The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations

Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS), quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2–4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen Campylobacter and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.     

Case studies on the use of biotechnologies and on biosafety provisions in four African countries

This review is based on a study commissioned by the European Commission on the evaluation of scientific, technical and institutional challenges, priorities and bottlenecks for biotechnologies and regional harmonisation of biosafety in Africa. Biotechnology was considered within four domains: agricultural biotechnologies (‘Green’), industrial biotechnologies and biotechnologies for environmental remediation (‘White’), biotechnologies in aquaculture (‘Blue’) and biotechnologies for healthcare (‘Red’). An important consideration was the decline in partnerships between the EU and developing countries because of the original public antipathy to some green biotechnologies, particularly genetically modified organisms (GMOs) and food from GM crops in Europe. The study focus reported here was West Africa (Ghana, Senegal, Mali and Burkina Faso).The overall conclusion was that whereas high-quality research was proceeding in the countries visited, funding is not sustained and there is little evidence of practical application of biotechnology and benefit to farmers and the wider community. Research and development that was being carried out on genetically modified crop varieties was concentrating on improving food security and therefore unlikely to have significant impact on EU markets and consumers. However, there is much non-controversial green biotechnology such as molecular diagnostics for plant and animal disease and marker-assisted selection for breeding that has great potential application. Regarding white biotechnology, it is currently occupying only a very small industrial niche in West Africa, basically in the sole sector of the production of liquid biofuels (i.e., bio-ethanol) from indigenous and locally planted biomass (very often non-food crops). The presence of diffused small-scale fish production is the basis to develop and apply new (Blue) aquaculture technologies and, where the research conditions and the production sector can permit, to increase this type of production and the economy of this depressed areas. However, the problems bound to environmental protection must not be forgotten; priority should be given to monitor the risks of introduction of foreign species. Red biotechnologies potentially bring a vast domain of powerful tools and processes to achieve better human health, most notably improved diagnostics by molecular techniques, better targeting of pathogens and a better knowledge of their sensitivities to drugs to permit better treatment.Biosafety regulatory frameworks had been initiated in several countries, starting with primary biosafety law. However, disparate attitudes to the purpose of biosafety regulation (e.g., fostering informed decision-making versus ‘giving the green-light for a flood of GMOs’) currently prevent a needed consensus for sub-regional harmonisation. To date, most R&D funding has come from North America with some commercial interests from Asia, but African biotechnology workers expressed strong desire for (re-)engagement with interested parties from the European Union. Although in some of the visited countries there are very well qualified personnel in molecular biology and biosafety/regulation, the main message received is that human resources and capacity building in-house are still needed. This could be achieved through home-based courses and capacity-building including funds for post-degree research to motivate and retain trained staff.     

Reproductive incompatibility and cytochrome oxidase I gene sequence variability amongst host-adapted and geographically separate Bemisia tabaci populations (Hemiptera: Aleyrodidae)

Abstract. Reciprocal‐crossing experiments were carried out and mitochondrial cytochrome oxidase I gene (mtCOI) sequences were compared for allopatric and sympatric Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) populations collected from Africa and India, and from the host‐plants cassava, sweet‐potato and a common weed, Euphorbia geniculata. Three incompatible mating groups were discovered, which involved the cassava B. tabaci colonies from Africa and India, the cassava and sweet‐potato B. tabaci populations from Uganda, and the cassava and E. geniculata B. tabaci from India. Successful reciprocal mating occurred between cassava‐specific B. tabaci from Uganda, Tanzania and Ghana, and between two Indian cassava B. tabaci populations. The parsimony and neighbour‐joining analyses of 699 bp mtCOI gene sequences divided the colonies primarily into those originating from Africa and India. Further subgrouping corresponded to host‐plant specialization. Cassava‐specific Ugandan, Tanzanian and Ghanaian colonies formed a single group and the sympatric sweet‐potato colony from Uganda grouped separately from them. The two geographically distant Indian cassava B. tabaci populations were similar and formed a single group, whereas the sympatric E. geniculata colony formed a sister clade. The clades generated by the phylogenetic analyses were maintained, with highly supported bootstrap values, when other published mtCOI gene sequences were included in the tree‐building process and the divisions matched those revealed by the reciprocal‐crossing experiments. These data suggest that biologically discrete populations exist within B. tabaci (sensu Russell, 1957 ).     

Exploring the binding dynamics of etoricoxib with human hemoglobin: A spectroscopic,calorimetric, and molecular modeling approach

Etoricoxib, widely used for the treatment of osteoarthritis, rheumatoid arthritis, ankylosing spondylitis, and related conditions has ample affinity to bind with globular proteins. Here, the molecular interaction between purified human hemoglobin (HHb), a major heme protein and etoricoxib, a cyclooxygenase-2 inhibitor was studied by various spectroscopic, calorimetric, and molecular modeling techniques. The binding affected hypochromic changes in the Soret band of hemoglobin (Hb) and induced remarkable quenching of the intrinsic fluorescence property of protein molecules. Synchronous fluorescence studies revealed alterations in tryptophan (Trp) and tyrosine (Tyr) microenvironments of HHb molecule in presence of etoricoxib. Flouremetric and isothermal titration calorimetric studies suggested two binding sites in HHb for etoricoxib at three different temperatures (298.15, 303.15, and 310.15 K). Negative values of Gibbs energy change (ΔG⁰) and enthalpy change (ΔH⁰) strongly suggest that it is spontaneous and exothermic reaction, mainly stabilized by hydrogen bonding as evidenced by sucrose binding assay. These findings support our in silico molecular docking study, which specified the binding site and the non-covalent interactions involved in the association. Moreover, the interaction impacts on structural integrity and functional aspects of HHb as confirmed by decreased α helicity, increased free iron release, increased rate of co-oxidation, and decreased rate of esterase activity. Overall, these studies conclude that etoricoxib leads to a remarkable alteration in the conformational aspects of binding to HHb.

