Advanced Nucleic Acids Research

Eukaryotic chromosomal DNA is packaged into nucleosomes, each consisting of 147 bp wrapped tightly around a core histone octamer . A recent genome-wide high-resolution microarray study states that ~80% of the yeast (Saccharomyces cerevisiae) genome consists of (translationally) positioned nucleosomes .This result is consistent with the conclusions of an earlier microarray study and a subsequent parallel sequencing study in which only portions of the yeast genome were examined. There are a variety of possible mechanisms that could lead to nucleosome positioning. For example, the base-pair-specific binding of a non-histone protein to DNA could exclude a nucleosome from that DNA region. Then, a regularly spaced array of adjacent nucleosomes would be positioned in the vicinity of the DNA-bound non-histone protein. Alternatively, an array of several regularly spaced nucleosomes could form adjacent to one sequence-positioned nucleosome. These mechanisms have been called statistical positioning . Statistical positioning would be most effective in yeast where the DNA linkers between adjacent nucleosomes are on average very short, only 18 bp for a 165-bp nucleosome repeat length (NRL) , and therefore not much statistical variation in nucleosome linker lengths can occur. Nucleosome positioning could also result from the boundary effect provided by the attachment of DNA regions to nuclear structures , chromatin remodeling or as a result of DNA replication from a bidirectional replication origin . In addition, nucleosome positioning could result from the DNA sequence preferences of the histones themselves. It has been known for some time that in vitro nucleosomes form with high preference on certain DNA sequences (10–13) and tend to avoid other sequences .

Evidence was provided that there is a genomic code for nucleosome positioning, and that ~50% of the nucleosome positions in yeast (±35 bp) result from histone preferences for certain DNA motifs (22). A different, complementary approach reported similar results for computationally predicting the positions of positioned yeast nucleosomes based on the genomic DNA sequence (±35 bp), but concluded that only ~25% of the positioned nucleosomes can be attributed to the preferences of certain DNA sequence motifs for histones , a value considered to be too low for the existence of a nucleosome positioning code. A critical evaluation of the statistics used by Segal et al. in 2006 also suggested that the performance of the proposed nucleosome positioning code is more modest than claimed . In 2007, Lee et al. reported that there was a poor correlation between their microarray-determined genome-wide nucleosome occupancy values and the predictions by Segal et al. in 2006. However, they found that there was a moderate correlation (R = 0.44) between their measured nucleosome occupancy values and a collection of DNA structural or sequence parameters. This degree of correlation suggests that only about 19% (R2 x 100%) of their nucleosome occupancy values are represented by the DNA structure/sequence parameters that they used in their model. Consistent with these findings, it was suggested that statistical positioning (discussed earlier), rather than intrinsic positioning, largely accounts for the nucleosome positioning observed in S. cerevisiae . In addition, it was reported in a genome-wide study, that Caenorhabditis elegans, which has (on average) longer nucleosome linkers than yeast, generally lacks sequence-dictated nucleosome positioning .

Recently, a direct genome-wide comparison of in vivo and in vitro nucleosome positioning in yeast was performed using the massively parallel Illumina sequencing system . The number of reads overlying each base pair for DNA sequences extracted from nucleosomes that were excised from native or reconstituted chromatin by micrococcal nuclease was used to assess the nucleosome occupancy at each base pair. This same sequencing approach had been used earlier to assess the nucleosome occupancy per base pair of the much smaller SV40 virus genome, where it was found that unique nucleosome positions did not occur . Control experiments were also performed by Kaplan et al. , using ~40 000 synthesized 150-bp DNA sequences to validate their yeast genomic DNA results. In these experiments, competitive reconstitution and microarray analysis were used to assess the affinities of each synthetic DNA sequence for histones to show that 5-mers contained in genomic sequences that had high (or low) affinities had corresponding affinities in the synthetic DNAs. Kaplan et al. concluded from their direct genome-scale experiment that intrinsic nucleosome sequence preferences do have a dominant role in determining the nucleosome organization in vivo.


