Dec 5, 2011

Virus size and Its Relationship to Genome Nature and Envelop

Preparation of notes during examinations preparation is one of the most tedious tasks, but key of my happiness is that it always give me some daunting clues about facts which are not provided in books. While I was preparing for my mid-terms at university. I came to know a great correlation in infection causing viruses size with other components. It is non-statistical analysis, performed on very limited number of viruses. But damn interesting.

Sizes of medically important viruses
These viruses are well-known and volumes of literature is available on all of them. Their sizes vary from 10nm to 380nm. But important thing to consider is that most of viruses concentrate from 50-100nm sizes. So viruses at other both extremes are very very less in number, but rare means something unique in all. So, I will be discussing them one by one.

DNA viruses
These viruses are in range of 50-100nm diameter, with Herpes virus and Pox virus as exceptions which are moderately larger than this range. Herpes and Pox viruses are different from other viruses in a sense that their sizes are very much variable as compared to other DNA viruses. Most of DNA viruses have size variation of about 10nm e.g Adenoviruses (70-80nm), Papovaviridae (45-55nm), while Herpes virus and Pox viruses are ranging from 120-150nm and 170-260nm respectively. Exceptions like Hepadna-viruses are discrete 42nm particles with partially double stranded genomes and associated reverse transcriptase enzyme.

RNA viruses
RNA viruses are categorized into (i) ssRNA and (ii) dsRNA viruses. RNA viruses which are single stranded can be of +ve polarity (sense) or -ve polarity, based upon their ability to translate directly or possession of RNA trancriptase association to RNA genome. 
When we check RNA viruses, we find them in all ranges of sizes. They are as small as 20nm diameter (Parvoviruses) and highly large viruses such as Rhabdoviridae. It was a thing of interest that +ve sense RNA viruses were relatively smaller in size as compared to -ve sense RNA viruses. For example, viruses of Flaviviridae are largest to all in +ve sense viruses, which vary in size from 40-70nm (although coronavirus is also larger than this but its exception in all). While viruses of dsRNA are also present at this upper limit, Reoviridae members vary in size from 60-80nm, almost same size as of Adenoviruses of ds-DNA viurses. As, size among RNA viruses start increasing from 80nm, virus type completely shifts to -ve sense, size variability begin to increase which become highest at Rhabdoviridae. Rhabdoviridae members are ranging from 130-380nm in size in one dimension. Another exception at this extreme of size is that genomes of Arenaviridae members can be linear or circular and these are the only viruses which have ribosomes in side nucleocapsid.

Size: A direct impact on viral symmetry
Most remarkable finding which was observed is that as sizes increase viruses start to be asymmetrical. Smallest viruses are very fine with ico-sahedral symmetry. And this thing was found common in all viruses including DNA and RNA. The largest viruses which were observed with icosahedon were Adenoviruses among DNA viruses and Reoviridae members of RNA viruses. Then, helical symmetry begins, which was optimistically ended at 180nm. Coronaviridae members are largest and most variable members with helical symmetry. Now, irregular shaped viruses with complex dimension appear. They are two which are Pox virus and Rhabdovirus. Rabdoviruses are bullet shaped having length (130-380nm) and diameter (50-95nm).

Viral envelop is size dependent
This was observed that viruses with smaller sizes were without any kind of envelop and outermost covering was capsid protein. As sizes continue to increase, envelop begins to incorporate in viral structures. Envelop was found to impart asymmetry in structure and viruses were begin to be more variable in shapes as compared to smaller sized viruses. It was also observed that all viruses which have historical importance such as Herpes and Pox Viridae members contain an envelop outside their nucleocapsid, which is usually host derived.

May 8, 2011

Test to Help Speed-Up Distinguishing Between MRSA and MSSA

Health experts will now be able to save time when trying to determine whether Staphylococcus aureus infections in patients are methicillin resistant (MRSA) or methicillin susceptible (MSSA), as the U.S. Food and Drug Administration (FDA) announced on Friday that it has cleared a test that will allow a speed-up in the process.

There are various types of Staphylococci bacteria, some of which are easily treated with antibiotics and some that are resistant to this treatment, such as MRSA.

