Tuesday 30 May 2017

How Gonorrhea manipulates the female reproductive tract

Gonorrhea is a widespread sexually transmitted disease caused when Neisseria gonorrhoeae bacteria infect the normally protective inner lining of human genital tissues. In women, the opening of the uterus, known as the endocervix, serves as a primary infection site for N. gonorrhoeae. However, the strategy used by N. gonorrhoeae to penetrate the lining of the endocervix has been unclear.

To investigate this mechanism, Liang-Chun Wang of the University of Maryland, College Park, and colleagues needed to develop an alternative to the mouse models normally used to study gonorrhea, since they have been inadequate for this purpose. The team developed a new model using tissue samples obtained from the human endocervix.

The researchers infected the endocervix tissue, as well as lab-grown cells of the same type as those that line the endocervix, with N. gonorrhoeae. They then employed a variety of molecular and imaging techniques to examine the infection mechanism.

The results demonstrate that N. gonorrhoeae penetrates the endocervix lining by interfering with a normally protective process. Usually, infected cells in the lining can be shed and disposed of without breaking the tight connections between cells that keep the lining uncompromised. N. gonorrhoeae appears to be able to break these connections and induce cell shedding, opening paths for penetration without reducing its ability to adhere to and invade the cells of the lining.


Liang-Chun Wang, Qian Yu, Vonetta Edwards, Brian Lin, Jessica Qiu, Jerrold R. Turner, Daniel C. Stein, Wenxia Song. Neisseria gonorrhoeae infects the human endocervix by activating non-muscle myosin II-mediated epithelial exfoliation. PLOS Pathogens, 2017; 13 (4): e1006269 DOI: 10.1371/journal.ppat.1006269

Posted by Dr. Tim Sandle

Saturday 27 May 2017

Synthetic biologists engineer inflammation-sensing gut bacteria

Synthetic biologists at Rice University have engineered gut bacteria capable of sensing colitis, an inflammation of the colon, in mice. The research points the way to new experiments for studying how gut bacteria and human hosts interact at a molecular level and could eventually lead to orally ingestible bacteria for monitoring gut health and disease.

The research, published in a new study in Molecular Systems Biology, involved a series of breakthroughs in the lab of Jeffrey Tabor, assistant professor of bioengineering and of biosciences at Rice, and key contributions from collaborators Robert Britton and Noah Shroyer at Baylor College of Medicine. Tabor's team, including lead co-author and postdoctoral researcher Kristina Daeffler, identified the first genetically encoded sensor of a novel biomarker linked to inflammation, inserted the genes for the sensor into a well-studied gut bacterium and collaborated with Shroyer and Britton to use the engineered bacteria to detect colon inflammation in mice.

"The gut harbors trillions of microorganisms that play key roles in health and disease," Tabor said. "However, it is a dark and relatively inaccessible place, and few technologies have been developed to study these processes in detail. On the other hand, bacteria have evolved tens of thousands of genetically encoded sensors, many of which sense gut-linked molecules. Thus, genetically engineered sensor bacteria have tremendous potential for studying gut pathways and diagnosing gut diseases."

Synthetic biologists like Tabor specialize in programming single-celled organisms like bacteria in much the same way an engineer might program a robot. In particular, Tabor's team is working to develop bacterial sensors that can detect disease signals in the gut. Like electrical engineers who build circuits from wires and electronic components, Tabor's team uses genetic circuits to program single-celled creatures to carry out complex information processing.

Previous work has suggested that alterations to the gut microbiota, genetic predisposition and other environmental factors may play key roles in inflammatory bowel disease, a condition that includes Crohn's disease and ulcerative colitis and which affects as many as 1.6 million Americans.

"Based on a number of previous studies, we hypothesized that the molecule thiosulfate may be elevated during colitis," Daeffler said. "It has been difficult for scientists to study this link because there aren't tools for reliably measuring thiosulfate in living animals. Our first goal in this project was to engineer such a tool."

