Non-invasive analysis of intestinal development in preterm and term infants using RNA-Sequencing : Scientific Reports. Nutritional regulation of intestinal development begins in utero with exposure to protein-rich amniotic fluid and continues after birth with human milk and/or infant formula1, 10. These developmental processes are essential for continued cellular differentiation of the gut and development of mucosal immunity18. In the healthy term infant, the continuum of enteral stimulation is continued postnatally, whereas the preterm infant is typically supported on parenteral nutrition with limited enteral stimulation in the first few weeks of life3. In addition, postnatal exposure to environmental organisms in the neonatal intensive care unit and the routine use of antibiotics can lead to aberrant intestinal development, microbial colonization and risk of intestinal disease in the preterm infant3, 6.
Hence, it is imperative to understand the transcriptional responses of the preterm gut so that specific nutritional practices can be employed in order to optimize intestinal development. Corrections. Characterisation of cytoplasmic DNA complementary to non-retroviral RNA viruses in human cells : Scientific Reports. Cell lines and plasmids The NP-2 cells were derived from human glioma cells. The N4R (NP-2/CD4/ecoR) cells were NP-2 cells transduced with CD4 and an ecotropic murine leukaemia virus (MuLV) receptor26. The N4R5X4/iGFP cells, which were used for HIV-1 titration, were N4R cells that were transduced with CXCR4, CCR5, and an HIV-LTR-driven GFP. The N4R5X4/iGFP cells clearly expressed GFP when HIV-1 infection was established. The NP-2/LINE-1 cells were NP-2 cells that were transfected with a LINE-1 (L1.2) expression plasmid with a pCEP4 backbone13.
VSV preparation and titration To prepare the VSV samples, 4.0 × 105 HOS cells were seeded onto 60 mm plates. VSV infection and DNA purification A total of 1.0 × 106 293T cells were infected with VSV at an MOI of 0.1 for 1 hr. PCR amplification Real-time PCR amplification PCR primers The oligonucleotide primers were synthesised by Hokkaido System Science Co., Ltd. Time course of VSV DNA synthesis and the treatment of cell lysates with RNase A or DNase I. Adenoviral vector delivery of RNA-guided CRISPR/Cas9 nuclease complexes induces targeted mutagenesis in a diverse array of human cells : Scientific Reports. Cells The U2OS human osteosarcoma and the HeLa cervix carcinoma cells (American Type Culture Collection) were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% and 5% fetal bovine serum (FBS), respectively, at 37°C in a 10% CO2 atmosphere.
The E1- and E2A-complementing AdV packaging cell line PER.E2A34, was kept in DMEM supplemented with 10% FBS, 10 mM MgCl2 and 250 μg/ml of Geneticin (Invitrogen). PER.E2A cells were regularly sub-cultured at 39°C and were shifted to 34°C during AdV production for the proper folding of their E2A-encoded thermo-sensitive DNA-binding protein. The origin of and culture conditions for the HeLa cell-derived clone H27, constitutively expressing eGFP, as well as those for myoblasts and hMSCs have been detailed elsewhere23, 35, 36. Recombinant DNA Standard recombinant DNA techniques were applied for the construction of the various AdV shuttle plasmids38.
Validation of Cas9- and gRNAS1-encoding AdV shuttle plasmids Transduction experiments. Silkworm sex factor is no ordinary gene. Munetaka Kawamoto, Laboratory of Insect Genetics and Bioscience, University of Tokyo An adult male silkmoth. In the silk business, sex is money. Male silkworms weave cocoons with more silk of a higher quality than females do, and the multibillion dollar sericulture industry has long sought an easy way to breed only males.
That might now be a realistic goal, as researchers have identified the process that determines sex in the silkworm Bombyx mori1. The sex factor is found to be a small RNA molecule — the first time that anything other than a protein has been implicated in a sex-detemination process. In nearly all Lepidoptera — the order that includes moths and butterflies — sex is determined by a WZ chromosome system, in contrast to the XY system used in mammals. Last year, researchers showed how to genetically modify silkworms so that the females would express a deadly protein (see 'Genetic kill switch eradicates female silkworms for a better crop'). Potent hepatitis C inhibitors bind directly to NS5A and reduce its affinity for RNA : Scientific Reports. In vitro NS5A binding assay We have used MST20 to develop an in vitro NS5A binding assay.
MST data arise from the spontaneous movement of fluorescently labelled protein in a glass capillary tube along induced microscopic temperature gradients generated by an infra-red laser. The thermophoretic movement can be monitored by measuring the local changes in fluorescence intensity emitted from the labelled protein. The rate of this thermophoresis is dependent on a number of factors including the solvent structure around a molecule, and crucially is altered by the binding of a ligand.
