Incredible Flu Fighting Tea that Gives Fast Results

Healthy Food Style

Being healthy means being happy

If you are one of those always stocking up flu and cold medications before the cold weather sets in, then the time has come to rethink your strategy. Embrace all the remedies that nature gives and combine them to create a powerful flu fighting tea that gives incredible results.

Ginger stimulates circulation and has been used for centuries as a remedy for sore throat. It warms the body and gives you instant cold relief. It has antiviral and anti-inflammatory properties and is effective for people experiencing respiratory problems.

 

Lemon has citric acid and bioflavonoids that boost immunity and fight infection and is an excellent source of Vitamin C. Regular consumption of lemon helps you stay healthy and protects you from many ailments. It is widely known as strong natural antiseptic and when combined with ginger helps with sinuses.

 

Ginger-lemon combination was traditionally used by many ancient cultures to relieve symptoms accompanied by flu, cold and infections. Most common symptoms included runny nose, fever, cough, chills, sneezing, muscles aches, mild tiredness, headache etc.

 

Cinnamon is considered as a “wonder spice” when it comes to flu and cold treatment. Using cinnamon as part of warm drinks significantly reduces cold and flu effects.

 

The preparation of this tea is always recommended as a prevention of common cold or as a remedy to help your body get rid of flu fast and effectively.

 

Ingredients:

• a thumb of ginger
• 1 lemon
• 1/2 tbsp. cinnamon
• 2 cups water

Instructions:

Put the water in a teapot and bring it to boiling point. Then add the grated ginger and the cinnamon. Let it boil for 5 minutes. Put it aside until it cools a bit ( but not completely). Strain the mixture, squeeze the lemon and stir well. Drink immediately.

November 8, 2014

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Opinion: The Planet Needs More Plant Scientists

Academia is not producing sufficient PhDs in the plant sciences to solve the crop production challenges facing a rapidly growing population.

By Alan M. Jones | October 1, 2014

 

FLICKR, JOI ITOWhile the message is not new, the declaration of the flaws of the US biomedical research system by four prominent life scientists this spring captured everyone’s attention. Bruce Alberts, Marc Kirschner, Shirley Tilghman, and Harold Varmus wrote in PNAS of how “demands for research dollars grew much faster than the supply . . . [due to] perverse incentives [that] encourage grantee institutions to grow without making sufficient investments in their faculty and facilities.” Rather than devote money to faculty salaries, universities built infrastructure to house more self-paid researchers able to bring in more money via research grants, of which a large fraction was used as revenue (overhead) for the university. More labs required more students to fill them, leading to a dramatic rise of PhDs in the biomedical sciences, which then produced more researchers competing for dwindling grant dollars. In short, research institutions have no incentive to support individual faculty and instead have perverse incentives to encourage further research spending: more grants = more overhead = more buildings = more PIs = more PhDs in an increasingly out-of-control spiral. (See “PhDs in the U.S.”) This is not sustainable, and we are now experiencing the consequences, with the most despairing being the lack of adequate jobs for our postdocs and perceived insufficient funding for all of us.

 

PhDs in the U.S.: From 1982 to 2012, the total number of PhDs in the life sciences (blue) has grown dramatically. Most of these PhDs are in biological, biomedical, and health sciences (red), however; the number of PhDs in the agricultural and natural sciences (green) has remained flat over that same time period. The unsustainable rate of PhDs awarded per year in the biomedical sciences does not extrapolate to the rate of PhDs in other life sciences, however, especially the agricultural sciences, where the rate of PhDs per year has remained flat for decades. Since 1982, we have consistently trained only about 1,000 PhDs in applied agricultural and related sciences each year. And over the last decade, the U.S. has annually produced only 800 or so plant scientists working in applied agricultural science and only 100 with the skills for basic plant research. (See “Plant science stagnates.”) Given the global agricultural challenges we now face, this is a problem.

 

The Earth must support another 1 billion humans in the coming decade, and must do so with less arable land and in an unpredictable climate. This means we must find innovative ways to produce crops with higher yields and novel traits—a feat that will require the work of PhDs trained in agriculture and plant sciences. But at this point we are not producing enough plant scientists to lead us out of this Malthusian dilemma.

 

The US Coalition for a Sustainable Agricultural Workforce recently completed a confidential survey among agricultural biotech companies to ascertain near-term needs for hiring domestic agricultural scientists. This survey generated an amazing result, given the tone of the PNAS perspective, predicting that by 2015, 1,000 new employees will be needed in the half-dozen largest plant-science companies in the US alone (Bayer Crop Science, Dow Agro Sciences, Dupont Pioneer Hybrid, Dupont Crop Protection, Monsanto, and Syngenta). Almost half of these anticipated new hires will hold PhDs. Unfortunately, with what appears to be a dwindling pool of qualified applicants applying to plant science PhD programs, we may not be keeping up with this demand.

 

Plant science stagnates: Selected subdisciplines relevant to a work force in plant industry (blue and green) have not increased this century, while selected biomedical subdisciplines (red) have grown steeply.