It is clear that there are apparent conflicts in the current literature on the question: are nucleosome positions in vivo primarily determined by histone–DNA sequence preferences?

In an attempt to resolve these apparent conflicts, in this study we first examined the degree of correlation between nucleosome occupancies from the yeast in vitro parallel sequencing data and those from the in vivo microarray data of Lee et al. (3). We found that nucleosome occupancies in vitro and in vivo correlate less well when the data from the two different studies are compared than when the parallel sequencing data of Kaplan et al. in vitro and in vivo are compared. We discuss a potential problem with correlation analysis using scatter plots, when large numbers of superimposed points are present. We then analyzed the synthetic DNA nucleosome occupancy data provided by Kaplan et al. in a more direct way than the authors reported and found that there is not a very good correlation between their parallel sequencing data and their microarray data for these sequences. We suggest possible causes for the apparent discrepancies between the Illumina-Solexa parallel sequencing data and the microarray data, and between the two recent genome-wide parallel sequencing studies . We precisely calculate the effect of ‘statistical positioning’ in yeast. Furthermore, we examine what it really means to say that genomes encode an intrinsic nucleosome organization that can explain approximately half of the in vivo nucleosome positions.

Improve Chi for an appetising meal

Whether you eat to live or live to eat, you'll find the experience much more enjoyable in a dining room that conforms to the principles of Vaastu and Feng Shui. When the energy flow is favourable, the flow of conversation improves, and you, your family and your guests will have an appetising meal without even realising how much the arrangement and decor of your dining room is contributing to your sense of satisfaction. In most modern houses and apartments, there is no separate dining room. So you only have a dining alcove to create the same feeling of a dining room. Since this room represents the heart of the house, it should be located at the centre of the house. It should ideally be laid out between the living room and the kitchen for good luck. Here are some more suggestions for ensuring your dining space has a favourable energy flow:

A round table symbolises heaven's blessings; a square means the blessing of earth; an octagonal table symbolises the gathering of heaven and earth with all their children. The circle, the square, and the octagon, as they have no place for the head of the table, show humbleness, compassion and love. The rectangle and the oval, on the other hand, are hierarchical, formal and less friendly. A big round table implies no number; it is the best for a large happy family. If the apartment is in a multi-storeyed building, try to ensure that the dining room is not located directly under the bathroom or kitchen of the floor above. The dining room is associated with the element Earth, so yellow and earthy tones would be most effective. Rooms with one wall shared with a toilet should not be used as a dining area. The seat of the main breadwinner, in particular, should have its back firmly against the supporting wall.

Recipe corner

Ingredients

Fusilli pasta 100g

Olive oil 50g

Tomatoes whole 2 nos

Garlic chopped 10g

Brocolli 100g

Fresh Mozzarella cheese 50g

Grated parmesan cheese 20g

Breadcrumbs dried 25g

Parsley chopped 10g

Thyme chopped 5g

Garlic powder 5g

Kashmiri chilli 1 no

Salt n Pepper

To prepare the pasta,

Heat olive oil in a pan.

Add chopped garlic and saute.

Add the broccoli, fusilli, mozzarella cheese and toss.

Add the tomatoes, parmesan cheese and garlic breadcrumbs.

Check the seasoning.

Toss once more and put in the plate

Garnish with fried Kashmiri chilli.

Serve piping hot.

Virus found to replicate four times faster than thought

Live video microscopy shows how vaccinia, a pox virus, spreads four times faster and in a different way than suspected earlier - a discovery that could open the way to the creation of better class of drugs to tackle some viruses.

Vaccinia is a pox virus and is the vaccine that was used to eradicate smallpox. Using live video microscopy.

Previously, viruses were thought to spread by entering a cell, replicating there, and then being released to infect new cells, so that the rate of spread of a virus would be limited by how quickly it could replicate in each cell.

Videos of virus-infected cells revealed that the bug spreads by surfing from cell to cell, using a mechanism that allows it to bounce past cells that are already infected and reach uninfected cells as quickly as possible.

Early after vaccinia infects a cell, it expresses two viral proteins on the cell surface, which marks the cell as infected.

