Identification of baboon microRNAs expressed in liver and lymphocytes

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are small noncoding RNAs (~22 nucleotides) that regulate gene expression by cleaving mRNAs or inhibiting translation. The baboon is a well-characterized cardiovascular disease model; however, no baboon miRNAs have been identified. Evidence indicates that the baboon and human genomes are highly conserved; based on this conservation, we hypothesized that comparative genomic methods could be used to identify baboon miRNAs.</p> <p>Methods</p> <p>We employed an <it>in silico </it>comparative genomics approach and human miRNA arrays to identify baboon expressed miRNAs in liver (n = 6) and lymphocytes (n = 6). Expression profiles for selected miRNAs in multiple tissues were validated by RT-PCR.</p> <p>Results</p> <p>We identified <it>in silico </it>555 putative baboon pre-miRNAs, of which 41% exhibited 100% identity and an additional 58% shared more than 90% sequence identity with human pre-miRNAs. Some of these miRNAs are primate-specific and are clustered in the baboon genome like human miRNA clusters. We detected expression of 494 miRNAs on the microarray and validated expression of selected miRNAs in baboon liver and lymphocytes by RT-PCR. We also observed miRNA expression in additional tissues relevant to dyslipidemia and atherosclerosis. Approximately half of the miRNAs expressed on the array were not predicted <it>in silico </it>suggesting that we have identified novel baboon miRNAs, which could not be predicted using the current draft of the baboon genome.</p> <p>Conclusion</p> <p>We identified a subset of baboon miRNAs using a comparative genomic approach, identified additional baboon miRNAs using a human array and showed tissue-specific expression of baboon miRNAs. Our discovery of baboon miRNAs in liver and lymphocytes will provide resources for studies on the roles of miRNAs in dyslipidemia and atherosclerosis, and for translational studies.</p

Potential miRNA biomarkers and therapeutic targets for early atherosclerotic lesions

Identification of potential therapeutic targets and biomarkers indicative of burden of early atherosclerosis that occur prior to advancement to life-threatening unstable plaques is the key to eradication of CAD prevalence and incidences. We challenged 16 baboons with a high cholesterol, high fat diet for 2 years and evaluated early-stage atherosclerotic lesions (fatty streaks, FS, and fibrous plaques, FP) in formalin-fixed common iliac arteries (CIA). We used small RNA sequencing to identify expressed miRNAs in CIA and in baseline blood samples of the same animals. We found 412 expressed miRNAs in CIA and 356 in blood samples. Eight miRNAs (miR-7975, -486-5p, -451a, -191-5p, -148a-3p, -17-5p, -378c, and -144-3p) were differentially expressed between paired fatty streak lesion and no-lesion sites of the tissue, and 27 miRNAs (e.g., miR-92a-3p, -5001, -342-3p, miR-28-3p, -21-5p, -221-3p, 146a-5p, and -16-5p) in fibrous plaques. The expression of 14 blood miRNAs significantly correlated with extent of lesions and the number of plaques. We identified coordinately regulated miRNA-gene networks in which miR-17-5p and miR-146a-5p are central hubs and miR-5001 and miR-7975 are potentially novel miRNAs associated with early atherosclerosis. In summary, we have identified miRNAs expressed in lesions and in blood that correlate with lesion burden and are potential therapeutic targets and biomarkers. These findings are a first step in elucidating miRNA regulated molecular mechanisms that underlie early atherosclerosis in a baboon model, enabling translation of our findings to humans

Identification of coordinately regulated microRNA-gene networks that differ in baboons discordant for LDL-cholesterol

Rationale Plasma low-density lipoprotein cholesterol (plasma LDL-C), vascular endothelial cells and peripheral blood mononuclear cells (PBMCs), particularly monocytes, play key roles in initiating atherosclerosis, the primary cause of cardiovascular disease (CVD). Although the mechanisms underlying development of atherosclerosis are not well understood, LDL-C is known to influence expression of endothelial microRNAs (miRNAs) and gene-targets of miRNAs to promote cell senescence. However, the impact of LDL-C on expression of PBMC miRNAs and miRNA targeted genes in response to an atherogenic diet is not known. In this study, we used unbiased methods to identify coordinately responsive PBMC miRNA- gene networks that differ between low and high LDL-C baboons when fed a high-cholesterol, high-fat (HCHF) diet. Methods and results Using RNA Seq, we quantified PBMC mRNAs and miRNAs from half-sib baboons discordant for LDL-C plasma concentrations (low LDL-C, n = 3; high LDL-C, n = 3) before and after a 7-week HCHF diet challenge. For low LDL-C baboons, 626 genes exhibited significant change in expression (255 down-regulated, 371 up-regulated) in response to the HCHF diet, and for high LDL-C baboons 379 genes exhibited significant change in expression (162 down-regulated, 217 up-regulated) in response to the HCHF diet. We identified 494 miRNAs identical to human miRNAs and 47 novel miRNAs. Fifty miRNAs were differentially expressed in low LDL-C baboons (21 up- and 29 down-regulated) and 20 in high LDL-C baboons (11 up- and 9 down-regulated) in response to the HCHF diet. Among the differentially expressed miRNAs were miR-221/222 and miR-34a-3p, which were down-regulated, and miR-148a/b-5p, which was up-regulated. In addition, gene-targets of these miRNAs, VEGFA, MAML3, SPARC, and DMGDH, were inversely expressed and are central hub genes in networks and signaling pathways that differ between low and high LDL-C baboon HCHF diet response. Conclusions We have identified coordinately regulated HCHF diet-responsive PBMC miRNA-gene networks that differ between baboons discordant for LDL-C concentrations. Our findings provide potential insights into molecular mechanisms underlying initiation of atherosclerosis where LDL-C concentrations influence expression of specific miRNAs, which in turn regulate expression of genes that play roles in initiation of lesions

