Impact of GC content on gene expression pattern in chicken

Background

GC content varies greatly between different genomic regions in many eukaryotes. In order to determine whether this organization named isochore organization influences gene expression patterns, the relationship between GC content and gene expression has been investigated in man and mouse. However, to date, this question is still a matter for debate. Among the avian species, chicken (Gallus gallus) is the best studied representative with a complete genome sequence. The distinctive features and organization of its sequence make it a good model to explore important issues in genome structure and evolution.

Methods

Only nuclear genes with complete information on protein-coding sequence with no evidence of multiple-splicing forms were included in this study. Chicken protein coding sequences, complete mRNA sequences (or full length cDNA sequences), and 5^′ untranslated region sequences (5^′ UTR) were downloaded from Ensembl and chicken expression data originated from a previous work. Three indices i.e. expression level, expression breadth and maximum expression level were used to measure the expression pattern of a given gene. CpG islands were identified using hgTables of the UCSC Genome Browser. Correlation analysis between variables was performed by SAS Proprietary Software Release 8.1.

Results

In chicken, the GC content of 5^′ UTR is significantly and positively correlated with expression level, expression breadth, and maximum expression level, whereas that of coding sequences and introns and at the third coding position are negatively correlated with expression level and expression breadth, and not correlated with maximum expression level. These significant trends are independent of recombination rate, chromosome size and gene density. Furthermore, multiple linear regression analysis indicated that GC content in genes could explain approximately 10% of the variation in gene expression.

Conclusions

GC content is significantly associated with gene expression pattern and could be one of the important regulation factors in the chicken genome.     

Do foods imported into the UK have a greater environmental impact than the same foods produced within the UK?

Purpose

This study of seven foods assessed whether there are modes or locations of production that require significantly fewer inputs, and hence cause less pollution, than others. For example, would increasing imports of field-grown tomatoes from the Mediterranean reduce greenhouse gas (GHG) emissions by reducing the need for production in heated greenhouses in the UK, taking account of the additional transport emissions? Is meat production in the UK less polluting than the import of red meat from the southern hemisphere?

Methods

We carried out a life-cycle inventory for each commodity, which quantified flows relating to life-cycle assessment (LCA) impact categories: primary energy use, acidification, eutrophication, abiotic resource use, pesticide use, land occupation and ozone depletion. The system boundary included all production inputs up to arrival at the retail distribution centre (RDC). The allocation of production burdens for meat products was on the basis of economic value. We evaluated indicator foods from which it is possible to draw parallels for foods whose production follows a similar chain: tomatoes (greenhouse crops), strawberries (field-grown soft fruit), apples (stored for year-round supply or imported during spring and summer), potatoes (early season imports or long-stored UK produce), poultry and beef (imported from countries such as Brazil) and lamb (imported to balance domestic spring–autumn supply).

Results and discussion

Total pre-farm gate global warming potential (GWP) of potatoes and beef were less for UK production than for production in the alternative country. Up to delivery to the RDC, total GWP were less for UK potatoes, beef and apples than for production elsewhere. Production of tomatoes and strawberries in Spain, poultry in Brazil and lamb in New Zealand produced less GWP than in the UK despite emissions that took place during transport. For foods produced with only small burdens of GWP, such as apples and strawberries, the burden from transport may be a large proportion of the total. For foods with inherently large GWP per tonne, such as meat products, burdens arising from transport may only be a small proportion of the total.

Conclusions

When considering the GWP of food production, imports from countries where productivity is greater and/or where refrigerated storage requirement is less will lead to less total GWP than axiomatic preference for local produce. However, prioritising GWP may lead to increases in other environmental burdens, in particular leading to both greater demands on and decreasing quality of water resources.     

Enrichment of hexachlorobenzene and 1,3,5-trichlorobenzene transforming bacteria from sediments in Germany and Vietnam

Bacterial cultures were enriched from sediments in Germany and Vietnam reductively dechlorinating hexachlorobenzene and the highly persistent 1,3,5-trichlorobenzene to monochlorobenzene. The main products of the reductive dechlorination of hexachlorobenzene were monochlorobenzene and dichlorobenzenes (1,2-; 1,3- and 1,4-dichlorobenzene) while no trichlorobenzenes accumulated. For the reductive dechlorination of 1,3,5-trichlorobenzene with the mixed culture from Vietnam sediment, 1,3- dichlorobenzene and monochlorobenzene were produced as intermediate and final end-product, respectively. The pattern of dechlorination did not change when the cultures were repeatedly exposed to oxygen over seven transfers demonstrating oxygen tolerance of the dechlorinating bacteria. However, reductive dechlorination of 1,3,5-trichlorobenzene was inhibited by vancomycin at a concentration of 5 mg L^?1. Vancomycin delayed reductive dechlorination of hexachlorobenzene in mixed cultures by about 6 months. When repeatedly applied, vancomycin completely abolished the ability of the mixed culture to transform hexachlorobenzene. Sensitivity to vancomycin and insensitivity to brief exposure of oxygen indicates that the dechlorinating bacteria in the mixed cultures did not belong to the genus Dehalococcoides.     

