59 research outputs found
Considering the Case for Biodiversity Cycles: Reexamining the Evidence for Periodicity in the Fossil Record
Medvedev and Melott (2007) have suggested that periodicity in fossil
biodiversity may be induced by cosmic rays which vary as the Solar System
oscillates normal to the galactic disk. We re-examine the evidence for a 62
million year (Myr) periodicity in biodiversity throughout the Phanerozoic
history of animal life reported by Rohde & Mueller (2005), as well as related
questions of periodicity in origination and extinction. We find that the signal
is robust against variations in methods of analysis, and is based on
fluctuations in the Paleozoic and a substantial part of the Mesozoic.
Examination of origination and extinction is somewhat ambiguous, with results
depending upon procedure. Origination and extinction intensity as defined by RM
may be affected by an artifact at 27 Myr in the duration of stratigraphic
intervals. Nevertheless, when a procedure free of this artifact is implemented,
the 27 Myr periodicity appears in origination, suggesting that the artifact may
ultimately be based on a signal in the data. A 62 Myr feature appears in
extinction, when this same procedure is used. We conclude that evidence for a
periodicity at 62 Myr is robust, and evidence for periodicity at approximately
27 Myr is also present, albeit more ambiguous.Comment: Minor modifications to reflect final published versio
Wolbachia in the flesh: symbiont intensities in germ-line and somatic tissues challenge the conventional view of Wolbachia transmission routes
Symbionts can substantially affect the evolution and ecology of their hosts. The investigation of the tissue-specific distribution of symbionts (tissue tropism) can provide important insight into host-symbiont interactions. Among other things, it can help to discern the importance of specific transmission routes and potential phenotypic effects. The intracellular bacterial symbiont Wolbachia has been described as the greatest ever panzootic, due to the wide array of arthropods that it infects. Being primarily vertically transmitted, it is expected that the transmission of Wolbachia would be enhanced by focusing infection in the reproductive tissues. In social insect hosts, this tropism would logically extend to reproductive rather than sterile castes, since the latter constitute a dead-end for vertically transmission. Here, we show that Wolbachia are not focused on reproductive tissues of eusocial insects, and that non-reproductive tissues of queens and workers of the ant Acromyrmex echinatior, harbour substantial infections. In particular, the comparatively high intensities of Wolbachia in the haemolymph, fat body, and faeces, suggest potential for horizontal transmission via parasitoids and the faecal-oral route, or a role for Wolbachia modulating the immune response of this host. It may be that somatic tissues and castes are not the evolutionary dead-end for Wolbachia that is commonly thought
Punctate White Matter Lesions Associated With Altered Brain Development And Adverse Motor Outcome In Preterm Infants.
Preterm infants who develop neurodevelopmental impairment do not always have recognized abnormalities on cerebral ultrasound, a modality routinely used to assess prognosis. In a high proportion of infants, MRI detects punctate white matter lesions that are not seen on ultrasonography. To determine the relation of punctate lesions to brain development and early neurodevelopmental outcome we used multimodal brain MRI to study a large cohort of preterm infants. Punctate lesions without other focal cerebral or cerebellar lesions were detected at term equivalent age in 123 (24.3%) (59 male) of the 506 infants, predominantly in the centrum semiovale and corona radiata. Infants with lesions had higher gestational age, birth weight, and less chronic lung disease. Punctate lesions showed a dose dependent relation to abnormalities in white matter microstructure, assessed with tract-based spatial statistics, and reduced thalamic volume (p < 0.0001), and predicted unfavourable motor outcome at a median (range) corrected age of 20.2 (18.4-26.3) months with sensitivity (95% confidence intervals) 71 (43-88) and specificity 72 (69-77). Punctate white matter lesions without associated cerebral lesions are common in preterm infants currently not regarded as at highest risk for cerebral injury, and are associated with widespread neuroanatomical abnormalities and adverse early neurodevelopmental outcome
Long-term cycles in the history of life: Periodic biodiversity in the Paleobiology Database
Time series analysis of fossil biodiversity of marine invertebrates in the
Paleobiology Database (PBDB) shows a significant periodicity at approximately
63 My, in agreement with previous analyses based on the Sepkoski database. I
discuss how this result did not appear in a previous analysis of the PBDB. The
existence of the 63 My periodicity, despite very different treatment of
systematic error in both PBDB and Sepkoski databases strongly argues for
consideration of its reality in the fossil record. Cross-spectral analysis of
the two datasets finds that a 62 My periodicity coincides in phase by 1.6 My,
equivalent to better than the errors in either measurement. Consequently, the
two data sets not only contain the same strong periodicity, but its peaks and
valleys closely correspond in time. Two other spectral peaks appear in the PBDB
analysis, but appear to be artifacts associated with detrending and with the
increased interval length. Sampling-standardization procedures implemented by
the PBDB collaboration suggest that the signal is not an artifact of sampling
bias. Further work should focus on finding the cause of the 62 My periodicity.Comment: Published in PLoS ONE. 5 pages, 3 figures. Version with live links,
discussion available at
http://www.plosone.org/article/info:doi/10.1371/journal.pone.0004044#to
Computational identification of ubiquitylation sites from protein sequences
