EPINEST, an agent-based model to simulate epidemic dynamics in large-scale poultry production and distribution networks

The rapid intensification of poultry production raises important concerns about the associated risks of zoonotic infections. Here, we introduce EPINEST (EPIdemic NEtwork Simulation in poultry Transportation systems): an agent-based modelling framework designed to simulate pathogen transmission within realistic poultry production and distribution networks. We provide example applications to broiler production in Bangladesh, but the modular structure of the model allows for easy parameterization to suit specific countries and system configurations. Moreover, the framework enables the replication of a wide range of eco-epidemiological scenarios by incorporating diverse pathogen life-history traits, modes of transmission and interactions between multiple strains and/or pathogens. EPINEST was developed in the context of an interdisciplinary multi-centre study conducted in Bangladesh, India, Vietnam and Sri Lanka, and will facilitate the investigation of the spreading patterns of various health hazards such as avian influenza, Campylobacter, Salmonella and antimicrobial resistance in these countries. Furthermore, this modelling framework holds potential for broader application in veterinary epidemiology and One Health research, extending its relevance beyond poultry to encompass other livestock species and disease systems.

Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant

Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health.

Transcriptome analysis of differentially expressed circRNAs miRNAs and mRNAs during the challenge of coccidiosis

Avian coccidiosis is a common enzootic disease caused by infection of Eimeria species parasites. It causes huge economic losses in the global poultry industry. Current control using anticoccidial drugs or vaccination is limited due to drug resistance and the relatively high cost of vaccines. Improving host genetic resistance to Eimeria species is considered an effective strategy for improved control of coccidiosis. Circular RNAs (circRNAs) have been found to function as biomarkers or diagnoses of various kinds of diseases. The molecular biological functions of circRNAs, miRNAs, and mRNAs related to Sasso chicken have not yet been described during Eimeria species challenge. In this study, RNA-seq was used to profile the expression pattern of circRNAs, miRNAs, and mRNAs in spleens from Eimeria tenella-infected and non-infected commercial dual-purpose Sasso T445 breed chickens. Results showed a total of 40 differentially expressed circRNAs (DEcircRNAs), 31 differentially expressed miRNAs (DEmiRNAs), and 820 differentially expressed genes (DEmRNAs) between infected and non-infected chickens. Regulatory networks were constructed between differentially expressed circRNAs, miRNAs, and mRNAs to offer insights into the interaction mechanisms between chickens and Eimeria spp. Functional validation of a significantly differentially expressed circRNA, circMGAT5, revealed that circMGAT5 could sponge miR-132c-5p to promote the expression of the miR-132c-5p target gene monocyte to macrophage differentiation-associated (MMD) during the infection of E. tenella sporozoites or LPS stimulation. Pathologically, knockdown of circMGAT5 significantly upregulated the expression of macrophage surface markers and the macrophage activation marker, F4/80 and MHC-II, which indicated that circMGAT5 might inhibit the activation of macrophage. miR-132c-5p markedly facilitated the expression of F4/80 and MHC-II while circMGAT5 could attenuate the increase of F4/80 and MHC-II induced by miR-132c-5p, indicating that circMGAT5 exhibited function through the circMGAT5-miR-132c-5p-MMD axis. Together, our results indicate that circRNAs exhibit their resistance or susceptive roles during E. tenella infection. Among these, circMGAT5 may inhibit the activation of macrophages through the circMGAT5-miR-132c-5p-MMD axis to participate in the immune response induced by Eimeria infection.

Biliary protozoa in a dog with acute cholangiohepatitis fed a raw food diet

A 1-year 11-month intact female Alaskan Malamute fed a raw food diet was referred to the Queen Mother Hospital for Animals for further investigation of hyporexia and increased hepatobiliary enzyme activities. Clinicopathological and imaging findings were consistent with cholangiohepatitis, with coccidial zoites identified on bile cytology. Polymerase chain reaction and amplicon sequencing from the bile identified Hammondia heydorni, a Sarcocytid coccidial protozoa with an obligate 2-host life cycle. The dog was treated with clindamycin, marbofloxacin, ursodeoxycholic acid (UDCA) and S-adenosylmethionine/silybin with complete clinical and biochemical resolution documented after 6 weeks. Infection with Hammondia spp. should be considered in patients receiving raw food diets in which coccidial zoites are identified in the bile, but the pathogenic potential of this organism is unknown and the possibility of its presence as a commensal cannot be discounted.

The complete genome sequence of Eimeria tenella (Tyzzer 1929), a common gut parasite of chickens

We present a genome assembly from a clonal population of Eimeria tenella Houghton parasites (Apicomplexa; Conoidasida; Eucoccidiorida; Eimeriidae). The genome sequence is 53.25 megabases in span. The entire assembly is scaffolded into 15 chromosomal pseudomolecules, with complete mitochondrion and apicoplast organellar genomes also present.

