Posts tagged: Biology

On a personal note: cancer genomics and personalized medicine

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Special issue GB cover-page-001

When I was three years old my grandma passed away after a long fight with cancer. I should disclaim quickly: it never affected me greatly, since I was too young to remember anything. I know, though, that that experience was a gruelling one for my mum, who cared for our grandma during the therapy – battle with cancer ain’t pretty in general, and it was even worse then.

It would of course be easy to blame the health system of the communist regime in which we lived at the time but the truth is that the treatment strategy was pretty much the same all over the place: surgery, radiotherapy, chemotherapy. It doesn’t work? Let’s try harsher treatment. And the understanding …

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Commonality and what is the hydrogen atom equivalent for cell shape?

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Stentor image 2 for cell geometry

The design principles of cell shape are the main focus of Wallace Marshall’s lab at the Department of Biochemistry & Biophysics, UCSF. As the inaugural contributor to our series on Cell geometry  (see: “Origins of cellular geometry”) he discusses in this guest post the role of mathematical modelling and the lessons of physics in the context of a new review article by Fred Chang and Kerwyn Casey Huang “How and why cells grow as rods”, just published in the series.

 

Predictive models are the difference between alchemy and chemistry. Everyone seems to agree that simple, quantitatively predictive models, of the type seen in physics, are something we should strive for in cell biology.

Just collecting lists of …

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July blogs digest: Impact Factors, swimmer’s itch, dodos, and more

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Impact factors planet

It’s been a bumper month on the BioMed Central blogs, so we wouldn’t be surprised if you’ve missed a few posts. Not to worry though, as we’ve pulled together all the highlights right here.

The new Impact Factors are coming…

(Or rather, they’ve now arrived!) Now is the time of year when journal editors all over the world sit repeatedly clicking ‘refresh’ on their browsers. Up? Down? Staying the same? What will happen to their journal’s Impact Factor when the Journal Citation Report is published? Diana Marshall, Senior Managing Editor of the BMC series, wrote about how the new Impact Factors will affect her journals, and the publishing world as a whole.

Swimmer’s itch: sailors, fishermen and swimmers beware

For those in the …

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Microbial monitoring: health forensics for the modern age

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Metadata plot

A new paper published in Genome Biology today uses smartphone tracking and additional observations to piece together a staggering amount of information about the research subjects and their individual microbiomes. In this guest post, Jack A Gilbert, Associate Professor at the University of Chicago and Group Leader at Argonne National Laboratory, delves into this promising new avenue of research and data collection.

At the beginning of September 2013 I weighed about 205lbs (92kg). I decided to do something about my weight, for my health and for the sake of my family and of course I approached this plan as a scientist. For me that meant parameterizing my inputs and outputs so I could control what I was doing to …

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Small microbes, big microbiome

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Microbiome logo

Our own bodies are teeming with microorganisms, not to mention those present in the environment we live in. Every time we touch something we transfer microbial life from one place to another. Understanding the genetic make-up of these microbes and how they interact with one another is crucial to increase our knowledge of all life forms and all environments on the planet.

 

Microbiome research involves identifying and characterising the genetic material of microorganisms found in a particular environment. This relatively young field has seen an explosion of research in the last few years, and is rapidly growing as more is discovered about the uses of microbiome data and methods and protocols are developed.

 

Scientists have been studying the microbial life which exists …

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Beyond ENCODE – let’s continue the conversation

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As the human genome sequence was completed, so the deep analysis of it began in earnest with the ENCyclopedia Of DNA Elements (ENCODE) project – intended to identify all functional elements in the human genome.

The project involved a worldwide consortium of research groups and the data emerging can be accessed through public databases. BioMed Central has published a selection of the early findings.

ENCODE initiatives lead to modENCODE a project aspiring to identify the functional elements in the genomes of the model organisms Caenorhabditis elegans (nematode) and Drosophila melanogaster (fruit fly). The extension of the ‘ENCODE approach’ to other model organisms allows further biological validation of the findings coming from the human genome project.

And building on ENCODE doesn’t …

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Cancer and diet – how to ask the right questions

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Apple&cells_2014_all green_small

In the panel discussion at the end of the first BioMed Central conference on Metabolism, diet and disease, the panellists confronted the overwhelming evidence for a link between obesity and cancer. The panel discussion at the second picked up where the first left off – Can cancer be prevented by diet?

The only categorical answer came from Stephen O’Keefe, starting from the epidemiology that shows a 100-fold difference in colon cancer risk between African Americans (high) and rural Africans (low). If you switch their diets – and he has done the experiment – the gut microbiota, he reports, switches within two weeks, with known carcinogens going up in the guts of the rural Africans and conversely down in African …

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June blogs digest: Alcohol and football, eating disorders in men, irreproducible research, and more

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Alcohol advertising Warsaw

Missed out on some of our posts in June? No need to trawl the archives – we’ve pulled together the highlights for you right here.

Do we need a red card for alcohol advertising in football?

With the World Cup kicking off on 12th June, we braced ourselves for the highs and lows of a month of football. But getting bitten by Luis Suarez might not be the only danger of the tournament. In a guest post, Dr Jean Adams, a Senior Lecturer in Public Health at Newcastle University, UK, told us about her latest research into alcohol advertising in football, published in BMC Public Health.

The perfect body? How eating disorders and body image are a threat to …

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Word of caution: a new method to study RNA-seq biases

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Shaury Nash CC BY-SA

As next generation sequencing methods quickly become ubiquitous tools of genomics, more and more effort is directed to understand what are the limitations of these approaches. These limitations present themselves quite often in the form of coverage biases.

Last year Genome Biology published a study from David Jaffe and colleagues that looked at coverage biases in DNA sequencing. The authors used a suite of computational tools for bias assessment and applied them to a number of commonly used technologies. It turned out that, for instance, PacBio coverage is the least biased; and that high- and low-CG regions and long runs of homopolymers are very prone to coverage biases. They emphasized that the presence of such biases may lead to …

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Can you show us that again please?

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Drosophila

For almost thirty years, David Stern has been obsessed with the fact that male fruit flies ‘sing’ to females. His work on this problem, published today in BMC Biology, has got him thinking about reproducibility in science. In this guest post, he sets out his prescription to help scientists check whether research results are reliable

As an undergraduate at Cornell in 1985, I looked for a research problem that combined my interests in genetics, evolution, and behavior. Kyriacou and Hall had recently reported that the period gene, which regulates circadian rhythms, also controlled a rhythm of fruit fly courtship song and that evolution of period explained a species difference in this courtship song rhythm. This seemed …

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