When further virus particles reach the infected cell, these proteins cause the host cell to push out snake-like projections called 'actin tails,' which drive the virus particles away towards other cells that they can infect.

The particles thus bounce from one cell surface to another until they land on an uninfected cell.

In the study, the researchers prevented the virus from making the proteins needed to make the actin tails in the early stages of infecting a cell and showed that this slowed the spread of the virus dramatically.

Scientists unravel secret of pink tomato

Diners in the Far East are quite partial to a variety of sweet, pink-skinned tomatoes. Now, a researcher has revealed the secret behind this pink vegetable.

Asaph Aharoni of the Weizmann Institute's Plant Sciences department in Israel says that a mutated gene, SIMYB12, is responsible for producing these pink tomatoes.

This gene acts as a 'master switch' that regulates the activities of a whole network of other genes, controlling the amounts of yellow pigments as well as a host of other substances in the tomato.

Aharoni's research focuses on plants' thin, protective outer layers, called cuticles, which are mainly composed of fatty, wax-like substances.

In the familiar red tomato, this layer also contains large amounts of antioxidants called flavonoids forming the tomatoes' first line of defence.

Some of these flavonoids also give the tomato cuticles a bright yellow cast - the colour component that is missing in the translucent pink skins of the mutants.

Using a lab system that's unique in Israel, and one of only a few in the world, Aharoni and his team are able to rapidly and efficiently identify hundreds of active plant substances called metabolites.

A multidisciplinary approach developed over the past decade, known as metabolomics, enables them to create a comprehensive profile of all these substances in mutant plants and compare it with that of normal ones.

The research showed that the differences between pink and red tomatoes go much deeper than skin colour, says a Weizmann release.

The pink tomato also has less lycopene, a red pigment known to be a strong antioxidant that's been shown to be associated with reduced risk of cancer, heart disease and diabetes.

These findings were published in the Friday issue of Science.

Microbe's toxic hunting habits could help curb massive fish kills

microbe commonly found in waterways emits a poison not just to protect itself, but to stun and immobilize the prey it plans to eat, which could help curb massive fish kills.

The researchers studied the behavior of the algal cell Karlodinium veneficum, known as a dinoflagellate and found in estuaries worldwide.

Each year, millions of dollars are spent on measures to control dinoflagellates around the globe.

This particular species is known to release a substance called karlotoxin, which is extremely damaging to the gills of fish.

Karlodinium veneficum has been known to form large algal blooms in the Chesapeake and elsewhere, triggering an immediate harmful impact on aquatic life, including fish kills.

The researchers found that K. veneficum microbes release toxins to stun and immobilize their prey prior to ingestion, probably to increase the success rate of their hunt and to promote their growth.

This significantly shifts the understanding about what permits harmful algal blooms to form and grow.

Instead of being a self-defense mechanism, the microbes' production of poison appears to be more closely related to growth through the ingestion of a "pre-packaged" food source, the cryptophyte cell.

"This new research opens the door to reducing bloom frequency and intensity by reducing the availability of its prey"As we reduce the nutrient load feeding Karlodinium's prey and bring back the bay's most prolific filter feeder, the Eastern oyster, we could essentially limit Karlodinium's ability to bloom"This is a major environmental problem, but we didn't know why these microbes were producing the toxins in the first place.
"Some people thought they were just using the toxins to scare away other predators and protect themselves.