From the outset of the project in 2015, Daeffler said, the idea was to use sensor bacteria, in this case an engineered form of Escherichia coli, to sense thiosulfate and related sulfur-containing compounds that may also be biomarkers of colitis. There were well-understood methods for programming E. coli to produce a fluorescent green protein in response to specific stimuli, but there were no known genes -- in any organism -- that were used to sense thiosulfate, and few for the other compounds.

"There's a link between gut sulfur metabolism and inflammation, and we knew that we needed to be able to measure sulfur metabolites accurately to diagnose colon inflammation," she said.

Tabor said study co-author Ravi Sheth, an undergraduate researcher in the group in 2015, used a computer program to identify potential sensors of thiosulfate and other sulfur compounds in the genome of Shewanella, a type of bacteria that live in marine sediment. Tabor's group believes that Shewanella likely breathe these molecules and use the sensors to turn on the proper enzymes in their presence.

Daeffler spent one year engineering E. coli to express the sensor genes, validate their function and optimize them to respond to the potential biomarkers by producing a green fluorescent protein signal. It took another year to prove that the system worked and detected colon inflammation in mice.

The researchers administered orally two drops containing about a billion sensor bacteria to both healthy mice and to mice with colitis. They measured the activity of the sensor bacteria in each group six hours later. The tell-tale green fluorescent protein showed up in the feces of the mice. Though it was not visible to the unaided eye, it could easily be measured with a standard laboratory instrument called a flow cytometer.

The team found that the thiosulfate sensor was activated in the mice with inflammation, and was not activated in the healthy mice. Furthermore, the researchers found that the more inflammation the mouse had, the more the sensor was activated.

Tabor said the study shows that gut bacteria can be outfitted with engineered sensors and used to noninvasively measure specific metabolites and that this result could open the door to many new studies that could help elucidate a wide range of gut processes.

Though it would likely take several additional years of development, and it remains unknown if thiosulfate is a biomarker of human colitis, the sensor bacteria might eventually be re-engineered to function as a diagnostic of human colitis, Tabor said. In particular, the green fluorescent protein could be replaced with an enzyme that makes a colored pigment.

"We'd like to develop a home inflammation test where a person prone to colitis flare-ups would eat yogurt that contained the engineered bacteria and see blue pigment in the toilet if they were sick," he said.

Tabor said such a test could reduce unneeded and costly trips to the doctor and unneeded colonoscopy procedures, which are both expensive and invasive. He said his team has begun collaborations with gastroenterologists at Baylor to achieve this goal.


Kristina NM Daeffler, Jeffrey D Galley, Ravi U Sheth, Laura C OrtizVelez, Christopher O Bibb, Noah F Shroyer, Robert A Britton, Jeffrey J Tabor. Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation. Molecular Systems Biology, 2017; 13 (4): 923 DOI: 10.15252/msb.20167416

Posted by Dr. Tim Sandle

Friday 26 May 2017

EMA: risk based prevention of cross contamination in production (draft)

The European Medicines Agency has issued a new draft document, with the lengthy title of “Questions and answers on implementation of risk based prevention of cross contamination in production and ‘Guideline on setting health based exposure limits for use in risk identification in the manufacture of different medicinal products in shared facilities’ (EMA/CHMP/CVMP/SWP/169430/2012).”

The document deals with highly hazardous products are those that can cause serious adverse effects at low doses and that therefore would benefit from a full toxicological assessment in order to derive a safe Health Based Exposure Limits. A health based exposure limit is a limit (permitted daily exposure (PDE) or equivalent) at which a product is regarded to be safe in humans. It can be based on either clinical dose or non-clinical safety data, depending on which would give the lower exposure limit.

