Cancer inhibitor

A TopoisomeraseIB protein (green) is hindered in unwinding DNA loops by the cancer inhibitor topotecan (red). The DNA polymerase protein (grey), a protein which duplicates DNA, is hindered by the DNA loops.

Credit: Delft University of Technology / Tremani


Researchers in Delft University of Technology's Kavli Institute of Nanoscience in The Netherlands have cast new light on the workings of the important cancer inhibitor topotecan. Little had been known about the underlying molecular mechanism, but the Delft scientists can now view the effects of the medicine live at the levelin of a single DNA molecule.

The medicine investigated, topotecan, interacts with an important protein (TopoIB), causing a (cancer) cell to malfunction. The TopoIB protein is responsible for the removal of loops from DNA, which arise amongst other things during cell division. The TopoIB protein binds to the DNA molecule, clamps around it and cuts one of the two DNA strands, after which it allows it to unwind and finally joins the broken ends together.

Until now it has been supposed that topotecan only causes the TopoIB protein to reside longer than normal on the DNA molecule, disturbing the cell division and damaging the (cancer) cell. But the Delft researchers have now discovered to their surprise that adding topotecan also dramatically impedes the unwinding and that DNA loops accumulate as a result. The accumulation of these DNA loops forms the basis for an alternative mechanism, and could help in the development of better cancer medicine.

PhD candidate Daniel Koster, Master's student Elisa Bot and researcher Nynke Dekker of the Molecular Biophysics group of the Kavli Institute of Nanoscience Delft have managed to unravel this mechanism in an extremely direct manner. In the laboratory they fixed a single DNA molecule between a glass plate and a magnetic sphere. With the help of two magnets they could both pull and twist the DNA molecule.

When they added TopoIB to a twisted piece of DNA, they saw that the loops were slowly removed. What is exceptional is that the action of one TopoIB enzyme on one DNA molecule could be observed live. In collaboration with St. Jude Children's Research Hospital Memphis (USA) the mechanism could also be observed in living yeast cells.

The research was published in the journal Nature (June 24). The lead author of the article, Daniel Koster, will receive his PhD at TU Delft partly on the results described in the article. The research is supported by the Foundation for Fundamental Research on Matter and the Netherlands Organisation for Scientific Research.

TU DElft - Delft Research Centres
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Toward a cure for inherited eye disease

Isolated mouse photoreceptor sensory cilium. Red is the rootlet, which helps connect the cilium to the cell. Green is the axoneme, the central part of the cilium. Scale bar 5 microns.
Credit: Qin Liu, MD, PhD and Eric A. Pierce, MD, PhD, University of Pennsylvania School of Medicine.

Researchers at the University of Pennsylvania School of Medicine have identified proteins in the rod and cones of the eye that could lead to the discovery of the genetic causes of a host of inherited eye diseases. The investigators hope to gain a clearer understanding of what goes wrong at the most basic level in these diseases that cause blindness and other disorders.

Specifically, they have identified and measured the types and amounts of proteins in the light-sensing parts of the eye’s retina. These light-sensitive structures, called photoreceptor sensory cilia, enable the rod and cone cells of the retina to detect light. While the proteins of cilia in single-celled organisms have been studied, this is the first time that a comprehensive description of the proteins of a mammalian cilium – used for movement and sensing – has been determined.

“We want to understand how cilia work normally and how their function is disrupted in disease, because their dysfunction is such an important cause of disease,” says senior author Eric A. Pierce, MD, PhD, Associate Professor of Ophthalmology at the F.M. Kirby Center for Molecular Ophthalmology at Penn. “One of the first steps to achieve this is to put together a complete parts list. Now that we have that, we can figure out how all 2000 proteins we’ve identified fit together correctly.”

Cilia, specialized structures that extend from cells, have recently taken the spotlight in studying genetic diseases. They are commonly used by cells for movement or sensory purposes, and, in many cases with mammals, have been thought to be remnants of evolution without much purpose. But new research has shown that mutations in genes that encode the proteins of cilia are common causes of a host of genetic diseases, including inherited retinal diseases and polycystic kidney disease.