Controlling the causative agents of coccidiosis in domestic chickens; an eye on the past and considerations for the future

Coccidiosis is a potentially severe enteritis caused by species of obligate intracellular parasites of the genus Eimeria. These parasites cause significant economic losses to the poultry industry, predominantly due to compromised efficiency of production as well as the cost of control. These losses were recently estimated to cost chicken producers approximately £10.4 billion worldwide annually. High levels of Eimeria infection cause clinical coccidiosis which is a significant threat to poultry welfare, and a pre-disposing contributory factor for necrotic enteritis. Control of Eimeria parasites and coccidiosis is therefore an important endeavour; multiple approaches have been developed and these are often deployed together. This review summarises current trends in strategies for control of Eimeria, focusing on three main areas: good husbandry, chemoprophylaxis and vaccination. There is currently no "perfect solution" and there are advantages and limitations to all existing methods. Therefore, the aim of this review is to present current control strategies and suggest how these may develop in the future.

Using infrared geostationary remote sensing to determine particulate matter ground-level composition and concentration

Speciated ground-level aerosol concentrations are required to understand and mitigate health impacts from dust storms, wildfires, and other aerosol emissions. Globally, surface monitoring is limited due to cost and infrastructure demands. While remote sensing can help estimate respirable (i.e. ground level) concentrations, current observations are restricted by inadequate spatiotemporal resolution, uncertainty in aerosol type, particle size, and vertical profile. One key issue with current remote sensing datasets is that they are derived from reflectances observed by polar-orbiting imagers, which means that aerosol is only derived during the daytime and only once or twice per day. Newer quantification methods using geostationary infrared (IR) data have focussed on detecting the presence, or absence, of an event. The determination of aerosol composition or particle size using IR exclusively has received little attention. This manuscript summarizes four scientific papers, published as part of a larger study, and identifies requirements for (a) using infrared radiance observations to obtain continual (i.e. day and night) concentration estimates; (b) increasing temporal resolution by using geostationary satellites; (c) utilizing all infrared channels to maximize spectral differences due to compositional changes; and (d) applying a high-pass filter (brightness temperature differences) to identify compositional variability. Additionally, (e) a preliminary calibration methodology was tested against three severe air quality case study incidents, namely, a dust storm, smoke from prescribed burns, and an ozone smog incident, near Sydney in eastern Australia which highlighted the ability of the method to determine atmospheric stability, clouds, and particle size. Geostationary remote sensing provides near-continuous data at a temporal resolution comparable to monitoring equipment. The spatial resolution (~ 4 km2 at NADIR) is adequate for large sources but coarse for localized sources. The spectral sensitivity of aerosol is limited and appears to be dominated by humidity changes rather than concentration or compositional changes. Geostationary remote sensing can be used to determine the timing, duration, and spatial extent of an air quality event. Brightness temperature differences can assist in qualifying composition with an order of magnitude estimate of concentration.

The proportion of endometrial cancers associated with Lynch syndrome: a systematic review of the literature and meta-analysis

Purpose

Endometrial cancer (EC) is often the sentinel cancer in women with Lynch syndrome (LS). However, efforts to implement universal LS screening in EC patients have been hampered by a lack of evidence detailing the proportion of EC patients that would be expected to screen positive for LS.

Methods

Studies were identified by electronic searches of Medline, Embase, Cochrane CENTRAL and Web of Science. Proportions of test positivity were calculated by random and fixed-effects meta-analysis models. I² score was used to assess heterogeneity across studies.

Results

Fifty-three studies, including 12,633 EC patients, met the inclusion criteria. The overall proportion of endometrial tumors with microsatellite instability or mismatch repair (MMR) deficiency by immunohistochemistry (IHC) was 0.27 (95% confidence interval [CI] 0.25–0.28, I²: 71%) and 0.26 (95% CI 0.25–0.27, I²: 88%), respectively. Of those women with abnormal tumor testing, 0.29 (95% CI 0.25–0.33, I²: 83%) had LS-associated pathogenic variants on germline testing; therefore around 3% of ECs can be attributed to LS. Preselection of EC cases did increase the proportion of germline LS diagnoses.

Conclusion

The current study suggests that prevalence of LS in EC patients is approximately 3%, similar to that of colorectal cancer patients; therefore our data support the implementation of universal EC screening for LS.

Modeling of x-ray fluorescence full field imaging using planar square pore micro-channel plate optics

X-ray fluorescence imaging using perfect planar square pore micro-channel plate x-ray optics (MPO) is investigated through the modeling of the MPO point spread function (PSF). A semi-continuous model based on the use of a simplified two parameters reflectivity curve is developed including, in particular, three kinds of contributions. A validation of this model is carried out by calculating variations of several PSF characteristics with the MPO and fluorescence imaging parameters and comparing the results with ray-tracing simulations. A good agreement is found in a large range of x-ray energies; however, it is shown that for the lower values of the working distance a discrete model should be used to take into account the periodic nature of the PSF. Ray-tracing simulated images of extended monochromatic sources are interpreted in light of both the semi-continuous and discrete models. Finally, solutions are proposed to improve the imaging properties of the MPOs.