Current approaches to native woodland restoration in Scotland

Summary

A large number of projects have recently been initiated in Scotland aiming to restore native woodland, which are being undertaken by a variety of organisations, often in partnership, with environmental NGOs playing a leading role. The objectives, constraints and methodologies of these projects are critically reviewed, partly through a questionnaire survey. Most aim to restore ‘natural’ woodland, but the lack of appropriate reference ecosystems and uncertainty about the characteristics of the original forest hinder the development of precise objectives, and consequently the criteria for success are poorly defined. Most projects face major practical constraints, particularly browsing by herbivores and invasion by exotic species, indicating that they will require long-term management interventions. Most woodlands are isolated from other woodlands, which threatens their long-term viability, restricting colonisation by woodland organisms. Greater reference to ecological theory in practical restoration projects such as these would enable objectives to be defined with more precision, encourage a greater emphasis on ecological processes rather than community composition, and improve management plans through use of predictive tools. In particular, the integration of woodlands into habitat networks, increasing ecological connectivity between woodland fragments, is considered essential to ensure success in the long term.     

Waist Circumference,Not Body Mass Index,Is Associated with Renal Function Decline in Korean Population: Hallym Aging Study

Background

Prospective investigation of obesity and renal function decline in Asia is sparse. We examined the associations of body mass index (BMI) and waist circumference (WC) with renal function decline in a prospective study of Korean population.

Methods

A total of 454 participants who had baseline estimated glomerular filtration rate (eGFR) levels of more than 60 mL/min/1.73 m² in Hallym Aging Study (HAS) were included and followed for 6 years. Renal function decline was defined as follows: (1) an eGFR decline ≥3 mL/min/1.73 m²/year (n = 82 cases); (2) an eGFR decrease of 20% or greater (n = 87 cases) at follow-up; (3) an eGFR decrease of 20% greater at follow-up or eGFR decline ≥3 mL/min/1.73 m²/year (n = 91 cases); and (4) an eGFR <60 mL/min/1.73 m² at follow-up (n = 54 cases). eGFR was determined based on the Modification of Diet in Renal Disease (MDRD) Study equation. Multivariate logistic regression model was used to determine the association between obesity and renal function decline.

Results

We found that central obesity was associated with faster renal function decline. Comparing WC of >95 cm in men or >90 cm in women with ≤90 cm in men or ≤85 cm in women, ORs (95% CIs) ranged from 2.31 (1.14–4.69) to 2.78 (1.19–6.50) for the 4 definitions of renal function decline (all p-values for trend <0.05). Waist-to-hip ratio (WHR) and waist-to-height ratio (WHtR) also was associated with renal function decline. There was no significant association of BMI with renal function decline.

Conclusions

Central obesity, but not BMI, is associated with faster renal function decline in Korean population. Our results provide important evidence that simple measurement of central fat deposition rather than BMI could predict decline in renal function in Korean population.     

Temporal and Pharmacological Characterization of Angiostatin Release and Generation by Human Platelets: Implications for Endothelial Cell Migration

Platelets play an important role in thrombosis and in neo-vascularisation as they release and produce factors that both promote and suppress angiogenesis. Amongst these factors is the angiogenesis inhibitor angiostatin, which is released during thrombus formation. The impact of anti-thrombotic agents and the kinetics of platelet angiostatin release are unknown. Hence, our objectives were to characterize platelet angiostatin release temporally and pharmacologically and to determine how angiostatin release influences endothelial cell migration, an early stage of angiogenesis. We hypothesized anti-platelet agents would suppress angiostatin release but not generation by platelets. Human platelets were aggregated and temporal angiostatin release was compared to vascular endothelial growth factor (VEGF). Immuno-gold electron microscopy and immunofluorescence microscopy identified α-granules as storage organelles of platelet angiostatin. Acetylsalicylic acid, MRS2395, GPIIb/IIIa blocking peptide, and aprotinin were used to characterize platelet angiostatin release and generation. An endothelial cell migration assay was performed under hypoxic conditions to determine the effects of pharmacological platelet and angiostatin inhibition. Compared to VEGF, angiostatin generation and release from α-granules occurred later temporally during platelet aggregation. Consequently, collagen-activated platelet releasates stimulated endothelial cell migration more potently than maximally-aggregated platelets. Platelet inhibitors prostacyclin, S-nitroso-glutathione, acetylsalicylic acid, and GPIIb/IIIa blocking peptide, but not a P2Y12 inhibitor, suppressed angiostatin release but not generation. Suppression of angiostatin generation in the presence of acetylsalicylic acid enhanced platelet-stimulated endothelial migration. Hence, the temporal and pharmacological modulation of platelet angiostatin release may have significant consequences for neo-vascularization following thrombus formation.