Massively parallel sequencing of millions of <30-nt class="search-term-highlight">RNAs expressed in mouse ovary, embryonic pancreas (E14.5), and insulin-secreting beta-cells (βTC-3) reveals that ∼50% of the mature miRNAs representing mostly the mmu-let-7 family display internal insertion/deletions and substitutions when compared to precursor miRNA and the mouse genome reference sequences.

Approximately, 12%–20% of species associated with mmu-let-7 populations exhibit sequence discrepancies that are dramatically reduced in nucleotides 3–7 (5′-seed) and 10–15 (cleavage and anchor sites). This observation is inconsistent with sequencing error and leads us to propose that the changes arise predominantly from post-transcriptional RNA-editing activity operating on miRNA:target mRNA complexes.

Internal nucleotide modifications are most enriched at the ninth nucleotide position. A common ninth base edit of U-to-G results in a significant increase in stability of down-regulated let-7a targets in inhibin-deficient mice (Inha^−/−). An excess of U-insertions (14.8%) over U-deletions (1.5%) and the presence of cleaved intermediates suggest that a mammalian TUTase (terminal uridylyl transferase) mediated dUTP-dependent U-insertion/U-deletion cycle may be a possible mechanism.

We speculate that mRNA target site-directed editing of mmu-let-7a duplex-bulges stabilizes “loose” miRNA:mRNA target associations and functions to expand the target repertoire and/or enhance mRNA decay over translational repression. Our results also demonstrate that the systematic study of sequence variation within specific RNA classes in a given cell type from millions of sequences generated by next-generation sequencing (NGS) technologies (“intranomics”) can be used broadly to infer functional constraints on specific parts of completely uncharacterized RNAs.

Source - http://genome.cshlp.org/content/18/10/1571.abstract?sid=40206306-7c2e-4b18-96b3-8319fa594a4b

We undertook a genome-wide search for novel noncoding RNAs (ncRNA) in the malaria parasite Plasmodium falciparum. We used the RNAz program to predict structures in the noncoding regions of the P. falciparum 3D7 genome that were conserved with at least one of seven other Plasmodium spp.

genome sequences. By using Northern blot analysis for 76 high-scoring predictions and microarray analysis for the majority of candidates, we have verified the expression of 33 novel ncRNA transcripts including four members of a ncRNA family in the asexual blood stage. These transcripts represent novel structured ncRNAs in P. falciparumand are not represented in any RNA databases.

We provide supporting evidence for purifying selection acting on the experimentally verified ncRNAs by comparing the nucleotide substitutions in the predicted ncRNA candidate structures in P. falciparum with the closely related chimp malaria parasite P. reichenowi. The high confirmation rate within a single parasite life cycle stage suggests that many more of the predictions may be expressed in other stages of the organism’s life cycle.

Source - http://genome.cshlp.org/content/18/2/281.abstract?sid=40206306-7c2e-4b18-96b3-8319fa594a4b

We have conducted a survey of RNA editing in human brain by comparing sequences of clones from a human brain cDNA library to the reference human genome sequence and to genomic DNA from the same individual. In the RNA sample from which the library was constructed, 01:2000 nucleotides were edited out of >3 Mb surveyed. All edits were adenosine to inosine (A→I) and were predominantly in intronic and in intergenic RNAs.

No edits were found in translated exons and few in untranslated exons. Most edits were in high-copy-number repeats, usually Alus. Analysis of the genome in the vicinity of edited sequences strongly supports the idea that formation of intramolecular double-stranded RNAwith an inverted copy underlies most A→I editing.

The likelihood of editing is increased by the presence of two inverted copies of a sequence within the same intron, proximity of the two sequences to each other (preferably within 2 kb), and by a high density of inverted copies in the vicinity. Editing exhibits sequence preferences and is less likely at an adenosine 3′ to a guanosine and more likely at an adenosine 5′ to a guanosine. Simulation by BLAST alignment of the double-stranded RNA molecules that underlie known edits indicates that there is a greater likelihood of A→I editing at A:C mismatches than editing at other mismatches or at A:U matches. However, because A:U matches in double-stranded RNA are more common than all mismatches, overall the likely effect of editing is to increase the number of mismatches in double-stranded RNA.

Source - http://genome.cshlp.org/content/14/12/2379.abstract?sid=4be18750-d5af-4896-b05e-eeb49c944425

One dose of vaccine may be effective to protect infants and children and reduce transmission of the H1N1 virus, according to a study in JAMA, just published online because of its public health implications. The study will appear in the January 6 print edition of the journal.

