Host‐microbe interaction in the gastrointestinal tract

The gastrointestinal tract is a highly complex organ in which multiple dynamic physiological processes are tightly coordinated while interacting with a dense and extremely diverse microbial population. From establishment in early life, through to host‐microbe symbiosis in adulthood, the gut microbiota plays a vital role in our development and health. The effect of the microbiota on gut development and physiology is highlighted by anatomical and functional changes in germ‐free mice, affecting the gut epithelium, immune system and enteric nervous system. Microbial colonisation promotes competent innate and acquired mucosal immune systems, epithelial renewal, barrier integrity, and mucosal vascularisation and innervation. Interacting or shared signalling pathways across different physiological systems of the gut could explain how all these changes are coordinated during postnatal colonisation, or after the introduction of microbiota into germ‐free models. The application of cell‐based in‐vitro experimental systems and mathematical modelling can shed light on the molecular and signalling pathways which regulate the development and maintenance of homeostasis in the gut and beyond.     

Carbon metabolism in in vitro cultures of date palm: the role of carboxylases (PEPC and RubisCO)

While describing major trends of carbon metabolism during the initiation and expression of somatic embryogenesis in date palm (Phoenix dactylifera L., cv. Deglet Nour), we have investigated the role of two carboxylases, namely PEPC (Phosphoenolpyruvate carboxylase, EC 4.1.1.31) and RubisCO (Ribulose 1,5-bisphosphate carboxylase/oxygenase, EC 4.1.1.39), in embryogenic and non-embryogenic cultures. The detection of PEPC activity on polyacrylamide native gels after electrophoresis revealed the presence of 3 active isoforms in crude extracts from the embryogenic (E) callus strain, whereas only a single band was present in the non-embryogenic (NE) one. The level of PEPC specific capacity was of the same order (3.9 ± 1.2 μmol CO₂ h⁻¹ mg⁻¹ TSP) in both types of cultures. Further changes in carboxylase (PEPC and RubisCO) activities during the growth and development of somatic embryo–derived plantlets were also analysed. The PEPC/RubisCO ratio was found to progressively decrease (from 17.7 to 0.2) throughout the in vitro development of plantlets, due to a substantial depletion of PEPC activity, which decreased from 5.3 to 1.2 μmol CO₂ h⁻¹ mg⁻¹ TSP. Concomitantly, RubisCO assumed greater importance (from 0.3 to 5.3 μmol CO₂ h⁻¹ mg⁻¹ _TSP ) and became the main route for inorganic carbon fixation. Western blot analysis using polyclonal antibodies raised against PEPC and RubisCO purified from tobacco leaves confirmed this trend in terms of relative enzyme abundance. This revised version was published online in June 2006 with corrections to the Cover Date.     

Soil moisture surpasses elevated CO2 and temperature as a control on soil carbon dynamics in a multi-factor climate change experiment

Some single-factor experiments suggest that elevated CO₂ concentrations can increase soil carbon, but few experiments have examined the effects of interacting environmental factors on soil carbon dynamics. We undertook studies of soil carbon and nitrogen in a multi-factor (CO₂ × temperature × soil moisture) climate change experiment on a constructed old-field ecosystem. After four growing seasons, elevated CO₂ had no measurable effect on carbon and nitrogen concentrations in whole soil, particulate organic matter (POM), and mineral-associated organic matter (MOM). Analysis of stable carbon isotopes, under elevated CO₂, indicated between 14 and 19% new soil carbon under two different watering treatments with as much as 48% new carbon in POM. Despite significant belowground inputs of new organic matter, soil carbon concentrations and stocks in POM declined over four years under soil moisture conditions that corresponded to prevailing precipitation inputs (1,300 mm yr^?1). Changes over time in soil carbon and nitrogen under a drought treatment (approximately 20% lower soil water content) were not statistically significant. Reduced soil moisture lowered soil CO₂ efflux and slowed soil carbon cycling in the POM pool. In this experiment, soil moisture (produced by different watering treatments) was more important than elevated CO₂ and temperature as a control on soil carbon dynamics.     

A Temporal Threshold for Formaldehyde Crosslinking and Fixation

Background

Formaldehyde crosslinking is in widespread use as a biological fixative for microscopy and molecular biology. An assumption behind its use is that most biologically meaningful interactions are preserved by crosslinking, but the minimum length of time required for an interaction to become fixed has not been determined.