Biomedical subdisciplines include bioinformatics, biomedical sciences, biometrics and biostatistics, cancer biology, computational biology, developmental biology/embryology, neurosciences and neurobiology, structural biology, virology. Basic plant biology subdisciplines (green) include botany/plant biology, plant genetics, plant pathology/phytopathology, plant physiology. Agricultural research subdisciplines (blue) include agricultural and horticultural plant breeding, agricultural economics, agronomy and crop science, forest engineering, forest sciences and biology, forestry and related science, horticulture science, plant pathology/phytopathology (applied), plant sciences (other), soil chemistry/microbiology, soil sciences, entomology, plant genetics, plant pathology/phytopathology applied plant physiology. The growing world population needs to eat, and it is past due that we elevate basic, translational, and applied plant research to the priority given to biomedical research, or more boldly, to defense. Stabilizing food supplies in a changing environment is integral not only to the world population’s health, as an estimated 50 percent of childhood disease globally is attributed to malnourishment, but also to national security. Moreover, a recent study found that, around the world, the rate of return for investment in agricultural research is ten to one, bringing into question the scaling back of funding for agriculture research and development in many rich countries.   

Going forward, we must infuse more resources into plant biology research, to boost research output and to train tomorrow’s plant scientists. In the early 1980s, the National Science Foundation (NSF) established an 11-year postdoctoral fellowship program with the primary objective to nurture future leaders of plant biology research. By many accounts, this program was successful; among a cohort of 236 fellows, four are members of the National Academy of Sciences today, and more than 80 percent remained in plant biology. Of those, the majority stayed in academic institutions, while an impressive number (25 percent) went to industry, where many now hold corporate officer positions. Anticipating the need for leaders to alleviate hunger and to prevent global instability, we should reinstate this program to recruit our best talent to plant science and agricultural research.

 

In conclusion, it is important that the sirens of a glut of biomedical PhDs do not fallaciously harm other areas of science that are still in desperate need of young researchers and more research funding. This is especially true for the plant sciences, where the next generation of researchers must conquer significant challenges to feed a growing world population in a changing environment.

    

Acknowledgement: I thank Machi Dilworth for providing annotated data on the NSF Postdoctoral Fellowship program. Data source: NSF.

 

Alan M. Jones is a Kenan Distinguished Professor at the University of North Carolina, Chapel Hill.

Tags

plant science, plant biology, PhD, jobs and agriculture

 

 

 

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Best Drink to Boost Metabolism and Reduce Weight Naturally

Healthy Food Style

Being healthy means being happy

You may feel frustrated about all your attempts at slimming your waistline and shedding all those extra pounds you have been carrying around for some time. You tried your best and still no evident results.

No magical pill or electronic device can substitute the good old exercise and proper diet. Choosing the right combination is the key to healthy weight loss management without being afraid of the pounds bouncing back. Yellow and orange color foods are excellent solution for losing weight and they are extra delicious. Moreover, they are recommended for improving mood, so if you are disappointed after so many failed attempts, now is the time to take control of the situation, reduce weight and boost your mood at the same time.

 

Apples and pears are high in dietary fiber which aid the weight loss process by speeding up metabolism and keeping you full for longer period thus preventing intake of more calories. They also prevent constipation and regulate blood sugar.

 

Oranges and lemons are perfect addition to your weight loss plan owing to their abundance of vitamin C which acts as a natural fat burning compound. Vitamin C helps the body burn calories, flushes out toxins accumulated in the body which improves liver health necessary for appropriate metabolism of fats.

 

Metabolism is regarded as a complex process in which the body transforms the consumed food into fuel. Flax seeds and ginger are natural metabolism boosters and their regular consumption will not only help you reduce weight but also burn fats especially accumulated in the stomach area.

 

Mix these healthy ingredients to prepare incredibly delicious beverage that will keep you healthy and melt pounds naturally. Prevent weight gain, overweight or obesity, shape your body the way you have always dreamed about and improve your health. Your body will be grateful one day.

 

Always choose fresh organic ingredients in order to avoid pesticides and other harmful and toxic substances.

 

Consume this drink twice, early in the morning and 3 hours later. Then take your lunch and eat something light for dinner ( seasonal salad or vegetable soup). Drink this beverage regularly, boost your metabolism and start losing weight naturally.You will be amazing by the results.

Best Drink to Boost Metabolism and Reduce Weight Naturally

Serving Size-2

Ingredients:

• 2 pears
• 1 apple
• 1 banana
• 1 orange
• 1 lemon
• 1 tbsp. ground flax seeds
• a thumb of ginger

Instructions:

Combine all the listed ingredients in a blender and blend till you get creamy smoothie with incredible taste.

 

 

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Delays hinder Ebola genomics

Infectious Diseases

As the Ebola epidemic sweeps through West Africa, scientists lack key genetic data to answer a question that has provoked much worried speculation: Is the virus becoming more transmissible or more deadly, or acquiring changes that would let it evade diagnostic tests or vaccines? Thousands of blood samples from Ebola patients have been sitting in refrigerators in Africa and Europe, untouched. And, as Science went to press, the few groups that have new sequence data have not made them public.

                 

Researchers are eager for a close-up look at how the virus may be evolving. Besides answering questions about its virulence, genomic data could reveal details about the epidemic, including hotspots of transmission and how often the virus has escaped from its animal reservoir to humans, says Andrew Rambaut, an evolutionary biologist who studies infectious diseases at the University of Edinburgh in the United Kingdom. “If it can be done on a timely basis, you can really get insight into what is going on.” But faced with the all-consuming public health response to the epidemic, bureaucratic obstacles, and chaotic record keeping, scientists have had to wait.