Such products are:

  1. Genotoxic (specifically mutagenic) compounds that are known to be, or highly likely to be, carcinogenic to humans. Compounds of this group are easily identifiable, since genotoxicity would be related to the pharmacology, e.g. as DNA alkylating cytostatics, and their use is usually restricted to oncology indications with respective warning statements in the Summary of Product Characteristics.
  2. Compounds that can produce reproductive and/or developmental effects at low dosages, for example where evidence exists of such effects being caused by a clinical dose of <10 mg/day (veterinary dose equivalent 0.2 mg/kg/day) or dosages in animal studies of ≤1 mg/kg/day.
  3. Compounds that can produce serious target organ toxicity or other significant adverse effects at low doses, for example where evidence exists of such effects being caused by a clinical dose of <10 mg/day (veterinary dose equivalent 0.2 mg/kg/day) or dosages in animal studies of ≤1 mg/kg/day.
  4. Compounds with a high pharmacological potency i.e. recommended daily dose of <1 mg (veterinary dose equivalent 0.02 mg/kg)

Compounds with a high sensitising potential.

The document can be accessed here: EMA

Posted by Dr. Tim Sandle

Thursday 25 May 2017

New assay for bioterrorism threat

Researchers in Spain are using RPA as the foundation for a highly sensitive and specific solid-phase optical assay that can detect the potential biowarfare agent, Y. pestis, in less than an hour. The enzyme-linked oligonucleotide assay (ELONA) approach developed by Ioanis Katakis and Ciara K. O’Sullivan, at the Universitat Rovira i Virgili’s Interfibio Research Group, and the ICREA (Catalan Institution for Research and Advanced Studies), uses conventional PCR primers to amplify both single- and double-stranded Y. pestis DNA. Their work provides proof of concept for applying RPA in a heterogeneous format, with one primer immobilized onto a solid surface. The researchers aim to further develop the technology into an integrated, portable lateral flow-type test device for the rapid amplification and detection of Y. pestis in resource limited and field settings.

For further details see:

Wednesday 24 May 2017

Too much pressure: a behavioral approach to Data Integrity

The MHRA has published an interesting article on the behavioral factors that shape data integrity.

Data integrity refers to maintaining and assuring the accuracy and consistency of data over its entire life-cycle, and is a critical aspect to the design, implementation and usage of any system which stores, processes, or retrieves data.

Here is an extract:

“Implementing a quality culture and ensuring job satisfaction is easier said than done, but relatively simple actions taken by management can make big differences in everyday operations.  Informal senior management visits to the shop floor enable an understanding of operational issues which are invisible from the boardroom. The ability of an individual to justify their decision to manipulate data can be reduced by making sure that all employees have ‘visibility to the patient’ and understand the impact of their actions. Senior management has the power to fix problematic test methods from the beginning, upgrade outdated equipment and software, encourage open reporting of deviations, and reward good behavior rather than speed.”

The full article can be accessed here.

Tim Sandle’s article on data integrity for the microbiology laboratory can be read here.

Posted by Dr. Tim Sandle

Tuesday 23 May 2017

How a beneficial gut microbe adapted to breast milk

Breast milk provides vital nutrients not only to infants, but also to beneficial microbes that inhabit the gastrointestinal tract. A new study shows that a bacterial species called Bifidobacterium longum has successfully adapted to the unique niche of the infant gut by producing an enzyme called LnbX, which enables this microbe to grow on a sugar that is abundant only in human milk.

Gut microbes in early life are thought to have long-lasting effects on human health, and studies have shown that diet strongly influences the composition of this population. For example, human milk sugars are known to selectively promote the growth of beneficial gut microbes such as Bifidobacteria, which prevent diarrhea and pathogenic infection in infants. One major component of human milk is a sugar called lacto-N-tetraose, which is virtually absent in the milk of other mammals. Bifidobacteria produce enzymes that break down this sugar, strongly suggesting that a symbiotic relationship recently evolved between these microorganisms and humans.

While investigating how this symbiotic relationship evolved, Katayama and co-senior study author Shinya Fushinobu of the University of Tokyo previously characterized LnbB and isolated LnbX -- enzymes that degrade lacto-N-tetraose in Bifidobacterium bifidum and Bifidobacterium longum, respectively. In the new study, the researchers set out to build on these findings by determining the X-ray crystal structure of the catalytic domain of LnbX. The crystal structure, in combination with mutation and pharmacological experiments, revealed that LnbX has a distinct structure and catalytic mechanism from LnbB and therefore belongs to a novel family of glycoside hydrolase enzymes called GH136.

