Chemical Science Blog

Researchers in the UK have developed a new method that uses surface enhanced Raman scattering (SERS) to quickly identify which meningitis causing bacteria is responsible for an infection.

Neisseria meningitidis is one of three pathogens that the technique can detect © Shutterstock

Onset of meningitis is often rapid and severe, particularly when a bacterial infection is the cause. Several types of bacteria cause meningitis and each is sensitive to different antibiotics.

The faster the type of bacteria can be identified by DNA analysis, the faster patients can receive the most effective antibiotic for their condition. This also reduces the need for broadband antibiotics, overuse of which is increasing bacterial resistance.

Karen Faulds’ group at the University of Strathclyde, Glasgow, used SERS, a spectroscopic imaging technique, to identify which of Haemophilus influenzae, Streptococcus pneumoniae and Neisseria meningitidisis were present in a single sample, with a view to analysing cerebral spinal fluid from patients suspected to have meningitis. A series of DNA probes containing dyes detectable by SERS make it possible to single out the different pathogens.

Read the full article in Chemistry World»

Read the original journal article in Chemical Science:
Simultaneous detection and quantification of three bacterial meningitis pathogens by SERS
Kirsten Gracie, Elon Correa, Samuel Mabbott, Jennifer A. Dougan, Duncan Graham, Royston Goodacre and Karen Faulds  
Chem. Sci., 2014, Advance Article, DOI: 10.1039/C3SC52875H, Edge Article

© Shutterstock

German scientists searching for a sustainable source of medically important polyunsaturated fatty acids (PUFAs) have shown they can be manufactured by soil-dwelling bacteria.

Research is ongoing to pinpoint who would benefit most from taking a fish oil supplement but there’s no denying that PUFAs – the good fats in fish and fish oil – have clear health benefits. However, overfishing, climate change and ocean acidification have left global fish populations, and supplies of high quality fish oil, in decline.

Rolf Müller and colleagues at Saarland University have identified that certain species of myxobacteria, also known as slime bacteria after the slime they produce to aid their movement, have the genes to synthesise certain omega-3 long-chain PUFAs de novo by employing enzymes known as PUFA synthases.

Read the full article in Chemistry World»

Read the original journal article in Chemical Science:
Polyunsaturated fatty acid biosynthesis in myxobacteria: Different PUFA synthases and their product diversity
Katja Gemperlein, Shwan Rachid, Ronald O. Garcia, Silke C. Wenzel and Rolf Mueller  
Chem. Sci., 2013, Accepted Manuscript, DOI: 10.1039/C3SC53163E, Edge Article

Everyone knows that like charges repel one another. But unusual coordination compounds bearing cationic ligands bound to cationic metals have been prepared by scientists in Israel, opening up fresh opportunities for organic transformations.

Gandelman's team have successfully made rhodium (pictured) and platinum forms of the unusual complexes

When two positively charged chemical species are brought together they experience counteracting forces. One is Coulombic repulsion, and the other is attraction due to the bonding interactions between the nuclei of one cation and the electrons of the other. Thermodynamically unstable bonds ensue from the interplay of these opposing interactions.

Rather than being thermodynamically stable, the transition metal complexes made by Mark Gandelman from the Israel Institute of Technology in Haifa and colleagues manage to be kinetically stable. Pincer-type ligands with nitrenium moieties at their centre, that are essentially the nitrogen analogues of N-heterocyclic carbenes, are central to the complexes’ creation. Computational investigations reveal that the coordination geometry of the pincer ligand provides the kinetic barrier to dissociation of the nitrogen–metal bond; the two phosphine arms aid coordination by bringing the metal within close proximity of the central nitrogen.

Read the full article in Chemistry World»

Read the original journal article in Chemical Science:
Cation-Cation Bonding in Nitrenium Metal Complexes
Mark Gandelman, Yuri Tulchinsky, Prasenjit Saha, Sebastian Kozuch, Mark M Botoshansky and Linda Shimon  
Chem. Sci., 2013, Accepted Manuscript, DOI: 10.1039/C3SC53083C, Edge Article

Many researchers use photographs of fluorescent solutions to illustrate their scientific papers but scientists in Germany have shown these photographs are more than just pictures and actually contain valuable information.