Methodology

Using a unique series of mutations in the DNA binding protein MeCP2, we show that in vivo interactions lasting less than 5 seconds are invisible in the microscope after formaldehyde fixation, though they are obvious in live cells. The stark contrast between live cell and fixed cell images illustrates hitherto unsuspected limitations to the fixation process. We show that chromatin immunoprecipitation, a technique in widespread use that depends on formaldehyde crosslinking, also fails to capture these transient interactions.

Conclusions/Significance

Our findings for the first time establish a minimum temporal limitation to crosslink chemistry that has implications for many fields of research.     

The E3 ubiquitin ligase RNF121 is a positive regulator of NF-κB activation

Background

The nuclear factor κB (NF-κB) family members regulate several biological processes as cell proliferation and differentiation, inflammation, immunity and tumor progression. Ubiquitination plays a key role in NF-κB activation and the ubiquitylated transmitters of the NF-κB signaling cascade accumulate in close proximity to endomembranes.

Findings

We performed an unbiased siRNA library screen targeting the 46 E3 ubiquitin ligases bearing transmembrane domains to uncover new modulators of NF-κB activation, using tumor necrosis factor–α (TNF-α) receptor (TNFR) stimulation as a model. We report here the identification of a new Golgi Apparatus-resident protein, RNF121, as an enhancer of NF-κB promoter activity through the catalytic function of its RING domain. From a molecular standpoint, while knocking down RNF121 did not alter RIP1 ubiquitination and IKK activation, the proteasomal degradation of IκBα was impaired suggesting that this E3 ubiquitin ligase regulates this process. However, RNF121 did not directly ubiquitinate IκBα While they were found in the same complex. Finally, we discovered that RNF121 acts as a broad regulator of NF-κB signaling since its silencing also dampens NF-κB activation following stimulation of Toll-Like Receptors (TLRs), Nod-Like Receptors (NLRs), RIG-I-Like Receptors (RLRs) or after DNA damages.

Conclusions

These results unveil an unexpected role of Golgi Apparatus and reveal RNF121 as a new player involved in the signaling leading to NF-κB activation.

     

Interleukin 1 can replace monocytes for the specific human B-cell response to a particulate antigen

It is shown that the anti-trinitrophenyl (TNP) response of human B cells to trinitrophenyl polyacrylamide beads (TNP-PAA) is monocyte dependent. This response is abolished by extensive adherent cell depletion and restored by the addition of monocytes. The optimal response is obtained with 3% monocytes, higher numbers being suppressive. Supernatants from muramyl dipeptide (MDP)-activated monocytes can restore the response of monocyte-depleted preparations even when cells are cultured at suboptimal concentration. A partially purified preparation of interleukin (IL-1) has a comparable restorative ability. The following arguments suggest that monocytes do not function as antigen-presenting cells for this particulate antigen: (i) anti-genpulsed monocytes induce neither an anti-TNP response nor a specific T-cell proliferative response; (ii) allogeneic monocytes function as well as autologous monocytes to restore the response of nonadherent cells; (iii) HLA-DR-negative cells from the human leukemia cell line K562 can replace monocytes for this response. Monocyte supernatants do not replace T cells for the response of B-enriched lymphocytes, showing that T cells are directly involved in B-cell activation.     

Biochemical and functional comparisons of Mcl-1 and Bcl-2 proteins: evidence for a novel mechanism of regulating Bcl-2 family protein function

