456 research outputs found
Transcriptomics and metatranscriptomics in zooplankton: wave of the future?
Abstract
Molecular tools have changed the understanding of zooplankton biodiversity, speciation, adaptation, population genetics and global patterns of connectivity. However, the molecular resources needed to capitalize on these advances continue to be limited in comparison with those available for other eukaryotic plankton. This deficiency could be addressed through an Ocean Zooplankton Open 'Omics Project (Ocean ZOOP) that would generate de novo assembled transcriptomes for hundreds of metazoan plankton species. A collection of comparable reference transcriptomes would generate a new framework for ecological and physiological studies. Defining species niches, identifying optimal habitats, assessing adaptive capacity and predicting changes in phenology are just a few examples of how such a resource could transform studies on zooplankton ecology
Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses
Many empirical studies show that there are unusual clusters of palindromes, closely spaced direct and inverted repeats around the replication origins of herpesviruses. In this paper, we introduce two new scoring schemes to quantify the spatial abundance of palindromes in a genomic sequence. Based on these scoring schemes, a computational method to predict the locations of replication origins is developed. When our predictions are compared with 39 known or annotated replication origins in 19 herpesviruses, close to 80% of the replication origins are located within 2% of the genome length. A list of predicted locations of replication origins in all the known herpesviruses with complete genome sequences is reported
Asymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI
Restriction enzymes share little or no sequence homology with the exception of isoschizomers, or enzymes that recognize and cleave the same DNA sequence. We present here the structure of a BamHI isoschizomer, OkrAI, bound to the same DNA sequence (TATGGATCCATA) as that cocrystallized with BamHI. We show that OkrAI is a more minimal version of BamHI, lacking not only the N- and C-terminal helices but also an internal 310 helix and containing β-strands that are shorter than those in BamHI. Despite these structural differences, OkrAI recognizes the DNA in a remarkably similar manner to BamHI, including asymmetric contacts via C-terminal ‘arms’ that appear to ‘compete’ for the minor groove. However, the arms are shorter than in BamHI. We observe similar DNA-binding affinities between OkrAI and BamHI but OkrAI has higher star activity (at 37°C) compared to BamHI. Together, the OkrAI and BamHI structures offer a rare opportunity to compare two restriction enzymes that work on exactly the same DNA substrate
Substrate Micropatterning as a New in Vitro Cell Culture System to Study Myelination
Artículo de publicación ISIMyelination is a highly regulated developmental
process whereby oligodendrocytes in the central nervous system
and Schwann cells in the peripheral nervous system ensheathe axons
with a multilayered concentric membrane. Axonal myelination
increases the velocity of nerve impulse propagation. In this work,
we present a novel in vitro system for coculturing primary dorsal root
ganglia neurons along with myelinating cells on a highly restrictive
and micropatterned substrate. In this new coculture system, neurons
survive for several weeks, extending long axons on defined Matrigel
tracks. On these axons, myelinating cells can achieve robust myelination, as demonstrated by the distribution of compact myelin
and nodal markers. Under these conditions, neurites and associated myelinating cells are easily accessible for studies on the
mechanisms of myelin formation and on the effects of axonal damage on the myelin sheath.Regenerative Medicine and Nanomedicine Initiative of the Canadian Institutes of Health Research (CIHR)
RMF-7028
FONDECYT
1080252
CIHR
Ministry of Industry of Canada
Rio Tinto Alcan
Molson Foundatio
Opportunities and challenges in incorporating ancillary studies into a cancer prevention randomized clinical trial
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