 

A changeable foe: The proteins that enable the Ebola virus to spread and cause disease are encoded by seven protein-sheathed genes. Mutations in the gene for the glycoprotein could affect the efficacy of antibody-based treatments. Other genes, such as those for polymerase and transcription factor VP30, can affect how quickly the virus replicates.                     

ILLUSTRATION: VIRALZONE/SIB SWISS INSTITUTE OF BIOINFORMATICS

In August, the world got its closest molecular look at the virus so far, when researchers published 99 genomes of viruses from 78 patients who were infected in or around Kenema, Sierra Leone, from late May to mid-June. That analysis, published online on 28 August in Science, included more than half of the known cases in Sierra Leone at the time.

                 

The sequence data, which the researchers deposited in public databases as soon as they were generated, showed how the virus changed as it passed from person to person at the start of the Sierra Leone outbreak, with one variant disappearing as another gained prominence among later cases. Since then, the outbreak has exploded into an epidemic—it has now sickened more than 13,000 and killed 5000—but the team, led by Pardis Sabeti and Stephen Gire at the Broad Institute in Cambridge, Massachusetts, has been unable to import any new samples from Sierra Leone. Other groups have been similarly stymied.

                 

Several researchers say that getting export approval from beleaguered health ministries has been tough. “I can only assume that the system is so overwhelmed that processing samples beyond simple diagnostic tests is not high priority,” says Rambaut, who was a co-author on the August sequence paper.

                 

Stephan Günther, a virologist at the Bernhard Nocht Institute for Tropical Medicine (BNI) in Hamburg, Germany, and coordinator of the European Mobile Laboratory (EMLab) consortium, says they have been unable to export samples from Nigeria or Liberia. But BNI has been receiving samples from the EMLab mission in Guinea since March and now has close to 3000, he says. (BNI is storing them in its high-security lab on behalf of the Guinean government, which still owns them.)

                 

Günther and his colleagues have not yet sequenced any of the samples, because consortium staff members have been busy supporting diagnostic centers in affected countries. “We are all busy with fieldwork,” Günther says. “Personnel is a bit of a problem.” That should ease, he says, with a new €1.7 million ($2.1 million) award from the European Union to EMLab for Ebola research.

                 

In France, the Institut Pasteur, where early samples from Guinea were first identified as Ebola, also experienced delays exporting samples from West Africa but plans to start sequencing new viral genomes soon. The institute's lab in Dakar recently received samples from Guinea, says Felix Rey, who is coordinating the institute's Ebola task force in Paris. The Dakar lab will extract RNA and send it to Paris for high-throughput sequencing. “We hope to have sequenced viruses from a couple of hundred samples in the next month or so,” Rey says.

                 

Sabeti and her colleagues should soon get their Sierra Leone samples, which finally were cleared for export and arrived in the United States last week, says Robert Garry of Tulane University in New Orleans, Louisiana, who collaborates with Sabeti. But to speed the research, she and her colleagues are trying to secure funding to send sequencing machines to West Africa. “If we can't get the samples here, we will get the sequencers there,” she says. The effort will build on the researchers' ongoing work with the African Centre of Excellence for Genomics of Infectious Diseases, a consortium of universities and research institutes in the United States, Nigeria, Sierra Leone, and Senegal, which for several years has been training African researchers in the use of genomics tools.

                 

Blood samples alone aren't enough for genomic studies. Investigators need to know at least where each patient was from; ideally they will also have clinical information such as whether he or she survived. “Only when you have those pieces of information can you come up with useful information from the sequences,” Günther says—and because of spotty record keeping, that information is often missing. He and his colleagues are working with Doctors Without Borders and the World Health Organization to match samples with relevant information, but setting up a database is time- and labor-intensive, he says.

                 

Meanwhile, the few Ebola virus sequences that have been generated since that initial batch from Sierra Leone have not been made public. The U.S. Centers for Disease Control and Prevention (CDC) announced in August that it had sequenced Ebola virus samples from patients treated in the United States. But the data have not been placed in any public sequence repositories. That's unfortunate, Rambaut says. “As the U.S. cases are from Liberia and we have zero sequences from there so far, even one genome would be interesting and potentially useful,” he says. Duncan MacCannell, a bioinformatics specialist at CDC in Atlanta, told Science that the sequences had been “actively shared and discussed with the public health community.” He says CDC is working to submit the sequences to a public database.

                 

New sequences probably won't show that the virus is finding new ways to attack or spread, Rambaut says. Instead, the prize is a clearer picture of the outbreak. A cluster of closely related viruses might point to a hotspot of transmission, he says, while unexpectedly diverse sequences would suggest that many cases were going undetected. Sequence data could also help researchers tell whether there has been more than one animal-to-human introduction.

                 

Earlier sequence data did suggest that the virus was undergoing rapid changes, but that is not necessarily a sign that it is becoming more dangerous, Rambaut says. “Most RNA viruses mutate quickly, but adaptation and functional change is a much slower process.” Measles mutates nearly as quickly as Ebola virus, but it has never evolved to escape the lifelong immunity of previously infected or vaccinated individuals. Even in an outbreak this big, Rambaut says, “I see no reason to suspect the virus will radically change its life cycle or its mode of transmission.”

