fMRI studies help to discover more about grief

I read this very interesting article on studies performed by clinical psychologists on 23 women who were divided into 2 groups based on their ability to handle grief. All of them had lost a loved one (mother/sister) to breast cancer and while some were able to accept it and move on, others were still in grief (state called 'complicated grief'). They were shown photos of their loved one or a stranger along with a word that was either grief-related or otherwise. The normal group, when shown the pic of their loved one, had activity in the region of the brain known to process pain. While the surprise was that the group belonging to 'complicated grief' not only had activity in those regions but also in the nucleus accumbens, the region of the brain related to pleasure. Mary-Frances O'Connor of the University of California, Los Angeles, who conducted this study, said this would help find a cure for people with this condition. Read more about it here.

In the news...

Latest lead in finding cure for Parkinson's
Researchers at Griffith University have recently published a study in the Journal Stem Cells, which could be a major step in finding the cure for Parkinson's disease. They created lesions in the brains of lab mice, similar to those found in Parkinson's patients due to the disease. They then planted adult stem cells from the olfactory nerves of patients in the brains of the mice and were able to see an improvement in the behavior of the mice, like regaining the ability to run in a straight line. The stem cells were able to differentiate into dopamine producing brain cells. These cells are damaged in the brains of Parkinson's patients.

Breaking News: Oldest mother found

Researchers in Melbourne, Australia have found, what they call, the oldest pregnant mother. This placoderm fossil is said to be 380 million years old and bears an embryo with an umbilical cord. This has proved that vertebrates have been giving birth (exhibiting viviparity) for at least 380 million years. To read the full story Click Here.

In the news: Parkinsons's Disease

• Study Links Parkinson's Disease With Chemical Exposure

Scientists have now discovered additional evidence of a connection between Parkinson's disease and long-term exposure to pesticides. Parkinson's disease strikes movements like walking, talking and writing. Symptoms of the disease first tend to appear in patients over 50. These symptoms may include tremors and muscle rigidity.

A study of over 300 people with Parkinson's found that sufferers were more than two times as likely to have had heavy exposure to pesticides over their lifetime as other members of their family without the disease.The new research observed the lifetime pesticide exposure of over 300 Parkinson's patients. Over 200 of their healthy relatives were also included in the study as a control group. The results showed that patients with Parkinson's were 1.6 times more likely to report an exposure to pesticides in their lifetimes compared with the control group.Additionally, people with Parkinson's were 2.4 times more likely than healthy people to report heavy exposure to pesticides. Heavy exposure is defined as more than 215 days over a lifetime.

A change in several genes has been identified as a precursor to the disease, however these variations are somewhat unusual and they only account for a small number of the incidence of the disease. The majority of cases are believed to be the result of a reaction between genes and the environment. Pesticides may be contributing to nerve cell death in some people who have Parkinson's. It is unlikely to be the only cause of the disease, however.

Read the article here

• Medical Breakthrough -- Tango For Parkinson's Disease

A new study is showing how a popular dance may help patients fight some of the effects. Researchers at Washington University are studying a unique treatment for those afflicted with Parkinson's -- the tango.

"It seemed to be a good fit because several of the movements that tango incorporates might specifically target some of the difficulties that people with Parkinson's disease have."

To tango, patients have to balance, turn, initiate steps, dance at different speeds and walk backwards.Researchers say it's these moves that help improve symptoms. Dr. Gammon Earhart says "given the challenges that they're facing on a day-to-day basis, but they come in here with such energy and enthusiasm, and they're so very, very appreciative." Researchers followed Parkinson's patients who attended 20 tango classes. The participants saw much more dramatic improvements in balance and mobility than those who did traditional exercise.
Study participants ranged from their mid-forties to age eighty-two. Researchers are now testing whether a more intense two-week dance course could benefit patients even more. The study was funded by the American Parkinson Association.

Read the article here

Tutorial Series

I will be visiting basics of computational biology in a series of tutorials that I will be preparing based on my knowledge of the subject. These will include sequence analysis methods, microRNAs: the biology, predictions and functions, modeling and simulation methods, basic genomics and much more... So keep reading and please feel free to post any comments...

miRNA companies

Asuragen Launches New Company Focused on miRNAs. Read more here.