Data equivalent to multiple emission spectra extracted from a single photograph

Emission spectroscopy is considered the gold standard for characterising fluorescent solutions but analysing this data can be time consuming and non-intuitive, especially when a lot of data is involved. This led Uwe Bunz’s team at Heidelberg University to ask if photography might be a better method for obtaining this information quickly and efficiently. And the answer is yes.

Photographic and spectroscopic data can be compared using the chromaticity coordinates, r,g. These can be easily extracted from emission spectra using colour matching functions. However, in order to extract chromaticity coordinates from photographs, we have to assume that the camera is using the same set of functions. ‘There was no good way to compare information gleaned from emission spectra and photographs,’ explains Bunz.

To get around this problem Bunz’s team used pseudo colour matching functions to give chromaticity coordinates specific to their camera. These values can then be directly compared to r,g values from emission spectra, converting the camera into a three filter detector. ‘We can now interconvert fluorescence spectral data and colour information gleaned from photographs,’ says Bunz. ‘The common denominators are the chromaticity coordinates r,g.’

They tested their method on light emitting diodes (LEDs) and solutions of inorganic quantum dots and organic fluorescent dyes. In all three cases, the photo-extracted coordinates were excellent matches with the spectroscopic values.

‘It’s a very simple but very effective method for analysing fast chemical processes,’ says Manijeh Razeghi, an expert in using cameras for spectroscopy from Northwestern University in Evanston, Illinois, US. ‘Its simplicity allows it to be used by a wide variety of people with different levels of knowledge about spectroscopy.’

Repurposing a camera as a spectrometer may sound a little unorthodox but a single photograph can simultaneously capture data on multiple coloured solutions making it cheap and efficient. Its applications range from the analysis of quality control test trips to adulterations of medical drugs.

You can read also this article in Chemistry World»

Read the original journal article in Chemical Science:
Photoscopy: Spectroscopic Information from Camera Snapshots?
Uwe Bunz, Thimon Schwaebel and Sebastian Menning  
Chem. Sci., 2013, DOI: 10.1039/C3SC52928B, Edge Article

The conformational behaviour of free D-glucose—at last
José L. Alonso, María A. Lozoya, Isabel Peña, Juan C. López, Carlos Cabezas, Santiago Mata and Susana Blanco
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52559G, Edge Article

Free to access until 19th January 2014

Simultaneous detection and quantification of three bacterial meningitis pathogens by SERS
Kirsten Gracie, Elon Correa, Samuel Mabbott, Jennifer A. Dougan, Duncan Graham, Royston Goodacre and Karen Faulds
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52875H, Edge Article

Free to access until 19th January 2014

Constraint-induced structural deformation of planarized triphenylboranes in the excited state
Tomokatsu Kushida, Cristopher Camacho, Ayumi Shuto, Stephan Irle, Masayasu Muramatsu, Tetsuro Katayama, Syoji Ito, Yutaka Nagasawa, Hiroshi Miyasaka, Eri Sakuda, Noboru Kitamura, Zhiguo Zhou, Atsushi Wakamiya and Shigehiro Yamaguchi
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52751D, Edge Article

Free to access until 19th January 2014

Direct observation of a lithiated oxirane: a synergistic study using spectroscopic, crystallographic, and theoretical methods on the structure and stereodynamics of lithiated ortho-trifluoromethyl styrene oxide
Antonio Salomone, Filippo M. Perna, Aurelia Falcicchio, Sten O. Nilsson Lill, Anna Moliterni, Reent Michel, Saverio Florio, Dietmar Stalke and Vito Capriati
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52099D, Edge Article

Free to access until 19th January 2014

Sugar-coated sensor chip and nanoparticle surfaces for the in vitro enzymatic synthesis of starch-like materials
Ellis C. O’Neill, Abdul M. Rashid, Clare E. M. Stevenson, Anne-Claire Hetru, A. Patrick Gunning, Martin Rejzek, Sergey A. Nepogodiev, Stephen Bornemann, David M. Lawson and Robert A. Field
Chem. Sci., 2014,5, 341-350
DOI: 10.1039/C3SC51829A, Edge Article