Initial reports of 2009 influenza A(H1N1) infection in many countries have largely involved children, especially those attending school. Reports have also indicated high hospitalization rates of children younger than 5 years of age in the current pandemic, according to background information provided by the authors. "The Advisory Committee on Immunization Practices also currently recommends that infants and children aged 9 years or younger receive two doses of H1N1 influenza vaccine at least 21 days apart, based on existing experience with seasonal trivalent influenza vaccines in this age group."

Terry Nolan, M.B.B.S., Ph.D., from the University of Melbourne, Australia and colleagues assessed the effectiveness and safety of two doses of a 2009 influenza A(H1N1) vaccine in 370 healthy infants and children ages six-months to less than 9 years living in Australia. The children were randomized into groups that received a two-injection regimen 21 days apart in doses of either 15-micrograms or 30-micrograms of the vaccine.

"Following the first dose of vaccine, antibody titers of 1:40 or greater were observed in 161 of 174 infants and children in the 15-microgram group (92.5 percent) and in 168 of 172 infants and children in the 30 microgram group (97.7 percent)," the authors report. "All participants demonstrated antibody titers of 1:40 or greater after the second vaccine dose," [which means that every child achieved an antibody level considered high enough to protect against the H1N1 virus]. The researchers note that the majority of adverse reactions to the vaccine were mild to moderate in severity. The immune responses to the vaccine were strong regardless of age, baseline antibody status, or whether the child had received a seasonal influenza vaccination prior to this study.

"Our findings suggest that a single dose 15-microgram dose vaccine regimen may be effective and well tolerated in children, and may have positive implications for disease protection and reduced transmission of pandemic H1N1 in the wider population," the authors conclude.

Editor's Note: This study was sponsored by CSL Limited with funding from the Australian government's Department of Health and Ageing.

Editorial: 2009 Influenza A(H1N1) Vaccines for Children

"Even though influenza activity has decreased in recent weeks in some states, there remains the possibility of continued activity through the traditional winter influenza season and the prospect of normal winter circulation of seasonal influenza viruses," and the authors of the editorial note that this pandemic has highlighted the fact the children have no measurable immunity against the H1N1 virus.

Anthony E. Fiore, M.D., M.P.H., from the National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, and Kathleen M. Neuzil, M.D., M.P.H., of PATH, Seattle, write that children have been a primary source of illness in community outbreaks of pandemic influenza with more severe complications, hospitalizations and deaths from this virus than what is usually seen for seasonal influenza.

The editorial authors urge caution at interpretation of the results of the study. "The hemagglutinin antigen content administered to six-month-old infants and children younger than 3 years in this study was 15-micrograms, the equivalent of two doses of the 7.5-microgram vaccine currently licensed in the United States for this age group."

"The immunogenicity data presented by Nolan et al suggest that at least some children will be protected after a single 15-microgram dose of the H1N1 vaccine used in this study, but the findings cannot be generalized with confidence to all children, epidemiological circumstances in every country, or different vaccine formulations."

In conclusion, the authors write: "… it remains prudent to continue to follow current recommendations for administering two doses to infants and young children while awaiting definitive vaccine effectiveness data."

In both yeast and mammalian systems, considerable progress has been made toward the characterization of the transcription factors required for transcription by RNA polymerase III. However, whereas in yeast all of the RNA polymerase III subunits have been cloned, relatively little is known about the enzyme itself in higher eukaryotes.

For example, no higher eukaryotic sequence corresponding to the largest RNA polymerase III subunit is available. Here we describe the isolation of cDNAs that encode the largest subunit of human RNApolymerase III, as suggested by the observations that

(1) antibodies directed against the cloned protein immunoprecipitate an active enzyme whose sensitivity to different concentrations of α-amanitin is that expected for human RNA polymerase III; and

(2) depletion of transcription extracts with the same antibodies results in inhibition of transcription from an RNA polymerase III, but not from an RNA polymerase II, promoter.

Sequence comparisons reveal that regions conserved in the RNA polymerase I, II, and III largest subunits characterized so far are also conserved in the human RNA polymerase III sequence, and thus probably perform similar functions for the human RNA polymerase III enzyme.

Source - http://genome.cshlp.org/content/7/10/1006.abstract?sid=4be18750-d5af-4896-b05e-eeb49c944425

A biochemist and cook explains that cooking is all about chemistry and knowing some facts can help chefs understand why recipes go wrong. Because cooking is essentially a series of chemical reactions, it is helpful to know some basics. For example, plunging asparagus into boiling water causes the cells to pop and result in a brighter green. Longer cooking, however, causes the plant's cell walls to shrink and releases an acid. This turns the asparagus an unappetizing shade of grey.

