The geology and palaeontology of the Jurassic rocks of Eathie (Cromarty)

1. The Jurassic rocks at Eathie Haven have been downfaulted against the pre-Mesozoic rocks with which they are in contact to the west. 2. With the exception of the rocks at Bow Buoy Skerry, which are of Upper Oxford Clay age, the Jurassic rocks exposed at Eathie are Lower Kimmeridgian. Three successive ammonite zones have been identified in the Kimmeridgian deposits: the zones of Rasenia cymodoce and Amoeboceras kitchini, Rasenia uralensis, and Rasenia pseadomutabilis. 3. The presence of 'marker beds' in the Kimmeridge shales enables them to be mapped and their stratigraphical succession determined. 4. Lines of weakness were developed in the Kimmeridgian strata by earth-movements during late Kimmeridgian times. Sand was injected along these lines of weakness, probably under pressure from below. The loose sand was consolidated after injection by the growth of calcite cement to form 'sandstone dykes' and 'sandstone sills'. 5. A rich microfauna is present in the Kimmeridgian rocks, ten genera of foraminifera and two of Radiolaria having been found. 6. Eight lamellibranch species were identified in the Kimmerig gian rocks, three new species being described. J. Weir's suggestion that Lima concentrica (J. de C. Sow) might be a synonym for Buchia concentrica (Rouillier) is confirmed. 7. One horizon of the Kimmeridgian yielded three species of gastropoda. 8. Ten ammonite species were obtained from the Kimmeridgian rocks, five Cardioceratids and five Perisphinctids. Prorasenia spp. were found in association with species of the 1 asenia uralensis group. 9. The Kimmeridgian yielded three Belemnite species including Pachyteuthis abbreviatus. 10. The Kimmeridgian rocks appear to have been deposited in a tranquil sea of moderate depth which cannot have been far from land. 11. The presence of a mixed Boreal and Mediterranean faunal assemblage at Eathie in north -east Scotland suggests that a sea connection existed between the Boreal and Mediterranean provinces, the gradual change of aspect of the ammonite assemblage between southern England and Greenland being due to the influence of climatic zones

The role of advocacy in promoting better child health

Child health professionals play a crucial role in advocating for children and it is incumbent on all who work with them to observe and enforce the maintenance of children's rights. In this article we summarise what advocacy is, its importance for child health and briefly how to go about it. Finally, we provide three differing examples of how advocacy has been used to improve the health of children

The negative acute phase response of serum transthyretin following Streptococcus suis infection in the pig

Peer reviewedPublisher PD

Maternal undernutrition and the ovine acute phase response to vaccination

Background: The acute phase response is the immediate host response to infection, inflammation and trauma and can be monitored by measuring the acute phase proteins (APP) such as haptoglobin ( Hp) or serum amyloid A (SAA). The plane of nutrition during pregnancy is known to affect many mechanisms including the neuroendocrine and neuroimmune systems in neonatal animals but effects on the APP are unknown. To investigate this phenomenon the serum concentration of Hp and SAA was initially determined in non-stimulated lambs from 3 groups (n = 10/group). The dams of the lambs of the respective groups were fed 100% of requirements throughout gestation (High/High; HH); 100% of requirements for the first 65 d of gestation followed by 70% of requirements until 125 d from when they were fed 100% of requirements (High/Low; HL); 65% of liveweight maintenance requirements for the first 65 d gestation followed by 100% of requirements for the remainder of pregnancy ( Low/High; LH). The dynamic APP response in the lambs was estimated by measuring the concentration of Hp and SAA following routine vaccination with a multivalent clostridial vaccine with a Pasteurella component, Heptavac P (TM) following primary and secondary vaccination. Results: The Hp and SAA concentrations were significantly lower at the time of vaccination ( day 8-14) than on the day of birth. Vaccination stimulated the acute phase response in lambs with increases found in both Hp and SAA. Maternal undernutrition led to the SAA response to vaccination being significantly lower in the HL group than in the HH group. The LH group did not differ significantly from either the HH or HL groups. No significant effects of maternal undernutrition were found on the Hp concentrations. A significant reduction was found in all groups in the response of SAA following the second vaccination compared to the response after the primary vaccination but no change occurred in the Hp response. Conclusion: Decreased SAA concentrations, post-vaccination, in lambs born to ewes on the HL diet shows that maternal undernutrition prior to parturition affects the innate immune system of the offspring. The differences in response of Hp and SAA to primary and secondary vaccinations indicate that the cytokine driven APP response mechanisms vary with individual AP

Acute phase protein response in an experimental model of ovine caseous lymphadenitis

