Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate

BACKGROUND: Development is largely driven by transitions between transcriptional programs. The initiation of transcription at appropriate sites in the genome is a key component of this and yet few rules governing selection are known. Here, we used cap analysis of gene expression (CAGE) to generate bp-resolution maps of transcription start sites (TSSs) across the genome of Oikopleura dioica, a member of the closest living relatives to vertebrates. RESULTS: Our TSS maps revealed promoter features in common with vertebrates, as well as striking differences, and uncovered key roles for core promoter elements in the regulation of development. During spermatogenesis there is a genome-wide shift in mode of transcription initiation characterized by a novel core promoter element. This element was associated with > 70% of male-specific transcription, including the use of cryptic internal promoters within operons. In many cases this led to the exclusion of trans-splice sites, revealing a novel mechanism for regulating which mRNAs receive the spliced leader. Binding of the cell cycle regulator, E2F1, is enriched at the TSS of maternal genes in endocycling nurse nuclei. In addition, maternal promoters lack the TATA-like element found in zebrafish and have broad, rather than sharp, architectures with ordered nucleosomes. Promoters of ribosomal protein genes lack the highly conserved TCT initiator. We also report an association between DNA methylation on transcribed gene bodies and the TATA-box. CONCLUSIONS: Our results reveal that distinct functional promoter classes and overlapping promoter codes are present in protochordates like in vertebrates, but show extraordinary lineage-specific innovations. Furthermore, we uncover a genome-wide, developmental stage-specific shift in the mode of TSS selection. Our results provide a rich resource for the study of promoter structure and evolution in Metazoa

Possible identifications of the 3.4 micrometer feature

A feature at 3.4 micrometer was first detected in Comet Halley by the IKS spectrometer on board the Vega 1 probe; and subsequently from the ground. The feature has since been reported in Comet Wilson. The presence of the feature is of considerable interest for a number of reasons. First, it may represent the detection of a new parent molecule, and when combined with data from Giotto and Vega yield new information on cometary chemistry and the early solar system composition. Secondly, it may represent a link to the interstellar medium, the feature corresponds in wavelength and shape with an interstellar feature seen in absorption in a luminous star, towards the Galactic center known as GC-IRS7. The feature in turn is thought to be related with a growing family of unidentified infrared emission features seen in stellar objects, planetary nebulae, reflection nebulae, HII regions and extra galactic sources. These features occur at wavelengths 3.3, 3.4, 3.5, 6.2, 7.7, 8.6, and 11.25 micrometers. Further identification theory is given

Spring and Early Summer Temperatures in a Shallow Arctic Pond

Temperatures were recorded continuously during spring and early summer in a shallow pond on Bathurst Island in the High Arctic; thawing was rapid. After the thaw, seasonal and diel differences within the water and mud showed that frozen substrate had a marked effect on mud temperature, but that the superficial mud received almost as much heat as the water immediately above it. Temperature summations suggested that even in favourable shallow habitats low mud temperatures dictate the life-cycles of more than one year of arctic chironomids. The maximum-minimum temperature midpoint was a satisfactory substitute for a recorder-obtained day-mean, and seasonal comparisons of pond temperatures in relation to bottom fauna could therefore be based on daily maximum and minimum mud surface temperatures.Températures du printemps et du début de l’été dans une mare peu profonde de l’Arctique.  Dans une mare peu profonde, sur l’île de Bathurst dans le Haut Arctique, on a enregistré de façon continue les températures du printemps et du début de l’été.  Après le dégel, les différences saisonnières et quotidiennes dans l’eau et dans la vase montrent que le substrat pergelé a un effet marqué sur la température de la vase, mais aussi que la vase superficielle reçoit presque autant de chaleur que l’eau qui la recouvre immédiatement.  Les compilations des températures suggèrent que même dans des habitats favorables parce que peu profonds, les basses températures de la vase dictent les cycles biologiques pluriannuels chez les chironomides de l’Arctique.  La médiane des températures maximum et minimum peut être substituée à la température moyenne enregistrée; les températures maximum et minimum quotidiennes de la surface de la vase peuvent donc servir de base aux comparaisons saisonnières des températures de la mare en relation avec la faune du fond

