Time-of-flight detection of ultra-cold atoms using resonant frequency modulation imaging.

Resonant frequency modulation imaging is used to detect free falling ultra-cold atoms. A theoretical comparison of fluorescence imaging (FI) and frequency modulation imaging (FMI) is made, indicating that for low optical depth clouds, FMI accomplished a higher signal-to-noise ratio under conditions necessary for a 200 µm spatially resolved atom interferometer. A 750 ms time-of-flight measurement reveals near atom shot-noise limited number measurements of 2×106 Bose-condensed Rb87 atoms. The detection system is applied to high precision spinor BEC based atom interferometer.

Non-destructive shadowgraph imaging of ultra-cold atoms.

An imaging system is presented that is capable of far-detuned non-destructive imaging of a Bose-Einstein condensate with the signal proportional to the second spatial derivative of the density. Whilst demonstrated with application to Rb85, the technique generalizes to other atomic species and is shown to be capable of a signal-to-noise of ∼25 at 1 GHz detuning with 100 in-trap images showing no observable heating or atom loss. The technique is also applied to the observation of individual trajectories of stochastic dynamics inaccessible to single shot imaging. Coupled with a fast optical phase locked loop, the system is capable of dynamically switching to resonant absorption imaging during the experiment.

Simultaneous Precision Gravimetry and Magnetic Gradiometry with a Bose-Einstein Condensate: A High Precision, Quantum Sensor.

A Bose-Einstein condensate is used as an atomic source for a high precision sensor. A 5×10^{6} atom F=1 spinor condensate of ^{87}Rb is released into free fall for up to 750 ms and probed with a T=130 ms Mach-Zehnder atom interferometer based on Bragg transitions. The Bragg interferometer simultaneously addresses the three magnetic states |m_{f}=1,0,-1⟩, facilitating a simultaneous measurement of the acceleration due to gravity with a 1000 run precision of Δg/g=1.45×10^{-9} and the magnetic field gradient to a precision of 120 pT/m.

Changing risk of environmental Campylobacter exposure with emerging poultry production systems in Ethiopia.

Campylobacter is a leading cause of diarrhoea, and its presence in chickens is a significant risk for zoonotic infection. Poultry production is becoming increasingly intensive in Ethiopia and is incorporating more high-producing breeds into traditionally managed smallholdings, especially in peri-urban areas. This cross-sectional study sampled 219 household environments in one peri-urban and two rural areas of Ethiopia, and an additional 20 semi-intensive farms in the peri-urban district. Campylobacter was detected by polymerase chain reaction (PCR)-specific assays in 44 samples; 16 of which could be identified as C. jejuni. Flocks in the peri-urban area were at significantly greater odds of detection, including those which only kept indigenous birds under a scavenging system. It was also noted that scavenging flocks of exotic high-production birds (Rhode Island Red) were at slightly greater risk, perhaps as exotic birds are under more stress when kept under traditional management systems. We suggest that changes to the system of chicken production may alter the ecology and epidemiology of Campylobacter in the environment, chickens and people, which may drive emergence of new epidemiological patterns of disease. Further research is needed to determine the extent to which the current management intensification and the distribution programmes of exotic and/or improved indigenous birds may alter Campylobacter epidemiology, ecology and public health risk, before their widespread adoption.

Soluble plantain nonstarch polysaccharides, although increasing caecal load, reduce systemic invasion of Salmonella Gallinarum in the chicken.