For further details see:

Chihaya Yamada, Aina Gotoh, Mikiyasu Sakanaka, Mitchell Hattie, Keith A. Stubbs, Ayako Katayama-Ikegami, Junko Hirose, Shin Kurihara, Takatoshi Arakawa, Motomitsu Kitaoka, Shujiro Okuda, Takane Katayama, Shinya Fushinobu. Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum. Cell Chemical Biology, 2017; DOI: 10.1016/j.chembiol.2017.03.012

Posted by Dr. Tim Sandle

Sunday 21 May 2017

Giant viruses found in Austrian sewage

Giant viruses are characterized by disproportionately large genomes and virions that house the viruses' genetic material. They can encode several genes potentially involved in protein biosynthesis, a unique feature which has led to diverging hypotheses about the origins of these viruses. But after discovering a novel group of giant viruses with a more complete set of translation machinery genes than any other virus known to date, scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, believe that this group (dubbed "Klosneuviruses") significantly increases our understanding of viral evolution. Thus the Klosneuviruses contradict the theory that viruses make up a distinct domain of life.
The predicted hosts for the Klosneuviruses are protists (single-celled eukaryotic (nucleus-containing) microorganisms) and while their direct impacts on protists are not yet worked out, these giant viruses are thought to have a large impact on these protists that help regulate the planet's biogeochemical cycles.

Scientists have been fascinated by giant viruses since 2003, when a group of French biologists led by Didier Raoult discovered the Mimiviruses. Since then, a handful of other giant virus groups have been found. The unique ability among them to encode proteins involved in translation (typically DNA to RNA to protein) piqued researchers' interests as to the origin of giant viruses. Since then, two evolutionary hypotheses have emerged. One posits that giant viruses evolved from an ancient cell, perhaps one from an extinct fourth domain of cellular life. Another -- a scenario championed by Koonin -- presents the idea that giant viruses arose from smaller viruses.

The discovery of Klosneuvirus supports the latter idea, according to Tanja Woyke, DOE JGI Microbial Genomics Program lead and senior author of the paper. "In this scenario, a smaller virus infected different eukaryote hosts and picked up genes encoding translational machinery components from independent sources over long periods of time through piecemeal acquisition," she said.

For further details see:

Frederik Schulz, Natalya Yutin, Natalia N. Ivanova, Davi R. Ortega, Tae Kwon Lee, Julia Vierheilig, Holger Daims, Matthias Horn, Michael Wagner, Grant J. Jensen, Nikos C. Kyrpides, Eugene V. Koonin, Tanja Woyke. Giant viruses with an expanded complement of translation system components. Science, 2017; 356 (6333): 82 DOI: 10.1126/science.aal4657

Posted by Dr. Tim Sandle

Friday 19 May 2017

European Pharmacopoeia 9th Edition (Supplement 9.1)

The 1st supplement to the 9th edition of the European Pharmacopeia became effective on 1st April 2017.

Of interest to readers:

Water for injections (0169)

Production: revision to include purification processes equivalent to distillation (such as reverse osmosis coupled with appropriate techniques) for producing water for injections (WFI), in addition to distillation; use of non-distillation technologies for the production of WFI requires that notice is given to the supervisory authority of the manufacturer before implementation.

A requirement for regular monitoring of total organic carbon has been added to further emphasize the specific test controls required in the Production section.

Posted by Dr. Tim Sandle

Wednesday 17 May 2017

Giant virus viewing required retrofitted microscope

In order to map one of the world’s largest viruses, scientists took a DIY approach to build a retrofitted cryo-electron microscope.

“If the common cold virus is scaled to the size of a ladder, then the giant Samba virus is bigger than the Washington Monument,” says Kristin Parent, assistant professor of biochemistry and molecular biology at Michigan State University and coauthor of the paper in the journal Viruses. “Cryo-EM allowed us to map this virus’ structure and observe the proteins it uses to enter, or attack, cells.”