 

 

By Gretchen Vogel 6 November 2014 5:17 am 0 Comments

 

 

Science 7 November 2014:
Vol. 346 no. 6210 pp. 684-685
DOI: 10.1126/science.346.6210.684

 

 

 

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A census of human RNA-binding proteins

Nature Reviews Genetics | Analysis

 Analyses of post-transcriptional gene regulation and the protein factors involved have been substantially driven forward by technological advances such as next-generation sequencing and modern protein mass spectrometry. This Analysis provides a census of 1,542 manually curated RNA-binding proteins, for which the authors have investigated interactions with different classes of RNA, evolutionary conservation, abundance and tissue-specific expression.

 

Stefanie Gerstberger,^1, Markus Hafner^2, & Thomas Tuschl^1,

Abstract

 

Post-transcriptional gene regulation (PTGR) concerns processes involved in the maturation, transport, stability and translation of coding and non-coding RNAs. RNA-binding proteins (RBPs) and ribonucleoproteins coordinate RNA processing and PTGR. The introduction of large-scale quantitative methods, such as next-generation sequencing and modern protein mass spectrometry, has renewed interest in the investigation of PTGR and the protein factors involved at a systems-biology level. Here, we present a census of 1,542 manually curated RBPs that we have analysed for their interactions with different classes of RNA, their evolutionary conservation, their abundance and their tissue-specific expression. Our analysis is a critical step towards the comprehensive characterization of proteins involved in human RNA metabolism. 

Key points

• Recent advances in next-generation sequencing methods and quantitative mass spectrometry have renewed the interest in RNA biology and the genome-wide investigation of post-transcriptional gene regulatory proteins. A global census that systematically lists the number of factors involved in post-transcriptional gene regulation (PTGR) is currently not available. Here, we provide an overall summary of the proteins involved in interactions with all classes of RNAs based on our current knowledge of PTGR; this will guide future systems-wide studies of PTGR.
• RNA-binding proteins (RBPs) are evolutionarily deeply conserved, and their structural domains diversified early in evolution.
• RBPs are among the most abundant proteins in the cell and are generally ubiquitously expressed, which mirrors their central and conserved role in gene regulation.
• Only ~2% of RBPs are tissue-specific, and most of these are mRNA- and non-coding RNA-binding proteins.
• Diseases involving RBPs show characteristic phenotypes depending on the type of RNA (for example, mRNA, ribosomal RNA and tRNA) predominantly bound by the RBPs.
• Correlated expression of RBPs across developmental processes can identify factors in shared PTGR pathways.

Introduction

Post-transcriptional gene regulation (PTGR) is essential to sustain cellular metabolism, coordinating maturation, transport, stability and degradation of all classes of RNAs (Fig. 1). Mechanistically, each of these events is regulated by the formation of different ribonucleoprotein (RNP) complexes with RNA-binding proteins (RBPs) at their core. Initially, it was thought that RNA mainly served either as the template, in the form of mRNA, or as an adaptor or a structural component during protein synthesis, provided by tRNAs and ribosomal RNAs. With the discovery of catalytic RNAs and a multitude of non-coding RNA (ncRNA) species, it was recognized that RNA is a highly versatile molecule that carries out many regulatory functions in the cell, either by acting as a guide to recognize RNA sequence motifs or RNA recognition elements present in their target RNAs, or by functioning as a scaffold and assembly platform for recruiting proteins to act synergistically¹. The characterization of the proteins transiently or stably interacting with RNAs is a prerequisite for the dissection of RNA regulatory processes.

Figure 1: Overview of the main post-transcriptional gene regulation pathways in eukaryotes.

