Bacterial identification gets a culture shock

Written for Chemistry World

Scientists in the UK have developed a new tool to distinguish bacterial strains from each other. This speedy method could help to minimise drug resistance by accurately directing antibiotic treatment at an early stage.

Antimicrobial resistance is a major health concern and its risk is growing evermore due to a lack of both new drugs and rapid point-of-care diagnostic tools to ensure best use of the drugs in hand. ‘Innovative solutions to identifying pathogens can be found – which is really needed as antibiotic resistance spreads – if different fields work together,’ explains Matthew Gibson from the University of Warwick, whose group developed the new diagnostic tool.

Current point-of-care methods to identify bacteria require culturing bacteria to grow them to higher density – a very slow process. New sequencing technologies are faster, but still require hours and special equipment. Gibson’s method makes use of adhesion between bacteria and other cells. Many bacteria bind to cells through protein or carbohydrate structures exposed on the surface of the bacterium called adhesins. Each bacterial strain has a very specific pattern of adhesins and therefore binds with different strength to different sugar-bearing cell surfaces.


Read the full story in Chemistry World


Read the original journal article in Molecular BioSystems – it is open access.

Discrimination between bacterial species by ratiometric analysis of their carbohydrate binding profile
L. Otten, E. Fullam and M. I. Gibson, Mol. Biosyst., 2016, Advance Article
DOI: 10.1039/C5MB00720H, Communication

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What are your colleagues reading in Molecular BioSystems?

The articles below are the most read Molecular BioSystems articles in July, August and September 2015.

Isothermal amplified detection of DNA and RNA
Lei Yan, Jie Zhou, Yue Zheng, Adam S. Gamson, Benjamin T. Roembke, Shizuka Nakayama and Herman O. Sintim
DOI: 10.1039/C3MB70304E, Review Article

Bridging the layers: towards integration of signal transduction, regulation and metabolism into mathematical models
Emanuel Gonçalves, Joachim Bucher, Anke Ryll, Jens Niklas, Klaus Mauch, Steffen Klamt, Miguel Rocha and Julio Saez-Rodriguez
DOI: 10.1039/C3MB25489E, Review Article

Why phosphoproteomics is still a challenge
Fiorella A. Solari, Margherita Dell’Aica, Albert Sickmann and René P. Zahedi
DOI: 10.1039/C5MB00024F, Opinion

Fatty acid biosynthesis revisited: structure elucidation and metabolic engineering
Joris Beld, D. John Lee and Michael D. Burkart
DOI: 10.1039/C4MB00443D, Review Article

Mechanism of action-based classification of antibiotics using high-content bacterial image analysis
Kelly C. Peach, Walter M. Bray, Dustin Winslow, Peter F. Linington and Roger G. Linington
DOI: 10.1039/C3MB70027E, Paper

Differential protein profile in sexed bovine semen: shotgun proteomics investigation
Michele De Canio, Alessio Soggiu, Cristian Piras, Luigi Bonizzi, Andrea Galli, Andrea Urbani and Paola Roncada
DOI: 10.1039/C3MB70306A, Paper

Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis
Aakash Chavan Ravindranath, Nolen Perualila-Tan, Adetayo Kasim, Georgios Drakakis, Sonia Liggi, Suzanne C. Brewerton, Daniel Mason, Michael J. Bodkin, David A. Evans, Aditya Bhagwat, Willem Talloen, Hinrich W. H. Göhlmann, QSTAR Consortium, Ziv Shkedy and Andreas Bender
DOI: 10.1039/C4MB00328D, Paper

NMR- and MS-based metabolomics: various organ responses following naphthalene intervention
Yee Soon Ling, Hao-Jan Liang, Meng-Hsuan Chung, Ming-Huan Lin and Ching-Yu Lin
DOI: 10.1039/C4MB00090K, Paper

Multifunctional polymeric micelles with folate-mediated cancer cell targeting and pH-triggered drug releasing properties for active intracellular drug delivery
Younsoo Bae, Woo-Dong Jang, Nobuhiro Nishiyama, Shigeto Fukushima and Kazunori Kataoka
DOI: 10.1039/B500266D, Paper

Development of novel assays for lignin degradation: comparative analysis of bacterial and fungal lignin degraders
Mark Ahmad, Charles R. Taylor, David Pink, Kerry Burton, Daniel Eastwood, Gary D. Bending and Timothy D. H. Bugg
DOI: 10.1039/B908966G, Paper

Read more »

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2016 RSC Prizes and Awards in Organic Chemistry & Chemical Biology now open for nomination

Nominate someone you know who is an exceptional talent in chemical sciences

The 2016 RSC Prizes and Awards are now open for nomination!

Nominations will close on 15 January 2016.


For more than 140 years, our Prizes and Awards programme has been acknowledging and celebrating exceptional talent in the chemical sciences, and with your support we are hoping that 2016 will even more successful!

Last year’s winners include Chemists such as Prof. Wilfred van der Donk (University of Illinois), Prof. Tim Donohoe (University of Oxford), Prof. Shuli You (Shanghai Institute of Organic Chemistry), Prof. Philip Gale (University of Southampton), Prof. Herman Overkleeft (Leiden University), Prof. Alison Ashcroft and Prof. Sheena Radford (University of Leeds).

