Development of a chicken 5 K microarray targeted towards immune function

<p>Abstract</p> <p>Background</p> <p>The development of microarray resources for the chicken is an important step in being able to profile gene expression changes occurring in birds in response to different challenges and stimuli. The creation of an immune-related array is highly valuable in determining the host immune response in relation to infection with a wide variety of bacterial and viral diseases.</p> <p>Results</p> <p>Here we report the development of chicken immune-related cDNA libraries and the subsequent construction of a microarray containing 5190 elements (in duplicate). Clones on the array originate from tissues known to contain high levels of cells related to the immune system, namely Bursa, Peyers patch, thymus and spleen. Represented on the array are genes that are known to cluster with existing chicken ESTs as well as genes that are unique to our libraries. Some of these genes have no known homologies and represent novel genes in the chicken collection. A series of reference genes (ie. genes of known immune function) are also present on the array. Functional annotation data is also provided for as many of the genes on the array as is possible.</p> <p>Conclusion</p> <p>Six new chicken immune cDNA libraries have been created and nearly 10,000 sequences submitted to GenBank [GenBank: <ext-link ext-link-type="gen" ext-link-id="AM063043">AM063043</ext-link>-<ext-link ext-link-type="gen" ext-link-id="AM071350">AM071350</ext-link>; <ext-link ext-link-type="gen" ext-link-id="AM071520">AM071520</ext-link>-<ext-link ext-link-type="gen" ext-link-id="AM072286">AM072286</ext-link>; <ext-link ext-link-type="gen" ext-link-id="AM075249">AM075249</ext-link>-<ext-link ext-link-type="gen" ext-link-id="AM075607">AM075607</ext-link>]. A 5 K immune-related array has been developed from these libraries. Individual clones and arrays are available from the ARK-Genomics resource centre.</p

Identification and characterisation of endogenous Avian Leukosis Virus subgroup E (ALVE) insertions in chicken whole genome sequencing data

Background: Endogenous retroviruses (ERVs) are the remnants of retroviral infections which can elicit prolonged genomic and immunological stress on their host organism. In chickens, endogenous Avian Leukosis Virus subgroup E (ALVE) expression has been associated with reductions in muscle growth rate and egg production, as well as providing the potential for novel recombinant viruses. However, ALVEs can remain in commercial stock due to their incomplete identification and association with desirable traits, such as ALVE21 and slow feathering. The availability of whole genome sequencing (WGS) data facilitates high-throughput identification and characterisation of these retroviral remnants. Results: We have developed obsERVer, a new bioinformatic ERV identification pipeline which can identify ALVEs in WGS data without further sequencing. With this pipeline, 20 ALVEs were identified across eight elite layer lines from Hy-Line International, including four novel integrations and characterisation of a fast feathered phenotypic revertant that still contained ALVE21. These bioinformatically detected sites were subsequently validated using new high-throughput KASP assays, which showed that obsERVer was highly precise and exhibited a 0% false discovery rate. A further fifty-seven diverse chicken WGS datasets were analysed for their ALVE content, identifying a total of 322 integration sites, over 80% of which were novel. Like exogenous ALV, ALVEs show site preference for proximity to protein-coding genes, but also exhibit signs of selection against deleterious integrations within genes. Conclusions: obsERVer is a highly precise and broadly applicable pipeline for identifying retroviral integrations in WGS data. ALVE identification in commercial layers has aided development of high-throughput diagnostic assays which will aid ALVE management, with the aim to eventually eradicate ALVEs from high performance lines. Analysis of non-commercial chicken datasets with obsERVer has revealed broad ALVE diversity and facilitates the study of the biological effects of these ERVs in wild and domesticated populations

Wave activity (planetary, tidal) throughout the middle atmosphere (20-100km) over the CUJO network: Satellite (TOMS) and Medium Frequency (MF) radar observations