Columbia University Medical Center and Rosetta Genomics Announce Columbia University's Submission of the First Cancer Diagnostic Test Based on Rosetta Genomics Proprietary MicroRNA Technology for Approval to the New York State Department of Health Clinical Laboratory Evaluation Program

new softwares for bioinformatics

RNACompress: A novel way to compress RNA sequence and secondary structure

Background
With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression.

Results
RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1) present a robust and effective way for RNA structural data compression; (2) design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers) compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective.

Conclusions
A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool for academic users. Extensive tests have shown that RNACompress is a universally efficient algorithm for the compression of RNA sequences with their secondary structures. RNACompress also serves as a good measurement of the informational complexity of RNA secondary structure, which can be used to study the functional activities of RNA molecules.

in the news...

• Merck & Co. Inc. (MRK) said two studies showed genetic susceptibility to obesity involves changes in entire networks of genes, not just mutations in several specific genes.Visit here for more.
• First study to show that microRNAs may also play a role in synaptic plasticity and the modulation of translation.Michael Greenberg's group at Harvard Medical School and Austrian colleagues hypothesized that microRNAs are involved in the regulation of protein synthesis in neuronal dendrites. To test this, they overexpressed a hippocampal microRNA, miR-134, and found that it reduced the size of dendritic spines by inhibiting a protein kinase that induces spine development.Read the paper here.
  

today in microRNA Research...

microRNAs play an important role in limb(fin) regeneration.
When the zebrafish is injured, the level of microRNA miR-133 drops and regeneration begins. In uninjured zebrafish, the level of this microRNA is quite high. This research was performed by researchers at Duke University and will feature in the 15th March issue of Genes & Development.
Read more here

events coming up...

Developmental Biology of the Sea Urchin XVIII
April 23-26, 2008
Marine Biological Laboratory, Woods Hole, MA
Click here for more information and to register

One day conference on sleep regulation and role of gene susceptibility in sleep disorders.
Jun 20, 2008 • 8:30 AM - 7:30 PM
The New York Academy of Sciences, 7 World Trade Center, 250 Greenwich St. at Barclay St., 40th fl.
Click here for more information and to register

hiatus...

Its been almost a year since I posted. Life moves fast and progress in Science, faster...

I am currently in my first year PhD Computational Biology at Carnegie Mellon University. You can check out what I work in RIGHT HERE.

You can come back daily for latest in the field and some interesting posts from me.

broadcast of the day:

Macaque Genome Analysis Will Help Find Human Disease Genes
The rhesus macaque (Macaca mulatta) is physiologically similar to humans. Its genome was sequenced in 2005 (2.9 billion DNA base pairs). The humans and chimpanzees are so closely related(6 million years) that a comaparative genomic study is not as informative as using the macaque. The different studies involve studying the common genes between these 3 genomes, differences between the Indian and Chinese macaques (for example, Chinese macaques develop AIDS-like symptoms more slowly than Indian macaques).

Full Article
Medicinal leeches have been misclassified for centuries
Until now, the leeches were assumed to be the species Hirudo medicinalis, but new research reveals they are actually a closely related but genetically distinct species, Hirudo verbana. Wild European medicinal leeches are at least three distinct species, not one.
Full Article

Human sperm made from bone marrow

Stem cells from the bone marrow have been used to create immature sperm cells. It is expected that this research can be be used in the future to find a cure for male infertility. Currently, mature sperms have not been created. Of course, with the bans, moral, ethical issues involved in stem cell research in addition to the scientific fact that manipulating stem cells can cause lasting genetic changes that may not all be desirable, its too early to jump to any conclusions.

paper of the day:

"A Systems Biology Dynamical Model of Mammalian G1 Cell Cycle Progression"
Thomas Haberichter, Britta Mädge, Renee A Christopher, Naohisa Yoshioka, Anjali Dhiman, Robert Miller, Rina Gendelman, Sergej V Aksenov, Iya G Khalil1 & Steven F Dowdy

The paper describes a combined experimental and computational approach used to understand progression of the mammalian G1 cell cycle, one of the phases in mammalian cell reproduction and tumor growth.
The GNS software was used to quantitatively model the cell cycle progression and then experimentally verified using cultured cells. An excellent example to demonstrate the power of the combinatorial approach.