<p>Abstract</p> <p>Background</p> <p>Ubiquitylation plays an important role in regulating protein functions. Recently, experimental methods were developed toward effective identification of ubiquitylation sites. To efficiently explore more undiscovered ubiquitylation sites, this study aims to develop an accurate sequence-based prediction method to identify promising ubiquitylation sites.</p> <p>Results</p> <p>We established an ubiquitylation dataset consisting of 157 ubiquitylation sites and 3676 putative non-ubiquitylation sites extracted from 105 proteins in the UbiProt database. This study first evaluates promising sequence-based features and classifiers for the prediction of ubiquitylation sites by assessing three kinds of features (amino acid identity, evolutionary information, and physicochemical property) and three classifiers (support vector machine, <it>k</it>-nearest neighbor, and NaïveBayes). Results show that the set of used 531 physicochemical properties and support vector machine (SVM) are the best kind of features and classifier respectively that their combination has a prediction accuracy of 72.19% using leave-one-out cross-validation.</p> <p>Consequently, an informative physicochemical property mining algorithm (IPMA) is proposed to select an informative subset of 531 physicochemical properties. A prediction system UbiPred was implemented by using an SVM with the feature set of 31 informative physicochemical properties selected by IPMA, which can improve the accuracy from 72.19% to 84.44%. To further analyze the informative physicochemical properties, a decision tree method C5.0 was used to acquire if-then rule-based knowledge of predicting ubiquitylation sites. UbiPred can screen promising ubiquitylation sites from putative non-ubiquitylation sites using prediction scores. By applying UbiPred, 23 promising ubiquitylation sites were identified from an independent dataset of 3424 putative non-ubiquitylation sites, which were also validated by using the obtained prediction rules.</p> <p>Conclusion</p> <p>We have proposed an algorithm IPMA for mining informative physicochemical properties from protein sequences to build an SVM-based prediction system UbiPred. UbiPred can predict ubiquitylation sites accompanied with a prediction score each to help biologists in identifying promising sites for experimental verification. UbiPred has been implemented as a web server and is available at <url>http://iclab.life.nctu.edu.tw/ubipred</url>.</p
Global cooling as a driver of diversification in a major marine clade
Climate is a strong driver of global diversity and will become increasingly important as human influences drive temperature changes at unprecedented rates. Here we investigate diversification and speciation trends within a diverse group of aquatic crustaceans, the Anomura. We use a phylogenetic framework to demonstrate that speciation rate is correlated with global cooling across the entire tree, in contrast to previous studies. Additionally, we find that marine clades continue to show evidence of increased speciation rates with cooler global temperatures, while the single freshwater clade shows the opposite trend with speciation rates positively correlated to global warming. Our findings suggest that both global cooling and warming lead to diversification and that habitat plays a role in the responses of species to climate change. These results have important implications for our understanding of how extant biota respond to ongoing climate change and are of particular importance for conservation planning of marine ecosystems
Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy
addresses: School of Biosciences, University of Exeter, Exeter EX4 5DE, UK. [email protected]: PMCID: PMC2777180types: Journal Article; Research Support, Non-U.S. Gov't© 2009 Yang; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Tyrosine sulfation is one of the most important posttranslational modifications. Due to its relevance to various disease developments, tyrosine sulfation has become the target for drug design. In order to facilitate efficient drug design, accurate prediction of sulfotyrosine sites is desirable. A predictor published seven years ago has been very successful with claimed prediction accuracy of 98%. However, it has a particularly low sensitivity when predicting sulfotyrosine sites in some newly sequenced proteins
First description of a fossil chamaeleonid from Greece and its relevance for the European biogeographic history of the group
The fossil record of Chamaeleonidae is very scarce and any new specimen is therefore considered important for our understanding of the evolutionary and biogeographic history of the group. New specimens from the early Miocene of Aliveri (Evia Island), Greece constitute the only fossils of these lizards from southeastern Europe. Skull roofing material is tentatively attributed to the Czech species Chamaeleo cf. andrusovi, revealing a range extension for this taxon, whereas tooth-bearing elements are described as indeterminate chamaeleonids. The Aliveri fossils rank well among the oldest known reptiles from Greece, provide evidence for the dispersal routes of chameleons out of Africa towards the European continent and, additionally, imply strong affinities with coeval chamaeleonids from Central Europe
Invading and expanding : range dynamics and ecological consequences of the Greater White-Toothed Shrew (Crocidura russula) invasion in Ireland
Establishing how invasive species impact upon pre-existing species is a fundamental question in ecology and conservation
biology. The greater white-toothed shrew (Crocidura russula) is an invasive species in Ireland that was first recorded in 2007
and which, according to initial data, may be limiting the abundance/distribution of the pygmy shrew (Sorex minutus),
previously Ireland’s only shrew species. Because of these concerns, we undertook an intensive live-trapping survey (and
used other data from live-trapping, sightings and bird of prey pellets/nest inspections collected between 2006 and 2013) to
model the distribution and expansion of C. russula in Ireland and its impacts on Ireland’s small mammal community. The
main distribution range of C. russula was found to be approximately 7,600 km2 in 2013, with established outlier populations
suggesting that the species is dispersing with human assistance within the island. The species is expanding rapidly for a
small mammal, with a radial expansion rate of 5.5 km/yr overall (2008–2013), and independent estimates from live-trapping
in 2012–2013 showing rates of 2.4–14.1 km/yr, 0.5–7.1 km/yr and 0–5.6 km/yr depending on the landscape features
present. S. minutus is negatively associated with C. russula. S. minutus is completely absent at sites where C. russula is
established and is only present at sites at the edge of and beyond the invasion range of C. russula. The speed of this invasion
and the homogenous nature of the Irish landscape may mean that S. minutus has not had sufficient time to adapt to the
sudden appearance of C. russula. This may mean the continued decline/disappearance of S. minutus as C. russula spreads
throughout the island
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