Planetary and tidal wave activity in the tropopause-lower stratosphere and mesosphere-lower thermosphere (MLT) is studied using combinations of ground-based (GB) and satellite instruments (2000-2002). The relatively new MFR (medium frequency radar) at Platteville (40&amp;deg; N, 105&amp;deg; W) has provided the opportunity to create an operational network of middle-latitude MFRs, stretching from 81&amp;deg; W-142&amp;deg; E, which provides winds and tides 70-100km. CUJO (Canada U.S. Japan Opportunity) comprises systems at London (43&amp;deg; N, 81&amp;deg; W), Platteville (40&amp;deg; N, 105&amp;deg; W), Saskatoon (52&amp;deg; N, 107&amp;deg; W), Wakkanai (45&amp;deg; N, 142&amp;deg; E) and Yamagawa (31&amp;deg; N, 131&amp;deg; E). It offers a significant 7000-km longitudinal sector in the North American-Pacific region, and a useful range of latitudes (12-14&amp;deg;) at two longitudes. Satellite data mainly involve the daily values of the total ozone column measured by the Earth Probe (EP) TOMS (Total Ozone Mapping Spectrometer) and provide a measure of tropopause-lower stratospheric planetary wave activity, as well as ozone variability. &lt;P style=&quot;line-height: 20px;&quot;&gt; Climatologies of ozone and winds/tides involving frequency versus time (wavelet) contour plots for periods from 2-d to 30-d and the interval from mid 2000 to 2002, show that the changes with altitude, longitude and latitude are very significant and distinctive. Geometric-mean wavelets for the region of the 40&amp;deg; N MFRs demonstrate occasions during the autumn, winter and spring months when there are similarities in the spectral features of the lower atmosphere and at mesopause (85km) heights. Both direct planetary wave (PW) propagation into the MLT, nonlinear PW-tide interactions, and disturbances in MLT tides associated with fluctuations in the ozone forcing are considered to be possible coupling processes. The complex horizontal wave numbers of the longer period oscillations are provided in frequency contour plots for the TOMS satellite data to demonstrate the differences between lower atmospheric and MLT wave motions and their directions of propagation

Latitudinal wave coupling of the stratosphere and mesosphere during the major stratospheric warming in 2003/2004

The coupling of the dynamical regimes in the high- and low-latitude stratosphere and mesosphere during the major SSW in the Arctic winter of 2003/2004 has been studied. The UKMO zonal wind data were used to explore the latitudinal coupling in the stratosphere, while the coupling in the mesosphere was investigated by neutral wind measurements from eleven radars situated at high, high-middle and tropical latitudes. It was found that the inverse relationship between the variability of the zonal mean flows at high- and low-latitude stratosphere related to the SSW is produced by global-scale zonally symmetric waves. Their origin and other main features have been investigated in detail. Similar latitudinal dynamical coupling has been found for the mesosphere as well. Indirect evidence for the presence of zonally symmetric waves in the mesosphere has been found

Using elemental chemostratigraphy on Mid-Late Frasnian platform-top successions from the Lennard Shelf outcrops, Canning Basin, Western Australia.

High-resolution chronostratigraphic correlation using elemental chemostratigraphy in platform carbonates is typically difficult to achieve. Here, elemental chemostratigraphy is used to correlate between two platform-top, carbonate-dominated field sections from the narrow Lennard Shelf that existed on the NE margin of the Canning Basin, Western Australia, during the mid–late Frasnian. The correlation, constrained by magnetic polarity reversals and physical ground truthing, is based on recognition of distinctive cyclical ‘‘stacking patterns’’ defined by changes in concentrations of the trace element zirconium (Zr). Zr concentrations are controlled by the amount of the heavy mineral zircon in the sediments, which is derived from a terrigenous source and is diagenetically very stable. The stacking patterns in the lower part of the study sections display gradually upward-increasing values of Zr to a maximum, followed by an almost immediate fall to a minimum. In the upper part of the study interval, the cycles are more symmetrical, with both gradually increasing and decreasing portions. The point at which the change in Zr stacking pattern occurs in the two sections is synchronous and occurs in association with a supersequence maximum flooding surface. The correlation based on maximum and minimum Zr values throughout the two sections is demonstrated to be chronostratigraphic by comparison with correlations based upon paleomagnetism and physical ground truthing. When element ratios commonly used as provenance and paleoclimate proxies are plotted, the variations between closely spaced samples are greater than any systematic variations throughout the study intervals. Therefore, no isochemical chemozones can be defined, implying that during deposition of the study intervals, there were no long-lived changes in sediment provenance or paleoclimate that the elemental chemistry can detect. The work presented here shows that the standard approach of defining isochemical chemozones for chemostratigraphic correlation is not always appropriate. However, an approach using cyclical changes in elemental variables for chemostratigraphic correlation between two closely spaced sections is chronostratigraphically valid. The greater challenge is in application of the same approach to more widely spaced sections, potentially in different facies of a carbonate setting

Latitudinal wave coupling of the stratosphere and mesosphere during the major stratospheric warming in 2003/2004

The coupling of the dynamical regimes in the high- and low-latitude stratosphere and mesosphere during the major SSW in the Arctic winter of 2003/2004 has been studied. The UKMO zonal wind data were used to explore the latitudinal coupling in the stratosphere, while the coupling in the mesosphere was investigated by neutral wind measurements from eleven radars situated at high, high-middle and tropical latitudes. It was found that the inverse relationship between the variability of the zonal mean flows at high- and low-latitude stratosphere related to the SSW is produced by global-scale zonally symmetric waves. Their origin and other main features have been investigated in detail. Similar latitudinal dynamical coupling has been found for the mesosphere as well. Indirect evidence for the presence of zonally symmetric waves in the mesosphere has been found