An overview is given for the biogenesis, decay and function of the most abundant RNAs: tRNAs, ribosomal RNAs, small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), mRNAs, microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs) and long non-coding RNAs (lncRNAs). Processes are described from left to right. Referenced gene names and complexes in the figure are listed in Supplementary information S3 (table) and within the listed references. a | tRNAs are transcribed by RNA polymerase III (Pol III); the 5′ leader and 3′ trailer sequences are removed, introns are spliced, and the ends are joined. CCA nucleotides are added to 3′ ends, and nucleotide modifications — such as methylation (M), pseudouridylation (ψ) and deamination of adenosines to inosines (I) — are introduced before tRNA aminoacylation¹⁹⁵. b | The 5S rRNA is transcribed by Pol III, whereas 28S, 18S and 5.8S rRNAs are transcribed as one transcript by Pol I. The precursor is processed by RNA exonucleases, endonucleases and the ribonucleoprotein (RNP) RNase MRP, guided by U3 small nucleolar RNP (snoRNP). Nucleotide modifications are introduced by snoRNPs. rRNAs are assembled together with ribosomal proteins into ribosomal precursor complexes in the nucleus and transported to the cytoplasm, where they mature to functional ribosomes^{92, 196, 197}. c | Most snRNAs are transcribed by Pol II, capped and processed in the nucleus. When exported to the cytoplasm, they undergo methylation and assemble with LSM proteins into small nuclear ribonucleic particles (snRNPs) in a process aided by the survival motor neuron 1 (SMN1). These snRNPs are re-imported into the Cajal body (CB) within the nucleus, where they undergo final maturation and snRNP assembly⁸¹. U6 and U6atac snRNAs are transcribed by Pol III and are alternatively processed in the nucleus and the nucleolus¹⁹⁸. Mature snRNPs form the core of the spliceosome. d | snoRNAs and small Cajal body-specific RNAs (scaRNAs) are processed from mRNA introns, capped and modified before they assemble into snoRNPs or scaRNPs in the CB. snoRNPs and scaRNPs carry out methylation and pseudouridylation of rRNAs, snoRNAs and snRNAs, or function in rRNA processing (for example, processing of U3 snoRNA)⁸¹. e | mRNAs are transcribed by Pol II, capped, spliced, edited and polyadenylated in the nucleus. Correctly matured mRNAs are exported into the cytoplasm. Regulatory RNA-binding proteins (RBPs) control correct translation, monitor stability, decay and localization, and shuttle mRNAs between actively translating ribosomes, stress granules and P bodies^{37, 141, 142, 199, 200, 201, 202}. f | miRNAs are either transcribed from separate genes by Pol II as long primary miRNA (pri-miRNA) transcripts or expressed from mRNA introns (mirtrons) and processed into hairpin pre-miRNAs in the nucleus. After transport into the cytoplasm, they are processed into 21-nucleotide-long double-stranded RNAs. One strand is incorporated into Argonaute (AGO) proteins (forming miRNA-containing RNPs (miRNPs)) and guides them to partially complementary target mRNAs to recruit deadenylases and repress translation²⁰³. g | piRNAs are ~28-nucleotides-long, germline-specific small RNAs. Primary piRNAs are directly processed and assembled from long, Pol II-transcribed precursor transcripts, whereas secondary piRNAs are generated in the 'ping pong' cycle by the cleavage of complementary transcripts by PIWI proteins. Mature piRNAs are 2′-O-methylated and incorporated into PIWI proteins. The piRNA–PIWI complexes (piRNPs) silence transposable elements (TEs) either by endonucleolytic cleavage in the cytoplasm or through transcriptional silencing at their genomic loci in the nucleus¹⁰⁷. h | Most lncRNAs are transcribed and processed in a similar way to mRNAs. Nuclear lncRNAs play an active part in gene regulation by directing proteins to specific gene loci, where they recruit chromatin modification complexes and induce transcriptional silencing or activation¹⁸⁵. Other non-coding RNAs (for example, 7SK RNA) regulate transcription elongation rates²⁰⁴ or induce the formation of paraspeckles (PS)²⁰⁵. Cytoplasmic non-coding RNAs can modulate mRNA translation²⁰⁶. i | Incorrectly processed RNAs are recognized by several complexes in the nucleus and cytoplasm that initiate and execute their degradation^{207, 208}. CPSF, cleavage and polyadenylation specificity factor; EJC, exon junction complex; hnRNP, heterogeneous nuclear RNP; NGD, no-go decay; NMD, nonsense-mediated RNA decay; NSD, non-stop decay; PABP, poly(A)-binding protein.

The recent development of large-scale quantitative methods, especially next-generation sequencing and modern protein mass spectrometry^{2, 3, 4, 5, 6}, facilitates genome-wide identification of RBPs, their protein cofactors and their RNA targets. Deep-sequencing approaches using immunoprecipitation of RBPs, with or without in vivo RNA–protein crosslinking (crosslinking and immunoprecipitation followed by sequencing (CLIP–seq) and RNA immunoprecipitation and sequencing (RIP-seq), respectively)^{2, 3}, as well as in vitro evolution methods^{7, 8}, revealed the binding ranges of RBPs and showed that many RBPs bind to thousands of transcripts in cells at defined binding sites.

 

Despite the growing amount of data collected on RBPs, many questions remain to be answered. Researchers still have an incomplete understanding of how binding specificity is achieved and how the regulatory function of an individual RBP is influenced by synergy and competition with other RBPs. We argue that a balanced approach of detailed biochemical and functional studies paired with complex systems-biology methods will ultimately lead to an understanding of the principles underlying PTGR networks.

 

Although much of the published research centres on mRNA-binding proteins (mRBPs) and messenger RNPs, PTGR is not limited to mRNA maturation and regulation; it also includes processes acting on ncRNAs. In this respect, it may not be surprising that, among the ~150 RBPs listed in the Online Mendelian Inheritance in Man (OMIM) database as being linked to human diseases, only one-third are described as directly binding mRNAs; the others target diverse ncRNAs⁹.

 

Here, we present a census of 1,542 human RBPs that interact with all known classes of RNAs, detail their families and evolutionary conservation across species, and analyse their expression across tissues and their potential roles in developmental processes. This catalogue of RBPs will guide future analyses of RBPs and provide an overview of known RNA pathways and their protein components.

 

......................................................................................................................................................................

...................................................................................................................................................................... 

Conclusions

A census of human RBPs is essential for organizing our current molecular and genetic understanding of the role of RNA in general gene expression and PTGR. This catalogue provides researchers with a newly curated resource to guide their investigations of PTGR processes and to systematically study RBPs. An analogous catalogue that assesses the abundance of all expressed RNAs (that is, the RBP targets) and that classifies them across tissues and cell types is still missing. Such a catalogue would be a useful complementary document to this census.