It seems counterintuitive that bigger organisms are harder to see, but they are when using cryo-electron microscopy. That’s because scientists usually use these microscopes to look at thin specimens. The microscopes can’t decipher larger organisms to reveal their biological mechanisms. For thick samples, scientists see only dark gray or black blobs instead of seeing the molecular framework.

Cryo-EM allowed Parent’s team to image the giant Samba virus and understand the structures that allow it to enter an amoeba. Once inside, Samba opens one of its capsid layers and releases its nucleocapsid—which carries the genetic cargo that sparks an infection. While Samba isn’t known to cause any diseases in humans, its cousin, the mimivirus, may be a culprit for causing some respiratory ailments in humans.

For more on this news item see: Laboratory Roots

Posted by Dr. Tim Sandle

Monday 15 May 2017

Cleanroom Management in Pharmaceuticals and Healthcare (new edition)

Everything you need to know about the operation and management of cleanrooms – a new edition of the book edited by Tim Sandle and Madhu Raju Saghee is now available from Euromed Communications.

In 26 Chapters and over 600 pages this book provides a unique tool to help you achieve regulatory compliance. It first creates a foundation in history and established practice and then helps you understand how state of the art technology and engineering solutions can deliver the best practice and so provide reliable systems performance.

An essential read for practitioners in cleanroom technology.

Since the first edition of this book in 2013 there have been many changes to the approach and methods for cleaning and certifying cleanrooms. This was most notable in the revised ISO 14644 cleanroom standard, parts 1 and 2. Numerous chapters have been updated to reflect the requirements of the new global standard.

In addition to incorporating the new standard, many of the other chapters in the book have been updated. For example, in bringing current practices and Good Manufacturing Practice regulations up-to-date. The book also details the leading international cleanroom requirements and regulations: U.S., FDA, EMA, and ISO. Many of the authors share best practice guidance.

The chapters on isolators and other barrier devices, contain added information about vapour phase bio-decontamination using hydrogen peroxide. There are also updates to those chapters surveying the future of aseptic processing and cleanroom technology, with a special focus on areas like automation.

This updated edition will prove an essential resource to all practitioners of operation and management of cleanrooms.

For further details see Euromed Communications

Sandle, T. and Saghee, M. R. (Eds) Cleanroom Management in Pharmaceuticals and Healthcare, 2nd Edition, Euromed Communications, Passfield, U.K.

See also:

Posted by Dr. Tim Sandle

Sunday 14 May 2017

Embracing the Cloud to Assure Data Integrity

Data integrity issues in the manufacturing of finished pharmaceuticals and active pharmaceutical ingredients (APIs) continue to be in the spotlight. Life sciences companies are under increased scrutiny by regulatory bodies, as the MHRA, FDA, EMA and WHO have all recently issued guidance on best practices for end-to-end management of data records throughout the drug development lifecycle.

Mike Jovanis has written an interesting article on this subject for Pharmaceutical Manufacturing.  Here is an extract: “Modernize with the cloud: Cloud applications tailored for life sciences quality processes can extend data integrity across every part of the supply chain by capturing every data-driven event. Easily configured to work with existing business processes, the cloud ensures anyone who touches data - whether it’s uploaded, reviewed or accepted - is automatically documented.”

The article can be accessed here: PM

Posted by Dr. Tim Sandle

Thursday 11 May 2017

Mapping giant viruses

In a laboratory at Michigan State University, scientists took a DIY approach to build a retrofitted cryo-electron microscope that allowed them to map a giant Samba virus -- one of the world's largest viruses.

"If the common cold virus is scaled to the size of a ladder, then the giant Samba virus is bigger than the Washington Monument," said Kristin Parent, assistant professor of biochemistry and molecular biology and co-author of the paper featured on the cover of the journal Viruses. "Cryo-EM allowed us to map this virus' structure and observe the proteins it uses to enter, or attack, cells."

It seems counterintuitive that bigger organisms are harder to see, but they are when using cryo-electron microscopy. That's because these microscopes usually are used to look at thin specimens and can't decipher larger organisms to reveal their biological mechanisms. For thick samples, scientists see only dark gray or black blobs instead of seeing the molecular framework.

