Propionibacterium acnes,the most common skin bacteria, secretes a protein with antioxidant capacity.

Nowadays, it is known that almost half of human being are bacteria. We call it microbiome. We read a lot of studies about gut microbiota as it is linked to gastrointestinal diseases.

Interestingly, in this study, the researchers studied skin microbiota.

P. acnes is the most ubiquitous bacteria in skin. It is well known for being associated with acne vulgaris. This bacteria is anaerobe meaning it grows in absence of oxygen. However, the skin can be subjected to several enviromental stress conditions like oxidative stress (ROS). In this study, the scientists show that P. acnes release an enzyme, RoxP that helps protecting the skin from oxydative stress.

RoxP is highly conserved amongst P.acnes strains. Using assays with heme, they showed in vitro that P. acnes acts as an antioxidant.

In previous studies, psoriasis was linked to decrease in P. acnes. We could think that the lack of RoxP is a significant element causing the disease. Other studies need to be led in other to know the extend of the benefit of RoxP.

Please I am thinking of was to improve my blog. Could you please leave me comment below ?

Thanks a lot,

USB stick: 

A new method to measure HIV-1 viral load in the blood stream!

Ok, ok, ...I extrapolate a lot.
However it could happen in a near future. A team of scientist in London developed a pH sensing semiconductor in order to measure HIV-1 viremia. A small sample of blood can be placed on phone chip and onto a USB spot. Any HIV-1 virus present will change the pH which translated into an electric signal. Innovative!

The technology could be used for other viruses like hepatitits.

If you want to read more:

HIV test performed on USB stick
Novel pH sensing semiconductor for point-of-care detection of HIV-1 viremia

Enjoy!

Nobel Prize 2016 

Dear Followers,

here comes again that time of the year....the 2016 Nobel Prize are being awarded. Exciting!

The Nobel Prize of Physiology and/or Medicine is awarded to Yoshinori Ohsumi for his discoveries of mechanisms of autophagy.

By 大臣官房人事課 - 平成27年度　文化功労者：文部科学省, CC BY 4.0,
https://commons.wikimedia.org/w/index.php?curid=52028935

What is autophagy?

The word "Autophagy" derived from Greek meaning "eating self". It was coined by the scientist Christian de Duve after he saw cells breaking their part inside the lysosymes, in 1963. Autophagy is a "cleaning" mechanism of cells. 

Ohsumi's discoveries? 
"They led to a new paradigm in our understanding of how the cell recycles its content. His discoveries opened the path to understanding the fundamental importance of autophagy in many physiological processes, such as in the adaptation to starvation or response to infection. Mutations in autophagy genes can cause disease, and the autophagic process is involved in several conditions including cancer and neurological disease."


The Nobel Prize in Physics has been awarded to three scientists, one half to David J. Thouless and the other half to F. Duncan M. Haldane and J. Michael Kosterlitz "for theoretical discoveries of topological phase transitions and topological phases of matter."

What is topology?

Topology is a branch of mathematics that describes properties that only change step-wise. Using topology, these scientists could demonstrate new matter phases.


David J. Thouless, F. Duncan M. Haldane and J. Michael Kosterlitz's discoveries?
"Michael Kosterlitz and David Thouless overturned the then current theory that superconductivity or suprafluidity could not occur in thin layers. They demonstrated that superconductivity could occur at low temperatures and also explained the mechanism, phase transition, that makes superconductivity disappear at higher temperatures."

"In the 1980s, Thouless was able to explain a previous experiment with very thin electrically conducting layers in which conductance was precisely measured as integer steps. He showed that these integers were topological in their nature. At around the same time, Duncan Haldane discovered how topological concepts can be used to understand the properties of chains of small magnets found in some materials."

The Nobel Prize in Chemistry has been awarded to Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Feringa "for the design and synthesis of molecular machines"


What are molecular machines?

Also called Nanomachines, they are tiny machines composed of one or few molecules and synthetised by several chemical reactions.

Jean-Pierre Sauvage, Sir J. Fraser Stoddart and Bernard L. Fering's discoveries?