 

Of the ~20,500 protein-coding genes in humans, we determined that 7.5% are directly involved in RNA metabolism by binding to and/or processing RNA, or by constituting essential components of RNPs. RBPs are structurally diverse and include many distinct classes of RBDs. Indeed, whereas the three most abundant DNA-binding domains account for 80% of all TFs⁵⁸, the three most abundant RBDs accounted for only 20% of all RBPs in our census. Based on target-RNA categorization, we found that nearly 50% of RBPs acted in mRNA metabolic pathways and 11% constituted ribosomal proteins, while the rest were involved in the diverse number of ncRNA metabolic processes. The target-based categorization of RBPs can assist interpretation of disease phenotypes and mutations emerging from rapidly increasing patient genome sequencing, and may guide future functional studies. When considering abundances, we found that ribosomal proteins and mRBPs were the most abundant RBPs in the cell. Nevertheless, most RBPs were ubiquitously expressed at higher levels than the residual protein-coding transcriptome, and up to 20% of the total expressed protein-coding transcripts encoded RBPs. Therefore, not only is RNA metabolism one of the most conserved cellular processes, but it also has one of the highest protein copy number demands.

 

Many details of PTGR remain to be revealed, including the dissection of newly discovered RNA regulatory processes^{1, 184, 185}. The investigation of PTGR networks is aided by the rapid development of next-generation sequencing-based methods, such as RIP- and CLIP-based methods^{2, 3, 14}, ribosome profiling¹⁸⁶, in vivo RNA secondary structure profiling^{187, 188, 189}, small and long RNA-seq^{6, 190, 191}, and 3′-end sequencing methods that profile alternative polyadenylation sites and poly(A) tail lengths^{158, 192, 193, 194}. These studies reveal an unanticipated complexity in RBP binding and targeting, and highlight the need to experimentally dissect PTGR networks in various cellular systems.

Published online 04 November 2014

 



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Macrophage subsets in atherosclerosis

Nature Reviews Cardiology

Atherosclerosis is characterized by increased accumulation of macrophages within the vessel wall. In response to stimuli such as modified lipids, cytokines, and senescent erythrocytes present in the atherosclerotic lesion, these macrophages can alter their functional phenotypes. Different macrophage subsets can influence the growth and composition of the atherosclerotic plaque in distinct ways. In this Review, Chinetti-Gbaguidi et al. highlight the diverse range of macrophage phenotypes present in atherosclerotic lesions, and their roles in both plaque progression and stability.

 

Giulia Chinetti-Gbaguidi,^1, Sophie Colin^1, & Bart Staels^1,

Abstract:

Macrophage accumulation within the vascular wall is a hallmark of atherosclerosis. In atherosclerotic lesions, macrophages respond to various environmental stimuli, such as modified lipids, cytokines, and senescent erythrocytes, which can modify their functional phenotypes. The results of studies on human atherosclerotic plaques demonstrate that the relative proportions of macrophage subsets within a plaque might be a better indicator of plaque phenotype and stability than the total number of macrophages. Understanding the function of specific macrophage subsets and their contribution to the composition and growth of atherosclerotic plaques would aid the identification of novel strategies to delay or halt the development of the disease and its associated pathophysiological consequences. However, most studies aimed at characterizing the phenotypes of human macrophages are performed in vitro and, therefore, their functional relevance to human pathology remains uncertain. In this Review, the diverse range of macrophage phenotypes in atherosclerotic lesions and their potential roles in both plaque progression and stability are discussed, with an emphasis on human pathology.

 Key points

• Only M1 proinflammatory and M2 anti-inflammatory macrophages have been described in vitro—however, a wide spectrum of intermediate phenotypes has been identified in in vivo studies

• Various stimuli (cytokines, lipids and their derivatives, senescent cells, iron) can influence macrophage phenotypes in atherosclerotic lesions

• Macrophages with different functional phenotypes are likely to perform different roles in the development of atherosclerosis

• M1 macrophages are associated with symptomatic and unstable plaques, whereas M2 macrophages are particularly abundant in stable zones of the plaque and asymptomatic lesions

• Modulation of macrophage phenotypes might be a novel strategy for the pharmacological treatment of atherosclerosis

Introduction

The development of atherosclerosis involves activation of various cell types (including endothelial cells, smooth muscle cells, lymphocytes, monocytes, and macrophages) in the intima of the arteries, which results in a local inflammatory response.¹ An increase in circulating LDL-cholesterol levels and the subsequent accumulation of oxidized LDL in the subendothelial space triggers the recruitment and retention of monocytes and lymphocytes in the arterial wall. In the intima, monocytes differentiate into macrophages, which scavenge lipoprotein particles, and eventually become foam cells.² These macrophage-derived foam cells secrete inflammatory molecules and factors that further promote lipoprotein retention, degrade the extracellular matrix, and sustain inflammation.^{3, 4}

 

Progression of atherosclerosis is characterized by apoptosis of these resident macrophages in the lipid core of the lesion. The clearance of apoptotic cells is mediated by phagocytes, mostly macrophages, which recognize and internalize dead cells in a process termed efferocytosis.⁵ In early lesions, phagocytes readily clear apoptotic cells, avoiding further progression of atherosclerosis. In chronic, advanced lesions, however, efferocytosis is no longer sufficient to engulf all dead cells, and the gradual accumulation of apoptotic debris results in formation of a necrotic core, which triggers further inflammation, necrosis, and thrombosis.⁵ Macrophages are crucial in the maintenance of efficient efferocytosis, and thereby contribute to both resolving inflammation and preventing the formation of a necrotic core within the plaque (Figure 1).⁶

 

Figure 1: Potential role of M2 macrophages in efferocytosis within atherosclerotic plaques.

