How we all kill whales Moore, Michael J
ICES journal of marine science,
06/2014, Volume:
71, Issue:
4
Journal Article
Peer reviewed
Open access
Today there is enormous popular interest in marine mammals. Western media tend to dwell on the ongoing debate about commercial whaling by Japan, Norway and Iceland. There is, however, relative ...silence as to how the shipping and fishing industries of many if not all maritime countries are also catching and sometimes killing whales, albeit unintentionally. Thus, western countries have, through the development and increase in fishing and shipping in continental shelf waters, essentially resumed whaling as vessel speeds and fishing gear strength have increased in recent decades. The ways in which these animals die, especially in fixed fishing gear that they become entangled in and swim off with, would raise substantial concern with consumers of seafood were they to be aware of what they were enabling.
microRNAs (miRNAs) act as sequence-specific guides for Argonaute (AGO) proteins, which mediate posttranscriptional silencing of target messenger RNAs. Despite their importance in many biological ...processes, rules governing AGO-miRNA targeting are only partially understood. Here we report a modified AGO HITS-CLIP strategy termed CLEAR (covalent ligation of endogenous Argonaute-bound RNAs)-CLIP, which enriches miRNAs ligated to their endogenous mRNA targets. CLEAR-CLIP mapped ∼130,000 endogenous miRNA-target interactions in mouse brain and ∼40,000 in human hepatoma cells. Motif and structural analysis define expanded pairing rules for over 200 mammalian miRNAs. Most interactions combine seed-based pairing with distinct, miRNA-specific patterns of auxiliary pairing. At some regulatory sites, this specificity confers distinct silencing functions to miRNA family members with shared seed sequences but divergent 3'-ends. This work provides a means for explicit biochemical identification of miRNA sites in vivo, leading to the discovery that miRNA 3'-end pairing is a general determinant of AGO binding specificity.
Although Pentapetalae (comprising all core eudicots except Gunnerales) include almost equal to70% of all angiosperms, the origin of and relationships among the major lineages of this clade have ...remained largely unresolved. Phylogenetic analyses of 83 protein-coding and rRNA genes from the plastid genome for 86 species of seed plants, including new sequences from 25 eudicots, indicate that soon after its origin, Pentapetalae diverged into three clades: (i) a "superrosid" clade consisting of Rosidae, Vitaceae, and Saxifragales; (ii) a "superasterid" clade consisting of Berberidopsidales, Santalales, Caryophyllales, and Asteridae; and (iii) Dilleniaceae. Maximum-likelihood analyses support the position of Dilleniaceae as sister to superrosids, but topology tests did not reject alternative positions of Dilleniaceae as sister to Asteridae or all remaining Pentapetalae. Molecular dating analyses suggest that the major lineages within both superrosids and superasterids arose in as little as 5 million years. This phylogenetic hypothesis provides a crucial historical framework for future studies aimed at elucidating the underlying causes of the morphological and species diversity in Pentapetalae.
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The reconstruction of soft tissue, such as that which is found in the nervous system, is governed by the mechanical cues of the growth microenvironment. The complexity of the nervous ...system, particularly in cases of nerve repair and reconstruction, necessitates the development of facile high-throughput investigational tools. This study assesses the hypothesis that a mechanically tunable photoreactive interpenetrating network (IPN) of hyaluronic acid and Puramatrix can be manipulated in order to demonstrate that 3-D environmental stiffness influences neurite growth and proliferation. For these studies we employed photocrosslinkable glycidyl methacrylate hyaluronic acid (GMHA) and Puramatrix, a self-assembling peptide scaffold, leading to a structurally adjustable IPN system. Our in vitro model provides us with a simple, reproducible environment to generate different properties in a single specimen. Mechanically manipulated IPN systems with different degrees of methacrylation were fabricated using a dynamic mask projection photolithography apparatus and characterized. To gauge the impact of IPN stiffness on neurite outgrowth, dorsal root ganglia (DRG) explants were cultured in the hydrogels. We found that neurite outgrowth in 3-D was more likely to happen in an environment with a lesser degree of methacrylation, which corresponded to structures that were more compliant and more porous. Overall, tuning the mechanical behavior of our IPN systems led to statistically significant (p<0.05) differences in cellular growth and extension that warrants further investigations.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
The cacti are one of the most celebrated radiations of succulent plants. There has been much speculation about their age, but progress in dating cactus origins has been hindered by the lack of fossil ...data for cacti or their close relatives. Using a hybrid phylogenomic approach, we estimated that the cactus lineage diverged from its closest relatives almost equal to35 million years ago (Ma). However, major diversification events in cacti were more recent, with most species-rich clades originating in the late Miocene, almost equal to10-5 Ma. Diversification rates of several cactus lineages rival other estimates of extremely rapid speciation in plants. Major cactus radiations were contemporaneous with those of South African ice plants and North American agaves, revealing a simultaneous diversification of several of the world's major succulent plant lineages across multiple continents. This short geological time period also harbored the majority of origins of Câ photosynthesis and the global rise of Câ grasslands. A global expansion of arid environments during this time could have provided new ecological opportunity for both succulent and Câ plant syndromes. Alternatively, recent work has identified a substantial decline in atmospheric COâ almost equal to15-8 Ma, which would have strongly favored Câ evolution and expansion of Câ-dominated grasslands. Lowered atmospheric COâ would also substantially exacerbate plant water stress in marginally arid environments, providing preadapted succulent plants with a sharp advantage in a broader set of ecological conditions and promoting their rapid diversification across the landscape.