Nutrition in karats

Have you heard that carrots are worth the other 'karat' (as in gold!)? This is in terms of the nutritional value in them! I see plenty of carrots right now: both the red and thick, ready to be grated and made into gajrela and the smaller, thinner orange version that spells magic into salads and stir fries. Spell magic with carrot The best role that this winter vegetable can play? Chomp on one as it is an excellent snack! Carrot is an all rounder and can be a part of all the meals throughout the day! Start with a smoothie or juice. Take a salad or pulao for lunch, or then have a pickle, finish with soup for dinner and dessert. Smoothie is a quick whir of carrots, tomatoes and celery in the blender with a salt, pepper and lemon juice. If you like it, add crushed ice. Last year at a show in the US, I made these small starters with carrot: Saute some onions, ginger and garlic. Add a few chopped button mushrooms, green chillies, salt and lemon juice. Now saute some neatly cut carrot roundels. Take some paneer cut into triangles. Place carrot roundels in a plate. Over each carrot roundel spread a layer of the mushroom mixture and top it with a paneer triangle. Top them up with more green chillies or jalapenos and serve immediately. They get over too immediately as the very sight of them is attractive. The demand for gajar halwa I remember going to Mahabaleshwar for the famed strawberries some years ago. We had a chance to pull out and have orange baby carrots straight from the field. The tops were attached and they had the perfect 'picture book' look. That the strawberry field had cauliflower, cabbage and knolknol growing in the furrows is another story! I also recall the time we had an order for gajar halwa for a wedding party when I was still in the hotel industry and at that time the red carrots were still not in season. But the orange ones were available. The client was insistent about the halwa and so asked them to come over for a trial. The colour of the halwa was not the traditional red, the texture too was different, the taste too was different but gajar halwa it was! And good to eat too! Was the client happy? Yes, and we were too. Sweet somethings Gajrela, as gajar halwa is nicknamed in the northern states, is the must dessert in winter. Our neighbour in Delhi had this peculiar liking for heating the halwa on the tawa and sauteing it to a crispy brown version. And then he would ask for vanilla ice cream to top it. On a cold winter night. I have tried it and it is superb (if you are not too bothered about the nutritional content of this twosome!). This same household made the best gajar ka murabba in our neighbourhood. It seems like eons have passed since I had gajar ka murabba. I have made use of gajar halwa in fusion desserts like a gajar halwa and sponge sizzler: sponge cake soaked in orange juice and sandwiched with gajar halwa and sizzled with rabdi. I have also made a recipe where I have removed some of the sugar content of the halwa by replacing it with chopped dates. Also try the gajar barfi and gajar ki kheer but the fact remains that gajar halwa, made the traditional way with khoya and nuts, is one of the most popular Indian desserts. Pickles and preserves Coming to other creations with carrots. Gajar matar ki sabzi. Gajar matar beans ka pulao. One more Punjabi favourite is the gajar gobhi shalgam achar made with mustard oil, ground mustard seeds, jaggery and vinegar. As it ferments with passage of time, the vegetables become softer, the colour darkens and as soon as the jar is opened the mouth waters due to the aroma that comes out. I love it and have actually asked my mother to prepare a jar of it this month. Another common winter offering from up North is the gajar ki kanji (made with purple carrots more often). As kids take to the terrace for kite flying this beverage is serve straight from the matka.cool, pungent, loaded with vitamins.this is one of favourite childhood memories of Delhi. Versatile vegetable So whether it is soup or a salad (rustle one up quickly: grated carrots, sliced apples, raisins and roasted cashew nuts with dressing of salad oil and lemon juice), or a hot and soft porridge of dalia (broken wheat) boiled with carrots and peas and topped with butter, carrots prove their versatility again and again. Will end now with something sweet for the cake tin. Recipecorner Golden Pineapple Carrot Coffee Cake

n Preheat oven to 180 degrees C. Grease a 6' cake tin with oil.

n In a medium sized bowl, mix together 1 cup grated carrots, 250 grams chopped tinned pineapple. Add 1/3 cup orange juice and mix. Add 1/3 cup sugar, 11/2 teaspoon

coffee powder and mix. Break one egg into it and mix.

n Sift 11/2 cups refined flour and 11/2 teaspoons soda bicarbonate into the egg mixture. Mix with a light hand. Add 1 teaspoon cinnamon powder, a pinch of salt and mix. Add 3 tablespoons oil and mix.

n Pour the batter into the greased cake tin.

n In another bowl mix together 1/3 cup finely chopped walnuts, 1/3 cup sugar and 1/2 teaspoon cinnamon powder. Sprinkle this over the cake batter.

n Bake in the preheated oven at 180 degrees C for twenty to twenty

five minutes.

n Cool slightly. Slice and serve.