Next Generation Sequencing of Actinobacteria for the Discovery of Novel Natural Products

Like many fields of the biosciences, actinomycete natural products research has been revolutionised by next-generation DNA sequencing (NGS). Hundreds of new genome sequences from actinobacteria are made public every year, many of them as a result of projects aimed at identifying new natural products and their biosynthetic pathways through genome mining. Advances in these technologies in the last five years have meant not only a reduction in the cost of whole genome sequencing, but also a substantial increase in the quality of the data, having moved from obtaining a draft genome sequence comprised of several hundred short contigs, sometimes of doubtful reliability, to the possibility of obtaining an almost complete and accurate chromosome sequence in a single contig, allowing a detailed study of gene clusters and the design of strategies for refactoring and full gene cluster synthesis. The impact that these technologies are having in the discovery and study of natural products from actinobacteria, including those from the marine environment, is only starting to be realised. In this review we provide a historical perspective of the field, analyse the strengths and limitations of the most relevant technologies, and share the insights acquired during our genome mining projects.     

Evaluating the protective efficacy of a trivalent vaccine containing Akabane virus,Aino virus and Chuzan virus against Schmallenberg virus infection

Schmallenberg virus (SBV), an arthropod borne pathogen, spread rapidly throughout the majority of Europe since 2011. It can cause a febrile disease, milk drop, diarrhea, and fetal malformation in ruminants. SBV, a member of the Simbu serogroup within the genus Orthobunyavirus, is closely related to Akabane virus (AKAV) and Aino virus (AINOV) among others. In the present study, 4 Holstein-Friesian calves were immunized twice four weeks apart with a multivalent, inactivated vaccine against AKAV and AINOV. Another 4 calves were kept as unvaccinated controls. All animals were clinically, serologically and virologically examined before and after challenge infection with SBV. AKAV- and AINOV-specific neutralizing antibodies were detected one week before challenge infection, while SBV-specific antibodies were detectable only thereafter. SBV genome was detected in all vaccinated animals and 3 out of 4 controls in serum samples taken after challenge infection. In conclusion, the investigated vaccine was not able to prevent an SBV-infection. Thus, vaccines for other related Simbu serogroup viruses can not substitute SBV-specific vaccines as an instrument for disease control.     

GnRH‐agonist deslorelin implant alters the progesterone release pattern during early pregnancy in gilts

The aim of this study was to investigate the relationship of progesterone (P) and luteinizing hormone (LH) during recognition and establishment of pregnancy in the gilt. Therefore, the effects of eliminating episodic LH pulses on P patterns were determined during early pregnancy. To this end, a slow‐release GnRH implant deslorelin was used for GnRH down‐regulation. A group of gilts (GnRHa, n = 8) was implanted with the GnRH‐agonist on Day 11 of pregnancy, while a control group (C, n = 5) was treated with a non‐impregnated placebo implant. Blood was collected via a vena cava caudalis catheter at 10‐min intervals for 8 hr on Day 16 and 21 of pregnancy. As expected, the GnRH implant reduced LH secretion (p < 0.01) and abolished LH pulses completely at Day 16 and Day 21 of pregnancy. On Day 16, there was no difference in P levels between the treatments. However, on Day 21, the GnRH‐agonist treatment led to significantly increased P concentrations (p < 0.01) compared with the control gilts. Progesterone was secreted in a pulsatile manner in both treatment groups and no relationship between LH pulsatility and P pulsatility was observed. In conclusion, abolishment of LH pulsatility did not affect the pulsatile pattern of P secretion but led to an unexpected overall increase in P on Day 21 of pregnancy; this effect was delayed and occurred 10 days after commencing treatment with the GnRH depot agonist. The elevation of P on Day 21 of pregnancy in the GnRHa group suggests either a reduced negative feedback effect or an increased autocrine response by the corpora lutea.     

Complement factor H variant increases the risk of age-related macular degeneration

Age-related macular degeneration (AMD) is a leading cause of visual impairment and blindness in the elderly whose etiology remains largely unknown. Previous studies identified chromosome 1q32 as harboring a susceptibility locus for AMD. We used single-nucleotide polymorphisms to interrogate this region and identified a strongly associated haplotype in two independent data sets. DNA resequencing of the complement factor H gene within this haplotype revealed a common coding variant, Y402H, that significantly increases the risk for AMD with odds ratios between 2.45 and 5.57. This common variant likely explains approximately 43% of AMD in older adults.     

Differences in the tissue tropism to chicken oviduct epithelial cells between avian coronavirus IBV strains QX and B1648 are not related to the sialic acid binding properties of their spike proteins

The avian coronavirus (AvCoV) infectious bronchitis virus (IBV) is a major poultry pathogen. A characteristic feature of IBV is the occurrence of many different strains belonging to different serotypes, which makes a complete control of the disease by vaccinations a challenging task. Reasons for differences in the tissue tropism and pathogenicity between IBV strains, e.g. a predilection for the kidneys or the oviduct are still an open question. Strains of the QX genotype have been major pathogens in poultry flocks in Asia, Europe and other parts of the world. They are the cause of severe problems with kidney disease and reproductive tract disorders. We analysed infectivity and binding properties of the QX strain and compared them with those of the nephropathogenic strain B1648. As most IBV strains do not infect permanent cell lines and show infection only in primary chicken cells of the target organs, we developed a culture system for chicken oviduct explants. The epithelial cells of the oviduct showed a high susceptibility to infection by the QX strain and were almost resistant to infection by the nephropathogenic B1648 strain. Binding tests with isolated primary oviduct epithelial cells and soluble S1 proteins revealed that S1 proteins of two IBV strains bound with the same efficiency to oviduct epithelial cells. This attachment was sialic acid dependent, indicating that the sugar binding property of IBV spike proteins is not the limiting factor for differences in infection efficiency for the oviduct of the corresponding viruses.     

Seroprevalence of chlamydial infection in cattle in Ireland

Although few studies have investigated the prevalence of chlamydial infections in cattle, reported prevalence rates vary hugely. In order to assess the prevalence of this infection in cattle in Ireland, serum samples (100 herds, 20 samples/herd) collected for statutory screening for brucellosis were examined by soluble chlamydial antigen indirect ELISA. The assay detects antibodies to the two most common Chlamydiaceae spp. affecting cattle, namely Chlamydia abortus and Chlamydia pecorum. A total of 95 samples from 57 herds were seropositive, representing an observed prevalence rate of 4.75%. The parametric bootstrap estimate of the mean disease prevalence in the population was 6.04% (95%, CI 4.70-7.50). The results suggest the prevalence of chlamydial infection is low in cattle in Ireland.