Free to access until 19th January 2014

Electrochemistry in a drop: a study of the electrochemical behaviour of mechanically exfoliated graphene on photoresist coated silicon substrate
Peter S. Toth, Anna T. Valota, Matěj Velický, Ian A. Kinloch, Kostya S. Novoselov, Ernie W. Hill and Robert A. W. Dryfe
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52026A, Edge Article

Free to access until 19th January 2014

Core solution: a strategy towards gold core/non-gold shell nanoparticles bearing strict DNA-valences for programmable nanoassembly
Huiqiao Wang, Yulin Li, Ming Gong and Zhaoxiang Deng
Chem. Sci., 2014, Advance Article
DOI: 10.1039/C3SC52445K, Edge Article

Free to access until 19th January 2014

Researchers in Germany looking to find unprecedented ways of combating bacterial infection have demonstrated that certain small molecules can reduce the ability of Staphylococcus aureus to cause disease. ‘The classic antibiotic approach puts bacteria in a life or death situation, meaning that they need to become resistant in order to survive. We aimed to find a way of reducing the ability of bacteria to make the toxins that harm eukaryote cells during infection, without putting them under selective pressure,’ explains Stephan Sieber of the University of Technology in Munich who led the study.

α-methylene-γ-butyrolactones can inhibit virulence factors like α-haemolysin (hla) to render pathogenic bacteria harmless

 Transcriptional regulators control the virulence factors in bacteria, that enable a microorganism to establish itself within a host or enhance its potential to cause disease, by directly binding to DNA promoter regions of toxin-encoding genes. In the study, the researchers identified a series of α-methylene-γ-butyrolactones that covalently modify cysteine residues on three transcriptional regulators in S. aureus, markedly decreasing the expression of α-haemolysin, one of the most prominent virulence factors.

Read the full article in Chemistry World»

Read the original journal article in Chemical Science:
α-Methylene-γ-butyrolactones attenuate Staphylococcus aureus virulence by inhibition of transcriptional regulation
Martin H Kunzmann, Nina C. Bach, Bianca Bauer and Stephan Axel Sieber  
Chem. Sci., 2013, Accepted Manuscript, DOI: 10.1039/C3SC52228H

When most people read a book they don’t remember every word. They compress the story down to the main points and remember those. The reverse is also true – given a few facts most people can embellish a story to a suitably lengthy tale of adventure and mystery.

These data compression/decompression processes are called logic operations and are a central theme in information theory. They are also replicated in biological systems where scaffolding proteins within the regulatory cellular networks carry out the operations. However, there has been no synthetic DNA-based system that can carry out this data compression/decompression process, until now.

Logic circuit showing how 4 inputs (I) can be compressed to one output (S)

Itamar Willner from the Hebrew University of Jerusalem and colleagues have developed such a system based on Mg²⁺-dependent DNAzyme subunits. Unlike previous approaches where the demonstration is done using two inputs and one output the team have investigated enhanced multiplexing in the compression process with four inputs producing one output.

Additionally they have also demonstrated the expansion of a single input to produce two outputs. Having such systems based on nucleic acids also raises the possibility of resetting the computational module. This means you could reconfigure and change its operation in situ by the addition of suitable complementary nucleic acid strands.

This article details important advances in DNA based logic networking and raises the potential to compress information held within genes into a single output. It also raises challenges for the future that must be overcome before these synthetic biomolecular computational systems can control natural intracellular processes.

For more, read the Chemical Science Edge article in full:

DNAzyme-Based 2:1 and 4:1 Multiplexers and 1:2 Demultiplexer
Ron Orbach, Francoise Remacle, R. D. Levine and Itamar Willner*
Chem. Sci., 2013, Accepted Article
DOI: 10.1039/C3SC52752B

Iain Larmour is a guest web writer for Chemical Science. He has researched a wide variety of topics during his years in the lab including nanostructured surfaces for water repellency and developing nanoparticle systems for bioanalysis by surface enhanced optical spectroscopies. He currently works in science management with a focus on responses to climate change.  In his spare time he enjoys reading, photography, art and inventing.