An aerosol particle containing enriched uranium encountered in the remote upper troposphere

We describe a submicron aerosol particle sampled at an altitude of 7 km near the Aleutian Islands that contained a small percentage of enriched uranium oxide. ²³⁵U was 3.1 ± 0.5% of ²³⁸U. During twenty years of aircraft sampling of millions of particles in the global atmosphere, we have rarely encountered a particle with a similarly high content of ²³⁸U and never a particle with enriched ²³⁵U. The bulk of the particle consisted of material consistent with combustion of heavy fuel oil. Analysis of wind trajectories and particle dispersion model results show that the particle could have originated from a variety of areas across Asia. The source of such a particle is unclear, and the particle is described here in case it indicates a novel source where enriched uranium was dispersed.

Veterinary parasitology teaching at London - Meeting the 'Day-One Competency' needs of new veterinarians

Over the past four decades, there has been an exponential increase in veterinary parasitology knowledge, coinciding with the advent of molecular biology in research. Therefore, it is unrealistic for teachers to expect students to graduate with an encyclopaedic knowledge of the subject. As a result, a new curriculum was introduced at The Royal Veterinary College (University of London) in 2007, designed to meet the needs of our new graduates, i.e. RCVS Day-One Competences. The aims of this curriculum are, inter alia, to ensure that new graduates have an up-to-date body of core knowledge and are able to apply such knowledge and newly-acquired information to scientific and clinical problem-solving. Veterinary parasitology is taught primarily in Year 2, following a brief introduction in Year 1; clinical aspects are covered in Year 3, with original research projects undertaken in Years 4 and 5. Parasitology is taught in parallel with other subjects, enabling both horizontal and vertical integration. Core material is provided in lectures supplemented by directed learning (DL) in small groups and interactive, clinical scenario-based practical classes. Student learning is supported by Moodle 3.2 (Virtual Learning Environment [VLE], RVC Learn) which provides access to an on-line study guide (annotated using Adobe Reader), PowerPoint presentations with synchronized lecturer commentary (Echo Active Learning Platform [ALP]), detailed feedback for DL and practical classes, parasite 'potcasts' and CAL packages, and a Clinical Skills Centre. A parasitology textbook has also been published recently to support courses taught at the College. Assessment of student learning is achieved using a variety of written formats (essay, problem-solving questions [PSQ], multiple choice questions [MCQ] and extended matching questions [EMQ]), integrated oral examinations and objective structured clinical examinations (OSCEs).

Eimeria tenella protein trafficking: differential regulation of secretion versus surface tethering during the life cycle

Eimeria spp. are intracellular parasites that have a major impact on poultry. Effective live vaccines are available and the development of reverse genetic technologies has raised the prospect of using Eimeria spp. as recombinant vectors to express additional immunoprotective antigens. To study the ability of Eimeria to secrete foreign antigens or display them on the surface of the sporozoite, transiently transfected populations of E. tenella expressing the fluorescent protein mCherry, linked to endogenous signal peptide (SP) and glycophosphatidylinositol-anchor (GPI) sequences, were examined. The SP from microneme protein EtMIC2 (SP2) allowed efficient trafficking of mCherry to cytoplasmic vesicles and following the C-terminal addition of a GPI-anchor (from surface antigen EtSAG1) mCherry was expressed on the sporozoite surface. In stable transgenic populations, mCherry fused to SP2 was secreted into the sporocyst cavity of the oocysts and after excystation, secretion was detected in culture supernatants but not into the parasitophorous vacuole after invasion. When the GPI was incorporated, mCherry was observed on the sporozites surface and in the supernatant of invading sporozoites. The proven secretion and surface exposure of mCherry suggests that antigen fusions with SP2 and GPI of EtSAG1 may be promising candidates to examine induction of protective immunity against heterologous pathogens.

Angiostrongylus vasorum Causing Severe Granulomatous Hepatitis with Concurrent Multiple Acquired PSS

A 14 mo old female Jack Russell terrier presented with a 12 hr history of vomiting and inappetence. She was subsequently diagnosed with multiple acquired portosystemic shunts during an exploratory celiotomy. Gross and histopathological hepatic abnormalities were consistent with chronic disease, including features suggestive of portal hypertension that was potentially caused by migrating and resident Angiostrongylus vasorum larvae. Fecal analysis and polymerase chain reaction of hepatic tissue confirmed the presence of Angiostrongylus vasorum . The dog recovered clinically following empirical treatment and supportive care. A lack of parasite burden was confirmed 9 wk postdiagnosis; however, serum biochemical analysis at that time was suggestive of ongoing hepatic dysfunction.

