For about two decades, chemists have been synthesizing libraries of single-stranded DNAs and screening them for ones that can catalyze specific reactions. Scientists think these DNA enzymes, or DNAzymes, could serve as medical diagnostics, functional components in nanotechnologies, or even drugs. In fact, some have been tested in clinical trials, but none have yet been approved. But until now, researchers haven’t been able to obtain a crystal structure or determine a catalytic mechanism for any DNAzyme. By sheer persistence, Claudia Höbartner, Vladimir Pena, and coworkers at the Max Planck Institute for Biophysical Chemistry and Georg-August University found the right conditions to crystallize and structurally analyze a DNAzyme called 9DB1 that stitches together, or ligates, RNA strands (Nature 2016, DOI: 10.1038/nature16471). They succeeded by crystallizing a form of 9DB1 in which its reaction product, a ligated RNA, is still attached. The structure enabled the researchers to propose the first molecular mechanism of action for any DNAzyme. The work could help researchers begin to rationally design DNAzymes to improve their catalytic activity or change their substrate selectivity. Indeed, the Höbartner-Pena team revised 9DB1’s substrate selectivity as part of the study. “It’s the missing piece,” says Gerald F. Joyce of Scripps Research Institute California, who, with Ronald R. Breaker of Yale University, discovered the first DNAzyme in 1994. “I know from personal experience how hard it’s been to get a DNAzyme structure, and this is the first one. It’s really cool to see DNA catalyzing a reaction like this.” “Many groups have tried to provide a crystal structure of a DNAzyme for the past two decades, and finally one has succeeded,” says functional nucleic acid specialist Yingfu Li of McMaster University. Mutagenesis studies had provided indirect evidence suggesting that single-stranded DNAzymes are capable of adopting intricate tertiary folds like those of enzymes and ribozymes—RNA enzymes—to form well-defined catalytic active sites. But this study is the first to make it crystal clear, Li says. Scott K. Silverman of the University of Illinois, Urbana-Champaign, who first identified 9DB1 and was Höbartner’s postdoc adviser, notes that the mechanistic analysis reveals how the positioning of key nucleotide pairs in 9DB1 enables it to catalyze 3’ to 5’ RNA ligation rather than 2’ to 5’ ligation. The study also highlights a difference between ribozymes and DNAzymes. Ribozymes use RNA’s 2’-hydroxyl groups, which are absent in DNA, for structural interactions or directly for catalysis. The new structure shows why the lack of these groups doesn’t diminish the catalytic activity of DNAzymes. The missing hydroxyls make DNA’s sugar-phosphate backbone more flexible, allowing acrobatic conformations that compensate for the absent hydroxyls in DNAzymes. Höbartner admits that the study could have provided more mechanistic information if the DNAzyme had been caught prior to or during catalysis, as such conformations are more mechanistically revelatory. “Our next goals are to obtain a structure of 9DB1’s precatalytic state and to get further insights into the mechanism,” she says. She and others in the field also hope eventually to structurally analyze other DNAzymes and compare their mechanisms with that of 9DB1. This article has been translated into Spanish by Divulgame.org and can be found here.
A study at the Las Cruces Biological Station in Costa Rica shows that when forests are linked by continuous corridors of trees, pollination has a greater likelihood of success. In contrast, when patches of forest are isolated from each other, pollinators are less abundant and plants frequently fail to reproduce. More than 94 percent of flowering tropical plants and 75 percent of the world's leading food crops require pollination by animals such as bees, bats and hummingbirds. Researchers have found that forest corridors enable specialized hummingbirds that prefer such landscapes to travel longer distances from one patch of trees to another, increasing pollen exchange between forest patches. Such patches not only harbor more hummingbirds but also display greater rates of pollination than plants in areas that are isolated from each other. These are among the results published today in the Proceedings of the Royal Society B, a technical journal, by scientists from the College of Forestry at Oregon State University and the Georg-August University Gottingen in Germany. "This work presents tropical forest landowners with a simple, relatively inexpensive solution to enhancing biodiversity and pollination of native forest plants—connect forest patches with hedgerows and wooded corridors," said Urs Kormann, the lead author of the study and a postdoctoral researcher at Oregon State. "This may complement national parks." "Wooded corridors remain abundant in many tropical landscapes," said Matthew Betts, co-author and assistant professor at Oregon State. "But as agricultural land use is expanding rapidly, quick action will be required to avert the disappearance of corridor elements between fragments. Otherwise, there may substantial losses of connectivity between forest remnants, leading to accelerated biodiversity loss." The researchers performed field experiments and conducted observations to arrive at