In 1983, Jean-Pierre Sauvage managed to link two ring-shaped molecules to form a chain called a catenane. In 1992, Sir J. Fraser Stoddart "threaded a molecular ring onto a thin molecular axle and demonstrated that the ring was able to move along the axle." Molecules called rotaxane.

In1999, Bernard L. Fering developped a molecular motor rotating a glass cylinder that is 10,000 times bigger than the motor and also designed a nanocar.

Nobel Prizes Animations

Dear followers,


This week, I would like to share with you a webpage on Nature.com.
It contains animations explaining the findings of 4 scientists who received the Nobel Prize:




1) Big box, small box, light-filled box with Serge Haroche
2) Tick-tock cold clock with Bill Phillips
3) Ain't no stopping them now with Art McDonald
4) No such animal with Dan Shechtman

I think it is a great initiative to break down complex research for everyone to understand and animation is a great way to illustrate.

Let me know what you think,

Have a nice week-end!

Map-reading can be difficult for women during ovulation

A team of scientists from Concordia University in Montreal studied the memory of women throughout their menstrual cycle. They found that oestrogen and progesterone cause the brain to favor one memory or strategy over the other.

As you may know, the menstrual cycles occurs with the variation of  two of the ovarian hormones called  estrogen and progesterone.

On the graph, we can observe a high increase of estrogen.

45 women who had regular tested where tested for two tasks. One group was asked to memorize a list of words and the other one was asked to find their way through a maze.
The results showed that women that were ovulation performed better in memorizing the list of words and women in their pre-menstrual phase were better at solving a maze.

This study's goal is to better understand the women brain. I hope it will not be used to discriminate more women at work.
Understanding the difference between women and men could trigger the research, notably pharmaceutical, to create targeted therapy.

What do you think ?

Changing the genetic code of life

In August, Science published a fascinating study from a team working in MIT.

The team has designed a synthetic Escherichia coli genome that could use a protein-coding scheme different from the one employed by all known life.

The team reduced the number of codons from 64 to 57 codons.

It is a new step in the engineering of E. Coli and synthetic biology.

The one of the overall goal of this kind of researcher is to create engineered bacteria for industrial purposes. But it also allow us to understand better our biology and its limits.

You can read more details on Science: http://science.sciencemag.org/content/353/6301/819

Enjoy!

New planet discovered !!!

Hi dear follower,

A new planet have been discovered :) The discovery has been reported this week in Nature.

Sun and solar system

It is a small planet orbiting Proxima, a red dwarf moderately active star. It's minimum size in around 1.3 Earth masses. The team, led by Guillem Anglada-Escudé, was analysing Doppler data previously obtained (pre-2016). They observed a signal that they could attribute to this new planet.

You. So can we think that the system solar has a new planet ?

Let me know what you think.

Have a nice Sunday :)

H

Hi Dear Followers,

How are you? Are you following the Olympic games ? Maybe you are in Rio watching and participating live. In any case, I wish you a nice time. I like watching athletism…Let's see what Usain Bolt will do in the 100 m and 200 m.

Let me know what are your favorite sport watching or doing. I would love to know!

This Olympic mood inspired me to write about a study from the University of Cardiff. A team led by Professor Roger Whitaker showed that the large human brain is a result of constantly sizing up each other.

Their study was focus on cooperation. It is a fundamental human trait and they were to understand more about it.

The team proposed that evolution favors those who prefer to help out others who are at least as successful as themselves.

The study was made by computer scientists and I must admit it is not my strong suit. As a molecular/ cellular/ biochemist, I find this research project interesting for social purposes.

On way of sizing up each other is sport. Could sport competition be a important activity to increase our collective brain size ?

You can read more on the article in Scientific Reports. Let me know what you think.

We can always learn :)

Lugdunin: a newly found potent antibiotic

Hi dear follower,

No new antibiotic has been discovered for year and how was my surprise when I read, in Nature, that a newly found potent antibiotic has been found in our nose: Lugdunin !

