Pyrosequencing and de novo assembly of Antarctic krill (Euphausia superba) transcriptome to study the adaptability of krill to climate-induced environmental changes

The Antarctic krill, Euphausia superba, has a key position in the Southern Ocean food web by serving as direct link between primary producers and apex predators. The south-west Atlantic sector of the Southern Ocean, where the majority of the krill population is located, is experiencing one of the most profound environmental changes worldwide. Up to now, we have only cursory information about krill’s genomic plasticity to cope with the ongoing environmental changes induced by anthropogenic CO₂ emission. The genome of krill is not yet available due to its large size (about 48 Gbp). Here, we present two cDNA normalized libraries from whole krill and krill heads sampled in different seasons that were combined with two data sets of krill transcriptome projects, already published, to produce the first knowledgebase krill ‘master’ transcriptome. The new library produced 25% more E. superba transcripts and now includes nearly all the enzymes involved in the primary oxidative metabolism (Glycolysis, Krebs cycle and oxidative phosphorylation) as well as all genes involved in glycogenesis, glycogen breakdown, gluconeogenesis, fatty acid synthesis and fatty acids β-oxidation. With these features, the ‘master’ transcriptome provides the most complete picture of metabolic pathways in Antarctic krill and will provide a major resource for future physiological and molecular studies. This will be particularly valuable for characterizing the molecular networks that respond to stressors caused by the anthropogenic CO₂ emissions and krill’s capacity to cope with the ongoing environmental changes in the Atlantic sector of the Southern Ocean.

Undulator beamline of the Brockhouse sector at the Canadian Light Source

The Brockhouse project at the Canadian Light Source plans the construction of three beamlines, two wiggler beamlines, and one undulator beamline, that will be dedicated to x-ray diffraction and scattering. In this work, we will describe the undulator beamline main components and performance parameters, obtained from ray tracing using XOP-SHADOW codes. The undulator beamline will operate from 4.95 to 21 keV, using a 20 mm period hybrid undulator placed upstream of the wiggler in the same straight section. The beamline optics design was developed in cooperation with the Brazilian Synchrotron - LNLS. The beamline will have a double crystal monochromator with the options of Si(111) or Si(311) crystal pairs followed by two mirrors in the KB configuration to focus the beam at the sample position. The high brilliance of the undulator source will produce a very high flux of ~10(13) photons/s and high energy resolution into a small focus of 170 μm horizontal and 20-60 μm vertical, depending on the optical configuration and energy chosen. Two multi-axis goniometer experimental stations with area detectors and analyzers are foreseen to enable diffraction, resonant and inelastic scattering experiments, and SAXS/WAXS experiments with high resolution and time resolving capabilities.

Anterior clinoidectomy

BACKGROUND

The optic nerve within the optic canal, the parophthalmic segment of the carotid artery, and the oculomotor nerve in the superior orbital fissure all lay against the anterior clinoid process. Bone resection uncovers these structures.

METHOD

For extradural resection of the anterior clinoid process and surrounding bone, two key steps are recommended: bony opening of the superior orbital fissure, and transection of the orbitotemporal periosteal fold.

CONCLUSION

Anterior clinoidectomy is technically challenging. Following a sequence of surgical steps to expose clearly-defined surgical landmarks helps to make this procedure simple and safe.

KEY POINTS

• Pterional craniotomy • Complete extradural anterior clinoidectomy • Slit dura (3 mm) to drain cerebrospinal fluid • Peel dura from orbital roof and lateral wall • Bony opening of superior orbital fissure to use it as surgical corridor • Drilling of optic canal • Transection of orbitotemporal periosteal fold • Hollow anterior clinoid process and piece-meal resection • Transection of falciforme ligament to free optic nerve • Replace falciforme ligament by extradural free pericranial flap.

Middle East Respiratory Syndrome coronavirus (MERS-CoV) serology in major livestock species in an affected region in Jordan, June to September 2013

Between June and September 2013, sera from 11 dromedary camels, 150 goats, 126 sheep and 91 cows were collected in Jordan, where the first human Middle-East respiratory syndrome (MERS) cluster appeared in 2012. All sera were tested for MERS-coronavirus (MERS-CoV) specific antibodies by protein microarray with confirmation by virus neutralisation. Neutralising antibodies were found in all camel sera while sera from goats and cattle tested negative. Although six sheep sera reacted with MERS-CoV antigen, neutralising antibodies were not detected.

Specific serology for emerging human coronaviruses by protein microarray

We present a serological assay for the specific detection of IgM and IgG antibodies against the emerging human coronavirus hCoV-EMC and the SARS-CoV based on protein microarray technology. The assay uses the S1 receptor-binding subunit of the spike protein of hCoV-EMC and SARS-CoV as antigens. The assay has been validated extensively using putative cross-reacting sera of patient cohorts exposed to the four common hCoVs and sera from convalescent patients infected with hCoV-EMC or SARS-CoV.

Contact investigation of a case of human novel coronavirus infection treated in a German hospital, October-November 2012

On 24 October 2012, a patient with acute respiratory distress syndrome of unknown origin and symptom onset on 5 October was transferred from Qatar to a specialist lung clinic in Germany. Late diagnosis on 20 November of an infection with the novel Coronavirus (NCoV) resulted in potential exposure of a considerable number of healthcare workers. Using a questionnaire we asked 123 identified contacts (120 hospital and three out-of-hospital contacts) about exposure to the patient. Eighty-five contacts provided blood for a serological test using a two-stage approach with an initial immunofluorescence assay as screening test, followed by recombinant immunofluorescence assays and a NCoV-specific serum neutralisation test. Of 123 identified contacts nine had performed aerosol-generating procedures within the third or fourth week of illness, using personal protective equipment rarely or never, and two of these developed acute respiratory illness. Serology was negative for all nine. Further 76 hospital contacts also tested negative, including two sera initially reactive in the screening test. The contact investigation ruled out transmission to contacts after illness day 20. Our two-stage approach for serological testing may be used as a template for similar situations.

Contact investigation of a case of human novel coronavirus infection treated in a German hospital, October-November 2012

On 24 October 2012, a patient with acute respiratory distress syndrome of unknown origin and symptom onset on 5 October was transferred from Qatar to a specialist lung clinic in Germany. Late diagnosis on 20 November of an infection with the novel Coronavirus (NCoV) resulted in potential exposure of a considerable number of healthcare workers. Using a questionnaire we asked 123 identified contacts (120 hospital and three out-of-hospital contacts) about exposure to the patient. Eighty-five contacts provided blood for a serological test using a two-stage approach with an initial immunofluorescence assay as screening test, followed by recombinant immunofluorescence assays and a NCoV-specific serum neutralisation test. Of 123 identified contacts nine had performed aerosol-generating procedures within the third or fourth week of illness, using personal protective equipment rarely or never, and two of these developed acute respiratory illness. Serology was negative for all nine. Further 76 hospital contacts also tested negative, including two sera initially reactive in the screening test. The contact investigation ruled out transmission to contacts after illness day 20. Our two-stage approach for serological testing may be used as a template for similar situations.

Assays for laboratory confirmation of novel human coronavirus (hCoV-EMC) infections

We present a rigorously validated and highly sensitive confirmatory real-time RT-PCR assay (1A assay) that can be used in combination with the previously reported upE assay. Two additional RT-PCR assays for sequencing are described, targeting the RdRp gene (RdRpSeq assay) and N gene (NSeq assay), where an insertion/deletion polymorphism might exist among different hCoV-EMC strains. Finally, a simplified and biologically safe protocol for detection of antibody response by immunofluorescence microscopy was developed using convalescent patient serum.