Mcl-1 is a recently described homologue of Bcl-2 whose function and biochemical characteristics remain poorly defined. Gene transfer experiments in lnterleukin-3 (IL-3)-dependent myeloid progenitor 32D.3 cells and pro-B-lymphoid FL5.12 cells demonstrated that enforced production of high levels of Mcl-1 protein failed to prolong the survival of cells when cultured in the absence of IL-3, whereas Bcl-2 did delay cell death. Mcl-1 also did not prolong the survival in vitro of 32D.3 cells that had been induced to differentiate into mature neutrophils using Granulocyte-Colony Stimulating Factor (G-CSF), whereas Bcl-2 did. 32D.3 and FL5.12 cells co-transfected with Mcl-1 and Bcl-2 displayed survival kinetics essentially identical to cells transfected with Bcl-2 alone, when cultured in the absence of IL-3, indicating that Mcl-1 neither enhances nor impairs Bcl-2 function. In contrast to the lack of effects of Mcl-1 in 32D.3 and FL5.12 cells, Mcl-1 (like Bcl-2) was able to neutralise Bax-induced cytotoxicity in yeast (S. cerevisiae). Moreover, the recombinant GST-Mcl-1 protein bound specifically to in vitro translated Bax protein, as well as to Bax protein present in detergent lysates prepared from 32D.3 and FL5.12 cells, based on in vitro binding assays. However, Mcl-1 and Bax proteins could not be co-immunoprecipitated from control and transfected 32D.3 and FL5.12 cells, whereas Bcl-2 and Bax were easily co-immunoprecipitated under the same conditions. The findings suggest that while Mcl-1 has the capacity to bind to and neutralise the cell death promoting activity of Bax, other factors such as perhaps additional proteins or undefined post-translational modifications may influence its ability to bind to Bax in vivo and thus affect its function as a cell death blocker.     

Global patterns and substrate‐based mechanisms of the terrestrial nitrogen cycle

Nitrogen (N) deposition is impacting the services that ecosystems provide to humanity. However, the mechanisms determining impacts on the N cycle are not fully understood. To explore the mechanistic underpinnings of N impacts on N cycle processes, we reviewed and synthesised recent progress in ecosystem N research through empirical studies, conceptual analysis and model simulations. Experimental and observational studies have revealed that the stimulation of plant N uptake and soil retention generally diminishes as N loading increases, while dissolved and gaseous losses of N occur at low N availability but increase exponentially and become the dominant fate of N at high loading rates. The original N saturation hypothesis emphasises sequential N saturation from plant uptake to soil retention before N losses occur. However, biogeochemical models that simulate simultaneous competition for soil N substrates by multiple processes match the observed patterns of N losses better than models based on sequential competition. To enable better prediction of terrestrial N cycle responses to N loading, we recommend that future research identifies the response functions of different N processes to substrate availability using manipulative experiments, and incorporates the measured N saturation response functions into conceptual, theoretical and quantitative analyses.     

Monitoring Great Ape and Elephant Abundance at Large Spatial Scales: Measuring Effectiveness of a Conservation Landscape

Protected areas are fundamental to biodiversity conservation, but there is growing recognition of the need to extend beyond protected areas to meet the ecological requirements of species at larger scales. Landscape-scale conservation requires an evaluation of management impact on biodiversity under different land-use strategies; this is challenging and there exist few empirical studies. In a conservation landscape in northern Republic of Congo we demonstrate the application of a large-scale monitoring program designed to evaluate the impact of conservation interventions on three globally threatened species: western gorillas, chimpanzees and forest elephants, under three land-use types: integral protection, commercial logging, and community-based natural resource management. We applied distance-sampling methods to examine species abundance across different land-use types under varying degrees of management and human disturbance. We found no clear trends in abundance between land-use types. However, units with interventions designed to reduce poaching and protect habitats - irrespective of land-use type - harboured all three species at consistently higher abundance than a neighbouring logging concession undergoing no wildlife management. We applied Generalized-Additive Models to evaluate a priori predictions of species response to different landscape processes. Our results indicate that, given adequate protection from poaching, elephants and gorillas can profit from herbaceous vegetation in recently logged forests and maintain access to ecologically important resources located outside of protected areas. However, proximity to the single integrally protected area in the landscape maintained an overriding positive influence on elephant abundance, and logging roads – even subject to anti-poaching controls - were exploited by elephant poachers and had a major negative influence on elephant distribution. Chimpanzees show a clear preference for unlogged or more mature forests and human disturbance had a negative influence on chimpanzee abundance, in spite of anti-poaching interventions. We caution against the pitfalls of missing and confounded co-variables in model-based estimation approaches and highlight the importance of spatial scale in the response of different species to landscape processes. We stress the importance of a stratified design-based approach to monitoring species status in response to conservation interventions and advocate a holistic framework for landscape-scale monitoring that includes smaller-scale targeted research and punctual assessment of threats.