Posts tagged: Biology

An update on the Earth Microbiome Project

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When BMC Biology launched its iconic image we acknowledged the extreme artistic licence of portraying selected vertebrate phyla pictorially while whole microbial kingdoms were denoted with a single blob. This was not intended to signify a lack of interest in the microbial world on our part, and to update our readers on a major effort to explore its taxonomic diversity and role in the biosphere, we invited the instigators of the Earth Microbiome Project (EMP), launched in 2010 with the aim of sampling the microbial diversity of the planet, to give us a progress report.

In their short comment article on the achievements and aspirations of the EMP, Jack Gilbert, Janet Jansson and Rob Knight deliver a positive …

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Twelve reasons you need to read about lactic acid bacteria

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Gouda

You may not know much about them, but you’ll almost certainly have eaten something that lactic acid bacteria have had a hand in. To mark a new supplement in Microbial Cell Factories, guest editor Eric Johansen tells us his 12 reasons why you ought to read it.

Lactic acid bacteria have a long history of use in the food industry where they are best known for turning milk into cheese or yoghurt, cabbage into sauerkraut or kimchi, and even improving the quality of wine. They’re also consumed in probiotic products for their health-promoting effects.

We’ve dedicated a whole supplement to these ‘friendly’ bacteria, and these are my 12 reasons why you need to read about them:

1. Their surface structure is

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Climate-smart agriculture: scientists show agricultural progress in responding to climate change

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Diversified landscapes offer benefits to farmers by providing many cropping options for climate change. And agroforestry and reduced deforestation increase carbon storage and reduce greenhouse emissions. Research helps determine ways to build resilience in different agricultural contexts. Image courtesy of Louise E Jackson

There are over seven billion people living on our planet and this vast population creates an equally vast demand for food and fuel. In this guest post, the authors of an article published today in Agriculture and Food Security tell us how climate-smart agriculture could help us to combat the threat of climate change to these in-demand resources.

Climate change is already putting food security at risk. Rising temperatures and extreme events, such as sudden droughts and floods, mean that it will be even harder to meet the growing demand for food, fiber and fuel, especially for poor countries with high population growth.

Unless immediate action is taken by policy-makers, the impacts on livelihoods will increase over the long-run, especially if agriculture …

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‘Prostate cancers’ not ‘prostate cancer’ – revealing the many faces of ‘one’ disease

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Iain Frame

New research published today in Genome Biology shows that RNA sequencing could lead the way towards more personalized treatments for prostate cancer. In this guest post, Dr Iain Frame, Director of Research at Prostate Cancer UK discusses what this could mean for patients and health services, and what more is needed to provide effective support and treatment for men with prostate cancer.

We are used to hearing and talking about prostate cancer as a single disease.  Albeit a disease with its tigers and pussycats – the tigers being the aggressive cancers that move out of the prostate gland to other parts of the body, and the pussycats being those cancers that may never cause any harm and won’t go …

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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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