Cold Spring Harbor Laboratory

Shape-Shifting Antibiotic against Resistant Superbugs

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In the United States, drug-resistant bacteria and fungi infect almost three million people per year and kill about 35,000. Antibiotics are essential and effective. However, in recent years overuse has led to some bacteria developing resistance to them. Now, researchers at Cold Spring Harbor Laboratory (CSHL) have created a new strategy against these drug-resistant superbugs.

Their findings, published in Proceedings of the National Academy of Sciences, in an article titled, “Shapeshifting bullvalene-linked vancomycin dimers as effective antibiotics against multidrug-resistant gram-positive bacteria,” report of a shape-shifting antibiotic that may lead to new therapies against deadly infections.

“The alarming rise in superbugs that are resistant to drugs of last resort, including vancomycin-resistant enterococci and staphylococci, has become a significant global health hazard,” wrote the researchers. “Here, we report the click chemistry synthesis of an unprecedented class of shapeshifting vancomycin dimers (SVDs) that display potent activity against bacteria that are resistant to the parent drug, including the ESKAPE pathogens, vancomycin-resistant Enterococcus (VRE), methicillin-resistant Staphylococcus aureus (MRSA), as well as vancomycin-resistant S. aureus (VRSA).”

John E. Moses, PhD, professor at CSHL, who led the study, came up with the idea of shape-shifting antibiotics while observing tanks in military training exercises.

A few years later, Moses learned of a molecule called bullvalene. Bullvalene is a fluxional molecule, meaning its atoms can swap positions. Several bacteria, including MRSA, VRSA, and VRE, have developed resistance to a potent antibiotic called vancomycin, used to treat everything from skin infections to meningitis. Moses thought he could improve the drug’s bacteria-fighting performance by combining it with bullvalene.

Moses turned to click chemistry. “Click chemistry is great,” said Moses, who studied this revolutionary development under two-time Nobel laureate K. Barry Sharpless. “It gives you certainty and the best chance you’ve got of making complex things.”

Moses and his team tested the new drug in collaboration with Tatiana Soares da-Costa, PhD, group leader at the University of Adelaide. The researchers gave the drug to VRE-infected wax moth larvae, which are commonly used to test antibiotics. They found the shape-shifting antibiotic significantly more effective than vancomycin at clearing the deadly infection.

“If we can invent molecules that mean the difference between life and death,” he said, “that’d be the greatest achievement ever.”

The new findings pave a way for further studies into shape-shifting antibiotic drugs and overcoming the rapid emergence of multidrug-resistant bacteria and pathogens.

WHICH ‘LETTERS’ IN THE HUMAN GENOME ARE FUNCTIONALLY IMPORTANT?

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In work published today in Nature Genetics, researchers at Cold Spring Harbor Laboratory (CSHL) have developed a new computational method to identify which letters in the human genome are functionally important. Their computer program, called fitCons, harnesses the power of evolution, comparing changes in DNA letters across not just related species, but also between multiple individuals in a single species. The results provide a surprising picture of just how little of our genome has been “conserved” by Nature not only across species over eons of time, but also over the more recent time period during which humans differentiated from one another.

“In model organisms, like yeast or flies, scientists often generate mutations to determine which letters in a DNA sequence are needed for a particular gene to function,” explains CSHL Professor Adam Siepel. “We can’t do that with humans. But when you think about it, Nature has been doing a similar experiment on a very large scale as species evolve. Mutations occur across the genome at random, but important letters are retained by natural selection, while the rest are free to change with no adverse consequence to the organism.”

It was this idea that became the basis of their analysis, but it alone wasn’t enough. “Massive research consortia, like the ENCODE Project, have provided the scientific community with a trove of information about genomic function over the last few years,” says Siepel. “Other groups have sequenced large numbers of humans and nonhuman primates. For the first time, these big data sets give us both a broad and exceptionally detailed picture of both biochemical activity along the genome and how DNA sequences have changed over time.”

Siepel’s team began by sorting ENCODE consortium data based on combinations of biochemical markers that indicate the type of activity at each position. “We didn’t just use sequence patterns. ENCODE provided us with information about where along the full genome DNA is read and how it is modified with biochemical tags,” says Brad Gulko, a Ph.D. student in Computer Science at Cornell University and lead author on the new paper. The combinations of these tags revealed several hundred different classes of sites within the genome each having a potentially different role in genomic activity.

The researchers then turned to their previously developed computational method, called INSIGHT, to analyze how much the sequences in these classes had varied over both short and long periods of evolutionary time. “Usually, this, kind of analysis is done comparing different species – like humans, dogs, and mice – which means researchers are looking at changes that occurred over relatively long time periods,” explains Siepel. But the INSIGHT model considers the changes among dozens of human individuals and close relatives, such as the chimpanzee, which provides a picture of evolution over much shorter time frames.