This year we have 63 prizes and awards open for nominations of individuals, teams and organisations covering the breadth of the chemical sciences across academia, education and industry.

This year’s prizes in the field of Organic Chemistry & Chemical Biology include:

CBID (Chemistry Biology Interface Division) awards –

Organic Awards –

For 2016 our Longstaff Prize is also open – since 1881 we have awarded this prize once every three years to one of our members who has achieved the most to advance the science of chemistry.

Submit your suggestions now!

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Prostate cancer detection comes of phage

Written by Laura Fisher for Chemistry World

Researchers in the US have wrapped bacteriophage with the polymer PEG (polyethylene glycol) to make a structure that detects PSMA, a molecular flag for prostate cancer. Their system could save lives by spotting aggressive forms of the disease at an earlier stage.

 Engineering chemically modified viruses for prostate cancer cell recognitionBacteriophage are harmless to humans, and their surfaces can be easily modified to grab onto cancer biomarkers, which can be indirectly quantified by measuring the levels of enzymes attached to these biomarkers with an ELISA (enzyme-linked immunosorbent assay). However, non-specific adhesion between cell surface receptors and phage can lead to a reduced signal-to-noise ratio and therefore make it difficult to distinguish cancer cells.

Greg Weiss and Kritika Mohan at the University of California have overcome this issue by wrapping PEG around the phage M13. This creates a hydration sphere around the phage and limits non-specific cell adhesion, allowing them to distinguish PSMA-positive from PSMA-negative cells.


Read the full story in Chemistry World»


Read the original journal article in Molecular BioSystems – it is free to access until 30 November 2015.

Engineering chemically modified viruses for prostate cancer cell recognition
K Mohan and G Weiss, Mol. Biosyst., 2015, Advance Article
DOI: 10.1039/
C5MB00511F, Paper

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Poster Prize Winners at Biorelevant Chemistry Symposium

We were please to present Poster Prizes at the 9th Symposium on Biorelevant Chemistry.

Congratulations to the winners:

  • Ryo Negshi (Tokyo University of Agriculture and Technology)
  • Yuta Niwa (Tokyo University of Agriculture and Technology)
  • Haruka Iki (University of Tokyo)
  • Hashiru Negishi (Tokyo Institute of Technology)
  • Takuma Sueoka (University of Tokyo)

Organized by the Chemical Society of Japan, the Biorelevant Chemistry Symposium took place from 10-12th Sept in Kumamoto, Japan.

From left to right: Professor Rie Wakabayashi (Poster award committee co-chair), Professor Hiroyuki Asanuma (Poster award committee chair), Ryo Negshi, Yuta Niwa, Haruka Iki, Hashiru Negishi, Takuma Sueoka, Professor Masahiro Takagi (Chair of the Division of Biotechnology, Chemical Society of Japan), Professor Itaru Hamachi (Vice-Chair of the Division of Biofunctional Chemistry, Chemical Society of Japan)

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Smorgasbord of chemical blueprints located in plain pond algae

Written by Jack Busby for Chemistry World

Euglena-gracilis

The pond algae Euglena gracilis has a surprising wealth of metabolic pathways for unexpected natural products, new research shows. Genes from this common single-celled organism could therefore be manipulated to synthesise a host of unusual, and potentially useful, compounds.

Euglenoids are a group of algae that grow abundantly in nutrient-rich freshwater environments, such as garden ponds. Euglena gracilis is known to produce many nutritional compounds including vitamins A, C and E, essential amino acids and polyunsaturated fatty acids. However, sequencing its genome in a bid to unlock these valuable natural products has proved very challenging due to its large size, complexity and incorporation of the unusual nucleotide base J.

Researchers, led by Rob Field at the John Innes Centre in the UK, have tackled this problem by instead looking at Euglena’s transcriptome – the mRNA transcribed from the genome that shows what genes an organism is using at a given time.



Read the full story in Chemistry World

Read the original journal article in Molecular BioSystems -  it is free to access until 15 October 2015

The transcriptome of Euglena gracilis reveals unexpected metabolic capabilities for carbohydrate and natural product biochemistry

Ellis C. O’Neill, Martin Trick, Lionel Hill, Martin Rejzek, Renata G. Dusi, Chris J. Hamilton, Paul V. Zimba, Bernard Henrissat and Robert A. Field.
Mol. BioSyst., 2015, Advance Article
DOI: 10.1039/C5MB00319A, Paper
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Protein labelling themed issue announced

We are pleased to announce an upcoming Molecular BioSystems issue on protein labelling. The Guest Editors for this issue are Dr Lyn Jones (Pfizer, USA) and Professor Eranthie Weerapana (Boston College, USA).