Contemporary and historic river channel change at Swinhope bum, Weardale: a study of river response to flood events in an upland, gravel-bed stream

The response of upland gravel-bed streams to floods has long been associated with high levels of erosion and deposition, often resulting in major changes in channel form. This largely stems from observations of upland channels immediately following large floods. The aim of this thesis is to identify the importance of flood events in contemporary and historic river channel change in an upland gravel-bed stream. Swinhope Bum, in upper Weardale, Northem Pennines is used as a basis for this study. An assessment of channel planform change over the historical period was made using historical maps and air photographs. The study reach has retained a stable meandering pattern over a period of 180 years, with a temporary but dramatic change to a straight, low sinuosity, partly braided channel identified in the 1844 Tithe Map. The probable cause is an increase in coarse sediment supply generated by floods in the 1820's and upstream mining activities. The passage of a major flood through Swinhope Bum in February, 1997 produced very little channel change with erosion being the same order of magnitude as deposition, indicating that the study reach is stable even during overbank flows. A sediment tracing experiment designed to assess the importance of sediment exchanges between the bed and lateral inputs from eroding banks and bluffs demonstrates the importance of within channel movements and the minor local influence of lateral sediment sources. This study shows that contemporary channel response to flood events is through vertical rather than lateral adjustment in channel form which is substantiated by channel planform stability over the historical period. Long-term channel stability is attributed to the presence of a local base-level imposed by the Greenly Hills moraine, which has resulted in a low channel gradient which inhibits coarse bedload transport and frequent, major channel change

Historians at the heart of the city: Manchester Metropolitan University

Manchester in the north west of England is a global city, which stresses innovation and education. Manchester Metropolitan University is located in the heart of the city and its historians, both staff and students, have access to libraries and archives of regional, national and internationa importance. Research-led teaching with a stress on internationalisation and employability, encompasses a wide geographical coverage and ranges from ancient to contemporary history. Манчестер на северо-западе Англии представляет собой универсальный город, приоритетными областями развития которого являются инновации и образование. Университет Манчестер Метрополитен расположен в центре города и работающие там историки, как профессионалы, так и студенты, имеют доступ к библиотекам и архивам регионального, национального и международного значения. Преподавание, включающее в себя элементы научно-исследовательской работы с акцентом на интернационализацию и возможности трудоустройства, предусматривает широкий географический охват и находится в диапазоне от древней до современной истории

Arctic Insects as Indicators of Environmental Change

The great diversity of terrestrial arthropods in the Arctic suggests that these organisms are especially useful to monitor environmental change there, where warming as a result of climatic change is expected to be especially pronounced and where current conditions are limiting for many organisms. Based on existing information about arctic faunas and how they differ from temperate ones, this paper suggests several elements, including ratios and other quantitative indexes, that can be used for long-term evaluations of change. These elements include composition indexes, range limits, marker species, interspecific ratios, relationship shifts, phenological and physiological indicators, and key sites. Using such elements in a planned way would exploit the diversity of arctic insects and emphasize their importance in arctic systems.Key words: arctic arthropods, arctic insects, arctic fauna, climatic change, environmental changem, onitoring, indicator species, long-term researchRÉSUMÉ. La grande diversité d’arthropodes terrestres dans l’Arctique suggère que ces organismes se prêtent particulièrement bien à la surveillance des changements qui prennent place dans cet environnement, où l’on s’attend à un réchauffement assez prononcé suite aux changements climatiques et où les conditions actuelles sont défavorables à beaucoup d’organismes. En s’appuyant sur l’information actuelle concernant les espèces arctiques et la façon dont elles diffèrent des espèces tempérées, cet article propose divers éléments, y compris des rapports et d’autres index quantitatifs, à utiliser pour effectuer une évaluation à long terme des changements. Ces éléments comprennent les index de composition, les limites de territoire, les espèces repères, les rapports interspécifiques, les modifications des liens, les indicateurs phénologiques et physiologiques ainsi que les sites clés. L’utilisation planifiée de ces éléments permettrait d’exploiter la diversité des insectes arctiques et de souligner leur importance dans les systèmes arctiques.Mots clés: arthropodes, insectes arctiques, faune arctique, changement climatique, changement environnemental, surveillance, espèces indicatrices, recherche à long term

Synergy

Special Section: Growt