Genome-wide meta-analysis identifies 93 risk loci and enables risk prediction equivalent to monogenic forms of venous thromboembolism

We report a genome-wide association study of venous thromboembolism (VTE) incorporating 81,190 cases and 1,419,671 controls sampled from six cohorts. We identify 93 risk loci, of which 62 are previously unreported. Many of the identified risk loci are at genes encoding proteins with functions converging on the coagulation cascade or platelet function. A VTE polygenic risk score (PRS) enabled effective identification of both high- and low-risk individuals. Individuals within the top 0.1% of PRS distribution had a VTE risk similar to homozygous or compound heterozygous carriers of the variants G20210A (c.*97 G > A) in F2 and p.R534Q in F5. We also document that F2 and F5 mutation carriers in the bottom 10% of the PRS distribution had a risk similar to that of the general population. We further show that PRS improved individual risk prediction beyond that of genetic and clinical risk factors. We investigated the extent to which venous and arterial thrombosis share clinical risk factors using Mendelian randomization, finding that some risk factors for arterial thrombosis were directionally concordant with VTE risk (for example, body mass index and smoking) whereas others were discordant (for example, systolic blood pressure and triglyceride levels).

MISCAST: MIssense variant to protein StruCture Analysis web SuiTe

Human genome sequencing efforts have greatly expanded, and a plethora of missense variants identified both in patients and in the general population is now publicly accessible. Interpretation of the molecular-level effect of missense variants, however, remains challenging and requires a particular investigation of amino acid substitutions in the context of protein structure and function. Answers to questions like 'Is a variant perturbing a site involved in key macromolecular interactions and/or cellular signaling?', or 'Is a variant changing an amino acid located at the protein core or part of a cluster of known pathogenic mutations in 3D?' are crucial. Motivated by these needs, we developed MISCAST (missense variant to protein structure analysis web suite; http://miscast.broadinstitute.org/). MISCAST is an interactive and user-friendly web server to visualize and analyze missense variants in protein sequence and structure space. Additionally, a comprehensive set of protein structural and functional features have been aggregated in MISCAST from multiple databases, and displayed on structures alongside the variants to provide users with the biological context of the variant location in an integrated platform. We further made the annotated data and protein structures readily downloadable from MISCAST to foster advanced offline analysis of missense variants by a wide biological community.

Metallothionein Zn2+- and Cu2+-clusters from first-principles calculations

Detailed electronic structures of Zn(II) and Cu(II) clusters from metallothioneins (MT) have been obtained using density functional theory (DFT), in order to investigate how oxidative stress-caused Cu(II) intermediates affect Zn-binding to MT and cooperatively lead to Cu(I)MT. The inferred accuracy is ∼0.02-0.03 Å for metal-thiolate bond lengths for the models that are the most realistic MT models so far studied by DFT. We find terminal Zn-S and Cu-S bond lengths of 2.35-2.38 Å and 2.30-2.34 Å, whereas bridging M-S bonds are 0.05-0.11 Å longer. This electronic effect is also reflected in changes in electron density on bridging sulfurs. Various imposed backbone constraints quantify the sensitivity of cluster electronic structure towards protein conformational changes. The large negative charge densities of the clusters are central to MT function, and the smaller β-clusters are more prone to modification. Oxidative stress-associated Cu(II) binding weakens the Zn-S bonds and is thus likely to impair the Zn(II) transfer function of MTs, providing a mechanism for cooperative Cu(II) binding leading to loss of Zn(II) and dysfunctional Cu(I)MT clusters.

Transmission of Salmonella between wildlife and meat-production animals in Denmark

AIMS

To investigate the transmission of Salmonella spp. between production animals (pigs and cattle) and wildlife on production animal farms in Denmark.

METHODS AND RESULTS

In the winter and summer of 2001 and 2002, 3622 samples were collected from Salmonella-infected and noninfected herds of pigs and cattle and surrounding wildlife. Salmonella was detected in wildlife on farms carrying Salmonella-positive production animals and only during the periods when Salmonella was detected in the production animals. The presence of Salmonella Typhimurium in wild birds significantly correlated to their migration pattern and food preference.

CONCLUSIONS

Salmonella was transmitted from infected herds of production animals (cattle and pigs) to wildlife that lived amongst or in close proximity to them.

SIGNIFICANCE AND IMPACT OF THE STUDY

Salmonella in animal food products is associated with the occurrence of Salmonella in primary animal production. Strategies to control the introduction and spread of infection should include wildlife management, as the nearby wildlife may act as reservoirs for Salmonella spp. and/or may be passive carriers of the bacteria.