White-Nose Syndrome fungus introduced from Europe to North America

The investigation of factors underlying the emergence of fungal diseases in wildlife has gained significance as a consequence of drastic declines in amphibians, where the fungus Batrachochytrium dendrobatidis has caused the greatest disease-driven loss of biodiversity ever documented [1]. Identification of the causative agent and its origin (native versus introduced) is a crucial step in understanding and controlling a disease [2]. Whereas genetic studies on the origin of B. dendrobatidis have illuminated the mechanisms behind the global emergence of amphibian chytridiomycosis [3], the origin of another recently-emerged fungal disease, White-Nose Syndrome (WNS) and its causative agent, Pseudogymnoascus destructans, remains unresolved [2,4]. WNS is decimating multiple North American bat species with an estimated death toll reaching 5-6 million. Here, we present the first informative molecular comparison between isolates from North America and Europe and provide strong evidence for the long-term presence of the fungus in Europe and a recent introduction into North America. Our results further demonstrate great genetic similarity between the North American and some European fungal populations, indicating the likely source population for this introduction from Europe.

Spatially directed vesicle capture in the ordered pores of breath-figure polymer films

This work describes a new method to selectively capture liposomes and other vesicle entities in the patterned pores of breath-figure polymer films. The process involves the deposition of a hydrophobe containing biopolymer in the pores of the breath figure, and the tethering of vesicles to the biopolymer through hydrophobic interactions. The process is versatile, can be scaled up and extended to the deposition of other functional materials in the pores of breath figures.

A selective review of advances in coccidiosis research

Coccidiosis is a widespread and economically significant disease of livestock caused by protozoan parasites of the genus Eimeria. This disease is worldwide in occurrence and costs the animal agricultural industry many millions of dollars to control. In recent years, the modern tools of molecular biology, biochemistry, cell biology and immunology have been used to expand greatly our knowledge of these parasites and the disease they cause. Such studies are essential if we are to develop new means for the control of coccidiosis. In this chapter, selective aspects of the biology of these organisms, with emphasis on recent research in poultry, are reviewed. Topics considered include taxonomy, systematics, genetics, genomics, transcriptomics, proteomics, transfection, oocyst biogenesis, host cell invasion, immunobiology, diagnostics and control.

Soil diversity and hydration as observed by ChemCam at Gale crater, Mars

The ChemCam instrument, which provides insight into martian soil chemistry at the submillimeter scale, identified two principal soil types along the Curiosity rover traverse: a fine-grained mafic type and a locally derived, coarse-grained felsic type. The mafic soil component is representative of widespread martian soils and is similar in composition to the martian dust. It possesses a ubiquitous hydrogen signature in ChemCam spectra, corresponding to the hydration of the amorphous phases found in the soil by the CheMin instrument. This hydration likely accounts for an important fraction of the global hydration of the surface seen by previous orbital measurements. ChemCam analyses did not reveal any significant exchange of water vapor between the regolith and the atmosphere. These observations provide constraints on the nature of the amorphous phases and their hydration.

Prevalence and molecular characterisation of Eimeria species in Ethiopian village chickens

BACKGROUND

Coccidiosis, caused by species of the apicomplexan parasite Eimeria, is a major disease of chickens. Eimeria species are present world-wide, and are ubiquitous under intensive farming methods. However, prevalence of Eimeria species is not uniform across production systems. In developing countries such as Ethiopia, a high proportion of chicken production occurs on rural smallholdings (i.e. 'village chicken production') where infectious diseases constrain productivity and surveillance is low. Coccidiosis is reported to be prevalent in these areas. However, a reliance on oocyst morphology to determine the infecting species may impede accurate diagnosis. Here, we used cross-sectional and longitudinal studies to investigate the prevalence of Eimeria oocyst shedding at two rural sites in the Ethiopian highlands.

RESULTS

Faecal samples were collected from 767 randomly selected chickens in May or October 2011. In addition, 110 chickens were sampled in both May and October. Eimeria oocysts were detected microscopically in 427 (56%, 95% confidence interval (95% CI) 52-59%) of the 767 faecal samples tested. Moderate clustering of positive birds was detected within households, perhaps suggesting common risk factors or exposure pathways. Seven species of Eimeria were detected by real time PCR in a subset of samples further analysed, with the prevalence of some species varying by region. Co-infections were common; 64% (23/36, 95% CI 46-79%) of positive samples contained more than one Eimeria spp. Despite frequent infection and co-infection overt clinical disease was not reported. Eimeria oocysts were detected significantly more frequently in October (248/384, 65%, 95% CI 60-69%), following the main rainy season, compared to May (179/383, 47%, 95% CI 42-52%, p < 0.001). Eimeria oocyst positivity in May did not significantly affect the likelihood of detecting Eimeria oocyst five months later perhaps suggesting infection with different species or immunologically distinct strains.

