111 research outputs found
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Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.
Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the "targeted" clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (ÎąâŻ=âŻ0.05) distributions in the targeted and random BAC clones (15.18 and 12.61âŻGM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08âŻGM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production
Late Holocene palynology and palaeovegetation of tephra-bearing mires at Papamoa and Waihi Beach, western Bay of Plenty, North Island, New Zealand.
The vegetation history of two mires associated with Holocene dunes near the western Bay of Plenty coast, North Island, New Zealand, is deduced from pollen analysis of two cores. Correlation of airfall tephra layers in the peats, and radiocarbon dates, indicate that the mires at Papamoa and Waihi Beach are c. 4600 and c. 2900 conventional radiocarbon years old, respectively. Tephras used to constrain the chronology of the pollen record include Rotomahana (1886 AD), Kaharoa (700 yr B.P.), Taupo (Unit Y; 1850 yr B.P.), Whakaipo (Unit V; 2700 yr B.P.), Stent (Unit Q; 4000 yr B.P.), Hinemaiaia (Unit K; 4600 yr B.P.), and reworked Whakatane (c. 4800 yr B.P.) at Papamoa, and Kaharoa and Taupo at Waihi Beach. Peat accumulation rates at Papamoa from 4600 - 1850 yr B.P. range from 0.94 to 2.64 mm/yr (mean 1.37 mm/yr). At Waihi Beach, from 2900 yr B.P. - present day, they range from 0.11 to 0.21 mm/yr (mean 0.20 mm/yr). Peat accumulation at both sites was slowest from 1850 to 700 yr B.P., suggesting a drier overall climate during this interval. At both sites, the earliest organic sediments, which are underlain by marine or estuarine sands, yield pollen spectra indicating salt marsh or estuarine environments. Coastal vegetation communities declined at both sites, as sea level gradually fell or the coast prograded, and were eventually superseded by a low moor bog at Papamoa, and a mesotrophic swamp forest at Waihi Beach. These differences, and the marked variation in peat accumulation rates, probably reflect local hydrology and are unlikely to have been climatically controlled. The main regional vegetation during this period was mixed northern conifer-angiosperm forest. Kauri (Agathis australis) formed a minor component of these forests, but populations of this tree have apparently not expanded during the late Holocene at these sites, which are near its present southern limit. Occasional shortlived forest disturbances are detectable in these records, in particular immediately following the deposition of Taupo Tephra. However, evidence for forest clearance during the human era is blurred by the downward dislocation of modern adventi ve pollen at these sites, preventing the clear differentiation of the Polynesian and European eras
Centralized Modularity of N-Linked Glycosylation Pathways in Mammalian Cells
Glycosylation is a highly complex process to produce a diverse repertoire of
cellular glycans that are attached to proteins and lipids. Glycans are involved
in fundamental biological processes, including protein folding and clearance,
cell proliferation and apoptosis, development, immune responses, and
pathogenesis. One of the major types of glycans, N-linked glycans, is formed by
sequential attachments of monosaccharides to proteins by a limited number of
enzymes. Many of these enzymes can accept multiple N-linked glycans as
substrates, thereby generating a large number of glycan intermediates and their
intermingled pathways. Motivated by the quantitative methods developed in
complex network research, we investigated the large-scale organization of such
N-linked glycosylation pathways in mammalian cells. The N-linked glycosylation
pathways are extremely modular, and are composed of cohesive topological
modules that directly branch from a common upstream pathway of glycan
synthesis. This unique structural property allows the glycan production between
modules to be controlled by the upstream region. Although the enzymes act on
multiple glycan substrates, indicating cross-talk between modules, the impact
of the cross-talk on the module-specific enhancement of glycan synthesis may be
confined within a moderate range by transcription-level control. The findings
of the present study provide experimentally-testable predictions for
glycosylation processes, and may be applicable to therapeutic glycoprotein
engineering
Geographic patterns of genetic variation in a broadly distributed marine vertebrate: new insights into loggerhead turtle stock structure from expanded mitochondrial DNA sequences