Communicated by Ramaswamy H. Sarma.     

Increasing temperatures can improve seedling establishment in arid-adapted savanna trees

Plant species are shifting their ranges in response to global climate change, thus intensifying the need to predict such changes accurately. As the environmental requirements controlling plant distribution act differently at each developmental stage, there is a need to acquire a demographic-specific understanding of the factors which determine these distributions. Here we investigated the germination niche of two common savanna species Acacia nigrescens and Colophospermum mopane, with the aims to disentangle the direct and indirect effects of temperature on seed germination and establishment and to explore the impact of higher temperatures on the establishment success of savanna trees. Under laboratory conditions, we used thermal gradient plates to determine the thermal germination niche of both species, and a water stress experiment was conducted on C. mopane to account for water–temperature interactions. Using these data we parameterised a soil-moisture model to determine germination and establishment success under field conditions at current and future temperatures (+4 °C). Based on this model, higher future temperatures will not limit germination directly, but they will reduce the number of germination events by reducing the time window of suitable available soil water. Conversely, warmer conditions will accelerate the rate of radicle extension and increase the frequency of seedling establishment events. An additional advantage of higher temperatures is that fewer seeds will germinate, resulting in slower seed bank depletion when successful seedling establishment events do occur.     

Scaling relative incentive value: different adjustments to incentive downshift in pigeons and rats

Previous research suggests that pigeons and rats show differences in their behavioral adjustments in spaced-trial, incentive-downshift situations. Also, Papini and Pellegrini [Papini, M.R., Pellegrini, S., 2006. Scaling relative incentive value in consummatory behavior. Learn. Motiv. 37, 357-378] and Pellegrini and Papini [Pellegrini, S., Papini, M.R., 2007. Scaling relative incentive value in anticipatory behavior. Learn. Motiv. 38, 128-154] showed that changes in the rat's lever-pressing performance, runway running, and consumption of sucrose solutions after downshifts in incentive magnitude were a function of the ratio of postshift/preshift incentive magnitudes. Here, two experiments using a Pavlovian autoshaping procedure studied the adjustment of pigeons and rats to changes in incentive magnitude. In Experiment 1, pigeons received light-food pairings, whereas in Experiment 2, rats received lever-sucrose pairings. As a result, key-pecking and lever-pressing developed in each experiment, respectively. Preshift incentive magnitudes were downshifted so as to obtain postshift/preshift ratios of 0.125 and 0.25. Pigeons responded during the postshift phase according to the preshift incentive value and independently of the ratio value. However, rats showed ratio constancy, responding during the postshift in accordance with the postshift/preshift ratio, rather than with the absolute magnitudes of either the preshift or postshift incentives. These results support the comparative hypothesis that the mechanisms underlying ratio constancy during incentive downshifts are unique to mammals.     

Sensorineural deafness and seizures in mice lacking vesicular glutamate transporter 3

The expression of unconventional vesicular glutamate transporter VGLUT3 by neurons known to release a different classical transmitter has suggested novel roles for signaling by glutamate, but this distribution has raised questions about whether the protein actually contributes to glutamate release. We now report that mice lacking VGLUT3 are profoundly deaf due to the absence of glutamate release from hair cells at the first synapse in the auditory pathway. The early degeneration of some cochlear ganglion neurons in knockout mice also indicates an important developmental role for the glutamate released by hair cells before the onset of hearing. In addition, the mice exhibit primary, generalized epilepsy that is accompanied by remarkably little change in ongoing motor behavior. The glutamate release conferred by expression of VGLUT3 thus has an essential role in both function and development of the auditory pathway, as well as in the control of cortical excitability.     

Natural Language Processing in aid of FlyBase curators

Background  

Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear.     

Thermal buffering capacity of the germination phenotype across the environmental envelope of the Cactaceae

Recruitment from seeds is among the most vulnerable stage for plants as global temperatures change. While germination is the means by which the vast majority of the world's flora regenerate naturally, a framework for accurately predicting which species are at greatest risk of germination failure during environmental perturbation is lacking. Taking a physiological approach, we assess how one family, the Cactaceae, may respond to global temperature change based on the thermal buffering capacity of the germination phenotype. We selected 55 cactus species from the Americas, all geo‐referenced seed collections, reflecting the broad environmental envelope of the family across 70° of latitude and 3700 m of altitude. We then generated empirical data of the thermal germination response from which we estimated the minimum (T_b), optimum (T_o) and ceiling (T_c) temperature for germination and the thermal time (θ₅₀) for each species based on the linearity of germination rate with temperature. Species with the highest T_b and lowest T_c germinated fastest, and the interspecific sensitivity of the germination rate to temperature, as assessed through θ₅₀, varied tenfold. A left‐skewed asymmetry in the germination rate with temperature was relatively common but the unimodal pattern typical of crop species failed for nearly half of the species due to insensitivity to temperature change at T_o. For 32 fully characterized species, seed thermal parameters correlated strongly with the mean temperature of the wettest quarter of the seed collection sites. By projecting the mean temperature of the wettest quarter under two climate change scenarios, we predict under the least conservative scenario (+3.7°C) that 25% of cactus species will have reduced germination performance, whilst the remainder will have an efficiency gain, by the end of the 21st century.