CONCLUSIONS

Eimeria spp oocysts may be frequently detected in faecal samples from village chickens in Ethiopia. Co-infection with multiple Eimeria spp was common and almost half of Eimeria positive birds had at least one highly pathogenic species detected. Despite this, all sampled birds were free of overt disease. Although there was no evidence of a difference in the prevalence of oocysts in faecal samples between study regions, there was evidence of variation in the prevalence of some species, perhaps suggesting regional differences in exposure to risk factors associated with the birds, their management and/or location-specific environmental and ecological factors.

Construction of a genetic map for Theileria parva: identification of hotspots of recombination

The tick-borne protozoan parasite Theileria parva is the causal agent of East Coast Fever (ECF), a severe lymphoproliferative disease of cattle in eastern, central and southern Africa. The life cycle of T. parva is predominantly haploid, with a brief diploid stage occurring in the tick vector that involves meiotic recombination. Resolved genetic studies of T. parva are currently constrained by the lack of a genome-wide high-definition genetic map of the parasite. We undertook a genetic cross of two cloned isolates of T. parva to construct such a map from 35 recombinant progeny, using a genome-wide panel of 79 variable number of tandem repeat markers. Progeny were established by in vitro cloning of cattle lymphocytes after infection with sporozoites prepared from Rhipicephalus appendiculatus ticks fed on a calf undergoing a dual infection with the two clonal parental stocks. The genetic map was determined by assigning individual markers to the four chromosome genome, whose physical length is approximately 8309 kilobasepairs (Kb). Segregation analysis of the markers among the progeny revealed a total genetic size of 1683.8 centiMorgans (cM), covering a physical distance of 7737.62 Kb (∼93% of the genome). The average genome-wide recombination rate observed for T. parva was relatively high, at 0.22 cM Kb(-1) per meiotic generation. Recombination hot-spots and cold-spots were identified for each of the chromosomes. A panel of 27 loci encoding determinants previously identified as immunorelevant or likely to be under selection were positioned on the linkage map. We believe this to be the first genetic linkage map for T. parva. This resource, with the availability of the genome sequence of T. parva, will promote improved understanding of the pathogen by facilitating the use of genetic analysis for identification of loci responsible for variable phenotypic traits exhibited by individual parasite stocks.

Peat fires and air quality: volatile organic compounds and particulates

There are numerous localized peat deposits on the Swan Coastal Plain, an urban and rural bioregion otherwise dominated by wetland ecosystems in southwestern Australia. Hydrological change is significant in the bioregion: urban development encroaches on wetlands, groundwater extraction provides the city population with most of its water, and rainfall declines will not recharge aquifers in the future. The wetland processes which contribute to the formation of these peat deposits have therefore changed and are becoming vulnerable to fire events with residents increasingly exposed to peat smoke. There is an imperative to characterise this peat smoke to determine if exposures are harmful or toxic, and opportunities to do so in this setting arise due to the absence of bushfire smoke which has confounded other international studies. We have measured volatile organic compounds (VOCs) and particulate concentrations from an opportunistic assessment of two peat fires. SUMMA canister grab samples and a portable GCMS were used to determine the VOCs with high 1h benzene concentrations of 16 and 30 ppm v/v. PM10 and PM2.5 particulate data were collected using an Osiris continuous analyser with 24h concentrations recorded at varying time periods (within a 5 months timeframe) ranging from 1h maximums of between 23-37 microgm(-3) for PM10 and 50.5-106 microgm(-3) for PM2.5. While the 24h averages were generally below national air quality standards, elevated 1h concentrations were observed on numerous occasions and on most days. Given the proximity of residential development to many peat deposits, a drying climate and the increased risk of arson in peri-urban environments, the health impacts of exposure to peat smoke need to be determined and if necessary measures developed to prevent exposure (which would include maintaining wetland sediment integrity so as to reduce its vulnerability to fire).

Short- and long-term olivine weathering in Svalbard: implications for Mars

Liquid water is essential to life as we know it on Earth; therefore, the search for water on Mars is a critical component of the search for life. Olivine, a mineral identified as present on Mars, has been proposed as an indicator of the duration and characteristics of water because it dissolves quickly, particularly under low-pH conditions. The duration of olivine persistence relative to glass under conditions of aqueous alteration reflects the pH and temperature of the reacting fluids. In this paper, we investigate the utility of 3 methodologies to detect silicate weathering in a Mars analog environment (Sverrefjell volcano, Svalbard). CheMin, a miniature X-ray diffraction instrument developed for flight on NASA's upcoming Mars Science Laboratory, was deployed on Svalbard and was successful in detecting olivine and weathering products. The persistence of olivine and glass in Svalbard rocks was also investigated via laboratory observations of weathered hand samples as well as an in situ burial experiment. Observations of hand samples are consistent with the inference that olivine persists longer than glass at near-zero temperatures in the presence of solutions at pH approximately 7-9 on Svalbard, whereas in hydrothermally altered zones, glass has persisted longer than olivine in the presence of fluids at similar pH at approximately 50 degrees C. Analysis of the surfaces of olivine and glass samples, which were buried on Sverrefjell for 1 year and then retrieved, documented only minor incipient weathering, though these results suggest the importance of biological impacts. The 3 types of observations (CheMin, laboratory observations of hand samples, burial experiments) of weathering of olivine and glass at Svalbard show promise for interpretation of weathering on Mars. Furthermore, the weathering relationships observed on Svalbard are consistent with laboratory-measured dissolution rates, which suggests that relative mineral dissolution rates in the laboratory, in concert with field observations, can be used to yield valuable information regarding the pH and temperature of reacting martian fluids.

