Left nose or Right – does it matter for Influenza?

Yes it does. A recent study in Belgium, done on 244 patients with Influenza like illness (ILI)  and/or acute Respiratory Tract Infection (RTI) showed this variability. This short report published at Virology Journal this January, described statistically, how the viral load,  varies with sample collection pattern and the load of human DNA present in the sample.

Typically samples for suspected Influenza is collected from nasopharyngial swabs, aspirates and washes. But here, mid-turbinate flocked swabs were taken. On a previous article by mayo clinic, this less invasive, patient friendly sample collection procedure showed very good response. Adults can safely collect samples from themselves and children at home, which effectively decreases the out-patient rush during flu season.

FIGURE 1
Patient instructions for midturbinate nasal swab collection.

This report has several shortcomings still. No specific data on left or right handed person, or any biological difference between two nostrils, is yet included, but may be solved on final version. Yet, this study is very important in Influenza study. till date, Flu surveillance studies focus  on viral characterization, typing. But quantity measurement can also be a effective endpoint related with the quantitative PCR variability.

The report ends up with proposals on proper sample collection, multiple swabs from one and both nostrils etc. Viral quantity measurement in the studies of HIV, Hepatitis C virus has already been successful. For Influenza, this study opens a door to study more on a standard procedure for sample collection.

Also posted at : http://www.sciencenutshell.com/left-nose-right-matter-influenza/

Woman cured of an immune genetic disease, spontaneously!

Biotechin.Asia

A 9-year old girl who had a very rare genetic immune disease called WHIM while growing up, was apparently cured in her 30s, spontaneously. Scientists have attributed it to a phenomena called Chromothripsis or ‘chromosome shattering’ during which chromosome pairs disintegrate and reassemble themselves into random and chaotic positions, with hundreds of gene alleles getting lost forever in the shuffling. Researchers claim that the woman might have got rid of the defective gene during one such scrambling of DNA in one of her blood stem cells. Their findings were published in the journal Cell.

The little girl was the first known case of a person who suffered from WHIM (Warts, Hypogammaglobulinemia, Infections, and Myelokathexis) syndrome back in 1964 and was documented in two reports in The New England Journal of Medicine. People who are afflicted with WHIM suffer from recurring infections due to poor immunity and when they grow into…

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Friends, Let’s get some EBOLA killed !

In response to The Daily Post’s writing prompt: “(Your Thing) for Dummies.”

I found the most favorite daily prompt on the least free day! I am quite sick, fever it is, and MUST rest now. But when I saw the prompt, I tried to do something… I can’t write much, so thought to share any video for my friends on “My Thing” “Biology”. And where rest? there’s tons of videos on PCR, Cell Biology, Cell structure, DNA replication, Protein synthesis etc etc etc..I started watching and knew a lot! Ha ha ! How many will I share?

Then found this video, on Ebola Virus, may be most media focused after Swine flu and HIV, or may be more than them! But is Ebola THAT important? This video will definitely answer that, and for that, PLEASE watch the video till end 😀

There is also a take home message from the sick teacher of today’s class. That is: “If YOU ALL want to stay out of deadly diseases, just stay in the NATURE’S LAW. Don’t make tree’s, animal’s, virus’s, bacteria’s lives hell; they would definitely make yours!”

Enjoy the class 🙂

learning virus genome is fun!

My Biologist and Non-biologist friends, you know, viruses are only microbes, who have either DNA or RNA as genetic material, never both…and for the complex world to be easier, I found a video out there.

you can also check out this awesome site,  http://www.shomusbiology.com/index.html by Suman Bhattacharjee

Hope you enjoy 🙂

also posted at : http://www.sciencenutshell.com/learning-virus-genome-fun/

6 Tips for a successful ELISA

Being bio-reactive

ELISA are immunoassays widely used in biomarker detection and validation. They have been used in research and clinical settings for more than 40 years, and they allow to quantify, in a simple way, thousands of biomarkers. New ELISAs are being developed every day, either for new biomarkers or new species. They can also be used to detect contaminants in food, water or industrial processes.Raybiotech ELISA Kits by tebu-bio

Technology-wise, there are several types of ELISAs, depending on whether they are based on double (or sandwich) antibody detection, direct detection, competitive detection, etc. It is not the scope of this post to enter into details about the different formats that an ELISA can have, but if you think that you need this info, feel free to suggest that I do a post on that!

Nevertheless, the aim of this post is to give some hints on how to reach the best result for your ELISA…

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Good News for Clinical Laboratory Scientists: iPad App For Medical Laboratory Pipetting Protects Lives and Jobs! Read more: Good News for Clinical Laboratory Scientists: iPad App For Medical Laboratory Pipetting Protects Lives and Jobs!

just wow 😀 😀

Subject alerts

Dark Daily Donna Marie Pocius 23 January 2015

Scientists at the prestigious Cambridge, Massachusetts-based Whitehead Institute for Biomedical Research at the Massachusetts Institute of Technology recently unveiled the iPipet system. This in an innovative system which employs tablet computers such as iPads to guide the tedious and often dangerous task of manual pipetting.