A chlorophyll-deficient, highly reflective soybean mutant: radiative forcing and yield gaps

Sunlight absorbed at the Earth’s surface is re-emitted as longwave radiation. Increasing atmospheric concentrations of CO2 and other greenhouse gases trap an increasing fraction of such heat, leading to global climate change. Here we show that when a chlorophyll (Chl)-deficient soybean mutant is grown in the field, the fraction of solar-irradiance which is reflected, rather than absorbed, is consistently higher than in commercial varieties. But, while the effect on radiative forcing during the crop cycle at the scale of the individual experimental plot was found to be large (−4.1± 0.6 W m−2 ), global substitution of the current varieties with this genotype would cause a small increase in global surface albedo, resulting in a global shortwave radiative forcing of −0.003 W m−2 , corresponding to 4.4 Gt CO2eq. At present, this offsetting effect would come at the expense of reductions to yields, probably associated with different dynamic of photosynthetic response in the Chl-deficient mutant. The idea of reducing surface-driven radiative forcing by means of Chl-deficient crops therefore requires that novel high-yielding and high-albedo crops are made available soon.publishedVersio

Biochar standardization and legislation harmonization

It is a relatively new concept to use biochar as soil amendment and for climate change mitigation. For this reason, the national and supranational legislation in the EU is not yet adequately prepared to regulate both the production and the application of biochar. Driven by this “regulatory gap”, voluntary biochar quality standards have been formed in Europe with the European Biochar Certificate, in the UK with the Biochar Quality Mandate and in the USA with the IBI Standard which is intended to be used internationally. In parallel to this, biochar producers and biochar users in a number of EU countries were partly successful in fitting the new biochar product into the existing national legislation for fertilisers, soil improvers and composts. The intended revision of the EC Regulation 2003/2003 on fertilisers offers the opportunity to regulate the use of biochar at the EU level. This publication summarizes the efforts on biochar standardization which have been carried out by voluntary products standards and illustrates existing legislation in EU member states, which apply to the production and use of biochar. It describes existing and planned EU regulations, which impact biochar applications and it develops recommendations on the harmonization of biochar legislation in the EU. &nbsp;First published online: 24 Jan 201

Recarga artificial en Bajos Submeridionales

Se presenta la experiencia en desarrollo en un sector de Bajos Submeridionales próximo a Tostado, para monitorear los efectos de la recarga artificial de acuíferos. El objetivo del estudio es mejorar la disponibilidad de agua en calidad y cantidad para uso ganadero y evaluar una obra de recarga a partir de un pozo doble propósito recarga – bombeo para mejorar su eficiencia, y difundir estas prácticas.El área piloto se ubica en un paleocauce arenoso del río Salado. En el mismo se han realizado numerosos estudios geoeléctricos, de infiltración, sedimentológicos, químicos recuperación de niveles, de suelos y de recarga. Además se dispone de una estación meteorológica automática, caudalímetro y freatímetros. Se realizó un análisis de eventos de recarga y su efecto sobre el sistema natural y en la obra. Se concluye que ha resultado exitosa y puede ser transferida a otros ambientes de paleocauces del chaco-santafesino.This work describes an artificial recharge experience of groundwater as source for animal beverage, de veloped on a livestock demonstrative unit, placed in Bajos Submeridionales, Santa Fe province, Argentina. The aim of this study is to improve quality and quantity of water for livestock use, analyze a recharge-pumping well efficiency, and finally to spread this practice in the region. The study area is located in a antique sandy channel of the Salado river, where have been conducted geoelectric studies, sedimentologic, soil and water analysis, pumping and recharge, and infiltration tests. Additionally, it counts with metheorological on-line data from an automatic station, flowmeter, and water-level measurements from digital and analogical devises. An analysis of a recharge event has been conducted in order to assess environmental changes and response of facilities. This successful experience suggests that these kinds of facilities could be applied in similar environments of chaco-santafesino region.Universidad Nacional de La Plat