This is the first time that an antibiotic has been discovered in the human microflora :)

A team of scientist in Tübigen, Germany, showed that nasal Staphylococcus lugdunensis strains produce a peptide called lugdunin. It is a novel thiazolidine-containing cyclic peptide antibiotic that prohibits colonization by S. aureus.

Knowing how rich is the human microflora, this study opens the door to a world of new discoveries.

Today, it is well-know that resistance to antibiotic have became a challenge to overcome. Finding new structure antibiotics is essential for the future and the fight against infectiouse diseases.

Source:

http://www.nature.com/nature/journal/v535/n7613/full/nature18634.html

In August, chinese scientists will start the first human CRISPR trial

Hi dear followers,
 

I am back from my vacations and I see that I missed many exciting science news. And I missed you !

For my come back, I chose to feature the news from Nature: Chinese scientists are close to be the first worldwide to inject patients with cells modified using the CRISPR-Cas9 technique. 

Cancer cells in culture from human connective tissue. 

This image was released by the National Cancer Institute, 

an agency part of the National Institutes of Health, 

with the ID 2306

It is an exciting new step in the gene editing area…well in the cancer cure area. Indeed the scientists led by Lu You are planning to edit immune cells, T cells in order to increase their attack on tumors. The team will test in people who have metastatic non-small cell lung cancer.

The target gene is PD-1. The encoded protein PD-1 is a receptor expressed at the surface of activated T cells. It binds two ligands PD-L1 and PD-L2. Both are expressed by tumor cells. Blocking PD-1 using antibodies is described as a potential way to boost the immune response against tumor cells.

The goal of Lu's team is to knockout PD-1 using CRISPR-Cas9 and see an increased immune response against tumors.

I wonder if they are anticipating the off-target response: Not only that a PD-1 KO could affect immune cells metabolism in the whole body but also that the CRISPR-Cas9 by itself could lead to unintended KO genes. The team will extract T cells from the enrolled patients and then knocked them out. I wonder if a quality check will be performed and how ?

It seems like the team had the same questions!

They are going to try to extract T near the tumor site where they are already specialized. However, the lung-cancer tumors are not easily accessible so the team is hoping for a low rate of immune response.

To prevent to pick cells with gene editing in the wrong place, a company Chengdu MedGenCell will validate the cells to make that only PD-1 is KO.

As you can imagine, this CRISPR gene editing studies are a race. US is also planning to make a similar study, knocking out PD-1  and other gene target and knocking in a third one. US researchers think they could start at the end of the year.

A video from Newsy explain quite well the study.

If you want to read more:

• http://www.nature.com/news/chinese-scientists-to-pioneer-first-human-crispr-trial-1.20302

Our ancestors evolved faster after dinosaur extinction

A team at University College London showed that the speed of evolution of placental mammals -- including humans- was stable in presence of dinosaurs and increased drastically after their extinction. An other team from UCL showed last year that the mammal diversity exploded after dinosaur extinction. I believe that these two studies show that the removal of the selection pressure, which was the presence of dinosaurs, allowed mammal evolution to flourish. I would love to know more from your side as I am not an expert in this domain.

Sources:

• Image: FlickR
• Please click on hyperlinks

Paternel obesity related to increased breast cancer risk in daughter, a mice study says

In mammals, epigenetic information is transmitted from one generation to the next one. Epigenetic information meaning DNA methylation, histone modification and also non-coding RNA. This information is also considered the memory of the previous generation and can be transmitted to the next one through the germ-line.

In this study, the authors tried to determine the contribution of paternal consumption of an obesity-diet and overweight around the time of conception on their daughters mammary development and breast cancer risk.

The male mice were fed from 3rd week to 10th week either with control diet or obesity-inducing diet (OID). An increased weight in the OID fathers and a mis-regulation of several miRNAs was observed.

After mating the OID father with female mice in a control diet, the female offsprings have been analysed. The authors observed that at birth the daughters show overweight. This weight increase persisted until puberty and disappeared compared to control in adult animals.