Atmospheric emissions and attenuation of non-methane organic compounds in cover soils at a French landfill

In addition to methane (CH(4)) and carbon dioxide (CO(2)), landfill gas may contain more than 200 non-methane organic compounds (NMOCs) including C(2+)-alkanes, aromatics, and halogenated hydrocarbons. Although the trace components make up less than 1% v/v of typical landfill gas, they may exert a disproportionate environmental burden. The objective of this work was to study the dynamics of CH(4) and NMOCs in the landfill cover soils overlying two types of gas collection systems: a conventional gas collection system with vertical wells and an innovative horizontal gas collection layer consisting of permeable gravel with a geomembrane above it. The 47 NMOCs quantified in the landfill gas samples included primarily alkanes (C(2)-C(10)), alkenes (C(2)-C(4)), halogenated hydrocarbons (including (hydro)chlorofluorocarbons ((H)CFCs)), and aromatic hydrocarbons (BTEXs). In general, both CH(4) and NMOC fluxes were all very small with positive and negative fluxes. The highest percentages of positive fluxes in this study (considering all quantified species) were observed at the hotspots, located mainly along cell perimeters of the conventional cell. The capacity of the cover soil for NMOC oxidation was investigated in microcosms incubated with CH(4) and oxygen (O(2)). The cover soil showed a relatively high capacity for CH(4) oxidation and simultaneous co-oxidation of the halogenated aliphatic compounds, especially at the conventional cell. Fully substituted carbons (TeCM, PCE, CFC-11, CFC-12, CFC-113, HFC-134a, and HCFC-141b) were not degraded in the presence of CH(4) and O(2). Benzene and toluene were also degraded with relative high rates. This study demonstrates that landfill soil covers show a significant potential for CH(4) oxidation and co-oxidation of NMOCs.

Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization

Eimeria tenella is an intracellular protozoan parasite that infects the intestinal tracts of domestic fowl and causes coccidiosis, a serious and sometimes lethal enteritis. Eimeria falls in the same phylum (Apicomplexa) as several human and animal parasites such as Cryptosporidium, Toxoplasma, and the malaria parasite, Plasmodium. Here we report the sequencing and analysis of the first chromosome of E. tenella, a chromosome believed to carry loci associated with drug resistance and known to differ between virulent and attenuated strains of the parasite. The chromosome--which appears to be representative of the genome--is gene-dense and rich in simple-sequence repeats, many of which appear to give rise to repetitive amino acid tracts in the predicted proteins. Most striking is the segmentation of the chromosome into repeat-rich regions peppered with transposon-like elements and telomere-like repeats, alternating with repeat-free regions. Predicted genes differ in character between the two types of segment, and the repeat-rich regions appear to be associated with strain-to-strain variation.

Assisted hatching on assisted conception (IVF & ICSI)

BACKGROUND

Failure of implantation and conception may result from an inability of the blastocyst to escape from its outer coat, know as the zona pellucida. In vitro culture conditions and/or advancing maternal age may alter the architecture of the zona pellucida and result in hatching difficulties. Artificial disruption of this coat is known as assisted hatching (AH) has been proposed as a method of improving the success of assisted conception.

OBJECTIVES

To determine whether assisted hatching (AH) of embryos facilitates live births and clinical pregnancy and whether it impacts on negative outcomes (such as multiple pregnancy and miscarriage).

SEARCH STRATEGY

We searched the Cochrane Menstrual Disorders and Subfertility Group trials register (1 June 2005), the Cochrane Controlled Trials Register (Cochrane Library Issue 2, 2005), MEDLINE (1996 to June 2003), EMBASE (1980 to June 2005) and reference lists of articles. Authors were contacted for missing and/or unpublished data.

SELECTION CRITERIA

Trials were identified and independently screened by two reviewers. Randomised controlled trials of AH (mechanical, chemical or laser disruption of the zona pellucida prior to embryo replacement) versus no AH that reported live birth, clinical pregnancy or implantation rates were included.

DATA COLLECTION AND ANALYSIS

Qualitative assessments and data extraction were performed independently by two reviewers. Outcomes were extracted as rates and combined using random effects meta-analysis, sensitivity analysis, sub grouping and meta-regression where appropriate.