Cryo-EM allowed Parent's team to image the giant Samba virus and understand the structures that allow it to enter an amoeba. Once inside, Samba opens one of its capsid layers and releases its nucleocapsid -- which carries the genetic cargo that sparks an infection. While Samba isn't known to cause any diseases in humans, its cousin, the mimivirus, may be a culprit for causing some respiratory ailments in humans.

"If you scoop up a handful of water from Lake Michigan, you are literally holding more viruses than there are people on the planet," said Parent, who published the paper with Jason Schrad and Eric Young, MSU biochemistry and molecular biology graduate students. "While scientists can't study every virus on Earth, the insights we glean from viruses like the giant Samba can help us understand the mechanisms of other viruses in its family, how they thrive and how we can attack them."

As bacteria become more resistant to antibiotics, looking for new ways to fight diseases will continue to grow in importance. Parent's lab also studies how bacteria-infecting viruses enter cells using this method, which could potentially lead to new antibacterial treatments. Yet the world's best cryo-EM microscope costs more than $5 million. Limited by funds but not drive, Parent was able to upgrade an existing microscope at MSU to do cryo-EM -- one that is a tinkerer's dream.

This traditional transmission electron microscope was retrofitted with a cryostage, which keeps viruses frozen in liquid nitrogen while they're being studied. Parent and her team then added a Direct Electron DE-20 detector, a powerful camera -- the mighty microscope's piece de resistance.

Parent didn't invent cryo-EM, but establishing it on campus serves as a viable proof-of-concept for MSU, opening the door for many interdisciplinary partnerships. This cutting-edge microscopy has applications across many fields, from those addressing a single protein to others studying entire cells. Virtually anyone studying complex molecular machines can advance their work with this tool, Parent added.

Parent has earned an AAAS Marion Milligan Mason Award for Women in the Chemical Sciences. This award, her paper in Viruses and being the co-author who performed cryo-EM work in a recent Nature Communications paper, lays the groundwork to someday have a more advanced cryo-EM microscope housed at MSU to be able to perform high-resolution structural studies.

"We've done quite a bit with our limited resources, but we're primed to do more," Parent said. "I think MSU could serve as a cryo-EM center and to increase the prevalence of this technology in the Midwest and beyond."

As one example, scientists from Universidade Federal de Minas Gerais (Brazil) and Universidade Federal do Rio de Janeiro (Brazil) also contributed to this study and benefitted from the technology MSU has to offer.


Jason Schrad, Eric Young, Jônatas Abrahão, Juliana Cortines, Kristin Parent. Microscopic Characterization of the Brazilian Giant Samba Virus. Viruses, 2017; 9 (2): 30 DOI: 10.3390/v9020030

Posted by Dr. Tim Sandle

Tuesday 9 May 2017

Pharmaceutical Manufacturing: Understanding Your Process Series

New from PDA -  collected bestsellers in electronic book form covering three vital topics: Cleaning and Cleanrooms; Sterilization and Environmental Monitoring.

These easily accessible, reasonably priced, informative collections offer background and handson applications that will help with a myriad of activities for manufacturers. These chapters were taken from books currently available at the PDA Bookstore website.

Posted by Dr. Tim Sandle

Pharmeuropa 29.1

Pharmeuropa is a free online EDQM publication. Draft monographs are published in Pharmeuropa for public enquiry, which lasts for three months.

Draft Monographs and General Texts for Comment.

2.3.2    Identification of fatty oils by thin-layer chromatography

Method A: chromatogram of hydrogenated arachis oil added.

2.2.32  Loss on drying

Due to its toxicity, the replacement of diphosphorus pentoxide with a molecular sieve is proposed.  The introduction of a standardised amount of desiccant to be used will also help to alleviate to a certain extent that variability.

The conditions of ‘high vacuum’, which were reported to be difficult to achieve with available instruments, are proposed for deletion; this would trigger a revision of the concerned monographs in due time.  Additional clarifications are proposed throughout the general chapter.