The mammary glad development has been analysed. The authors looked at mammary tissue susceptible to carcinogen induced initiation in breast cancer in rodents (TEBs). The number of TEBs was higher in daughters from OID fathers compared to controls. The authors measured an other parameter, the elongation of the mammary ductal adjusted to body weight and observed a higher one from OID female. It could correlate with and increased cell proliferation.

The link between the miRNA mis-regulation in the OID father and OID females and the risk of cancer has been strongly established. 

This study will need to be confirmed and performed in human in order to really be sure that there is a link between fathers obesity and daughters risk of breast cancer. 

I also think that this study increase our awareness.
We can always learn!

Source:

• Image: Common creative
•  Fontelles, C. C. et al. Paternal overweight is associated with increased breast cancer risk in daughters in a mouse model. Sci. Rep. 6, 28602; doi: 10.1038/srep28602 (2016).

MS breakthrough: Replacing diseased immune system halts progression, allows repair

Hi Everyone,

A clinical trial, in Canada, managed to eliminate all signs of damaging brain inflammation in people with early, agressive multiple sclerosis (MS). Amazing? right!

How did they do?

24 participant were included in trial that lasted for 13 years. The authors removed all the immune system and regenerated a new one using blood stem cells. This procedure also lead to lasting recovery.

Unfortunately this treatment option is very complex and cannot be used for every patient worldwide. It should be performed in specialized centers.

Source:

• Ottawa Hospital Research Institute. "MS breakthrough: Replacing diseased immune system halts progression, allows repair." ScienceDaily. ScienceDaily, 9 June 2016. <www.sciencedaily.com/releases/2016/06/160609222439.htm>

Monetary reward do not increase reactivated human memory, a study shows

Imagine you are studying for a test. Then the memory of the lecture needs to be kept and reactivated for the actual test. It would be nice to find ways to ensure the strength of that reactivation.
Dayan and colleagues studied the impact of monetary reward on the strength of reactivated skill memory.
They asked 36 people right-handed to tap repeatedly with their left hand 5-digit as quickly and as accuretely as possible.
They realised that monetary reward did not reinforce skill memory reactivation.
I found it surprising. I am not expert in such study but could it be that motivation left by the simple feedback is more important for skill memory reactivation? What do you think ?


Source:

• http://rdcu.be/iUAd

In Cinema, chemical composition of audiences breathe varies during specific movie scenes

A study in Germany lead by Jonathan Williams measured the air composition during movies screening. They tested different genres of movies, Suspense, Comedy, Romantic comedy, Mystery, Romance and Drama, including The Hunger Games: Catching Fire, Belle and Sebastian and Carrie.

During 6 weeks between 2013 and 2014, Williams and colleages collected air samples and analysed them using Mass-Spectroscopy. Then they tried to find association between air composition and movies scenes.

“The chemical signature of The Hunger Games was very clear; even when we repeated the measurements with different audiences,” Indeed, two significant peaks of CO2 were measure when the heroine fought for her life. A suggested explanation is that the viewers are more tense and breathe faster.

This original study may bring answer to medical fields. The field of medicinal breathe analysis could use these data to estimate the emotion state of patients.

Even more in entertainment industries, could one influence people emotional state using air chemical composition ?

I contacted Jonathan Williams to ask him questions. He nicely answered. Please find below his answers to my 2 questions:

1) Did you use the cinema set up in order to show that breathe chemical composition depends one’s emotion, specially « suspense » and « comedy » ?

"Yes that's right, we asked ourselves the question, do the chemicals we breathe out in any way reflect our emotional state? The idea came when we were measuring the air at a football match with the aim of getting an average breath spectrum from 30 000 people. Although we did get the average breath spectrum, the game ended goaless and so we could not characterize chemically what happens when a goal is scored. So we thought, where can we really investigate this questions under controlled conditions. The answer was, in a cinema. A cinema is simply people in a ventilated box and if you show the people films to make them laugh or scare them any changes in the air composition they induce will be detectable where the air is vented to outside."

2) I noticed that you performed the experiment around Christmas and New year’s (26th to 30th). People  in Germany are quite emotionally affected by all the festivities. Do you thing it could have influenced your data ?