You love to cook, but have you whipped up some disasters? Even the best recipes can sometimes go terribly wrong. A nationally recognized scientist and chef says knowing a little chemistry could help.

Long before she was a cook, Shirley Corriher was a biochemist. She says science is the key to understanding what goes right and wrong in the kitchen.

"Cooking is chemistry," said Corriher. "It's essentially chemical reactions."

This kind of chemistry happens when you put chopped red cabbage into a hot pan. Heat breaks down the red anthocyanine pigment, changing it from an acid to alkaline and causing the color change. Add some vinegar to increase the acidity, and the cabbage is red again. Baking soda will change it back to blue.

Cooking vegetables like asparagus causes a different kind of reaction when tiny air cells on the surface hit boiling water.

"If we plunge them into boiling water, we pop these cells, and they suddenly become much brighter green," Corriher said.

Longer cooking is not so good. It causes the plant's cell walls to shrink and release acid.

"So as it starts gushing out of the cells, and with acid in the water, it turns cooked green vegetables into [a] yucky army drab," Corriher said.

And that pretty fruit bowl on your counter? "Literally, overnight you can go from [a] nice green banana to an overripe banana," Corriher said.

The culprit here is ethylene gas. Given off by apples and even the bananas themselves, it can ruin your perfect fruit bowl -- but put an apple in a paper bag with an unripe avocado, and ethylene gas will work for you overnight.

"We use this as a quick way to ripen," Corriher said. Corriher says understanding a little chemistry can help any cook.

"You may still mess up, but you know why," she said. When it works, this kind of chemistry can be downright delicious.

WHAT ARE ACIDS AND BASES? An acid is defined as a solution with more positive hydrogen ions than negative hydroxyl ions, which are made of one atom of oxygen and one of hydrogen. Acidity and basicity are measured on a scale called the pH scale. The value of freshly distilled water is seven, which indicates a neutral solution. A value of less than seven indicates an acid, and a value of more than seven indicates a base. Common acids include lemon juice and coffee, while common bases include ammonia and bleach.

WHY DOES FOOD SPOIL? Processing and improper storage practices can expose food items to heat or oxygen, which causes deterioration. In ancient times, salt was used to cure meats and fish to preserve them longer, while sugar was added to fruits to prevent spoilage. Certain herbs, spices and vinegar can also be used as preservatives, along with anti-oxidants, most notably Vitamins C and E. In processed foods, certain FDA-approved chemical additives also help extend shelf life.

Natural antisense transcripts (NATs) have been shown to play important roles in post-transcriptional regulation through the RNA interference pathway. We have combined pyrophosphate-based high-throughput sequencing and computational analysis to identify and analyze, in genome scale, cis-NAT and trans-NAT small RNAs that are derived under normal conditions and in response to drought and salt stresses in the staple plant Oryza sativa.

Computationally, we identified 344 cis-NATs and 7142 trans-NATs that are formed by protein-coding genes. From the deep sequencing data, we found 108 cis-NATs and 7141trans-NATs that gave rise to small RNAs from their overlapping regions. Consistent with early findings, the majority of these 108 cis-NATs seem to be associated with specific conditions or developmental stages. Our analyses also revealed several interesting results.

The overlapping regions of the cis-NATs and trans-NATs appear to be more enriched with smallRNA loci than non-overlapping regions. The small RNAs generated from cis-NATs and trans-NATs have a length bias of 21 nt, even though their lengths spread over a large range. Furthermore, >40% of the small RNAs from cis-NATs and trans-NATs carry an A as their 5′-terminal nucleotides.

A substantial portion of the transcripts are involved in both cis-NATs and trans-NATs, and many trans-NATs can form many-to-many relationships, indicating that NATs may form complex regulatory networks in O. sativa. This study is the first genome-wide investigation of NAT-derived small RNAs in O. sativa. It reveals the importance of NATs in biogenesis of small RNAs and broadens our understanding of the roles of NAT-derived smallRNAs in gene regulation, particularly in response to environmental stimuli.

Source - http://genome.cshlp.org/content/19/1/70.abstract?sid=40206306-7c2e-4b18-96b3-8319fa594a4b

Omega-3 fatty acids, commonly found in fish, appears to play a significant role in improving nervous system function, reveals a new study.