MST was initially used to confirm the interaction of short, single stranded RNA [consisting of four, five or ten uridines (4rU, 5rU or 10rU respectively) or five adenines (5rA)] or double stranded 5rU (ds(5rU)) with NS5A domain 1. The MST data show that NS5A33–202 binds 4rU with a KD of 650 ± 39, 5rU with a KD of 50 ± 15, 10rU with a KD of 20 ± 9 nM and 5rA with a KD of 1.0 ± 0.2 μM (Fig. 2a–d). Sperm RNA carries marks of trauma. Tiripero/iStock/Thinkstock Mice exposed to stress have male offspring that show depressive behaviour across three generations.
Trauma is insidious. It not only increases a person’s risk for psychiatric disorders, but can also spill over into the next generation. People who were traumatized during the Khmer Rouge genocide in Cambodia tended to have children with depression and anxiety, for example, and children of Australian veterans of the Vietnam War have higher rates of suicide than the general population.
Trauma’s impact comes partly from social factors, such as its influence on how parents interact with their children. But stress also leaves ‘epigenetic marks’ — chemical changes that affect how DNA is expressed without altering its sequence. A study published this week in Nature Neuroscience finds that stress in early life alters the production of small RNAs, called microRNAs, in the sperm of mice (K. “Dad is having a much larger role … than just delivering his genome.” A color-tunable molecular beacon to sense miRNA-9 expression during neurogenesis : Scientific Reports. Cell culture CHO cells (Chinese hamster ovary cells) and P19 cells (mouse embryonic teratocarcinoma cell line) were purchased from the American Type Culture Collection (ATCC). CHO cells were cultured on growth media consisting of Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum (FBS). P19 cells were maintained in DMEM containing 10% FBS, 1% antibiotics, non essential amino acid solution (NEAA, Sigma, St Louis, MO) and β-melcaptoethanol in a 5% CO2-humidified chamber.
For the induction of neuronal differentiation of P19 cells, the cells were cultured with DMEM/F12 (1:1) medium (Gibco, Grand Island, NY) containing N2 supplement (Gibco) and 0.5 mM all-trans-retinoic acid (RA, Sigma, St Louis, MO). After 2 days, the differentiation medium was replaced without RA. Quantification of expression in miRNA For qRT-PCR of miRNAs, 200 ng of RNA were performed by using miR-Q-assay21. Confirmation of neuronal differentiation with immuno-fluorescence staining Design of the ColoR9 MB. Human evolution: Fifty years after Homo habilis. Natural History Museum/Mary Evans Picture Library The foot of 'handy man', Homo habilis. Half a century ago, the British–Kenyan palaeoanthropologist Louis Leakey and his colleagues made a controversial proposal: a collection of fossils from the Great Rift Valley in Tanzania belonged to a new species within our own genus1. The announcement of Homo habilis was a turning point in palaeoanthropology.
It shifted the search for the first humans from Asia to Africa and began a controversy that endures to this day. Even with all the fossil evidence and analytical techniques from the past 50 years, a convincing hypothesis for the origin of Homo remains elusive. In 1960, the twig of the tree of life that contains hominins — modern humans, their ancestors, and other forms more closely related to humans than to chimpanzees and bonobos — looked remarkably straightforward. Betting on Africa Until the 1960s, H. erectus had been found only in Asia. Listen Handy hypotheses Drawing the line. A day in the life of the spliceosome : Nature Reviews Molecular Cell Biology. Is this really the RNAissance? : Nature Biotechnology. Champagne corks have been popping at several RNAi drug developers in recent weeks.
The New Year celebrations started when RNAi bellwether Alnylam announced it had brokered deals to acquire Merck's entire Sirna Therapeutics portfolio for just $175 million and to sell rights to several of its rare disease assets to Sanofi/Genzyme, the latter company taking a 12% stake in the Cambridge, Massachusetts–based biotech (p. 203). In February, fellow RNAi developer Dicerna staged a staggeringly successful initial public offering, raising $90 million (p. 204). Festivities continued over at Arrowhead Research, which raised $104.2 million in a follow-on financing. This influx of investment into the sector is enabling RNAi companies to push ahead with clinical testing of lead candidates. But even though some pundits have greeted these announcements as signs of an “RNAissance,” is this really what we're witnessing? But it is perhaps delivery where the greatest strides have been made.
Corrigendum: Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories : Nature Biotechnology. RNA activity mapped across cells. Scientists can now take snapshots of where and how thousands of genes are expressed in intact tissue samples, ranging from a slice of a human brain to the embryo of a fly. The technique, reported today in Science1, can turn a microscope slide into a tool for creating data-rich, three-dimensional maps of how cells interact with one another — a key to understanding the origins of diseases such as cancer. The methodology also has broader applications, enabling researchers to create, for instance, unique molecular ‘barcodes’ to trace connections between cells in the brain, a stated goal of the US National Institutes of Health's Human Connectome Project. Previously, molecular biologists had a limited spatial view of gene expression, the process by which a stretch of double-stranded DNA is turned into single-stranded RNAs, which can in turn be translated into protein products.