"What a good question, I did not think of that before. The reason for working at Christmas is because in summer we investigate photochemistry (most active when the sun and emissions from plants is strongest). In the winter we tend not to measure and the instruments remain in the lab over Christmas holiday. However, for cinemas, Christmas is the best time to measure. This is when most new films come out and most people go the cinema. In this way the work fits nicely together with our main job, which is to investigate atmospheric chemistry.
My feeling is that when we watch films, we lose ourselves in the emotion of the film, independent of when we go and see it, so I would guess that this would not be a factor. However, it is an intriguing idea and worth thinking about, thanks for the question."

We can always learn :)

Sources:

• Williams, J. et al. Cinema audiences reproducibly vary the chemical composition of air during films, by broadcasting scene specific emissions on breath. Sci. Rep. 6, 25464; doi: 10.1038/srep25464 (2016).
• http://www.mpic.de/en/news/press-information/news/spannung-in-der-kinoluft.html

Is there a reproducibility crisis in science?

I am glad to read that lately journal like Nature are taking reproducibility and plagiat seriously.

I think it should be even be a high priority in my field of expertise (molecular, cellular biology and biochemistry). 

Who never managed to reproduce a result published? Who never managed to reproduce a result from a co-worker (from the previous post-doc/PhD student or PI)?

It is also very frustrating because the persons who produce the results sometimes cannot explain how they got it. 

Should we not believe the publications ? I would not be so categorical but the research community should be looking at statistics a little more.

In the video below are presented the data from a survey Nature performed. Half of the researchers thinks there is a crisis in reproducility.

What do you think? Are facing this reproducibility issues ? What solution could be used to decrease the problem ?

Source:

• http://www.nature.com/nature/videoarchive/reproducibility/index.html

CRISPR/Cas Nature Protocol calendar 2016

Hi everyone,

It is June 2016 already. Do you still need a calendar for 2016? Nature Protocol and Origen created a CRISPR/Cas9 calendar: Download it here
It is full of nice schemes. Here are the theme, you can expect:

• January: RNA-guided genome editing using the CRISPR/Cas9 system
• February: Cas9 therapeutics
• March: Procedure for the generation of gene-modified mice by CRISPR/Cas
• April: The RNA-guided Cas9 nuclease
• May: Types of therapeutic gene modifications
• June: Construction of rat gene-targeting vector through overlapping PCR
• July: Platform for multiplex biological screens
• August: Creating customized sgRNA for transcriptional repression of any gene
• September: DSB repair promotes gene editing
• October: sgRNA construction
• November: Highly specific gene editing by Cas9 nickase (Cas9n)
• December: Ex vivo versus in vivo editing therapy

Enjoy! We can always learn!

Source:

• Crystal structure: By Hiroshi Nishimasu, F. Ann Ran, Patrick D. Hsu, Silvana Konermann, Soraya I. Shehata, Naoshi Dohmae, Ryuichiro Ishitani, Feng Zhang, and Osamu Nureki [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

• http://www.nature.com/nprot/calendars/2016/index.html

Look at them so they wash their hands properly...

By "them", I mean physiciens in hospitals. According to a study from the infection prevention department at Santa Clara Valley Medical Center in San Jose, California, 'when healthcare providers know they are being watched, they are twice as likely to comply with hand hygiene guidelines.'

This phenomenon is called the Hawthorne effect. It is the modification of behaviour upon observation of the subject. It is known as 'the observer effect' in physics. 

It is concerning, don't you think? This type of studies will always be biaised in that case. 

A comparable study was performed in France at Marseille's hospital. There, less than 1 out of 5 healthcare providers did not wash their hands before entering in contact with patients.

This is not know new information but it is reminder for all of us who deal with medical professionals.