UNLABELLED: Soluble plantain (Musa paradisiaca) nonstarch polysaccharides (NSPs) have previously been shown to prevent pathogenic interaction with the intestinal epithelium. Here, we examined whether plantain NSP could prevent the invasion of the intestinal mucosa by Salmonella enterica Gallinarum, a causative agent of fowl typhoid. In vitro assays using B1OXI cells were performed with monolayers pretreated with/without plantain NSP, before inoculation with Salm. Gallinarum 287/91. Chicks were fed from hatch on a pellet diet containing 50 mg day(-1) plantain NSP, followed by oral inoculation with Salm. Gallinarum 287/91 at the age of 6 days. Bacteria were enumerated from the liver, spleen and caecal contents 3 days postinfection. Adhesion and invasion of Salm. Gallinarum to B1OXI cells were inhibited by 10 mg ml(-1) plantain NSP (reduction in invasion 52%; 95% CI 27-77; P < 0.05). In vivo diet supplemented with 50 mg day(-1) plantain NSP reduced the invasion of Salm. Gallinarum in the chick liver (control 4.05 Log10 CFU g(-1) , SE 0.28, vs plantain 2.07 Log10 CFU g(-1) , SE 0.65; P < 0.01) and nonsignificantly in the spleen. Conversely, CFUs were significantly increased in the caeca (control 1.27 Log10 CFU g(-1), SE 0.65, vs plantain 6.04 Log10 CFU g(-1) , SE 0.17; P < 0.001). Plantain NSP feed reduced the systemic infection by Salm. Gallinarum and may have potential in reducing the impact of the disease in avian salmonellosis. The caveat is the increased caecal load of Salm. Gallinarum, although this may reflect both the reduced intestinal invasion and the bacterial multiplication in the caeca. SIGNIFICANCE AND IMPACT OF THE STUDY: Nonstarch polysaccharide (NSP) derived from the plantain (Musa paradisiaca) inhibits interaction with epithelial cells by Salmonella enterica Gallinarum, a causative agent of the disease fowl typhoid. Incorporation of plantain NSP into the poultry feed reduced Salm. Gallinarum levels in the spleen and liver of chicks following experimental infection, although their numbers in the caeca increased. These data demonstrate that alternatives to antimicrobials such as NSP may be useful in the control of invasive salmonellosis in poultry.

The contribution of systemic Escherichia coli infection to the early mortalities of commercial broiler chickens.

Avian pathogenic Escherichia coli (APEC) are a substantial burden to the global poultry industry. APEC cause a syndromic poultry infection known as colibacillosis, which has been previously associated with broiler chickens over 2 weeks old. We recently reported that the intestinal tract of 1-day-old broilers harbours a rich reservoir of potentially pathogenic E. coli. Prior infections of the reproductive tract of breeders, egg hygiene and transportation all contribute to early colonization of the neonatal gut. Up to one-half of all flock deaths occur in the first week of production, but few data are available describing the contribution of E. coli. In the present study, all dead birds collected on the first daily welfare walk 48 and 72 h after chick placement underwent post-mortem examination. Diseased tissues were selectively cultured for E. coli and isolates subsequently virulotyped using 10 APEC virulence-associated genes (VAGs): astA, iss, irp2, iucD, papC, tsh, vat, cvi, sitA and ibeA. Approximately 70% of birds displayed signs of colibacillosis. Thirty distinct virulence profiles were identified among 157 E. coli. Isolates carried between zero and seven VAGs; ∼ 30% of E. coli isolates carried five to seven VAGs, with 12.7% sharing the same VAG profile (astA, iss, irp2, iucD, tsh, cvi and sitA). Overall, this study demonstrates the significant contribution of E. coli infections to early broiler mortalities. The identification of a diverse E. coli population is unsurprising based on our previous findings. This work emphasizes the need for an effective vaccination programme and provides preliminary data for vaccine production.

Infection of chickens with antimicrobial-resistant Salmonella enterica Typhimurium DT193 and monophasic Salmonella Typhimurium-like variants: an emerging risk to the poultry industry?

Antimicrobial-resistant Salmonella enterica poses a particular risk to public health, and in particular isolates belonging to clonal lineages such as Salmonella Typhimurium DT104 cause epidemics across species including poultry. In recent years, antimicrobial-resistant S. Typhimurium DT193 and specifically the monophasic S. Typhimurium-like variants of this phage type, serotypes 4,12:i:- and 4,5,12:i:-, have become an increasing risk to public health in Europe and the USA and now account for nearly one-half of human S. Typhimurium infections in the UK. Unlike S. Typhimurium that possesses two forms of flagella which can vary between phase 1 and phase 2 during infection, monophasic variants possess only phase 1 flagella. These monophasic antimicrobial-resistant variants have become a major problem in pig production but human cases have also been associated with poultry consumption and have been found in UK flocks through surveillance schemes since 2010. In this study we determined the ability of antimicrobial-resistant DT193 serotype 4,12:i:- and 4,5,12:i:- isolates from pigs to infect chickens. All isolates were found to colonize the caeca and liver. All but one isolate of serotype 4,5,12:i:- also infected the spleen. Levels of infection and pathology were comparable with those found with the virulent S. Typhimurium isolate 4/74. These findings indicate that both S. Typhimurium DT193 and monophasic variants of this phage type usually associated with pigs are capable of colonizing the chicken. This shows that both S. Typhimurium DT193 and monophasic variants represent a significant and potential emerging threat to poultry production from "spill-over" of these isolates from the pig industry or other sources.

The long view: Salmonella--the last forty years.