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Alternative splicing is a vast source of biological regulation and diversity that is misregulated in cancer and other diseases. To investigate global control of alternative splicing in human cells, ...we analyzed splicing of mRNAs encoding Bcl2 family apoptosis factors in a genome-wide siRNA screen. The screen identified many regulators of
Bcl-x and
Mcl1 splicing, notably an extensive network of cell-cycle factors linked to aurora kinase A. Drugs or siRNAs that induce mitotic arrest promote proapoptotic splicing of
Bcl-x,
Mcl1, and
caspase-9 and alter splicing of other apoptotic transcripts. This response precedes mitotic arrest, indicating coordinated upregulation of prodeath splice variants that promotes apoptosis in arrested cells. These shifts correspond to posttranslational turnover of splicing regulator ASF/SF2, which directly binds and regulates these target mRNAs and globally regulates apoptosis. Broadly, our results reveal an alternative splicing network linking cell-cycle control to apoptosis.
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► Functional genomic screen defines regulators of alternative splicing in apoptosis ► Disruption of cycle factors promotes coordinated proapoptotic mRNA splicing ► A major RNA-binding protein, ASF/SF2, mediates this proapoptotic splicing network
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the ...last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes (almost equal to42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae + magnoliids as sister to a well supported clade of monocots + (Ceratophyllum + eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 ± 4.8 and 140.3 ± 4.8 Mya.
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The systems of distributed molecular machines (i.e., devices with a size in the nano- to micro-scale range) are anticipated to perform nanoscale to microscale precision functions for future medical ...applications with cells and for manufacturing applications to pattern molecules. In these applications, molecular machines are mobile and distributed about an environment. The molecular machines coordinate to perform system-level functionality. One common form of coordination is synchronization of molecular machines. Since a single molecular machine has limited ability, multiple molecular machines may synchronize to perform some functionality at the same time to produce a larger scale effect. Synchronization may also be required for multiple molecular machines to coordinate a sequential process. This paper focuses on a simple model for oscillation by molecular machines which release pulses of inhibitory molecules. The inhibitory molecules diffuse and cause synchronization of pulses. Analysis was performed to determine how the number of oscillators, distance between oscillators, and noise of measured concentration impacted the period of oscillation and phase difference among molecular machines.
Angiosperm phylogeny: 17 genes, 640 taxa Soltis, Douglas E.; Smith, Stephen A.; Cellinese, Nico ...
American journal of botany,
April 2011, Volume:
98, Issue:
4
Journal Article
Peer reviewed
Open access
Premise of the study. Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the ...hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. Methods: We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i. e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). Key results: Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + Ceratophyllaceae + Eudicotyledoneae. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, CaryophyHales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. Conclusions: Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need ...comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications.
We assembled a data set of transcriptomes and genomes from 168 species in Caryophyllales, of which 43 transcriptomes were newly generated for this study, representing one of the most densely sampled genomic-scale data sets available. We carried out phylogenomic analyses using a modified phylome strategy to reconstruct the species tree. We mapped the phylogenetic distribution of polyploidy events by both tree-based and distance-based methods, and explicitly tested scenarios for allopolyploidy.
We identified 26 ancient and more recent polyploidy events distributed throughout Caryophyllales. Two of these events were inferred to be allopolyploidy.
Through dense phylogenomic sampling, we show the propensity of polyploidy throughout the evolutionary history of Caryophyllales. We also provide a framework for utilizing transcriptome data to detect allopolyploidy, which is important as it may have different macroevolutionary implications compared with autopolyploidy.
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