Read more

Request the source article from Information & Research Services (QH Staff only)

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Metagenomic virus detection in clinical specimens : a new era

As seen in this Chinese doll picture, the organisms in our nature is not only they look like, they live in an intermingling fashion, which calls for the whole study of them , or the Metagenomics. With the advancement of newer sequencing methods, the area of metagenomics has largely expanded, or on the other way, the broad-range studies of microorganisms in genetic level has geared up the newer and newer inventions of high-throughput sequencing systems. Okay, what it is, Metagenomics is a beautiful study, nothings less important here.

But when we come to the world of viruses, they are not the main ones in the environmental pool. Sure they are present there, but the main sphere of viruses are living cells as they only live well in intracellular condition. In many cases, viruses enter in a body, replicate here, fight with each other or live in peace, spread infections, and when they are shed, from the host body, they are not the same, they have mutated and changed by this time. This made the theory of Quasispecies. So, the environmental study of metagenomics can not be applied here.

Another matter is the studies of Zoonosis. Everyday, there is a new evidence coming out, about, this or that newly emerged disease has come from this or that animals. When a case is found, with no former case, its very difficult to find out the causative agent. So, the specific and effective study of Metagenomics from clinical sample is very important.

This study comes forward with a very new method, tissue-based unbiased virus detection for viral metagenomics (TUViD-VM). Formerly there were many methods available for viral metagenomic study as Hybridization, Sequence independent single primer amplification( SISPA), Arbitrary primed PCR (AP-PCR), Rolling circle amplification etc. This study group from Robert Koch Institute, Germany, not only established a new protocol, but also have shown the efficacy very well.

Schematic description of tissue-based universal virus detection for viral metagenomics protocol. Estimated durations of each step are shown in parentheses. The protocol takes 12 h to complete

This study compared the protocol in different virus groups, different hosts, different extraction, PCR and sequencing methods. The only limitation of this study might be the higher cost for sample processing. It also need high capacity computational analyses as both the viral and host genomes are mixed in a clinical sample gene pool. The researchers nullified the constrain, as sequence data for mammalian hosts are very limited.

This study opened a new era of viral study. Where a newly emerged disease call for an outbreak, and we find nothing in our hands to search the causative agent, as we saw for Ebola just a few days earlier, an established protocol of tissue based viral metagenomics can  help a lot!

Links : http://wwwnc.cdc.gov/eid/article/21/1/14-0766_article

            http://onlinelibrary.wiley.com/doi/10.1002/rmv.532/abstract

also posted at : http://www.sciencenutshell.com/metagenomic-virus-detection-clinical-specimens-new-era/

Next Generation Genome Sequencing – Today And Tommorrow

When Human Genome Project was running, and finally done in 2003, I was in school. The total thing was a sci-fi to me. As they are pouring a drop of blood or a string of hair, and  getting the whole secret story of human written in ATGC ! There were several fun facts published that time, like the distance of sun and earth relative to the length of whole DNA, or the about the mass of it. Sequencing DNA seemed very easy to me until I entered in the Virology lab, where we answer about any unknown thing, like, ahh, do the PCR and sequence it!

In molecular Biology, this thing is common for all organisms, doing PCR and sequencing. The genome is consisted of RNA (only RNA for some viruses) and DNA, but all tends to DNA sequencing, as the RNA is converted into DNA by reverse transcription. DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases—adenine, guanine, cytosine, and thymine—in a strand of DNA.

DNA sequencing is largely done by Sanger sequencing along with Maxam-Gilbert sequencing in some little cases. When we talk about sequencing, we usually refer to the chain termination or Sanger sequencing method. We use this in our lab too, for sequencing several parts of viruses to characterize them. I have never done any whole genome sequence, but some here do it by sequencing part by part and then aligning them.

When I came to know about Metagenomics and Next generation Sequencing that sci-fi feeling came back, but in a polished and I-can-do-it version 🙂 So, I decided to share them with my friends, who may know them already. Here I am skipping the whole thing about Sanger method, just adding a schematic picture to differentiate the two generations.