The scientists found that, at most, only about 7% of the letters in the human genome are functionally important. “We were impressed with how low that number is,” says Siepel. “Some analyses of the ENCODE data alone have argued that upwards of 80% of the genome is functional, but our evolutionary analysis suggests that isn’t the case.” He added, “other researchers have estimated that similarly small fractions of the genome have been conserved over long time evolutionary periods, but our analysis indicates that the much larger ENCODE-based estimates can’t be explained by gains of new functional sequences on the human lineage. We think most of the sequences designated as ‘biochemically active’ by ENCODE are probably not evolutionarily important in humans.”

According to Siepel, this analysis will allow researchers to isolate functionally important sequences in diseases much more rapidly. Most genome-wide studies implicate massive regions, containing tens of thousands of letters, associated with disease. “Our analysis helps to pinpoint which letters in these sequences are likely to be functional because they are both biochemically active and have been preserved by evolution.” says Siepel. “This provides a powerful resource as scientists work to understand the genetic basis of disease.”

Brain: Protein That Regulates Key ‘Fate’ Decision in Cortical Progenitor Cells Identified

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Researchers at Cold Spring Harbor Laboratory (CSHL) have solved an important piece of one of neuroscience’s outstanding puzzles: how progenitor cells in the developing mammalian brain reproduce themselves while also giving birth to neurons that will populate the emerging cerebral cortex, the seat of cognition and executive function in the mature brain.

CSHL Professor Linda Van Aelst, Ph.D., and colleagues set out to solve a particular mystery concerning radial glial cells, or RGCs, which are progenitors of pyramidal neurons, the most common type of excitatory nerve cell in the mature mammalian cortex.

In genetically manipulated mice, Van Aelst’s team demonstrated that a protein called DOCK7 plays a central regulatory role in the process that determines how and when an RGC “decides” either to proliferate, i.e., make more progenitor cells like itself, or give rise to cells that will mature, or “differentiate,” into pyramidal neurons. The findings are reported in the September 2012 issue of Nature Neuroscience.

DOCK7 was already known to be highly expressed in various parts of the developing rodent brain, including the hippocampus and cortex. It had been shown by Van Aelst and colleagues to control the formation of axons — wiring that connects neurons.

Balancing proliferation and differentiation

In their newly published research, Van Aelst, along with Drs. Yu-Ting Yang and Chia-Lin Wang, a graduate student and postdoctoral fellow, respectively, in the Van Aelst lab, elucidate DOCK7’s regulatory role in experiments in which the protein was alternately silenced and overexpressed.

When the protein was silenced in mouse embryos, neuronal differentiation was impeded; RGCs remained in their progenitor state. When DOCK7 was overexpressed, RGCs differentiated prematurely, resulting in more neurons and fewer RGCs.

These and related experiments revealed the mechanism through which DOCK7 expression affects the two essential but contrasting functions of RGCs. “Self-renewability of RGCs must be tightly balanced with differentiation for proper cortical development,” says Van Aelst.

“The mechanism we discovered to be central in the determination of RGC fate is called interkinetic nuclear migration, or INM,” she continues, “and you can see it in action in the movies made by Drs. Wang and Yang.”

In INM, an RGC cell nucleus visibly travels over the course of the cell cycle “upward” and “downward” between opposing sides of the apical-most region of the neuroepithelium, called the ventricular zone or VZ. Nuclei move away from the apical surface during the G1 phase, undergo S phase at a basal location in the VZ, and return to the apical surface during G2 to divide at the apical location. [see diagram below]

It is DOCK7 that regulates this movement; in particular, the movement from the basal to apical location, the CSHL team has now demonstrated. On what appears to be the lower surface of the VZ, the apical surface, signals directing the RCG toward proliferation — i.e., reproduction of other RGCs — are dominant. On the upper or ‘basal’ side of the VZ, dominant signals coax the RGC to split into new intermediate progenitors or neurons.

Migration explained: DOCK7, TACC3 and centrosomes

“The cellular machinery that controls INM involves a protein complex of actin and myosin, called actomyosin, as well as microtubule-dependent systems,” notes Dr. Wang. “We show how DOCK7 exerts its effects by antagonizing the microtubule growth-promoting function of a protein called TACC3.” That protein, tellingly, is associated with the centrosome, the cellular organ that organizes microtubules, and regulates the growth of microtubules emanating from the centrosome, thereby coupling the centrosome and nucleus .

As Dr. Yang points out, DOCK7 acts by antagonizing the microtubule growth-promoting function of TACC3. Silencing of DOCK7 accelerates the movement of RGC nuclei from the basal to apical side of the VZ, resulting in extended apical residency of RGC nuclei and apical mitoses that lead to an increase in RGCs and a reduction in neurons. DOCK7 overexpression, on the other hand, leads to extended residence of RGC nuclei at basal locations and mitoses away from the apical surface, where the production of new neurons increases, at the expense of the proliferation of more progenitors.

Beyond elucidating an important mechanism of cortical development, the new research may shed light on pathologies seen in microcephaly, a condition marked by an abnormally small brain size, as well as neurodevelopmental disorders such as schizophrenia. “If DOCK7 expression is abnormal, you perturb normal neurogenesis,” says Van Aelst. “In future work we hope to explore whether an imbalance in neurogenesis caused by DOCK7 aberrations is associated with a subsequent imbalance in cortical circuitry, and various known pathologies.”

Source: science daily.