Scope

This issue will cover the discovery, development and application of protein labelling to advance chemical biology. Relevant topics include:

  • Bioconjugation and site-specific labelling
  • Activity-based protein profiling
  • Target identification and validation
  • New click reactions
  • Chemical mutagenesis
  • Advances in –omics technologies underpinned by breakthroughs in protein labelling techniques
  • Imaging and screening technologies
  • Advances in pharmacological and therapeutic modalities (e.g. hydrophobic tagging, synthetic vaccines, antibody-drug conjugates)

Deadline for Submission: 11 December 2015

Please e-mail the Editorial Office if you are interested in contributing an article.

Manuscripts can be submitted using the Royal Society of Chemistry’s online article submission service. Please clearly state that the manuscript is submitted for the themed issue on protein labelling. The level of quality of this issue will be high, and all manuscripts will undergo the journal’s normal peer review processes.

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10th annual meeting of Japanese Society for Chemical Biology

The 10th annual meeting of the Japanese Society for Chemical Biology was held in Sendai from 10-12th June 2015 and Molecular BioSystems was pleased to award two poster prizes.

Congratulations to the winners:

Mizuki Watanabe (left) , an Assistant Professor for Professor Uesugi Motonari at Kyoto University, for his poster entitled:
The action mechanism of endogenous small molecules that suppress the lipid biosynthesis

Syusuke Egoshi (right), working for Professor Minoru Ueda at Tohoku University, for his poster entitled:
In vivo Raman Imaging in living guard cells for elucidating the localization of the plant toxin coronatine

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Drawing order from disorder to unravel Ebola’s lethality

Christopher Barnard writes about a hot Molecular BioSystems article for Chemistry World

The virulence of Ebola virus strains appears to be innately linked to the degree of disorder in proteins that form their nucleocapsids. Computational analysis has revealed that strains responsible for the most lethal outbreaks of Ebola show significantly higher levels of intrinsic protein disorder than less virulent strains, in a discovery that could constitute a major breakthrough in understanding the pathogen’s behaviour.

With over 27,000 confirmed, probable and suspected cases and more than 11,000 fatalities worldwide, the ongoing Ebola outbreak has resulted in considerably more casualties since late 2013 than all other outbreaks combined. There are no effective treatments or vaccines against the haemorrhagic fever that evinces Ebola infection; however, strains of the virus with drastically different virulence have emerged since the first outbreak in 1976, with fatality rates ranging from 25 to 90%.

In an effort to explain such radical variations in lethality, researchers Gerard Goh, from Goh’s BioComputing in Singapore, Keith Dunker, from the Indiana University School of Medicine in the US, and Vladimir Uversky, from the University of South Florida in the US, have computationally explored links between the virulence of different Ebola virus strains and their predicted protein structures. The group discovered that intrinsically disordered proteins (IDPs) encapsidating the virus’ genetic material appear to play a large role, with increasing levels of disorder correlating with greater virulence.


Read the full story in Chemistry World»

Read the original journal article in Molecular BioSystems – it is free to access until 24 July 2015.

Detection of links between Ebola nucleocapsid and virulence using disorder analysis
Gerard Kian-Meng Goh, Keith Dunker and Vladimir N. Uversky
Mol. BioSyst., 2015, Accepted Manuscript
DOI: 10.1039/C5MB00240K, Paper

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Editor’s Choice: Chemical Biology

Looking for the best articles in Chemical Biology?

Dr Lyn Jones, Editorial Board member

Molecular BioSystems Editorial Board member Dr Lyn Jones (Pfizer) has picked some of his favourite articles recently published in the journal. You can read these articles for free for a limited period by clicking on the links below.

Did you know?

Molecular BioSystems publishes experimental and theoretical research at the interface of chemistry and biology, covering both chemical tools for biological questions, and molecular-level understanding, control and manipulation of biological processes. Access our full scope

As a journal published by the Royal Society of Chemistry, Molecular BioSystems benefits from free colour artwork, no page charges, attractive journal design and a professional editorial team. The journal is included in MEDLINE, ISI and SCOPUS and is NIH compliant.

Read our chemical biology Editor’s Choice selection for FREE today:

Probing the effect of an inhibitor of an ATPase domain of Hsc70 on clathrin-mediated endocytosis
Hyungseoph J. Cho, Gun-Hee Kim, Seong-Hyun Park, Ji Young Hyun, Nak-Kyoon Kim and Injae Shin
Mol. BioSyst., 2015, Advance Article
DOI:
10.1039/C4MB00695J

Selection of LNA-containing DNA aptamers against recombinant human CD73
Ida C. Elle, Kasper K. Karlsen, Mikkel G. Terp, Niels Larsen, Ronni Nielsen, Nicola Derbyshire, Susanne Mandrup, Henrik J. Ditzel and Jesper Wengel
Mol. BioSyst., 2015,11, 1260-1270
DOI: 10.1039/C5MB00045A

Probing the effect of minor groove interactions on the catalytic efficiency of DNAzymes 8–17 and 10–23
Michael H. Räz and Marcel Hollenstein
Mol. BioSyst., 2015,11, 1454-1461
DOI: 10.1039/C5MB00102A

You can find many more excellent articles on chemical biology on our dedicated online collection at :

http://rsc.li/mb-chemical-biology

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