MAIN RESULTS

Twenty-three randomised controlled trials consisting of 2668 women reported on 849 pregnancy outcomes. There was no significant difference in the odds of live births in the AH compared with control groups (6 RCTs; OR 1.19 95% CI 0.81 to 1.73; 163 births from 516 women). Women undergoing assisted hatching were significantly more likely to achieve clinical pregnancy (23 RCTs, OR 1.33, 95% CI 1.12 to 1.57). Miscarriage rates per woman were similar in both groups (12 RCTs OR 1.23 (95% CI 0.73 to 2.05). Multiple pregnancy rates per woman was increased in women who were randomised to AH compared with control women (9 RCTs OR 1.83 (95% CI 1.19 to 2.83). The improvement in clinical pregnancy rate means for a clinic with a success rate of 25% could anticipate improving the CPR to between 28 and 39%, all things being equal. The trials provided insufficient data to investigate the impact of assisted hatching on several important outcomes, including monozygotic twinning, embryo damage, congenital and chromosomal abnormalities, and in vitro blastocyst development.

AUTHORS' CONCLUSIONS

Despite significantly improved odds of clinical pregnancy, there is insufficient evidence to determine any effect of AH on live birth rates. The increased multiple pregnancy rate is of concern although it likely that with a policy of single embryo transfer this may be lowered. Currently, there is insufficient evidence to recommend assisted hatching.

Cleavage stage versus blastocyst stage embryo transfer in assisted conception

BACKGROUND

In the past decade, advances in the understanding of nutrient requirements of embryos, has led to the evolution of culture media designed to support extended culture of embryos in vitro from the standard procedure of 2 to 3 days (for early cleavage embryo transfer) to 5 to 6 days (blastocyst culture). The rationale for blastocyst culture is to improve the synchronicity of uterine and embryonic development and provide a mechanism for self-selection of viable embryos. Since the initial widespread introduction of blastocyst culture in 1998, there has been conflicting reports about the clinical benefits of this technique.

OBJECTIVES

To determine if blastocyst stage embryo transfers (ETs) affects success rates compared with cleavage stage ETs and investigate what factors may influence this.

SEARCH STRATEGY

We searched the Cochrane Menstrual Disorders and Subfertility Group Specialised Register of controlled trials. We also searched the Cochrane Controlled Trials Register (CENTRAL) (The Cochrane Library), MEDLINE, EMBASE and Bio extracts. Attempts were made to identify trials from the National Research Register, the Clinical Trials Register and the citation lists of review articles and included trials. The last search date was May 2005. The first or corresponding author of each included trial was contacted for additional information.

SELECTION CRITERIA

Trials were included if they were randomised and compared the effectiveness of early cleavage versus blastocyst stage transfers.

DATA COLLECTION AND ANALYSIS

Of the 45 trials that were identified, 16 trials met the inclusion criteria and were reviewed. Primary outcomes were rates of live birth, clinical pregnancy and multiple-pregnancy rates per couple. Secondary outcomes were rates of miscarriage, failure to transfer embryos, freezing, implantation and high order pregnancy and per cycle data. Quality assessment and data extraction were performed independently by two review authors. Meta-analysis was performed using odds ratios (OR) for dichotomous outcomes and weighted mean differences for binary outcomes with 95% confidence intervals (CI).

MAIN RESULTS

There was no evidence of a difference in live-birth rate per couple between the two treatment groups (7 RCTs; OR 1.16, 95% CI 0.74 to 1.44 [Day 2/3 34.3% vs. Day 5/6 35.4%]); in the clinical pregnancy rate per couple (15 RCTs; OR 1.05, 95% CI 0.88 to 1.26 [Day 2/3 38.8% vs. 40.3%]) even for good prognosis patients (6 RCTs: OR 96% 1.06 CI 0.83 to 1.34). There was also no difference in multiple-pregnancy rate per couple (12 RCTs; OR 0.85, 95% CI 0.63 to 1.13) particularly in trials where equal numbers of embryos were transferred in both groups (6 RCTs: OR 0.91, 95% CI 0.63 to 1.32). There was no evidence of a difference in high order multiple-pregnancy rates per couple (5 RCTs; OR 0.44, 95% CI 0.15 to 1.33) or miscarriage rate per couple between the two groups (9 RCTs; OR 1.33, 95% CI 0.89 to 2.01). Rates of embryo freezing per couple was significantly higher in Day 2 to 3 transfers (9 RCTs; OR 0.45, 95% CI 0.36 to 0.57). Failure to transfer any embryos per couple was significantly higher in the Day 5 to 6 group (10 RCTs: OR 3.21, 95% CI 2.15 to 4.81[Day 2/3 3.5% vs D 5/6 10.1%]), but was not significantly different for good prognosis patients (7RCTs, OR 1.58 95% CI 0.65 to 3.82).

