BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads

Epidemiologists aim to inform the design of public health interventions with evidence on the evolution, emergence and spread of infectious diseases. Sequencing of pathogen genomes, together with date, location, clinical manifestation and other relevant data about sample origins, can contribute to describing nearly every aspect of transmission dynamics, including local transmission and global spread. The analyses of these data have implications for all levels of clinical and public health practice, from institutional infection control to policies for surveillance, prevention and treatment. This review highlights the range of epidemiological questions that can be addressed from the combination of genome sequence and traditional ‘line lists’ (tables of epidemiological data where each line includes demographic and clinical features of infected individuals). We identify opportunities for these data to inform interventions that reduce disease incidence and prevalence. By considering current limitations of, and challenges to, interpreting these data, we aim to outline a research agenda to accelerate the genomics-driven transformation in public health microbiology.     

Artemis deficiency confers a DNA double-strand break repair defect and Artemis phosphorylation status is altered by DNA damage and cell cycle progression

Mutations in the Artemis gene are causative in a subset of human severe combined immunodeficiencies (SCIDs) and Artemis-deficient cells exhibit radiation sensitivity and defective V(D)J recombination, implicating Artemis function in non-homologous end joining (NHEJ). Here we show that Artemis-deficient cells from Athabascan-speaking Native American SCID patients (SCIDA) display significantly elevated sensitivity to ionizing radiation (IR) but only a very subtle defect in DNA double-strand (DSB) break repair in contrast to the severe DSB repair defect of NHEJ-deficient cells. Primary human SCIDA fibroblasts accumulate and exhibit persistent arrest at both the G1/S and G2/M boundaries in response to IR, consistent with the presence of persistent DNA damage. Artemis protein is phosphorylated in a PI3-like kinase-dependent manner after either IR or a number of other DNA damaging treatments including etoposide, but SCIDA cells are not hypersensitive to treatment with etoposide. Inhibitor studies with various DNA damaging agents establish multiple phosphorylation states and suggest multiple kinases function in Artemis phosphorylation. We observe that Artemis phosphorylation occurs rapidly after irradiation like that of histone H2AX. However, unlike H2AX, Artemis de-phosphorylation is uncoupled from overall DNA repair and correlates instead with cell cycle progression to or through mitosis. Our results implicate a direct and non-redundant function of Artemis in the repair of a small subset of DNA double-strand breaks, possibly those with hairpin termini, which may account for the pronounced radiation sensitivity observed in Artemis-deficient cells.     

Ontogeny of lymphoid organs and development of IgM-bearing cells in Atlantic halibut (Hippoglossus hippoglossus L.)

In teleost fish, the head kidney, thymus, and spleen are generally regarded as important immune organs. In this study, the ontogeny of these organs was studied in Atlantic halibut (Hippoglossus hippoglossus), larvae at various stages of development. We observed that the kidney was present at hatching, the thymus at 33 days post hatch (dph), while the spleen was the last organ to be detected at 49 dph. All three lymphoid organs were morphologically well developed during late metamorphic stages. Real time RT-PCR analysis showed that IgM mRNA expression could be observed at 66 dph and later, which correlates well with in situ hybridisation data showing that a few IgM positive cells could be detected in the anterior kidney and spleen from 66 dph. Our data also showed that the highest levels of IgM mRNA could be detected in halibut spleen. Immunostaining using a monoclonal antibody against halibut IgM detected IgM positive cells at 94 dph in both the head kidney and the spleen, which is much later than the IgM mRNA. Numerous cells expressing both IgM mRNA and protein could be detected in the spleen and anterior kidney and also to some extent in thymus specimens from adult halibut.     

Effects of Proportions of Dietary Macronutrients on Glucocorticoid Metabolism in Diet-Induced Obesity in Rats