<p>Abstract</p> <p>Background</p> <p>Caseous lymphadenitis (CLA) is a disease of small ruminants caused by <it>Corynebacterium pseudotuberculosis</it>. The pathogenesis of CLA is a slow process, and produces a chronic rather than an acute disease state. Acute phase proteins (APP) such as haptoglobin (Hp) serum amyloid A (SAA) and α₁acid glycoprotein (AGP) are produced by the liver and released into the circulation in response to pro-inflammatory cytokines. The concentration of Hp in serum increases in experimental CLA but it is not known if SAA and AGP respond in parallel or have differing response profiles.</p> <p>Results</p> <p>The concentration in serum of Hp, SAA and AGP in 6 sheep challenged with 2 × 10⁵cells of <it>C. pseudotuberculosis </it>showed significant increases (P < 0.05) compared to 3 unchallenged control sheep. By day 7 post infection. (p.i.) the Hp and SAA concentrations reached mean (± SEM) values of 1.65 ± 0.21 g/L and 18.1 ± 5.2 mg/L respectively. Thereafter, their concentrations fell with no significant difference to those of the control sheep by day 18 p.i.. In contrast, the serum AGP concentration in infected sheep continued to rise to a peak of 0.38 ± 0.05 g/L on day 13 p.i., after which a slow decline occurred, although the mean concentration remained significantly higher (P < 0.05) than the control group up to 29 days p.i.. Specific IgG to phospholidase D of <it>C. pseudotuberculosis </it>became detectable at 11 days p.i. and continued to rise throughout the experiment.</p> <p>Conclusion</p> <p>The serum concentrations of Hp, SAA and AGP were raised in sheep in an experimental model of CLA. An extended response was found for AGP which occurred at a point when the infection was likely to have been transforming from an acute to a chronic phase. The results suggest that AGP could have a role as a marker for chronic conditions in sheep.</p

Genomic Selective Constraints in Murid Noncoding DNA

Recent work has suggested that there are many more selectively constrained, functional noncoding than coding sites in mammalian genomes. However, little is known about how selective constraint varies amongst different classes of noncoding DNA. We estimated the magnitude of selective constraint on a large dataset of mouse-rat gene orthologs and their surrounding noncoding DNA. Our analysis indicates that there are more than three times as many selectively constrained, nonrepetitive sites within noncoding DNA as in coding DNA in murids. The majority of these constrained noncoding sites appear to be located within intergenic regions, at distances greater than 5 kilobases from known genes. Our study also shows that in murids, intron length and mean intronic selective constraint are negatively correlated with intron ordinal number. Our results therefore suggest that functional intronic sites tend to accumulate toward the 5' end of murid genes. Our analysis also reveals that mean number of selectively constrained noncoding sites varies substantially with the function of the adjacent gene. We find that, among others, developmental and neuronal genes are associated with the greatest numbers of putatively functional noncoding sites compared with genes involved in electron transport and a variety of metabolic processes. Combining our estimates of the total number of constrained coding and noncoding bases we calculate that over twice as many deleterious mutations have occurred in intergenic regions as in known genic sequence and that the total genomic deleterious point mutation rate is 0.91 per diploid genome, per generation. This estimated rate is over twice as large as a previous estimate in murids

Copy number variant detection in inbred strains from short read sequence data

Summary: We have developed an algorithm to detect copy number variants (CNVs) in homozygous organisms, such as inbred laboratory strains of mice, from short read sequence data. Our novel approach exploits the fact that inbred mice are homozygous at virtually every position in the genome to detect CNVs using a hidden Markov model (HMM). This HMM uses both the density of sequence reads mapped to the genome, and the rate of apparent heterozygous single nucleotide polymorphisms, to determine genomic copy number. We tested our algorithm on short read sequence data generated from re-sequencing chromosome 17 of the mouse strains A/J and CAST/EiJ with the Illumina platform. In total, we identified 118 copy number variants (43 for A/J and 75 for CAST/EiJ). We investigated the performance of our algorithm through comparison to CNVs previously identified by array-comparative genomic hybridization (array CGH). We performed quantitative-PCR validation on a subset of the calls that differed from the array CGH data sets

Melatonin Alters Age-Related Changes in Transcription Factors and Kinase Activation

Male mice were fed 40 ppm melatonin for 2 months prior to sacrifice at age 26 months, and compared with both 26 and 4 month-old untreated controls. The nuclear translocation of NF-κB increased with age in both brain and spleen and this was reversed by melatonin only in brain. Another transcription factor, AP-1 was increased with age in the spleen and not in brain and this could be blocked by melatonin treatment. The fraction of the active relative to the inactive form of several enabling kinases was compared. The proportion of activated ERK was elevated with age in brain and spleen but this change was unresponsive to melatonin. A similar age-related increase in glial fibrillary acidic protein (GFAP) was also refractory to melatonin treatment. The cerebral melatonin M1 receptor decreased with age in brain but increased in spleen. The potentially beneficial nature of melatonin for the preservation of brain function with aging was suggested by the finding that an age-related decline in cortical synaptophysin levels was prevented by dietary melatonin

Expedited batch processing and analysis of transposon insertions

<p>Abstract</p> <p>Background</p> <p>With advances in sequencing technology, greater and greater amounts of eukaryotic genome data are becoming available. Often, large portions of these genomes consist of transposable elements, frequently accounting for 50% or more in vertebrates. Each transposable element family may have thousands or tens of thousands of individual copies within a given genome, and therefore it can take an exorbitant amount of time and effort to process data in a meaningful fashion.</p> <p>Findings</p> <p>In order to combat this problem, we developed a set of bioinformatics techniques and programs to streamline the analysis. This includes a unique Perl script which automates the process of taking BLAST, Repeatmasker and similar data to extract and manipulate the hit sequences from the genome. This script, called Process_hits uses an object-oriented methodology to compile all hit locations from a given file for processing, organize this data into useable categories, and output it in multiple formats.</p> <p>Conclusions</p> <p>The program proved capable of handling large amounts of transposon data in an efficient fashion. It is equipped with a number of useful sub-functions, each of which is contained within its own sub-module to allow for greater expandability and as a foundation for future program design.</p