The researchers insist two omega-3 fatty acids – docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) have been found to avoid sensory overload, maybe by maintaining nerve-cell membranes.
The finding connects low omega-3s to the information-processing problems found in people with schizophrenia; bipolar, obsessive-compulsive, and attention-deficit hyperactivity disorders; Huntington’s disease; and other afflictions of the nervous system.
"It is an uphill battle now to reverse the message that ‘fats are bad,’ and to increase omega-3 fats in our diet," said Norman Salem Jr., PhD, who led this study at the Laboratory of Membrane Biochemistry and Biophysics at the National Institute on Alcohol Abuse and Alcoholism.
The body cannot make these essential nutrients from scratch. It gets them by metabolizing their precursor, á-linolenic acid (LNA), or from foods or dietary supplements with DHA and EPA in a readily usable form.
"Humans can convert less than one percent of the precursor into DHA, making DHA an essential nutrient in the human diet," said Irina Fedorova, PhD, one of the paper’s co-authors.
EPA is already known for its anti-inflammatory and cardiovascular effects, but DHA makes up more than 90 percent of the omega-3s in the brain (which has no EPA), retina and nervous system in general.
During the study, the researchers fed four different diets with no or varying types and amounts of omega-3s to four groups of pregnant mice and then their offspring.
They measured how the offspring, once grown, responded to a classic test of nervous-system function in which healthy animals are exposed to a sudden loud noise. Normally, animals flinch. However, when they hear a softer tone in advance, they flinch much less.
It appears that normal nervous systems use that gentle warning to prepare instinctively for future stimuli, an adaptive process called sensorimotor gating.
The mice raised on DHA and EPA showed normal, adaptive sensorimotor gating by responding in a significantly calmer way to the loud noises that followed soft tones.
The research is published in journal Behavioural Neuroscience .

Source: http://timesofindia.indiatimes.com/life/health-fitness/health/Fish-can-help-improve-nervous-system-function/articleshow/5347748.cms

Alternative splicing can enhance transcriptome plasticity and proteome diversity. In plants, alternative splicing can be manifested at different developmental stages, and is frequently associated with specific tissue types or environmental conditions such as abiotic stress. We mapped the Arabidopsis transcriptome at single-base resolution using the Illumina platform for ultrahigh-throughput RNA sequencing (RNA-seq).

Deep transcriptome sequencing confirmed a majority of annotated introns and identified thousands of novel alternatively spliced mRNA isoforms. Our analysis suggests that at least ∼42% of intron-containing genes in Arabidopsisare alternatively spliced; this is significantly higher than previous estimates based on cDNA/expressed sequence tag sequencing.

Random validation confirmed that novel splice isoforms empirically predicted by RNA-seq can be detected in vivo. Novel introns detected by RNA-seq were substantially enriched in nonconsensus terminal dinucleotide splice signals. Alternative isoforms with premature termination codons (PTCs) comprised the majority of alternatively spliced transcripts.

Using an example of an essential circadian clock gene, we show that intron retention can generate relatively abundant PTC⁺ isoforms and that this specific event is highly conserved among diverse plant species. Alternatively spliced PTC⁺isoforms can be potentially targeted for degradation by the nonsense mediated mRNA decay (NMD) surveillance machinery or regulate the level of functional transcripts by the mechanism of regulated unproductive splicing and translation (RUST).

We demonstrate that the relative ratios of the PTC⁺ and reference isoforms for several key regulatory genes can be considerably shifted under abiotic stress treatments. Taken together, our results suggest that like in animals, NMD and RUST may be widespread in plants and may play important roles in regulating gene expression.

Source - http://genome.cshlp.org/content/early/2009/11/18/gr.093302.109.abstract

Natural antisense transcripts (NATs) have been shown to play important roles in post-transcriptional regulation through the RNA interference pathway. We have combined pyrophosphate-based high-throughput sequencing and computational analysis to identify and analyze, in genome scale, cis-NAT and trans-NAT small RNAs that are derived under normal conditions and in response to drought and salt stresses in the staple plant Oryza sativa. Computationally, we identified 344 cis-NATs and 7142 trans-NATs that are formed by protein-coding genes. From the deep sequencing data, we found 108 cis-NATs and 7141trans-NATs that gave rise to small RNAs from their overlapping regions. Consistent with early findings, the majority of these 108 cis-NATs seem to be associated with specific conditions or developmental stages. Our analyses also revealed several interesting results. The overlapping regions of the cis-NATs and trans-NATs appear to be more enriched with smallRNA loci than non-overlapping regions. The small RNAs generated from cis-NATs and trans-NATs have a length bias of 21 nt, even though their lengths spread over a large range. Furthermore, >40% of the small RNAs from cis-NATs and trans-NATs carry an A as their 5′-terminal nucleotides. A substantial portion of the transcripts are involved in both cis-NATs and trans-NATs, and many trans-NATs can form many-to-many relationships, indicating that NATs may form complex regulatory networks in O. sativa. This study is the first genome-wide investigation of NAT-derived small RNAs in O. sativa. It reveals the importance of NATs in biogenesis of small RNAs and broadens our understanding of the roles of NAT-derived smallRNAs in gene regulation, particularly in response to environmental stimuli.