As a part of the 40th anniversary celebrations of Avian Pathology we review the last four decades of Salmonella research which has led to major progress in our understanding of the bacteriology and infection biology of the organism through the huge advances in molecular biology and immunology that have accompanied technical advances in biology generally. In many countries combinations of improvements in management, sometimes under legislative pressure and supported by a number of basic biological interventions, have resulted in reductions in incidence in the Salmonella serovars that are commonly associated with food-poisoning to unprecedented low levels in parent flocks, broilers and layers. Utilisation of the information generated during the past few decades should improve the efficacy of surveillance and biological interventions both for the intestinal carriage that is associated most frequently with human infection and also for systemic diseases, including fowl typhoid and pullorum disease. These two diseases continue to be major economic problems in many countries where the possibilities for improvements in hygiene may be limited but which, nevertheless, are increasingly a significant part of the global economy in poultry meat.

Poor body condition is associated with lower hippocampal plasticity and higher gut methanogen abundance in adult laying hens from two housing systems.

It is still unclear which commercial housing system provides the best quality of life for laying hens. In addition, there are large individual differences in stress levels within a system. Hippocampal neurogenesis or plasticity may provide an integrated biomarker of the stressors experienced by an individual. We selected 12 adult hens each with good and poor body condition (based on body size, degree of feather cover and redness of the comb) from a multi-tier free range system containing H&N strain hens, and from an enriched cage system containing Hy-Line hens (n = 48 total). Immature neurons expressing doublecortin (DCX) were quantified in the hippocampus, contents of the caecal microbiome were sequenced, and expression of inflammatory cytokines was measured in the spleen. DCX+ cell densities did not differ between the housing systems. In both systems, poor condition hens had lower DCX+ cell densities, exhibited elevated splenic expression of interleukin-6 (IL6) mRNA, and had a higher relative caecal abundance of methanogenic archea Methanomethylophilaceae. The findings suggest poor body condition is an indicator that individual hens have experienced a comparatively greater degree of cumulative chronic stress, and that a survey of the proportion of hens with poor body conditions might be one way to evaluate the impact of housing systems on hen welfare.

Salmonella Virchow isolates from human and avian origins in England--molecular characterization and infection of epithelial cells and poultry.

AIMS: To characterize 12 Salmonella Virchow isolates from human and avian sources to begin to determine the genetic relationships within the serovar, determine its capacity to invade and induce inflammatory responses in human intestinal epithelial cells and investigate its ability to colonize the chicken gastrointestinal tract. METHODS AND RESULTS: Multi-Locus Sequence Typing (MLST) revealed that 11 isolates belonged to sequence type 16 (ST16). Pulsed Field Gel Electrophoresis (PFGE) grouped the isolates into two main clusters. All isolates contained genes associated with virulence determined through PCR virulotyping. All the S. Virchow isolates had the ability to invade human epithelial cells and elicit high levels of production of the pro-inflammatory chemokine interleukin-8 (IL-8). Experimental infection of poultry showed S. Virchow colonizes the caeca and spleen. CONCLUSIONS: Isolates within the serovar show high levels of genetic relatedness regardless of the source. The data indicates S. Virchow is an invasive and inflammatory serovar, consistent with its association with invasive salmonellosis in humans. SIGNIFICANCE AND IMPACT OF THE STUDY: The poultry infection experiment included in this study shows S. Virchow can colonize the gastrointestinal tract rapidly and to high levels with the chickens showing no clinical signs of infection. The asymptomatic colonization of chickens indicates an increased ability of S. Virchow to enter the food chain undetected and cause human salmonellosis which because of the invasive and inflammatory nature of S. Virchow seen during the Caco2 invasion assay and previous studies showing its invasive nature in humans and increasing resistance to antibiotics is a public health concern.

Multi-locus sequence typing of Salmonella enterica serovar Typhimurium isolates from wild birds in northern England suggests host-adapted strain.

