: A single construct was assembled using Golden Gate cloning. Two sgRNAs were used to introduce a precise 37 nt deletion early in the coding region of the urease gene. A high percentage of bi-allelic mutations (≤61.5%) were observed in clones with the CRISPR-Cas construct. Growth of bi-allelic mutants in urea led to a significant reduction in growth rate and cell size compared to growth in nitrate. Conclusions: CRISPR-Cas can precisely and efficiently edit the genome of T. pseudonana. The use of Golden Gate cloning to assemble CRISPR-Cas constructs gives additional flexibility to the CRISPR-Cas method and facilitates modifications to target alternative genes or species

An internal ribosome entry site in the 5′ untranslated region of epidermal growth factor receptor allows hypoxic expression

The expression of epidermal growth factor receptor (EGFR/ERBB1/HER1) is implicated in the progress of numerous cancers, a feature that has been exploited in the development of EGFR antibodies and EGFR tyrosine kinase inhibitors as anti-cancer drugs. However, EGFR also has important normal cellular functions, leading to serious side effects when EGFR is inhibited. One damaging characteristic of many oncogenes is the ability to be expressed in the hypoxic conditions associated with the tumour interior. It has previously been demonstrated that expression of EGFR is maintained in hypoxic conditions via an unknown mechanism of translational control, despite global translation rates generally being attenuated under hypoxic conditions. In this report, we demonstrate that the human EGFR 5′ untranslated region (UTR) sequence can initiate the expression of a downstream open reading frame via an internal ribosome entry site (IRES). We show that this effect is not due to either cryptic promoter activity or splicing events. We have investigated the requirement of the EGFR IRES for eukaryotic initiation factor 4A (eIF4A), which is an RNA helicase responsible for processing RNA secondary structure as part of translation initiation. Treatment with hippuristanol (a potent inhibitor of eIF4A) caused a decrease in EGFR 5′ UTR-driven reporter activity and also a reduction in EGFR protein level. Importantly, we show that expression of a reporter gene under the control of the EGFR IRES is maintained under hypoxic conditions despite a fall in global translation rates

Comparison of IRES and F2A-Based Locus-Specific Multicistronic Expression in Stable Mouse Lines

Efficient and stoichiometric expression of genes concatenated by bi- or multi-cistronic vectors has become an invaluable tool not only in basic biology to track and visualize proteins in vivo, but also for vaccine development and in the clinics for gene therapy. To adequately compare, in vivo, the effectiveness of two of the currently popular co-expression strategies - the internal ribosome entry site (IRES) derived from the picornavirus and the 2A peptide from the foot-and-mouth disease virus (FDMV) (F2A), we analyzed two locus-specific knock-in mouse lines co-expressing SRY-box containing gene 9 (Sox9) and enhanced green fluorescent protein (EGFP) linked by the IRES (Sox9IRES-EGFP) or the F2A (Sox9F2A-EGFP) sequence. Both the constructs expressed Sox9 and EGFP proteins in the appropriate Sox9 expression domains, with the IRES construct expressing reduced levels of EGFP compared to that of the F2A. The latter, on the other hand, produced about 42.2% Sox9-EGFP fusion protein, reflecting an inefficient ribosome ‘skipping’ mechanism. To investigate if the discrepancy in the ‘skipping’ process was locus-dependent, we further analyzed the FLAG3-Bapx1F2A-EGFP mouse line and found similar levels of fusion protein being produced. To assess if EGFP was hindering the ‘skipping’ mechanism, we examined another mouse line co-expressing Bagpipe homeobox gene 1 homolog (Bapx1), Cre recombinase and EGFP (Bapx1F2A-Cre-F2A-EGFP). While the ‘skipping’ was highly efficient between Bapx1 and Cre, the ‘skipping’ between Cre and EGFP was highly inefficient. We have thus demonstrated in our comparison study that the efficient and close to equivalent expression of genes linked by F2A is achievable in stable mouse lines, but the EGFP reporter may cause undesirable inhibition of the ‘skipping’ at the F2A sequence. Hence, the use of other reporter genes should be explored when utilizing F2A peptides

Equal abundance of summertime natural and wintertime anthropogenic Arctic organic aerosols

Organic aerosols in the Arctic are predominantly fuelled by anthropogenic sources in winter and natural sources in summer, according to observations from eight sites across the Arctic Aerosols play an important yet uncertain role in modulating the radiation balance of the sensitive Arctic atmosphere. Organic aerosol is one of the most abundant, yet least understood, fractions of the Arctic aerosol mass. Here we use data from eight observatories that represent the entire Arctic to reveal the annual cycles in anthropogenic and biogenic sources of organic aerosol. We show that during winter, the organic aerosol in the Arctic is dominated by anthropogenic emissions, mainly from Eurasia, which consist of both direct combustion emissions and long-range transported, aged pollution. In summer, the decreasing anthropogenic pollution is replaced by natural emissions. These include marine secondary, biogenic secondary and primary biological emissions, which have the potential to be important to Arctic climate by modifying the cloud condensation nuclei properties and acting as ice-nucleating particles. Their source strength or atmospheric processing is sensitive to nutrient availability, solar radiation, temperature and snow cover. Our results provide a comprehensive understanding of the current pan-Arctic organic aerosol, which can be used to support modelling efforts that aim to quantify the climate impacts of emissions in this sensitive region.Peer reviewe

Improving educational achievement and anaemia of school children: design of a cluster randomised trial of school-based malaria prevention and enhanced literacy instruction in Kenya

BACKGROUND: Improving the health of school-aged children can yield substantial benefits for cognitive development and educational achievement. However, there is limited experimental evidence on the benefits of school-based malaria prevention or how health interventions interact with other efforts to improve education quality. This study aims to evaluate the impact of school-based malaria prevention and enhanced literacy instruction on the health and educational achievement of school children in Kenya. DESIGN: A factorial, cluster randomised trial is being implemented in 101 government primary schools on the coast of Kenya. The interventions are (i) intermittent screening and treatment of malaria in schools by public health workers and (ii) training workshops and support for teachers to promote explicit and systematic literacy instruction. Schools are randomised to one of four groups: receiving either (i) the malaria intervention alone; (ii) the literacy intervention alone; (iii) both interventions combined; or (iv) control group where neither intervention is implemented. Children from classes 1 and 5 are randomly selected and followed up for 24 months. The primary outcomes are educational achievement and anaemia, the hypothesised mediating variables through which education is affected. Secondary outcomes include malaria parasitaemia, school attendance and school performance. A nested process evaluation, using semi-structured interviews, focus group discussion and a stakeholder analysis will investigate the community acceptability, feasibility and cost-effectiveness of the interventions. DISCUSSION: Across Africa, governments are committed to improve health and education of school-aged children, but seek clear policy and technical guidance as to the optimal approach to address malaria and improved literacy. This evaluation will be one of the first to simultaneously evaluate the impact of health and education interventions in the improvement of educational achievement. Reflection is made on the practical issues encountered in conducting research in schools in Africa. TRIAL REGISTRATION: National Institutes of Health NCT00878007