Source - http://genome.cshlp.org/content/19/1/70.abstract?sid=40206306-7c2e-4b18-96b3-8319fa594a4b

Which metal is always found in free state in nature-Gold.
• Bauxite is an ore of-Aluminum.
• Material used for bleaching pulp is-Sodium Hypo -chlori
• Which gas is leaked in Bhopal gas tragedy-Methyl Isocyanides.
Which element is common in all organic compounds is -Chlorine.
• What is the function of Green leaves in plants –Photosynthesis.
• Which is largest Gland in human body- Liver
• Which is largest Organ in human body –Skin
• Which is longest Bone in human body –Femur• Malaraia is a disease which effect the –Spleen
• Leukemia is a disease of the –Blood.
• Rickets is a disease of the –Bones.
• ECG is used for the diagnosis of ailments of –Heart.
• Food is normally digested in the –Small intestines.
• The main function of the kidney is –To remove waste product from body
• The human cells contains –46 Chromosomes• Centigrade and Fahrenheit scales resemble at ( –40C).
• Study of insects is called – Entomology.
• The inner layer of the skin is called – Dermis
• Nucleus of an atom has – Neutrons and Protons
• Marsh gas is – Methane
• In fireworks the green flame is produced because of – Barium
• Nuclear fission is caused by the impact –Neutron
• Atom Bomb is based on principal of – Nuclear Fission.
• Glass is made from the mixture of – Sand and Salt.
• Permanent hardness of water may be removed by the addition of – Sodium Carbonate.
• P.V.C is obtained by the polymerization of – Vinylchtoride
• The pursuit form of iron is – Cast Iron
• The element found on the surface of the moon is –Titanium
• One joule is equivalent to-10 ergs
• The most efficient engine is –Electric• Wisdom teeth normally grow during the age of- 17- 30 years
• The yellow colures of urine is due to the presence of –Urochrome.
• Life of RBC in human blood is of –120 days.
• How many teeth are known as milk teeth in human beings – 20.
• Colure of the skin due to presence of -Melanin
• Bile juice secreted by -Lactro meter
• The smallest cell in the human body are –Blood cells.
• Food is mainly digested in –small intestine.
• The number of ribs in human body is –24

• A nuclear reactor uses as fuel –Uranium.
• The Velocity of light was first measured by –Roemer.
• The purity of milk is checked by –Lacto meter.
• The hottest part of the flame lies in its –Non luminous Zone.
• The first life came on this earth –In Water
• An object weights maximum in –Vacuum
• Which is the semiconductor –Silicon
• Ic Chips for Computers are usually made of –Silicon
• A device used for converting AC into DC is called-Rectifier.
• The volume Urine produced in an adult human every 24 hours is-1.5Liters.
• The average Gestation period of Sheep is –150 days.
• The Smallest possible unit of a comical compounds is –Molecule
• The Vitamin which contains Cobalt is –B12
• The first metal to used by man was Copper
• All acid essentially contain the element –Hydrogen
• The main active continent of tea and coffee is –Caffeine.
• Pencil lead is made up of –Graphite.
• The human body contains the maximum amount of –water.
• The smallest bone in the human body is – Stirrup
• Total number of bones in human skill are- 30
• The hitting element in an electric iron is made of –Tungsten.• Acquired immune-deficiency syndrome(AIDS)is caused by –Virus
• The light with the longest wave length in the visible spectrum is – Red.
• In the electric bulb, the gas used is – Inert.
• Which Gland is called the master Gland –Pituitary
• How many Bones in adult human body –206
• How many Bones in child’s body –300
• What is the temperature of normal human body –36.9C.
• Which is the helps in clotting in blood –Vitamin K.
• Total volume of blood in normal adult human body 5-6iiters.
• Red blood corpuscles(RBC)are formed in the bone marrow
• The largest part of the human brain is the –cerebrum
• What is main component of the bone and teeth –Calcium Phosphate
• The main constituent of hemoglobin is –Transport Oxygen
• The main function of Hemoglobin is - Transport Oxygen.• The chemical name of table salt is-Sodium Chloride.
• Chemical name of Vitamin C is –Ascorbic Acid.
• Bone is used as fertilizer because it contains the plant nutrient-Phosphorus.
• Baking soda is-Sodium Bicarbonat.
• Plaster of Paris is made from-Gypsum.
• Which element is common in all acids-Hydrogen.