Previous genetic studies have demonstrated that natal homing shapes the stock structure of marine turtle nesting populations. However, widespread sharing of common haplotypes based on short segments of the mitochondrial control region often limits resolution of the demographic connectivity of populations. Recent studies employing longer control region sequences to resolve haplotype sharing have focused on regional assessments of genetic structure and phylogeography. Here we synthesize available control region sequences for loggerhead turtles from the Mediterranean Sea, Atlantic, and western Indian Ocean basins. These data represent six of the nine globally significant regional management units (RMUs) for the species and include novel sequence data from Brazil, Cape Verde, South Africa and Oman. Genetic tests of differentiation among 42 rookeries represented by short sequences (380 bp haplotypes from 3,486 samples) and 40 rookeries represented by long sequences (~800 bp haplotypes from 3,434 samples) supported the distinction of the six RMUs analyzed as well as recognition of at least 18 demographically independent management units (MUs) with respect to female natal homing. A total of 59 haplotypes were resolved. These haplotypes belonged to two highly divergent global lineages, with haplogroup I represented primarily by CC-A1, CC-A4, and CC-A11 variants and haplogroup II represented by CC-A2 and derived variants. Geographic distribution patterns of haplogroup II haplotypes and the nested position of CC-A11.6 from Oman among the Atlantic haplotypes invoke recent colonization of the Indian Ocean from the Atlantic for both global lineages. The haplotypes we confirmed for western Indian Ocean RMUs allow reinterpretation of previous mixed stock analysis and further suggest that contemporary migratory connectivity between the Indian and Atlantic Oceans occurs on a broader scale than previously hypothesized. This study represents a valuable model for conducting comprehensive international cooperative data management and research in marine ecology
On the number of purkinje cells in the human cerebellum: Unbiased estimates obtained by using the âfractionatorâ
Stereological estimates of the numbers of Purkinje cell nucleoli in human cerebellar cortex have been obtained from systematic random samples of tissue by using the fractionator. The estimates are unbiased by fixation, section thickness, or sampling errors and are independent of any assumptions about cell shape, size, or spatial orientation. Twelve brains from aged subjects of both sexes were examined. The average complement of nucleoli in four female brains (age range 71â93 years) amounted to 14.8 millions (with an observed coefficient of variation between subjects of 29%). For three male brains (76â91 years), the corresponding estimates were 15.7 millions (10%). No significant sex differences were found for these small samples. Five brains of unknown sex and age yielded values of 15.8 millions (18%). For the twelve brains examined, the total number of Purkinje cell nucleoli per cerebellum was found to be 15.4 millions (19%). Estimated numbers showed a significant positive correlation with cerebellar weights. The number of nucleoli in an individual cerebellum was obtained with high precision in as short a time as 4 hours
Isolation And Characterization Of Tetranucleotide Microsatellites From The Leatherback Turtle (Dermochelys Coriacea)
The leatherback turtle (Dermochelys coriacea) is a globally endangered marine species. Numerous questions regarding life history and demographics that are of conservation interest remain and many of these can be addressed through the use of highly polymorphic nuclear markers. We describe primers and polymerase chain reaction conditions to amplify 19 tetranucleotide microsatellite loci from the leatherback turtle. The primers were tested on samples from 22 females that nested at Archie Carr National Wildlife Refuge, Melbourne Beach, Florida, USA. The primers developed in this study yielded an average of 9.4 alleles per locus (range of 5-19) and an average observed heterozygosity of 0.84 (range 0.36-1.00). These markers should prove useful in supplementing existing markers for individual and population level analyses. Š Springer Science+Business Media B.V. 2011
Crowning glory: public law, power and the monarchy
âNew public lawâ has a keen interest in the deployment of power and the shifting nature of the public and private. In this article, we argue that the historical legacy of the Crown has hindered the ability of public lawyers to respond to changes in modes of governance in the UK. The constitutional law textbook tradition has played a key role in limiting critiques of the Crown because of the obfuscation that surrounds the legal and political status of the Monarch. However, instead of discounting the significance of the monarchy, we use it as a resource for exploring governing power, the blurring of boundaries and constitutional renewal.
Our starting point is the life, death and, most importantly, the funeral of Diana, Princess of Wales. The latter event exposed the political relevance of the âpersonalâ in a most dramatic way, generating claims about the âfeminisation of the governmentâ and âemotions augmenting democracyâ. We follow through on these claims in order to focus on the effects of adopting private, intimate-sphere norms in the public sphere, in particular public-sphere decision making. While aware of the risks associated with this âtransformationâ of democracy, we conclude that the increasing centrality of the intimate merits onsideration in new public lawâs search for progressive tools of modern governance
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