Tissue glucocorticoid levels in the liver and adipose tissue are regulated by regeneration of inactive glucocorticoid by 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) and inactivation by 5α- and 5β-reductases. A low carbohydrate diet increases hepatic 11β-HSD1 and reduces glucocorticoid metabolism during weight loss in obese humans. We hypothesized that similar variations in macronutrient proportions regulate glucocorticoid metabolism in obese rats. Male Lister Hooded rats were fed an obesity-inducing ad libitum ‘Western’ diet (37% fat, n = 36) for 22 weeks, then randomised to continue this diet (n = 12) or to switch to either a low carbohydrate (n = 12) or a moderate carbohydrate (n = 12) diet for the final 8 weeks. A parallel lean control group were fed an ad libitum control diet (10% fat, n = 12) throughout. The low and moderate carbohydrate diets decreased hepatic 11β-HSD1 mRNA compared with the Western diet (both 0.7±0.0 vs 0.9±0.1 AU; p<0.01), but did not alter 11β-HSD1 in adipose tissue. 5α-Reductase mRNA was increased on the low carbohydrate compared with the moderate carbohydrate diet. Compared with lean controls, the Western diet decreased 11β-HSD1 activity (1.6±0.1 vs 2.8±0.1 nmol/mcg protein/hr; p<0.001) and increased 5α-reductase and 5β-reductase mRNAs (1.9±0.3 vs 1.0±0.2 and 1.6±0.1 vs 1.0±0.1 AU respectively; p<0.01) in the liver, and reduced 11β-HSD1 mRNA and activity (both p<0.01) in adipose tissue. Although an obesity-inducing high fat diet in rats recapitulates the abnormal glucocorticoid metabolism associated with human obesity in liver (but not in adipose tissue), a low carbohydrate diet does not increase hepatic 11β-HSD1 in obese rats as occurs in humans.     

Identification of a siderophore utilization locus in nontypeable <Emphasis Type="Italic">Haemophilus influenzae</Emphasis>

Background  

Haemophilus influenzae has an absolute aerobic growth requirement for either heme, or iron in the presence of protoporphyrin IX. Both iron and heme in the mammalian host are strictly limited in their availability to invading microorganisms. Many bacterial species overcome iron limitation in their environment by the synthesis and secretion of small iron binding molecules termed siderophores, which bind iron and deliver it into the bacterial cell via specific siderophore receptor proteins on the bacterial cell surface. There are currently no reports of siderophore production or utilization by H. influenzae.     

Form and functional morphology of Raetellops pulchella (Bivalvia: Mactridae): an example of convergent evolution with anomalodesmatans

Abstract. The bivalve Raetellops pulchella is a highly specialized, deposit-feeding member of the Mactridae. Studies of its form and function provide an example of how the bivalve body plan can be modified to facilitate the exploitation of mud as a food resource, and help in understanding how this lifestyle has evolved. Adaptations to this lifestyle include an overall reduction in ctenidial size and loss of the descending lamellae of both outer demibranchs. This reduction is associated with the enlargement of the labial palps to process inhaled sediment. In the mantle cavity, a waste canal below the posterior mantle flaps facilitates pseudofeces removal. The midgut is long and capacious, presumably to cope with the large amounts of ingested organic material. In addition, individuals of R. pulchella have unusually thin, brittle, and rostrate shells, with narrow siphonal gapes. They possess a shell buttress in each valve extending from the hinge plate to above the posterior adductor muscle. This buttress functions to prevent the brittle shell valves from fracturing when adduction occurs. A buttress is also seen in some representatives of the Anomalodesmata; in particular, the situation in R. pulchella is most like that seen in individuals of the similarly deposit-feeding species Offadesma angasi (Anomalodesmata: Periplomatidae). I interpret the similar shell form of these deposit-feeding clams as an example of convergent evolution.     

Assessing the welfare of genetically altered mice

In 2003, under the auspices of the main UK funders of biological and biomedical research, a working group was established with a remit to review potential welfare issues for genetically altered (GA) mice, to summarize current practice, and to recommend contemporary best practice for welfare assessments. The working group has produced a report which makes practical recommendations for GA mouse welfare assessment and dissemination of welfare information between establishments using a 'mouse passport'. The report can be found at www.nc3rs.org.uk/GAmice and www.lal.org.uk/gaa and includes templates for the recommended welfare assessment scheme and the mouse passport. An overview is provided below.     

Correspondence of low mean shear and high harmonic content in the porcine iliac arteries

BACKGROUND: Temporal variations in shear stress have been suggested to affect endothelial cell biology. To better quantify the range of dynamic shear forces that occur in vivo, the frequency content of shear variations that occur naturally over a cardiac cycle in the iliac arteries was determined. METHOD OF APPROACH: Computational fluid dynamic calculations were performed in six iliac arteries from three juvenile swine. Fourier analysis of the time-varying shear stress computed at the arterial wall was performed to determine the prevalence of shear forces occurring at higher frequencies in these arteries. RESULTS: While most of each artery experienced shear forces predominantly at the frequency of the heart rate, the frequency spectra at certain regions were dominated by shear forces at higher frequencies. Regions whose frequency spectra were dominated by higher harmonics generally experienced lower mean shear stress. The negative correlation between shear and dominant harmonic was significant (p=0.002). CONCLUSIONS: Since lesion development typically occurs in regions experiencing low time-average shear stress, this result suggests that the frequency content of the shear exposure may also be a contributing factor in lesion development. A better understanding of the vascular response to shear components of different frequencies might help rationalize the notion of "disturbed flow" as a hemodynamic entity.