Figure 1.

http://circgenetics.ahajournals.org/content/6/4/427.figures-only

I collected some stuff from Wikipedia and technique types were from just one source, EMBL-EBI website, as anyone can take the online course at a glance. But there are many other methods, maybe I’ll discuss some if the mood comes back 🙂

Next-generation sequencing (NGS), also known as high-throughput sequencing, is the catch-all term used to describe a number of different modern sequencing technologies, which are given below-

Illumina sequencing

Illumina dye sequencing was based on inventions of S Balasubramanian and D Klenerman of Cambridge University. Here, the slide is flooded with nucleotides and DNA polymerase. These nucleotides are fluorescently labelled, with the colour corresponding to the base. They also have a terminator, so that only one base is added at a time. An image is taken of the slide. In each read location, there will be a fluorescent signal indicating the base that has been added.  The process is repeated, adding one nucleotide at a time and imaging in between. All of the sequence reads will be the same length, as the read length depends on the number of cycles carried out.

http://www.nature.com/nbt/journal/v29/n11/fig_tab/nbt.1996_F1.html

This technique offers a number of advantages over traditional sequencing methods. Due to the automated nature it is possible to sequence multiple strands at once and gain actual sequencing data quickly. Additionally, this method only uses DNA polymerase as opposed to multiple, expensive enzymes required by other sequencing techniques.

454 sequencing

The system relies on fixing nebulized and adapter-ligated DNA fragments to small DNA-capture beads in a water-in-oil emulsion. The DNA fixed to these beads is then amplified by PCR. Each DNA-bound bead is placed into a ~29 μm well on a PicoTiterPlate, a fiber optic chip. A mix of enzymes such as DNA polymerase, ATP sulfurylase, and luciferase are also packed into the well. The PicoTiterPlate is then placed into the GS FLX System for sequencing.

http://www.csulb.edu/~cohlberg/DNAsequencing.html

Ion semiconductor sequencing

Unlike Illumina and 454, Ion torrent and Ion proton sequencing do not make use of optical signals. Instead, they exploit the fact that addition of a dNTP to a DNA polymer releases an H+ ion. Like 454, the slide is flooded with a single species of dNTP, along with buffers and polymerase, one NTP at a time. The pH is detected is each of the wells, as each H+ ion released will decrease the pH. The changes in pH allow us to determine if that base, and how many thereof, was added to the sequence read.

http://dnamismatch.com/dna-sequencing/next-generation-methods/ion-semiconductor-sequencing/

NGS is significantly cheaper, quicker and is more accurate and reliable than Sanger sequencing. It needs least amount of template DNA, as mainly works on the synthesis process, where Sanger methods depends on chain termination. only one read (maximum ~1kb) can be taken at a time in Sanger sequencing, whereas NGS is massively parallel, allowing 300Gb of DNA to be read on a single run on a single chip. It is also useful for shorter and repeated sequences. Today, Next Generation Sequencing are just outside our lab door, and tomorrow we will slide the door and let it in! 😀

also posted at: http://www.sciencenutshell.com/next-generation-genome-sequencing-today-tommorrow/

An answer to getting rid of HIV?

Biotechin.Asia

Scanning electron micrograph of HIV-1 budding (in green) from cultured lymphocyte. Source and photo Credit: C. Goldsmith Content Providers: CDC/ C. Goldsmith, P. Feorino, E. L. Palmer, W. R. McManus - This media comes from the Centers for Disease Control and Prevention's Public Health Image Library (PHIL), with identification number #10000. Scanning electron micrograph of HIV-1 budding (in green) from cultured lymphocyte. Source and photo Credit: C. Goldsmith Content Providers: CDC/ C. Goldsmith, P. Feorino, E. L. Palmer, W. R. McManus – This media comes from the Centers for Disease Control and Prevention’s Public Health Image Library (PHIL), with identification number #10000.

Researchers have been working on targeted therapies to combat HIV for a long time now. Early last year, scientists from USA showed that the addition of an immunotoxin significantly reduced the number of cells with HIV in multiple organs. They had discovered a toxin that kills HIV-infected cells, specifically. This has paved way for researchers around the world to probe more into targeted therapies for viruses as dangerous as HIV. An HIV-specific poison can kill cells in which the virus is still reproducing despite antiretroviral therapy. This study, performed in mice, was published in January, 2014 in PLOS Pathogens

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Enteroviruses as causative agents in type 1 diabetes: loose ends or lost cause?

there’s a lot thing to know!!

MicrobiologyBytes

Coxsackie virus I’ve just been marking some student work about Group B coxsackieviruses as the cause of type 1 diabetes (T1D). This is a very old story, going back to the 1960s. In 1973 the discovery that Coxsackie virus B4 could induce insulin-dependent diabetes in suckling mice caused a lot of excitement, some of which is still bubbling away. The problem is that it is clear that Group B coxsackievirus infection in humans does not “cause” diabetes – in the sense of get infected, get diabetes. But the link won’t go away, so what is the connection between CVB and type 1 diabetes. A recent paper proposes a model which could explain the involvement of CVB as a contributory factor – if not the cause – of diabetes:

Summary:

  • Human β cells express enterovirus entry receptors and can sustain enterovirus replication.
  • Acute infection of β cells can lead to extensive islet damage…

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