Scanning electron microscopy of foreleg tarsal sense organs of the poultry red mite, Dermanyssus gallinae (DeGeer) (Acari:Dermanyssidae)

Scanning electron microscopy (SEM) studies on the poultry red mite, Dermanyssus gallinae (DeGeer), showed that the tip of the foreleg tarsus of both sexes and early instar stages (larvae, protonymph and deutonymph) bears a cluster of 10 blunt peg-type sensillae. Diversity in size, shape and surface features of the wall of these sensillae characterize the sensilla complex (sensory field). Two short setae (1 and 2) with smooth walls lack detectable pores, whereas three medium-sized setae (4, 5 and 8) bear pores in the wall. Four medium or long setae (3, 6, 7 and 9) have longitudinal grooves or ribs in the wall, whilst one seta (10) possesses both pores and grooves in the wall. Based on the morphology, it is suggested that the porous setae could be olfactory receptors, and the grooved setae could be mechanoreceptors.

Five decades of tick-man interaction in Denmark--an analysis

The tick Ixodes ricinus (L.) is a known vector of several zoonotic diseases such as Tick Borne Encephalitis (TBE), Lyme borreliosis and ehrlichiosis. The interaction between humans and ticks are at the very core of our understanding of the epidemiology of tick borne zoonoses, but only few experimental studies have been performed. Hence our understanding of the epidemiology of tick-borne disease has to rest on the assumption that the potential tick activity, which is reflected in tick samples from the vegetation or samples from animals, corresponds with tick-human interaction. Observations which may reflect the long term tick-human contact are available in Denmark. These observations are records of requests for information on I. ricinus forwarded to the Danish Pest Infestation Laboratory (DPIL). This article was based on the assumption that the request could be seen as a measure of tick-human interaction reflecting the tick densities in relative terms. The perceived tick densities given by the number of requests on I. ricinus divided by the total number of requests to DPIL was fairly stable from 1965 to 1985, while it doubled during the late 1980's reaching a higher level in the beginning of the 1990's. The perceived density was well explained by the variation in temperature, solar radiation (monthly measurement) and deer abundance (yearly assessments). The measure of deviation, i.e. the ratio between observed requests + 1 and modelled requests + 1, for the individual years varied between 0.91 and 1.20, with considerable within-year variation. A gradual change in periodicity of the residual might suggest gradually changing tick population dynamics. In conclusion, the perceived tick densities appear to be consistent with the current knowledge of tick ecology and tick-transmitted diseases.

The role of volatile semiochemicals in mediating host location and selection by nuisance and disease-transmitting cattle flies

The role of volatile semiochemicals in mediating the location and selection within herds of Holstein-Friesian heifers by nuisance and disease-transmitting cattle flies was investigated using coupled gas chromatography-electrophysiology (GC-EAG), coupled gas chromatography-mass spectrometry (GC-MS), electrophysiology (EAG), laboratory behaviour and field studies. Using volatile extracts collected by air entrainment from heifers in the Netherlands, a number of active peaks were located by coupled GC-EAG for Musca autumnalis (de Geer) (Diptera: Muscidae) and Haematobia irritans (L.) (Diptera: Muscidae). Volatile samples were also collected from two heifers in Denmark shown in previous counting experiments to differ significantly in their fly loads. Coupled GC-EAG using Ha. irritans antennae revealed differences in the EAG response to the samples, with additional EAG activity in the sample collected from the heifer with the lower fly load. To identify more EAG active compounds, volatiles were also collected from 48-h-old urine by air entrainment. In total, 23 compounds were located and identified by coupled GC-EAG and GC-MS. Further electrophysiological testing of these compounds with five fly species [M. autumnalis, Ha. irritans, Hydrotaea irritans (L.) (Diptera: Muscidae), Stomoxys calcitrans (L.) (Diptera: Musicidae) and Wohlfahrtia magnifica (Schiner) (Diptera: Sarcophagidae)] showed that only some of the compounds were physiologically active across the range of flies tested. These included 1-octen-3-ol, 6-methyl-5-hepten-2-one, (Z)-3-hexen-1-ol, naphthalene, and all EAG active compounds identified from urine. Compounds showing significant EAG activity were tested for behavioural activity using a wind-tunnel designed for measuring upwind flight behaviour. At certain concentrations, 1-octen-3-ol, 6-methyl-5-hepten-2-one and 3-octanol increased upwind flight, whereas naphthalene, propyl butanoate and linalool reduced upwind flight. In field studies using small herds of heifers ranked according to their fly load, individual slow-release formulations of 1-octen-3-ol and 6-methyl-5-hepten-2-one, when applied to low and high fly loading heifers, reduced fly loads on these individuals. This study provides evidence for the hypothesis that the natural differential attractiveness within herds of Holstein-Freisian heifers, i.e. a single host species, for cattle flies is partly due to differences in volatile semiochemicals emitted from the host. It is suggested that this phenomenon applies to other vertebrate host species and their associated insect pests.