The method hinges on ‘fossilizing’ the RNA in place in the cell and sequencing it. A complete ancient RNA genome: identification, reconstruction and evolutionary history of archaeological Barley Stripe Mosaic Virus : Scientific Reports. Presence of BSMV in archaeological barley The detection of ancient BSMV virus requires the preservation of ancient RNA in the archaeological record. To date there have been few studies on RNA26, 27 because it is highly labile relative to DNA, with an expected 50-fold increased rate of degradation28. RNA is highly vulnerable to hydrolytic attack relative to DNA, but less prone to depurination29, 30.
Therefore in very dry environments, the rate of RNA degradation may be greatly reduced30. Archaeological barley samples were selected from Qasr Ibrim, a site in North Africa where BSMV has been reported. The arid conditions of the site are expected to be conducive to RNA preservation as has been observed for other biomolecules in samples of comparable age31, 32, 33. Genome reconstruction and authentication of an archaeological BSMV virus The small RNA fraction of sample QI84/71 was sequenced on the Illumina Hi-Seq platform. The age of origin of BSMV Evolution and spread of BSMV. Systemic delivery of miR-126 by miRNA-loaded Bubble liposomes for the treatment of hindlimb ischemia : Scientific Reports. Preparation of liposomes and BLs To prepare liposomes for BLs that do not contain cationic lipid, 1,2-distearoyl-sn-glycero-phosphatidylcholine (DSPC) and 1,2-distearoylphosphatidylethanolamine-methoxy-polyethylene glycol (PEG2000) were mixed at a molar ratio of 94:6.
Both lipids were purchased from NOF Corporation (Tokyo, Japan). For BLs containing cationic lipid, 1,2-distearoyl-3-dimethylammonium-propane (DSDAP) from Avanti Polar Lipids (Alabaster, AL) was used. Liposomes with various lipid compositions were prepared using the reverse phase evaporation method as described previously7. Briefly, DSPC, cationic lipid, and PEG2000 were mixed at a molar ratio of 64:30:6 and dissolved in 1:1 (v/v) chloroform/diisopropylether. HEPES-buffered glucose (HBG: 5% glucose, 10 mM HEPES) was added to the lipid solution, and the mixture was sonicated and then evaporated. The liposome concentration was determined using a phosphorus assay. Cell cultures Transfection of miRNA into cells Hemolysis assay. Comet craft ready to wake. ATG medialab/ESA In November 2014, the Philae lander will be the first to try to land on the surface of a comet, 67P/Churyumov–Gerasimenko, as shown in this artist’s impression.
Space scientists are used to moments of high tension. They often have just one chance to get things right, and experiments can hinge on the success of equipment that may be millions of kilometres away. So there will be considerable anxiety on 20 January at the European Space Agency (ESA) when the comet-hunting spacecraft Rosetta is due to stir after almost three years of hibernation. With Rosetta now some 800 million kilometres from Earth, and rapidly approaching its target — comet 67P/Churyumov–Gerasimenko — the first sign that things are going to plan on Rosetta will be the activation of a pre-set alarm.
Once Rosetta is awake, the stakes will get higher. The €1-billion (US$1.4-billion) mission has been hurtling through the Solar System since 2004. Comets are primitive objects. Technical Variations in Low-Input RNA-seq Methodologies : Scientific Reports. Experimental design For each amplification-based method, viz., Smart-seq, DP-seq and CEL-seq, we constructed sequencing libraries using the same mRNA source (Figure 1). The mRNA was derived from an in vitro cell culture based model of primitive streak (PS) induction in mouse embryonic stem cells (mESCs)16, 17. Activation of Activin A/TGFβ pathway by high dosage of Activin A (100 ng/mL) induced mes-endoderm tissue18, 19, 20, 21, 22.
Absence of Activin A, however, resulted in negligible activation of Activin A/TGFβ pathway leading to neuro-ectoderm induction23. Mouse ESCs were differentiated in serum-free conditions and the mRNA was collected at day 4 (equivalent to 6.5 – 7.5 days per coitum) from embroid bodies maintained in control serum free media (SFM) and those subjected to Activin A treatment (AA100). Next, serial dilutions of mRNA ranging from 50 ng – 25 pg were prepared. Mouse ESCs were differentiated in serum free conditions for four days. Full size image (235 KB) Std. Adenovirus vectors lacking virus-associated RNA expression enhance shRNA activity to suppress hepatitis C virus replication : Scientific Reports.