M2 macrophages localized in areas of neovascularization or outside the lipid core can phagocytose apoptotic M1 macrophages, contributing to the resolution of inflammation. If efferocytosis is insufficient, dead M1 macrophages accumulate and undergo postapoptotic necrosis, leading to the formation of a necrotic core, which contributes to plaque instability and rupture.

Novel observations have challenged these previously well-established concepts. Whereas atherosclerosis was initially considered a type 1 T helper cell (T_H1)-driven inflammatory process, the concept of heterogeneity of macrophages resident within lesions has gradually emerged over the past decade.^{7, 8} Firstly, several studies revealed that both monocytes and macrophages comprise heterogeneous cell populations that adapt their functional phenotype in response to specific microenvironmental signals and molecules.^{9, 10} These different monocyte and macrophage subtypes can be identified based on their differential expression of surface markers and chemokine receptors.^{9, 10} Secondly, the general dogma that tissue-resident macrophages are incapable of proliferating was challenged by investigators who observed macrophages in mouse lungs that proliferated independently of monocyte recruitment.¹¹ Both resident and recruited macrophages can be induced to proliferate by IL-4.¹¹ Moreover, in mice, macrophages in early atherosclerotic lesions are predominantly derived from recruited monocytes, whereas macrophage proliferation is a preponderant feature of advanced plaques and is influenced by microenvironment signals.¹² Accordingly, differences in resident macrophage phenotypes can also influence their capacity to proliferate locally, which can alter the abundance of macrophages with a given phenotype.^{11, 13}

 

In this Review, we describe and discuss the reported functional phenotypes of macrophages in atherosclerotic plaques, focusing mainly on human pathology. The correlative studies suggesting a link between such macrophage phenotypes and the structure or progression of atherosclerotic lesions will also be discussed.

Figure 2: Main macrophage subtypes found in atherosclerotic lesions.

Stimuli present in atherosclerotic lesions drive the differentiation of monocytes towards different macrophage phenotypes. a | M1 macrophages release proinflammatory cytokines. b | M(Hb), Mhem, and M2 macrophages are resistant to lipid accumulation, possess iron-handling capacities, and have anti-inflammatory effects. c | Mox macrophages display an antioxidant gene expression profile. d | M4 macrophages, like M1 macrophages, are proinflammatory, but lack the capacity for phagocytosis. Abbreviations: COX-2, cyclooxygenase; CXCL4, C-X-C motif chemokine 4; HMOX-1, haem oxygenase (decycling) 1; LDL, low-density lipoprotein; LXR, liver X receptor; MMP-7, matrix metalloproteinase-7; NFE2L2, nuclear factor (erythroid-derived 2)-like 2; NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells; TLR, toll-like receptor; TNF, tumour necrosis factor.

Figure 3: Localization of macrophage subsets in human atherosclerotic lesions.

M1 macrophages are predominantly found in the plaque shoulder and lipid core, whereas M2 macrophages are most abundant in the adventitia and areas of neovascularization, which also contain iron deposits. Fibrous caps contain similar amounts of both macrophage subsets.

Conclusions

 Macrophages are important in the development of atherosclerotic lesions because they participate in all stages of plaque formation and progression.⁷⁷ During their lifetime, macrophages are exposed to a plethora of microenvironmental signals and stimuli (including cytokines modified lipids, senescent erythorocytes, and iron) that influence their transcriptional programme and functional phenotype. The intensity of these signals changes during plaque progression, and varies between plaque regions. Therefore, macrophages adapt their phenotype both over time and in response to their physical location, contributing to and modulating plaque progression and composition. The local accumulation of macrophage subpopulations that are highly competent in clearing apoptotic cells (such as M2 macrophages) can sustain efferocytosis, thereby contributing to the resolution of inflammation and prevention of necrotic core formation within plaques.

 

Whether the distinct macrophage phenotypes represent different stages of differentiation of a single population of phenotypically and functionally plastic resident macrophages, or are consequences of the recruitment and differentiation of specific monocyte subpopulations in the lesion, is still a matter of debate. However, despite rapid advances in this field, novel studies and research methods need to be developed to determine whether monocyte subpopulations give rise to specific macrophage phenotypes. Our current knowledge suggests that M2 macrophages, owing to their localization within human plaques and their intrinsic anti-inflammatory properties, are primarily associated with plaque stability. However, one of the most important challenges in this field will be to demonstrate a direct causative link between macrophage phenotype and the structure or progression of atherosclerotic lesions. Given that only correlation studies are feasible in humans, specific mouse models need to be developed.

 

Further identification of novel phenotypic and functional markers, and the use of novel large-scale expression profiling approaches and imaging technology, is expected to lead to an improved definition and understanding of the specific functions of the different macrophage subtypes identified within the plaque. The identification of biological stimuli that can modulate macrophage phenotypes could lead to the development of novel therapeutic approaches for the treatment of atherosclerosis.