Variation in the load of the horn fly, Haematobia irritans, in cattle herds is determined by the presence or absence of individual heifers

The distribution of horn flies, Haematobia irritans (L.) (Diptera: Muscidae), in herds of Danish Holstein-Friesian cattle was investigated in two studies conducted during two field seasons. In the first study, highly significant differences in fly distribution between the most and the least fly-susceptible heifers were observed. In one herd, the mean difference between the most fly-susceptible and the most fly-resistant heifers was 268 Ha. irritans specimens. The highest ratio between upper and lower mean fly number was 64.1:1, whereas the lowest was 3.1:1. In the second year, it was demonstrated that the heifers kept their rank in fly attraction over time. The trial clearly demonstrated that some heifers were attracting flies, whereas others, even in the same herd, only carried a few. In the second study, heifers were moved in and out of herds in an attempt to manipulate fly loads in the herds. In year 1, one herd (herd A) received four fly-resistant heifers from another herd (herd B), resulting in a drop in the mean number of flies, whereas herd B received four fly-susceptible heifers from herd A, resulting in an elevation of the mean number of flies. In year 2, a similar pattern emerged using herds C and D, and when the cattle were later returned to their original herds, the fly loads returned to their original distribution. The data presented here show unequivocally that, for horn flies, there can be considerable differences in fly loads for individual heifers within the Holstein-Friesian breed. Furthermore, the overall fly load within herds can be manipulated, and can be reversed. Thus, the distribution in the number of flies within a herd appears to depend on the number of fly-resistant or fly-susceptible heifers. The possible role of chemical factors emitted by heifers, i.e. volatile semiochemicals, in determining differences in fly loads is discussed, whereby attractants are emitted by fly-susceptible heifers and enable flies to locate their host, and repellents are emitted by fly-resistant heifers such that the flies are actively repelled from the herd.

Topical treatment of calves with synthetic pyrethroids: effects on the non-target dung fly Neomyia cornicina (Diptera: Muscidae)

Dung from calves treated with synthetic pyrethroids negatively influenced, in varying degrees, survival, reproduction and size of the common dung fly Neomyia cornicina (Fabricius). This was documented in assays where the coprophagous larvae and adults of N. cornicina were exposed to dung collected from calves dosed with topical preparations of deltamethrin, flumethrin, cyfluthrin, and alpha-cypermethrin. Larval mortality was significantly increased in dung collected up to at least seven days after treatment with deltamethrin, alpha-cypermethrin and cyfluthrin. Alpha-cypermethrin caused significant mortality of adults allowed to feed on moist dung. Nulliparous flies fed for six days on dung collected three days after treatment of calves with alpha-cypermethrin or deltamethrin showed little or no ovarian development. A tendency for a comparable effect with flumethrin was also observed. A connection between ovarian development and inhibition of feeding was indicated by the observation of significantly lowered excretion rates in flies exposed to residues of deltamethrin, alpha-cypermethrin and flumethrin. Larvae that survived exposure to dung from calves dosed with deltamethrin, alpha-cypermethrin, or cyfluthrin gave rise to smaller flies. The effect on adult fly size decreased when larvae were exposed to dung collected at longer times after treatment of the calves. Adult fly size was significantly reduced in dung collected up to 14 days (alpha-cypermethrin) or up to 28 days after treatment (deltamethrin and cyfluthrin). Fluctuating asymmetry of a wing vein character did not reflect the anticipated levels of exposure. The study strongly indicated that the use of synthetic pyrethroids affected the insect dung fauna and that such use may reduce dung decomposition.