AUTHORS' CONCLUSIONS

There is no evidence of a difference in live birth or pregnancy outcomes between Day 2 to 3 and Day 5 to 6 transfer of embryos. Blastocyst transfer was associated with an increase in failure to transfer any embryos in a cycle and a decrease in embryo freezing rates. In the absence of data on cumulative live birth rates resulting from fresh and thawed cycles, it is not possible to determine if this represents an advantage or disadvantage.

Assisted hatching on assisted conception (IVF & ICSI)

BACKGROUND

Failure of implantation and conception may result from an inability of the blastocyst to escape from its outer coat, know as the zona pellucida. In vitro culture conditions and/or advancing maternal age may alter the architecture of the zona pellucida and result in hatching difficulties. Artificial disruption of this coat is known as assisted hatching (AH) has been proposed as a method of improving the success of assisted conception.

OBJECTIVES

To determine whether assisted hatching (AH) of embryos facilitates live births and clinical pregnancy and whether it impacts on negative outcomes (such as multiple pregnancy and miscarriage).

SEARCH STRATEGY

We searched the Cochrane Menstrual Disorders and Subfertility Group trials register (1 June 2005), the Cochrane Controlled Trials Register (Cochrane Library Issue 2, 2005), MEDLINE (1996 to June 2003), EMBASE (1980 to June 2005) and reference lists of articles. Authors were contacted for missing and/or unpublished data.

SELECTION CRITERIA

Trials were identified and independently screened by two reviewers. Randomised controlled trials of AH (mechanical, chemical or laser disruption of the zona pellucida prior to embryo replacement) versus no AH that reported live birth, clinical pregnancy or implantation rates were included.

DATA COLLECTION AND ANALYSIS

Qualitative assessments and data extraction were performed independently by two reviewers. Outcomes were extracted as rates and combined using random effects meta-analysis, sensitivity analysis, sub grouping and meta-regression where appropriate.

MAIN RESULTS

Twenty-three randomised controlled trials consisting of 2668 women reported on 849 pregnancy outcomes. There was no significant difference in the odds of live births in the AH compared with control groups (6 RCTs; OR 1.19 95% CI 0.81 to 1.73; 163 births from 516 women). Women undergoing assisted hatching were significantly more likely to achieve clinical pregnancy (23 RCTs, OR 1.33, 95% CI 1.12 to 1.57). Miscarriage rates per woman were similar in both groups (12 RCTs OR 1.23 (95% CI 0.73 to 2.05). Multiple pregnancy rates per woman was increased in women who were randomised to AH compared with control women (9 RCTs OR 1.83 (95% CI 1.19 to 2.83). The improvement in clinical pregnancy rate means for a clinic with a success rate of 25% could anticipate improving the CPR to between 28 and 39%, all things being equal. The trials provided insufficient data to investigate the impact of assisted hatching on several important outcomes, including monozygotic twinning, embryo damage, congenital and chromosomal abnormalities, and in vitro blastocyst development.

AUTHORS' CONCLUSIONS

Despite significantly improved odds of clinical pregnancy, there is insufficient evidence to determine any effect of AH on live birth rates. The increased multiple pregnancy rate is of concern although it likely that with a policy of single embryo transfer this may be lowered. Currently, there is insufficient evidence to recommend assisted hatching.

Integrating genetics and genomics to identify new leads for the control ofEimeriaspp

Eimerian parasites display a biologically interesting range of phenotypic variation. In addition to a wide spectrum of drug-resistance phenotypes that are expressed similarly by many other parasites, theEimeriaspp. present some unique phenotypes. For example, unique lines ofEimeriaspp. include those selected for growth in the chorioallantoic membrane of the embryonating hens egg or for faster growth (precocious development) in the mature host. The many laboratory-derived egg-adapted or precocious lines also share a phenotype of a marked attenuation of virulence, the basis of which is different as a consequence of thein ovoorin vivoselection procedures used. Of current interest is the fact that some wild-type populations ofEimeria maximaare characterized by an ability to induce protective immunity that is strain-specific. The molecular basis of phenotypes that defineEimeriaspp. is now increasingly amenable to investigation, both through technical improvements in genetic linkage studies and the availability of a comprehensive genome sequence for the caecal parasiteE. tenella. The most exciting phenotype in the context of vaccination and the development of new vaccines is the trait of strain-specific immunity associated withE. maxima. Recent work in this laboratory has shown that infection of two inbred lines of White Leghorn chickens with the W strain ofE. maximaleads to complete protection to challenge with the homologous parasite, but to complete escape of the heterologous H strain, i.e. the W strain induces an exquisitely strain-specific protective immune response with respect to the H strain. This dichotomy of survival in the face of immune-mediated killing has been examined further and, notably, mating between a drug-resistant W strain and a drug-sensitive H strain leads to recombination between the genetic loci responsible for the specificity of protective immunity and resistance to the anticoccidial drug robenidine. Such a finding opens the way forward for genetic mapping of the loci responsible for the induction of protective immunity and integration with the genome sequencing efforts.