AIMS: Recent studies have suggested that Salmonella Typhimurium strains associated with mortality in UK garden birds are significantly different from strains that cause disease in humans and livestock and that wild bird strains may be host adapted. However, without further genomic characterization of these strains, it is not possible to determine whether they are host adapted. The aim of this study was to characterize a representative sample of Salm. Typhimurium strains detected in wild garden birds using multi-locus sequence typing (MLST)to investigate evolutionary relationships between them. METHODS AND RESULTS: Multi-locus sequence typing was performed on nine Salm. Typhimurium strains isolated from wild garden birds. Two sequence types were identified, the most common of which was ST568. Examination of the public Salmonella enterica MLST database revealed that only three other ST568 isolates had been cultured from a human in Scotland. Two further isolates of Salm. Typhimurium were determined to be ST19. CONCLUSIONS: Results of MLST analysis suggest that there is a predominant strain of Salm. Typhimurium circulating among garden bird populations in the United Kingdom, which is rarely detected in other species, supporting the hypothesis that this strain is host adapted. SIGNIFICANCE AND IMPACT OF THE STUDY: Host-pathogen evolution is often assumed to lead to pathogens becoming less virulent to avoid the death of their host; however, infection with ST568 led to high mortality rates among the wild birds examined, which were all found dead at wild bird-feeding stations. We hypothesize that by attracting unnaturally high densities of birds, wild bird-feeding stations may facilitate the transmission of ST568 between wild birds, therefore reducing the evolutionary cost of this pathogen killing its host, resulting in a host-adapted strain with increased virulence.

An atomic Fabry-Perot interferometer using a pulsed interacting Bose-Einstein condensate.

We numerically demonstrate atomic Fabry-Perot resonances for a pulsed interacting Bose-Einstein condensate (BEC) source transmitting through double Gaussian barriers. These resonances are observable for an experimentally-feasible parameter choice, which we determined using a previously-developed analytical model for a plane matter-wave incident on a double rectangular barrier system. Through numerical simulations using the non-polynomial Schödinger equation-an effective one-dimensional Gross-Pitaevskii equation-we investigate the effect of atom number, scattering length, and BEC momentum width on the resonant transmission peaks. For [Formula: see text]Rb atomic sources with the current experimentally-achievable momentum width of [Formula: see text] [[Formula: see text]], we show that reasonably high contrast Fabry-Perot resonant transmission peaks can be observed using (a) non-interacting BECs, (b) interacting BECs of [Formula: see text] atoms with s-wave scattering lengths [Formula: see text] ([Formula: see text] is the Bohr radius), and (c) interacting BECs of [Formula: see text] atoms with [Formula: see text]. Our theoretical investigation impacts any future experimental realization of an atomic Fabry-Perot interferometer with an ultracold atomic source.

Developmental regulation of the cell cycle.

The control of metazoan cell proliferation, a problem long the domain of cell culture studies, is now being examined in developing animals. Surprisingly, developmental regulation is mediated at a variety of cell-cycle stages. Highly conserved cell-cycle control mechanisms provide a focus for studying the regulatory processes involved.

Integrated immunogenomics in the chicken: deciphering the immune response to identify disease resistance genes.

Resistance to infection takes place at many levels, and involves both non-specific and specific immune mechanisms. The chicken has a different repertoire of immune genes, molecules, cells and organs compared to mammals. To understand the role of any disease resistance gene(s), it is therefore important to understand these different repertoires, and the bird's response to a particular pathogen. Our studies focus on the innate immune response, as responses of macrophages from inbred lines of chickens, and heterophils from commercial birds, correlate with resistance or susceptibility to Salmonella infection with a variety of Salmonella serovars and infection models. To map disease resistance genes, we are using a combination of expression quantitative trait loci (eQTLs) from microarray studies, allied with whole genome SNP arrays (WGA) and a candidate gene approach. There are over 500 human genes with the Gene Ontology term "innate immunity". We have identified over 400 of these genes in the chicken genome, and are actively identifying informative SNPs in them. The segregation of 6000 WGA SNPs across all of our inbred lines was also assessed, which should yield approximately 900 informative SNPs for a cross between any two lines. The initial focus of these studies is on mapping resistance genes in our inbred lines, but the studies will be extended to commercial flocks.

H5 gene specific trans-activation by nuclear extracts from avian erythroid cells.

Nuclear extracts from chicken erythroid cells selectively stimulate transcription of the chicken histone H5 gene (and not of other chicken histone genes) after coinjection into frog oocytes. This effect is shown to involve an enhancerlike activity, and a region of the H5 gene sufficient to mediate trans-activation is defined.