Have a great day :)

Sources:

• Henry A. Landsberger, Hawthorne Revisited, Ithaca, 1958.
• Association for Professionals in Infection Control. (2016, June 10). The Hawthorne Effect hinders accurate hand hygiene observation, study says. ScienceDaily. Retrieved June 12, 2016 from www.sciencedaily.com/releases/2016/06/160610094406.htm
• http://sante.lefigaro.fr/actualite/2015/03/04/23469-lhopital-soignants-negligent-regles-dhygiene

10 facts about Zika virus (ZIKV)

1. The name Zika comes from the Zika forest in Uganda where the virus was first described in 1947 from a rhesus monkey

2. ZIKV belongs to the Flavivirus genus and is related to dengue, West Nile, and Japanese encephalitis

3. Zika virus has a 11 kb positive-stranded RNA genome

4. ZIKV RNA genome contains a single long open reading frame (ORF) that encodes the viral polyprotein, subsequently processed into the 3 structural proteins and 7 enzymatic components

5. Mosquitoes, Aedes africanus, inhabiting the Zika forest are capable of transmitting ZIKV

6. 3 potential ways of transmission of ZIKV:  mosquitoes Aedes africanus, sexual transmission and placental transmission during pregnancy

7. Zika virus is strongly suspected to induce microcephaly in the fetus

8. Symptoms of Zika fever may be mild fever, skin rash, conjunctivis, muscle and joint pain, malaise or headhache. These symptoms last for 2-7 days.

9. A diagnosis of Zika virus infection can only be confirmed through laboratory tests on blood or other body fluids, such as urine, saliva or semen.

10. There is no specific treatment for the Zika fever. Paracetamol may help with the symptoms.

Sources:

• Image: Zika virus capsid, colored per chains. Manuel Almagro Rivas - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curid=47941048. Source: Sirohi, D., Chen, Z., Sun, L., Klose, T., Pierson, T., Rossmann, M. and Kuhn, R. (2016). The 3.8Å resolution cryo-EM structure of Zika virus.
• Sikka V, Chattu VK, Popli RK, Galwankar SC, Kelkar D, Sawicki SG, Stawicki SP, Papadimos TJ. The emergence of zika virus as a global health security threat: A review and a consensus statement of the INDUSEM Joint working Group (JWG). J Global Infect Dis 2016;8:3-15
• van Hemert and Ben Berkhout. Nucleotide composition of the Zika virus RNA genome and its codon usage. Virology Journal (2016)
• http://www.who.int/mediacentre/factsheets/zika/en/

Stunnig news about our "Hobbit"  relatives

Homo Floresiensis also known as 'Hobbit' has been discovered in 2003 in the Indonesian Island of Flores. They are described as shorter and smaller in size compared to Homo Sapiens.

This week, Gerrit van den Bergh and team described the finding of 700,000 -yr-old teeth and a partial jaw from ancestor from H. Floriensis after a decade of research at the site of excavation. The jaw and teeth seem to be from human and children.

This findings are great to confirm more the presence of that ancestors but it also opens up many questions.

Why are they so small ? How did they get there ? How did the extinction happened? and interesting questions could also be to know their lifestyle and so on?

So far scientists were not sure if H. floresiensis was more similar to H. erectus or H. habilis/Australopithecus. The jaw newly discovered seem to look more like that of H. erectus. According to van den Berg, the oldest artefacts in the region suggests that H. erectus arrived on Flores around 1 million years ago.

Gerrit van den Berg is explaining it in the following video:

I hope you like this post. It seems like this week I am more inspired by evolution studies :)

We can always learn! :)

Sources:
Images from G.D. van den Bergh et al., Nature, 2016
G. D. van den Bergh et al. Nature 534, 245–248; 2016
d A. Brumm et al. Nature 534, 249–253; 2016

Evolution happening in nature ... so cool 

Hi Science lovers,

My knowledge on evolution dates from school so Darwin and the Origin of Species but I kept fascinated by those theories.

This week, an article in Science featured an interesting observation in lizard...well... central bearded dragons to be more precise. In those lizards, sex is determined genetically and environmentally. At high temperature, male embryos turn into females. They will still have male genetical information but they become superfemales, producing more eggs than regular females!

With the current climate change, we could literally observe the apparition of a new "third sex".

We always learn :-) Don't you think ?