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Robison K.,Omics | Robison K.,Infinity Pharmaceuticals Inc.
BMC Genomics

Background: Anamika et al1 recently published in this journal a sequence alignment analysis of protein kinases encoded by the chimpanzee genome in comparison to those in the human genome. From this analysis they concluded that several chimpanzee kinases have unusual domain arrangements.Results: Re-examination of these kinases reveals claimed novel arrangements cannot withstand scrutiny; each is either not novel or represents over-analysis of weakly confident computer generated gene models. Additional sequence evidence available at the time of the paper's submission either directly contradict the gene models or suggest alternate gene models. These alternate models would minimize or eliminate the observed differences between human and chimp kinases.Conclusion: None of the proposed novel chimpanzee kinase architectures are supported by experiment evidence. Guidelines to prevent such erroneous conclusions in similar papers are proposed. © 2010 Robison; licensee BioMed Central Ltd. Source

Crawled News Article
Site: http://phys.org/space-news/

But what happens to these processes when we leave the planet? In Earth orbit and beyond, where gravity is counteracted by a constant state of freefall and cosmic radiation intensifies, the molecular inner-workings of the human body may change. To find out how, NASA has entered a realm of bio-research known as "-omics." "Omics" refers to the collection of data on the medley of microcosms that regulate our bodies at a molecular level. Things that work with the metabolism are grouped underneath the term "metabolome." All of the lipids in the body are called the "lipidome." All of the proteins? You guessed it—"proteome." "We have launched a one-year study to understand the omics of space travel," says Craig Kundrot, Ph.D. in the Office of the Chief Scientist at NASA Headquarters. "Astronauts are spending a year on the International Space Station, and we are looking at what happens to them on the molecular level." This project is really two projects: First, there is the "Twins Study. NASA has twin astronauts: One of them, Mark Kelly (retired), is staying on Earth while his brother, Scott Kelly, orbits Earth. For one year, Mark and Scott will be poked, prodded, and questioned to learn if the omics of identical twins show more signficant differences than normal aging would cause after one of them spends a year in space. At the same time, Scott Kelly is involved in a separate project called the "One Year Mission." Unlike previous expeditions to the space station, which lasted only 6 months, Scott Kelly is spending a full year onboard the station alongside Russian cosmonaut Mikhail Kornienko. This One Year Mission has its own battery of tests designed to reveal the physiological effects of long-term space flight. "NASA knows a lot about what happens to astronauts after 6 months in orbit," says Kundrot. "Deep space missions are going to take much longer than that. A round trip to Mars, for instance, might take thirty months or more. This 1-year experiment is the next, natural step in that direction." Kundrot also notes the intangible significance of 1 year to humans. "When we leave home for 6 months, it's like a long business trip. Leaving home for a year is a different thing. We are going to miss every birthday, anniversary, graduation and many other milestones. It feels like a big chunk of life—and this could affect the mood or behavior of the space travelers." Indeed, some of the studies focus the astronauts' psychological state. At the same time that blood is drawn and other samples are taken, the astronauts will be filling out questionnaires about their mood, thoughts and dreams. This approach could reveal links between the astronaut's mental state and their molecular state. In total, more than 30 research proposals have been approved for the Twin Study and the One Year Mission—and they are well underway. The experiments began on March 27, 2015, when Kelly and Kornienko blasted off onboard a Russian rocket for their year in space.

Undheim E.A.B.,University of Queensland | Sunagar K.,University of Porto | Sunagar K.,The Interdisciplinary Center | Hamilton B.R.,Omics | And 5 more authors.
Journal of Proteomics

Arthropod toxins are almost invariably encoded by transcripts encoding prepropeptides that are posttranslationally processed to yield a single mature toxin. In striking contrast to this paradigm, we used a complementary transcriptomic, proteomic and MALDI-imaging approach to identify four classes of multidomain centipede-toxin transcripts that each encodes multiple mature toxins. These multifunctional warheads comprise either: (1) repeats of linear peptides; (2) linear peptides preceding cysteine-rich peptides; (3) cysteine-rich peptides preceding linear peptides; or (4) repeats of linear peptides preceding cysteine-rich peptides. MALDI imaging of centipede venom glands revealed that these peptides are posttranslationally liberated from the original gene product in the venom gland and not by proteases following venom secretion. These multidomain transcripts exhibit a remarkable conservation of coding sequences, in striking contrast to monodomain toxin transcripts from related centipede species, and we demonstrate that they represent a rare class of predatory toxins that have evolved under strong negative selection. We hypothesize that the peptide toxins liberated from multidomain precursors might have synergistic modes of action, thereby allowing negative selection to dominate as the toxins encoded by the same transcript become increasingly interdependent. Biological significance: These results have direct implications for understanding the evolution of centipede venoms, and highlight the importance of taking a multidisciplinary approach for the investigation of novel venoms. The potential synergistic actions of the mature peptides are also of relevance to the growing biodiscovery efforts aimed at centipede venom. We also demonstrate the application of MALDI imaging in providing a greater understanding of toxin production in venom glands. This is the first MALDI imaging data of any venom gland. © 2014 Elsevier B.V. Source

Yarnold J.E.,Griffith University | Hamilton B.R.,Omics | Welsh D.T.,Griffith University | Pool G.F.,Omics | And 2 more authors.
Molecular BioSystems

A number of pharmacologically active brominated pyrrole-2-aminoimidazole (B-P-2-AI) alkaloids have been isolated from several families of marine sponges, including those belonging to the genus Stylissa. In the present study, MALDI mass spectrometry imaging (MALDI-imaging) was applied to determine the spatial distribution of B-P-2-AIs within 20 μm cross sections of S. flabellata. A number of previously characterised B-P-2-AIs were readily identified by MALDI-imaging and confirmed by MS-MS and NMR profiling. Unknown B-P-2-AIs were also observed. Discrete microchemical environments were revealed for several B-P-2-AIs including dibromophakellin which was localised within the external pinacoderm and internal network of choanoderm chambers. Additionally, dibromopalau'amine and konbu'acidin B were also found to be confined to the choanoderm, while sceptrin was found to be highly abundant within the mesohyl. Further brominated compounds of unknown structure were also observed to have distinct localisation in both choanoderm chambers and the pinacoderm. These findings provide insights into the chemical ecology of S. flabellata, as most B-P-2-AIs were found on highly exposed surfaces, where they may act to prevent pathogens, predation and/or biofouling. Moreover this study demonstrates the power of MALDI-imaging to visualise the location of a range of metabolites in situ and to characterise compounds by MS-MS directly from intact specimens without the need for extraction. These methodologies facilitate selective targeting of micro-regions of sponge to screen for symbiotic microbial candidates or genes that may be involved in the production of the correlated compounds, and may represent a change in paradigm for natural product drug development. © 2012 The Royal Society of Chemistry. Source

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