Published online 04 November 2014

 

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Epigenetics of Trained Innate Immunity

The Scientist » News & Opinion » Daily News             

Documenting the epigenetic landscape of human innate immune cells reveals pathways essential for training macrophages.

By Ruth Williams | September 25, 2014

 

WIKIMEDIA, CHRISTOPH BOCK (MAX PLANCK INSTITUTE FOR

INFORMATICS)

Genome-wide epigenetic and transcription analyses of monocytes and macrophages have uncovered two crucial pathways driving macrophage training—a recently discovered form of innate immune memory—according to two studies published in Science today (September 25). Together with a third paper documenting the transcriptional diversity of early immune cell progenitors, the studies present the latest results from the ongoing European BLUEPRINT initiative, which aims to decipher the epigenomes of blood cells during health and disease.

 

“They did a very thorough transcriptomic and epigenomic analysis of these cells and . . . they uncover not just immunologic pathways, which would be expected, but also, interestingly, some metabolic pathways that may be important to the different immunologic phenotypes of these cells,” said Ofer Levy of Boston Children’s Hospital and Harvard Medical School who was not involved in the studies.

 

Monocytes are part of the innate immune system. They circulate in the blood, but also exit to surrounding tissues, differentiate into macrophages, and patrol the body disposing of pathogens and dead cells. Under certain conditions, macrophages can become either tolerant of pathogens or trained to react against additional infections. This training of macrophages is a recently discovered process, and aside from providing a physiological answer for some previously unexplained effects of vaccination, it also challenges the established dogma of innate immunity.

 

In humans, the immune system has two arms: innate and adaptive. The traditional view is that innate immunity is broad-acting and non-specific, while adaptive immunity establishes memories for very specific pathogens, explained Christine Stabell Benn, a professor of global health at the Statens Serum Institute in Copenhagen who also did not participate in the studies. “So, if you give a vaccine against measles you induce protective immunity against measles and nothing else.” But, she added, “what we have seen in our epidemiological studies is that vaccines [also] have non-specific effects.” The Bacille Calmette-Guérin (BCG) vaccine, for example, confers protection against a variety of infections with other microorganisms—and trained macrophages appear to be responsible. The new papers, said Stabell Benn, “are now providing the molecular mechanisms behind these epidemiological observations.”

 

Mihai Netea, a professor of medicine at Radboud University in the Netherlands and an author on two of the papers, has characterized trained macrophages in the dish, in animals and in healthy people, comparing the trained phenotype to tolerant macrophages, naive macrophages (neither trained not tolerant), and monocytes. But to get the bigger picture of what defines these different yet related cells, “I went to the group of Hank [Hendrik] Stunnenberg and asked for his help with the epigenetics,” Netea said. Stunnenberg is a professor of molecular biology at Radboud University, an author on all three papers and the coordinator of the BLUEPRINT consortium.

 

Netea, Stunnenberg, and their colleagues collected monocytes from healthy people and from them derived the three macrophage types—tolerant, trained, and naive. In these four cell types, they then analyzed genome-wide distributions of four epigenetic indicators of gene activity: DNAse hypersensitivity and three different histone modifications—trimethylation of histone H3 at lysine 4, monomethylation of histone H3 at lysine 4, and acetylation of histone H3 at lysine 27. They also analyzed genome-wide transcription and transcription factor binding.

 

Together the analyses pointed to specific genes and pathways that defined the four cell types, as well as the genes’ surrounding regulatory regions. Of particular interest was the discovery that genes associated with signaling via cyclic adenosine monophasphate (cAMP)—a molecule regulating cell metabolism, among other processes—and glycolysis—a pathway that produces energy from glucose—were specifically activated in the trained macrophages.

 

The team went on to show that these two pathways were necessary for developing the trained phenotype. Cultured monocytes in which cAMP signaling or the glycolysis pathway were inhibited exhibited impaired production of training-induced cytokines. Inhibition of cAMP or glycolysis in mice increased susceptibility to secondary infections following trained innate immunity.

 

Both training and tolerance induction in macrophages have a number of clinical implications, explained Netea. For example, too much tolerance can cause immunoparalysis—a life-threatening complication of sepsis, he said. Such patients could be helped, added Stunnenberg, “if we could turn around a paralyzed cell and activate it.” But training “can probably also in some situations be detrimental to the host,” said Stabell Benn, by potentially causing excessive inflammation, for example. Having the epigenomic information about these cells, she added, is therefore important “in the first place, to understand what is going on, and in the second place, because it offers the potential of both down-regulating over-energetic cells but also revitalizing those that have been paralyzed.”

 

L. Chen et al., “Transcriptional diversity during lineage commitment of human blood progenitors,” Science, doi: 10.1126/science.1251033, 2014.

 

S. Cheng et al., “mTOR- and HIF-1a–mediated aerobic glycolysis as metabolic basis for trained immunity,” Science, doi: 10.1126/science.1250684, 2014.

 

S. Saeed et al., “Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity,” Science, doi: 10.1126/science.1251086, 2014.

Tags

vaccination, macrophage, innate immunity, immunology, genetics & genomics, epigenetics and disease/medicine

 

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