Mapping the phosphoproteome of influenza A and B viruses by mass spectrometry

Protein phosphorylation is a common post-translational modification in eukaryotic cells and has a wide range of functional effects. Here, we used mass spectrometry to search for phosphorylated residues in all the proteins of influenza A and B viruses – to the best of our knowledge, the first time such a comprehensive approach has been applied to a virus. We identified 36 novel phosphorylation sites, as well as confirming 3 previously-identified sites. N-terminal processing and ubiquitination of viral proteins was also detected. Phosphorylation was detected in the polymerase proteins (PB2, PB1 and PA), glycoproteins (HA and NA), nucleoprotein (NP), matrix protein (M1), ion channel (M2), non-structural protein (NS1) and nuclear export protein (NEP). Many of the phosphorylation sites detected were conserved between influenza virus genera, indicating the fundamental importance of phosphorylation for all influenza viruses. Their structural context indicates roles for phosphorylation in regulating viral entry and exit (HA and NA); nuclear localisation (PB2, M1, NP, NS1 and, through NP and NEP, of the viral RNA genome); and protein multimerisation (NS1 dimers, M2 tetramers and NP oligomers). Using reverse genetics we show that for NP of influenza A viruses phosphorylation sites in the N-terminal NLS are important for viral growth, whereas mutating sites in the C-terminus has little or no effect. Mutating phosphorylation sites in the oligomerisation domains of NP inhibits viral growth and in some cases transcription and replication of the viral RNA genome. However, constitutive phosphorylation of these sites is not optimal. Taken together, the conservation, structural context and functional significance of phosphorylation sites implies a key role for phosphorylation in influenza biology. By identifying phosphorylation sites throughout the proteomes of influenza A and B viruses we provide a framework for further study of phosphorylation events in the viral life cycle and suggest a range of potential antiviral targets

Disentangling habitat concepts for demersal marine fish management

Fishing and other anthropogenic impacts have led to declines in many fish stocks and modification of the seabed. As a result, efforts to restore marine ecosystems have become increasingly focused on spatially explicit management methods to protect fish and the habitats they require for survival. This has led to a proliferation of investigations trying to map ‘habitats’ vulnerable to anthropogenic impacts and identify fish resource requirements in order to meet conservation and management needs. A wide range of habitat-related concepts, with different uses and understandings of the word ‘habitat’ itself has arisen as a consequence. Inconsistencies in terminology can cause confusion between studies, making it difficult to investigate and understand the ecology of fish and the factors that affect their survival. Ultimately, the inability to discern the relationships between fish and their environment clearly can hinder conservation and management measures for fish populations. This review identifies and addresses the present ambiguity surrounding definitions of ‘habitat’ and habitat-related concepts currently used in spatial management of demersal marine fish populations. The role of spatial and temporal scales is considered, in addition to examples of how to assess fish habitat for conservation and management purposes

An assessment of juvenile Atlantic cod distribution and growth using diver operated stereo-video surveys

Protecting juvenile fish habitat is of particular importance for their survival. However, in many cases fish habitat requirements are poorly understood. Stereo-video methods can provide non-destructive quantitative information on fish abundance and size in relation to their surrounding environment. Stereo-video SCUBA transects were conducted during daylight hours from June to September 2013 within a proposed Marine Protected Area (MPA) in the Firth of Clyde, west of Scotland. More juvenile Atlantic cod Gadus morhua of size range 6 – 11 cm were observed in substrata containing mixed gravel, including maerl, than in boulder-cobble substrata with high algal cover, or sand with low density seagrass. Community composition was significantly different between substratum types. A decrease in G. morhua abundance was observed over the period of data collection. Over time, mean and variance in fish size increased, indicating multiple recruitment events. Protecting mixed gravel substrata could be a beneficial management measure to support the survival and recruitment of juvenile G. morhua, other substrata might be important at night given their diel migratory behaviour. Stereo-video cameras provide a useful non-destructive fisheries independent method to monitor species abundance and length measurements

Climate fluctuations and the spring invasion of the North Sea by Calanus finmarchicus