their findings. They measured rates of hummingbird visits to feeders and to live plants (Heliconia tortuosa) placed in forest patches. They tracked the flow of pollen from one patch to another and evaluated the presence of two groups of hummingbird species, one that prefers forested habitats and one that does not. "Simple wooded corridors can boost landscape connectivity for pollinators and animal-pollinated plants," the researchers wrote. "Our findings may also apply to other organism groups that move along corridors, potentially providing other ecosystem services." Explore further: Beneficial plant 'spillover' effect seen from landscape corridors More information: Corridors restore animal-mediated pollination in fragmented tropical forest landscapes, Proceedings of the Royal Society B: Biological Sciences, rspb.royalsocietypublishing.org/lookup/doi/10.1098/rspb.2015.2347
If farmers don’t want big cats to kill their livestock, they should make sure that the kitties have enough wild prey to eat. Lions, tigers and other big cats tend to hunt cattle, goats and sheep only after their regular prey has fallen below certain thresholds, a new study finds. The seven species that make up the big cats — lions, tigers, jaguars, cougars, leopards, snow leopards and cheetahs — are favorites for those of us who only encounter them in zoos or on safari. But people who have to live with these animals aren’t often fans. It’s not good for farmers when the cats kill animals in their herds, and it’s not good for the kitties, since people sometimes kill the big cats in retaliation or to prevent more attacks. But studies have suggested that the cats aren’t killing livestock willy-nilly and that the animals would prefer their natural, wild diet. So Igor Khorozyan and colleagues at the Georg-August University of Göttingen in Germany wondered if what the balance was between a wild diet and the easy prey of a livestock herd. They gathered data on the seven big cats from more than 100 studies and applied some statistical analyses. They report their findings in the December issue of Biological Conservation. “The probability of livestock killing by big cats significantly increased when prey biomass fell below minimum thresholds,” the team writes. When that “prey biomass” fell below 812 kilograms per square kilometer, the cats started killing cattle in higher numbers. And when the level fell below 545 kilograms per square kilometer, cats went for the smaller goats and sheep. (The numbers aren’t easily translated into numbers of animals per area because prey come in a variety of sizes. But they will be useful for people who manage animals and lands.) When the kitties’ prey starts becoming scarce, the cats start hunting the easiest and most-profitable animal alternatives — cattle. When even the cattle can’t compensate for the cats’ missing prey, then the cats go after the smaller goats and sheep. In other words, it appears that big cats don’t really want to kill livestock as a first choice for dinner, but they will if they have few other alternatives. The researchers found a few exceptions to this trend, such as when big cats were able to supplement the lack of their regular prey with other, non-livestock species, like giant anteaters or domestic dogs. But the livestock trend held for all seven of the cats, and it showed why in some protected areas in India, Nepal and South Africa, big cats tend not to kill livestock: They have plenty of wild animals to eat.
Gawinecka J.,August University |
Dieks J.,August University |
Asif A.R.,August University |
Carimalo J.,August University |
And 5 more authors.
Journal of Proteome Research | Year: 2010
Cerebrospinal fluid (CSF) contains a dynamic and complex mixture of proteins, which can reflect a physiological and pathological state of the central nervous system. In our present study, we show CSF protein patterns from patients with the two most frequent subtypes of sporadic Creutzfeldt-Jakob disease (sCJD) defined by the codon 129 genotype (MM, MV, and VV) and the protease-resistant form of prion protein (type 1 and type 2). The densitometric analysis of 2D gels showed up-regulation of 27 and down-regulation of 3 proteins in the MM-sCJD as well as the up-regulation of 24 proteins in the VV-sCJD as compared to nondemented control. Almost 40% of sCJD specific regulated proteins in CSF are involved in glucose metabolism, regardless of the codon 129 polymorphism. The increase in CSF levels of lactate dehydrogenase (LDH), glucose-6-phosphate isomerase (G6PI), and fructose-bisphosphate aldolase A (ALDOA) were validated on a larger group of sCJD patients including three possible codon 129 polymorphism carriers and three control groups consisting of nondemented, neurological cases as well as patients suffering from Alzheimer's disease or vascular dementia. Subsequently, the abundance of these glycolytic enzymes in the brain as well as their cellular localization were determined. This study demonstrates for the first time the implication of G6PI in prion-induced pathology as well as its cellular translocalization in sCJD. The identification of sCJD-regulated proteins in CSF of living symptomatic patients in our study can broaden our knowledge about pathological processes occurring in sCJD, as they are still not fully understood. © 2010 American Chemical Society. Source