Cilia diseases can also affect multiple organ systems in such disorders as Bardet-Biedl Syndrome, which causes kidney disease, obesity, polydactyly, diabetes, and retinal degeneration; Senior-Loken Syndrome, which causes kidney disease and retinal degeneration; Joubert Syndrome, which causes neurological disease, kidney disease, and retinal degeneration; Usher Syndrome, which causes deafness and blindness; and Meckel Syndrome, which causes kidney disease and neural tube defects.

Lead author Qin Liu, MD, PhD, Research Assistant Professor, and Pierce collaborated with a team at The Wistar Institute led by David Speicher to perform the analyses for this study. The researchers used mass spectrometry to identify and measure the amounts of proteins in mouse photoreceptor sensory cilia. They found many proteins in the cilia that had not been identified in photoreceptors before. This includes proteins involved in intraflagellar transport, which is a process that moves materials from the cell body into the cilia. Mutations in proteins associated with this transport system lead to a number of cilia-related diseases.

The investigators also found 60 proteins encoded by genes on chromosomes implicated in 23 inherited cilia-related disorders. Armed with this knowledge, researchers hope to be able to more quickly find the exact genetic mutations that cause these 23 cilia diseases, which include eye and kidney diseases, among others.

Pierce is a pediatric ophthalmologist who specializes in caring for children with inherited retinal degenerations. He says that about half of his patients with degenerative eye diseases have a type of disease that can be identified according to its genetic mutation. He believes that this research will help identify the genetic causes behind the other half of his patients’ conditions.
“We’re narrowing the field,” says Pierce. “This research in and of itself can’t find a cure, but it’s a great start because it tells you what proteins to study.”

University of Pennsylvania - School of Medicine
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Have I Been Here Before?

New research could lead to treatments for memory-related disorders.

Dentate Gyrus NMDA Receptors Mediate Rapid Pattern Separation in the Hippocampal Network.
Dentate gyrus pattern.
(Credit: Matt Jones)


In today's fast-moving world of look-alike hotel rooms and comparable corridors, it can take a bit of thinking to answer this simple question. University of Bristol neuroscientists working with colleagues at the Massachusetts Institute of Technology (MIT) report in the June 7 early online edition of Science that they have identified a neuronal mechanism that our brains may use to rapidly distinguish similar, yet distinct places.

The work could lead to treatments for memory-related disorders, as well as for the confusion and disorientation that plague elderly individuals who have trouble distinguishing between separate but similar places and experiences.

Forming memories of places and contexts in which episodes occur engages a part of the brain called the hippocampus. The laboratory of Nobel Laureate, Susumu Tonegawa, Picower Professor of Biology and Neuroscience at MIT, has been exploring how each of the three hippocampal subregions-the dentate gyrus, CA1 and CA3-contribute uniquely to different aspects of learning and memory.

In the current study, co-authors Matthew Jones, Research Councils UK (RCUK) Academic Fellow in the Department of Physiology at the University of Bristol and Dr Thomas McHugh, a Picower Institute research scientist, have revealed that the learning in the dentate gyrus is crucial in rapidly recognizing and amplifying the small differences that make each place unique.

"We constantly make split-second decisions about how best to behave at a given place and time. To achieve this, our nervous system must employ highly efficient ways of rapidly recognising and learning important changes in our environment" said Dr Jones.

"This paper demonstrates that a particular protein signalling molecule (the NMDA receptor) in a particular network of brain neurons (the dentate granule cells of the hippocampus) is essential for these rapid discrimination processes, hopefully paving the way for therapies targeting learning and behavioural disorders."

Researchers believe that a set of neurons called 'place cells' fire to provide a sort of blueprint for any new space we encounter. The next time we see the space, those same neurons fire. Thus we know when we've been somewhere before and don't have to relearn our way around familiar turf. But similar spaces may activate overlapping neuronal blueprints, leaving room for confusion if the neurons are not fine-tuned.

In this study, the researchers used a line of genetically altered mice to pinpoint how the dentate gyrus contributes to the kind of pattern separation involved in identifying new and old spaces. Whilst the mice behaved normally in most situations, they became confused when required to discriminate between different spaces. This may model the difficulties in forming distinct memories for similar but distinct places and experiences that afflicts some elderly individuals.

Have I Been Hear Before?
Neuronal Mechanism Could Help Explain Déjà-vu
Bristol University Press release issued 7 June 2007
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