ShRNA-expressing unit inserted at the E4 position worked more efficiently than that at the E1 position in the AdV genome We constructed four VA-deleted AdVs containing shRNA that suppresses GFP expression (Fig. 1a). Cassettes containing anti-GFP shRNA under the control of the human U6 promoter were inserted at the E1 and E4 insertion positions in left (L) and right (R) orientations (AxdV-aGFP-E1L, -E1R, -E4L, and -E4R, respectively). To assay shRNA suppression we used FC-18 cells that constitutively express GFP under the control of the EF1α promoter from its gene integrated in the chromosome20. The cells were infected with these AdVs at a multiplicity of infection (MOI) of 50, and the copy numbers of the GFP mRNA present in the cells were measured using quantitative PCR (qPCR).
The suppression efficiency of the E4L vector (Fig. 1b, left, bar 3) was significantly higher than those of the E1L and E1R vectors (bars 1and 2). (a) Structures of AdV-aGFP vectors. Full size image (143 KB) Generation of mutant mice by pronuclear injection of circular plasmid expressing Cas9 and single guided RNA : Scientific Reports. Modifying cellular properties using artificial aptamer-lipid receptors : Scientific Reports. ERRATUM: Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions : Scientific Reports. Mammals chop up viral RNA to attack infection. Corrigendum: A CRISPR/Cas system mediates bacterial innate immune evasion and virulence : Nature. Can matter cycle through shapes eternally?
The brain microenvironment negatively regulates miRNA-768-3p to promote K-ras expression and lung cancer metastasis : Scientific Reports. Novel Insights into Breast Cancer Genetic Variance through RNA Sequencing : Scientific Reports. p38[ggr] overexpression in gliomas and its role in proliferation and apoptosis : Scientific Reports. Molecular dissection of human Argonaute proteins by DNA shuffling : Nature Structural & Molecular Biology.
Cold-induced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation : Scientific Reports. A novel protocol for three-dimensional structure prediction of RNA-protein complexes : Scientific Reports. Wide support in UK for novel DNA 'transplants' in human egg cells. Circular RNAs throw genetics for a loop. Barnacles trust their sperm to the waves. Genome interpretation and assembly[mdash]recent progress and next steps : Nature Biotechnology. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond : Abstract : Nature Reviews Genetics.
Centenarians, but not octogenarians, up-regulate the expression of microRNAs : Scientific Reports. SpotOn NYC: DIY science | SpotOn. 14th Xenopus International Conference - Days 4 & 5 | ConferenceCast | Learn Science at Scitable. The primary transcriptome of the major human pathogen Helicobacter pylori : Abstract : Nature. Sensitive Real-Time Monitoring of Refractive Indexes Using a Novel Graphene-Based Optical Sensor : Scientific Reports. European ministers back research-buddy plan.
Animation : Nature Reviews Genetics. Past 5,000 years prolific for changes to human genome. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants : Nature. The difficult calls in RNA editing : Nature Biotechnology. Animation : Nature Reviews Genetics. X-ray crystallographer - Cornell University (298935) : ithaca, NY, United States : Naturejobs. Home : Nature Status. Blue whales pirouette for food. Applying Shannon's information theory to bacterial and phage genomes and metagenomes : Scientific Reports.
Hkat, a novel nutritionally regulated transmembrane protein in adipose tissues : Scientific Reports. GTPases IF2 and EF-G bind GDP and the SRL RNA in a mutually exclusive manner : Scientific Reports. Corrigendum: RNA sequencing of pancreatic circulating tumour cells implicates WNT signalling in metastasis : Nature. Comprehensive molecular portraits of human breast tumours : Nature. Research Post-Doctoral Fellow Curie Institute - Group “RNA Biology and Genotoxic Stress” (300972) : Paris, France : Naturejobs. Centenarians, but not octogenarians, up-regulate the expression of microRNAs : Scientific Reports. The long-range interaction landscape of gene promoters : Nature. Landscape of transcription in human cells : Nature. Fathers bequeath more mutations as they age. Seven days: 3–9 August 2012. Dissecting the genomic complexity underlying medulloblastoma : Nature.
Comprehensive molecular characterization of human colon and rectal cancer : Nature. Ultraviolet Shadowing of RNA Can Cause Significant Chemical Damage in Seconds : Scientific Reports. Phylogeny: Rewriting evolution. Involvement of RDR6 in short-range intercellular RNA silencing in Nicotiana benthamiana : Scientific Reports. Correction. RNA studies under fire. EMT and induction of miR-21 mediate metastasis development in Trp53-deficient tumours : Scientific Reports. SiRNA off-target effects in genome-wide screens identify signaling pathway members : Scientific Reports. RNA studies under fire. Subscribe to Nature this Holiday season 50% discount!