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Prostate cancer biopsies linked to risk of serious infection

The specter of prostate cancer is alarming enough – and it just got even more alarming. Some doctors are reporting that men who get biopsies for prostate cancer may be putting themselves at risk for infection by drug-resistant bacteria.
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New contraceptive in the pipeline

It's still at least a decade off, but Professor John Aitken, says the gel could be applied to a small, pliable sponge and inserted in the vagina up to 48 hours before sexual intercourse.
As soon as semen makes contact with the gel, the sperm are paralysed and any STI-causing organisms are killed.
At present, there are not any "local compounds" available that can be applied to prevent STIs, just the "classic" spermicide, which was a "crude inhibitor of fertility", Prof Aitken said.
"Women who use a lot of this stuff, especially commercial sex workers, are significantly more likely to get HIV than women who don't use it ... it just destroys everything around it," he said.

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Gut microbes: What's your type?

When European researchers set out to use gene sequencing to catalog the hundreds of species of microbes in the human gut, they expected to find variation between individuals and perhaps even between geographic groups -- but they assumed that there would be a large number of different possible combinations of bacteria.

Instead, said bioinformatics expert Peer Bork of the European Molecular Biology Laboratory in Heidelberg, Germany, gut bacteria seem to cluster into just three distinct and stable combinations that show up across populations from a variety of backgrounds -- a discovery that could have implications for medicine in the future. 

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Feb 10, 2011

Gut microbes influence behavior

Gut microbes acquired early in life can impact brain development in mice and subsequent behavior, such as decreasing physical activity and increasing anxiety, according to a study published this week in the Proceedings of the National Academy of Sciences.

This paper opens the door to new studies in at least two directions," Yale University microbiologist Andrew Goodman, who was not involved in the research, told The Scientist in an email. "First, determining how differences between complete host-associated microbial communities lead to differences in behavior, and second, exploring the contributions of microbes during specific developmental periods in the host."

Gut microbiota often colonize their hosts early in life, either during pregnancy or following birth, and play an integral role in the health of developing organisms. Previous research has shown that the bacteria affect the development of liver function, the protection epithelial cells afford underlying digestive tissue, gut regulation and the growth of new capillary blood vessels. But this is the first time gut flora have been linked to brain development and behavior.

Harmful microbial infections, on the other hand, have been linked to neurodevelopmental disorders, including autism and schizophrenia. And rodents infected by microbial pathogens before and after birth demonstrated behavioral abnormalities, such as anxiety-like behavior and impaired cognitive function, leading Rochellys Diaz Heijtz, a neurobiologist at the Karolinska Institute in Sweden, and her colleagues to wonder if the gut's normal microbial residents may similarly influence brain development.

The researchers tested exploratory activity in germ-free mice and mice with normal gut microbiota by tracking their movements across open space. They also tested anxiety of the two groups in two classic rodent behavioral tests -- the light-dark box and the elevated maze. Spending more time in lit areas and along unwalled, elevated maze portions equated to less anxiety.

Germ-free mice appeared to be more exploratory than mice with normal microbiota, venturing farther and to more areas of the space provided. Germ-free mice also spent more time in the light and engaged in riskier behavior in the maze, indicating they suffered from less anxiety than their microbe-filled counterparts.

The team then infected germ-free mice with normal gut microbiota when they were born to test whether the gut flora could alter the mice's activity and anxiety levels. Sure enough, the newly infected mice spent less time exploring and engaging in risky behavior, like the normal mice in the initial experiments. The results further supported the argument that the microorganisms can affect brain and behavior when introduced early enough in development.

"These microorganisms communicate in a systemic fashion to the developmental programming of a new individual and can influence fundamental aspects of behavior," said Diaz Heijtz. "We should start to consider the possibility that the microbiome and/or its composition may contribute to psychiatric problems."

Looking more closely at the gut flora's effects on the brain, the researchers found that germ-free mice had lower turnover rates of certain neurotransmitters in the striatum, the part of the brain involved in the regulation of motor and cognitive function, than in mice with normal gut microbiota. There were also differences in the levels of key synaptic-related proteins and signaling molecules involved in central nervous system communication.

"This all means that there has been an evolutionary adaption of host-microbe interactions to the most complex organ in the body, the brain," said coauthor Sven Pettersson, a neuro- and microbiologist at the Karolinska Institute.

The scientists stress that there are still many unanswered questions and further research is needed to understand the broad implications of the research. For example, the study didn't distinguish the effects of maternally inherited microbes from those acquired shortly after birth, Goodman noted. "It is also not clear whether microbes residing in other body habitats are playing a role," he said, such as those located in the nose, ears, mouth or vagina.

Next up, Diaz Heijtz and her colleagues are hoping to pinpoint which gut microbiota are affecting brain development and behavior. They also plan to identify which brain cells are responding, and work out the details of the signaling pathways that allow the microbiota to communicate with the brain.

Read more: Gut microbes influence behavior - The Scientist - Magazine of the Life Sciences