Posted by Dr. Tim Sandle

Monday 8 May 2017

Pharmig Guide to Disinfectants

The Pharmig guide on disinfectants has been update and it captures the latest changes to global disinfection standards and provides updated best practice. The guide features a foreword by MHRA together with photographs and illustrations.

The objective of the guide is to review current standards to aid in the selection and validation of disinfectants. This includes a review of the types and selection of disinfectants, the validation of disinfectants detailing global test methods and the practical use of disinfectants.


Blount, R., Gaurdi, L., Morwood, K. and Sandle, T. (2017) Pharmig Guide to Disifectants and their us in the pharmaceutical industry, Pharmig, Stanstead Abbotts, UK

For further information, see: Pharmig

Also purchase:

Posted by Dr. Tim Sandle

Sunday 7 May 2017

Cleanroom Management - new book

New book - Cleanroom Management

In 26 chapters and over 600 pagesthis book provides a unique tool to help you achieve regulatory compliance. It first creates a foundation in history and established practice and then helps you understand how state of the art technology and engineering solutions can deliver the best practice and so provide reliable systems performance.

Posted by Dr. Tim Sandle

CDC Report on Incidence in Pathogens Transmitted Through Food for 2016

The CDC report describes surveillance data for 2016 nine pathogens (CampylobacterCryptosporidiumCyclosporaListeriaSalmonella, STEC, ShigellaVibrio, and Yersinia. The data of 2016 is compared with the data from 2013-2015. FoodNet identified 24,029 infections, 5,512 hospitalizations, and 98 deaths caused by these pathogens. The data include both incidents confirmed by culturing the organisms and culture-independent diagnostic tests (CIDTs). The change from culture methodology to CIDT creates new problem comparing data from this year to previous years … Read More

Posted by Dr. Tim Sandle

Tuesday 2 May 2017

Hidden structures in bacterial DNA revealed

Researchers have described the 3D structure of the genome in the extremely small bacteria Mycoplasma pneumoniae. They discovered previously unknown arrangements of DNA within this tiny bacteria, which are also found in larger cells. Their findings suggest that this type of organization is a universal feature of living cells.

Using a technique called Hi-C, which reveals the interactions between different pieces of DNA, the researchers created a three-dimensional 'map' of the Mycoplasma chromosome. They then used super-resolution microscopy to prove that this computer-generated map matched up with the real-life chromosome organisation inside bacterial cells.
The researchers discovered that Mycoplasma's circular chromosome is consistently organised the same way in all the cells, with a region called the Origin (where DNA copying begins) at one end of the structure and the midpoint of the chromosome located at the opposite end. This is a similar arrangement to that seen in some other larger bacterial species.

The scientists also used the Hi-C technique to study more detailed patterns of organisation within the Mycoplasma genome. In recent years, scientists all over the world have investigated the organisation of chromosomes inside cells from species ranging from larger bacteria to human. Next Generation Sequencing has allowed scientists to 'read' the DNA sequence of any genome, but this doesn't reveal how genetic information is managed and organised in the crowded and bustling biological environment inside a cell. Now, new tools have revealed complex organisational structures within the genomes of larger organisms, with certain regions of chromosomes clustered together to form domains containing genes that are switched on or off together.

However, it was thought that these domains would not be found in Mycoplasma, because its genome is so small and it only makes around 20 different DNA binding proteins responsible for organising the chromosome, compared to the hundreds made by other bacterial species.

Intriguingly, the researchers found that even the tiny Mycoplasma chromosome is organised into distinct structural domains, each containing genes that are also turned on or off in a co-ordinated way.

For further details see:

Marie Trussart, Eva Yus, Sira Martinez, Davide Baù, Yuhei O. Tahara, Thomas Pengo, Michael Widjaja, Simon Kretschmer, Jim Swoger, Steven Djordjevic, Lynne Turnbull, Cynthia Whitchurch, Makoto Miyata, Marc A. Marti-Renom, Maria Lluch-Senar, Luís Serrano. Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniaeNature Communications, 2017; 8: 14665 DOI: 10.1038/ncomms14665

Posted by Dr. Tim Sandle

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