Polyadenylation of mRNA: minimal substrates and a requirement for the 2' hydroxyl of the U in AAUAAA.

mRNA-specific polyadenylation can be assayed in vitro by using synthetic RNAs that end at or near the natural cleavage site. This reaction requires the highly conserved sequence AAUAAA. At least two distinct nuclear components, an AAUAAA specificity factor and poly(A) polymerase, are required to catalyze the reaction. In this study, we identified structural features of the RNA substrate that are critical for mRNA-specific polyadenylation. We found that a substrate that contained only 11 nucleotides, of which the first six were AAUAAA, underwent AAUAAA-specific polyadenylation. This is the shortest substrate we have used that supports polyadenylation: removal of a single nucleotide from either end of this RNA abolished the reaction. Although AAUAAA appeared to be the only strict sequence requirement for polyadenylation, the number of nucleotides between AAUAAA and the 3' end was critical. Substrates with seven or fewer nucleotides beyond AAUAAA received poly(A) with decreased efficiency yet still bound efficiently to specificity factor. We infer that on these shortened substrates, poly(A) polymerase cannot simultaneously contact the specificity factor bound to AAUAAA and the 3' end of the RNA. By incorporating 2'-deoxyuridine into the U of AAUAAA, we demonstrated that the 2' hydroxyl of the U in AAUAAA was required for the binding of specificity factor to the substrate and hence for poly(A) addition. This finding may indicate that at least one of the factors involved in the interaction with AAUAAA is a protein.

Cross-reactive cellular and humoral immune responses to Salmonella enterica serovars Typhimurium and Enteritidis are associated with protection to heterologous re-challenge.

Chickens infected with Salmonella enterica serovars Typhimurium (ST) and Enteritidis (SE) still represent a major source of human food poisoning via consumption of contaminated meat and eggs. Vaccination represents a sustainable approach to control Salmonella in the chicken and the serovar specificity of immunity has the potential to impact on the need for multivalent vaccines. The issue of cross-reactive immune responses and cross-serovar protection was examined in these experiments. Cellular and humoral immune responses were measured by antigen-specific ELISA and splenocyte proliferation assays during primary infections (with ST and SE) and during a second challenge with homologous or heterologous serovars. Primary infection with ST or SE induced strong lymphocyte proliferation and high levels of specific antibody (IgM, IgG and IgA) responses with substantial serovar cross-reactivity. The occurrence of high levels of splenocyte proliferation and strong antibody responses corresponded to the initiation of clearance with both ST and SE. Re-challenge of ST and SE infection-primed chickens with either serovar resulted in significant levels of protection (assessed by bacterial numbers and rate of clearance) with little difference between homologous or heterologous challenge schedules. Relatively low levels of antigen-specific splenocyte proliferation were detected during secondary infection, which may be caused by splenic T cells exiting to the gut. In contrast, the more rapid specific antibody responses (compared with primary infection controls) indicate the development of a secondary antigen-specific adaptive response. The substantial level of cross-protection between serovars and the level of antigenic cross-reactivity indicates the potential for single serovar live vaccines to protect against both group B and D salmonellae.

Fast machine-learning online optimization of ultra-cold-atom experiments.

We apply an online optimization process based on machine learning to the production of Bose-Einstein condensates (BEC). BEC is typically created with an exponential evaporation ramp that is optimal for ergodic dynamics with two-body s-wave interactions and no other loss rates, but likely sub-optimal for real experiments. Through repeated machine-controlled scientific experimentation and observations our 'learner' discovers an optimal evaporation ramp for BEC production. In contrast to previous work, our learner uses a Gaussian process to develop a statistical model of the relationship between the parameters it controls and the quality of the BEC produced. We demonstrate that the Gaussian process machine learner is able to discover a ramp that produces high quality BECs in 10 times fewer iterations than a previously used online optimization technique. Furthermore, we show the internal model developed can be used to determine which parameters are essential in BEC creation and which are unimportant, providing insight into the optimization process of the system.

The tissue-specific chicken histone H5 gene is transcribed with fidelity in Xenopus laevis oocytes.

Vectors containing the chicken H5 gene were micro-injected into the nucleus of Xenopus laevis oocytes. Transcription of the H5 gene was accurately initiated and H5 transcripts with discrete 3' termini were produced. H5 transcripts were not polyadenylated in oocyte nuclei.

Histone H5 and H1 cross-reacting material is restricted to erythroid cells in chicken.

Monoclonal H5 antibodies and a polyclonal antiserum, raised against the globular domain of chicken H5 (GH5) but which cross-reacts with histone H1(0) from mouse liver, were used to search for H5 or H1 (0)-like proteins in chicken embryo and adult tissue sections by indirect immunofluorescence. Chicken cell lines in culture were examined for H5 protein and H5 mRNA. Histone H5 was detected only in erythroid cells in tissue sections of chicken embryos or adult livers. H5 protein and H5 mRNA were found only in erythroid cells in culture. No cross-reacting proteins were detected in any other tissue or cell line examined.