The population of Calanus finmarchicus in the North Sea is replenished each spring by invasion from an overwintering stock located beyond the shelf edge. A combincation of field observations, statistical analysis of Continuous Plankton Recorder (CPR) data, and particle tracking model simulations, was used to investigate the processes involved in the cross-shelf invasion. The results showed that the main source of overwintering animals entering the North Sea in the spring is at depths of greater than 600m in the Faroe Shetland Channel, where concentrations of up to 620m -3 are found in association with the overflow of Norwegian Sea Deep Water (NSDW) across the Iceland Scotland Ridge. The input of this water mass to the Faroe Shetland Channel, and hence the supply of overwintering C. finmarchicus, has declined since the late 1960s due to changes in convective processes in the Greenland Sea. Beginning in February, animals start to emerge from the overwintering state and migrate to the surface waters, where their transport into the North Sea is mainly determined by the incidence of north-westerly winds that have declined since the 1960s. Together, these two factors explain a high proportion of the 30-year trends in spring abundance in the North Sea as measured by the CPR survey. Both the regional winds and the NSDW overflow are connected to the North Atlantic Oscillation Index (NAO), which is an atmospheric climate index, but with different time scales of response. Thus, interannual fluctuations in the NAO can cause immediate changes in the incidence of north-westerly winds without leading to corresponding changes in C. finmarchicus abundance in the North Sea, because the NSDW overflow responds over longer (decadal) time scales

An assessment of juvenile Atlantic cod distribution and growth using diver operated stereo-video surveys

Protecting juvenile fish habitat is of particular importance for their survival. However, in many cases fish habitat requirements are poorly understood. Stereo-video methods can provide non-destructive quantitative information on fish abundance and size in relation to their surrounding environment. Stereo-video SCUBA transects were conducted during daylight hours from June to September 2013 within a proposed Marine Protected Area (MPA) in the Firth of Clyde, west of Scotland. More juvenile Atlantic cod Gadus morhua of size range 6 – 11 cm were observed in substrata containing mixed gravel, including maerl, than in boulder-cobble substrata with high algal cover, or sand with low density seagrass. Community composition was significantly different between substratum types. A decrease in G. morhua abundance was observed over the period of data collection. Over time, mean and variance in fish size increased, indicating multiple recruitment events. Protecting mixed gravel substrata could be a beneficial management measure to support the survival and recruitment of juvenile G. morhua, other substrata might be important at night given their diel migratory behaviour. Stereo-video cameras provide a useful non-destructive fisheries independent method to monitor species abundance and length measurements

Application of molecular dynamics techniques and luminescent probes to the study of glass structure: the SiO2–GeO2 case

In this paper, we report on the results obtained from molecular dynamic simulation of a Eu3+-doped germanosilicate glass. This simulation provides further information on the structure. In particular it reveals a homogeneous distribution of SiO4 and GeO4 units, a decrease of defects compared to SiO2 and GeO2 glasses, and a trend to clustering of the doping ions. Using the modified crystal-field theory, the luminescence spectroscopic properties have been computed and comparison with experimental data has allowed a correlation of the spectral features with two main types of local environment depending on the coordination number and on the medium-range arrangement around the doping ions

Solid molecular hydrogen: The Broken Symmetry Phase

By performing constant-pressure variable-cell ab initio molecular dynamics simulations we find a quadrupolar orthorhombic structure, of $Pca2_1$ symmetry, for the broken symmetry phase (phase II) of solid H2 at T=0 and P =110 - 150 GPa. We present results for the equation of state, lattice parameters and vibronic frequencies, in very good agreement with experimental observations. Anharmonic quantum corrections to the vibrational frequencies are estimated using available data on H2 and D2. We assign the observed modes to specific symmetry representations.Comment: 5 pages (twocolumn), 4 Postscript figures. To appear in Phys. Rev. Let

Birthing practices of traditional birth attendants in South Asia in the context of training programmes

Traditional Birth Attendants (TBA) training has been an important component of public health policy interventions to improve maternal and child health in developing countries since the 1970s. More recently, since the 1990s, the TBA training strategy has been increasingly seen as irrelevant, ineffective or, on the whole, a failure due to evidence that the maternal mortality rate (MMR) in developing countries had not reduced. Although, worldwide data show that, by choice or out of necessity, 47 percent of births in the developing world are assisted by TBAs and/or family members, funding for TBA training has been reduced and moved to providing skilled birth attendants for all births. Any shift in policy needs to be supported by appropriate evidence on TBA roles in providing maternal and infant health care service and effectiveness of the training programmes. This article reviews literature on the characteristics and role of TBAs in South Asia with an emphasis on India. The aim was to assess the contribution of TBAs in providing maternal and infant health care service at different stages of pregnancy and after-delivery and birthing practices adopted in home births. The review of role revealed that apart from TBAs, there are various other people in the community also involved in making decisions about the welfare and health of the birthing mother and new born baby. However, TBAs have changing, localised but nonetheless significant roles in delivery, postnatal and infant care in India. Certain traditional birthing practices such as bathing babies immediately after birth, not weighing babies after birth and not feeding with colostrum are adopted in home births as well as health institutions in India. There is therefore a thin precarious balance between the application of biomedical and traditional knowledge. Customary rituals and perceptions essentially affect practices in home and institutional births and hence training of TBAs need to be implemented in conjunction with community awareness programmes