Entomopathogenic Fungi in Flies Associated with Pastured Cattle in Denmark

Cattle flies, including Musca autumnalis, Haematobia irritans, and Hydrotaea irritans, are pests of pastured cattle. A 2-year study of the natural occurrence of entomopathogenic fungi in adult cattle flies and other flies associated with pastures showed that the four species included in the Entomophthora muscae species complex (E. muscae sensu lato) caused high infection levels in several species of flies. However, only a few specimens of cattle flies were infected by E. muscae sensu stricto despite the fact that cattle flies were observed to perch on spear thistles, which acted as transmission site for all four Entomophthora species. Transmission experiments with E. muscae s.l. supported the field data. Of the two species considered host specific, E. syrphi caused substantial infection in a muscid, and E. scatophagae likewise could be transmitted to a muscid. This emphasizes the need for a revision of the two species. Low prevalences were recorded of another entomophthoralean, Furia americana, and of the hyphomycetes Beauveria bassiana and Verticillium lecanii.

The status and development of insecticide resistance in Danish populations of the housefly Musca domestica L

Samples of housefly (Musca domestica) field populations were collected from Danish livestock farms in 1997. The tolerance of the first-generation offspring was determined for a number of insecticides. Dose-response values were obtained by topical application for the pyrethroids bioresmethrin and pyrethrum, both synergised with piperonyl butoxide, and the organophosphate dimethoate. The organophosphates azamethiphos and propetamphos and the carbamate methomyl were tested in discriminating dose feeding bioassays. Resistance was low to moderate in most of the populations for most of the compounds tested, but this study also revealed the existence of high resistance to pyrethroid, organophosphate and carbamate insecticides in some populations. The resistance factors at LD50 for bioresmethrin/piperonyl butoxide ranged between 2 and 98, and for pyrethrum/piperonyl butoxide between 2 and 29. Our results indicate that pyrethroid resistance in Denmark is increasing, since four of the 21 farms showed more than 100-fold resistance at LD95, a level of resistance only observed once before. Resistance factors at LD50 for dimethoate ranged from 9 to 100, and showed two distinct trends: populations with either decreasing or increasing resistance. Resistance to azamethiphos was found to be widespread and high. Although two strains with high methomyl and propetamphos resistance were observed, methomyl and propetamphos resistance is moderate and appears not to be increasing.

Selection and reversion of azamethipos-resistance in a field population of the housefly Musca domestica (Diptera: Muscidae), and the underlying biochemical mechanisms

The organophosphorus insecticide, azamethiphos, is widely used throughout the world to control the housefly, Musca domestica (L.). Since its commercial introduction to Denmark in 1983 for this purpose, we have monitored the toxicity of azamethiphos to housefly populations at livestock farms throughout the country and carried out regular field studies. The findings of our field studies, which have revealed a strong potential for resistance development, have been born out by regular surveys showing that resistance has increased in recent years. Through the analysis of a field derived laboratory strain, we have implicated oxidative and hydrolytic mechanisms together with altered acetylcholinesterase in this resistance. Our field and laboratory studies have also indicated that resistance is relatively unstable, and can revert in the absence of selection. The implications of our findings for the continued efficacy of azamethiphos are discussed.

Non-biting Muscidae and control methods

Many non-biting muscids (filth flies) are characterised by the habit of visiting manure or rotting organic material to feed and/or oviposit. As these flies also often have close associations with human beings, as well as human habitations and domestic animals, they are potentially both a nuisance and a contributory factor in the transmission of diseases. The authors examine the biology, economic importance and control of four of the most important non-biting muscids: housefly, Musca domestica; face fly, Musca autumnalis; Australian bush fly, Musca vetustissima; sheep head fly, Hydrotaea irritans.

Variation in density of cattle-visiting muscid flies between Danish inland pastures

The density of cattle-visiting flies (Muscidae) and the load of black-flies (Simulium spp.) were estimated in twelve and eighteen inland pastures in Denmark in 1984 and 1985 respectively. No differences in the geographical distribution pattern of the predominant cattle-visiting Muscidae were recorded, whilst the relative abundance and density of the species and the total fly-load varied considerably between pastures. In most cases the mean loads of Haematobia irritans (L.) and Hydrotaea irritans (Fall.) on heifers varied significantly in relation to site topography and shelter. These crude site variables explained 65-98% of the variation in densities of horn flies and sheep head flies observed between pastures. Highest densities of Hydrotaea irritans were primarily associated with permanent, low-lying, fairly sheltered grassland sites, whereas the density was low in temporary, dry, wind-exposed pastures. A comparable relationship was found for Haematobia irritans. With Haematobosca stimulans (Mg.) and Morellia spp. no relation between grassland environment and fly density was detected.