Toxoplasma gondii and mucosal immunity

Toxoplasma gondii, an intracellular parasite infects the host through the oral route. Infection induces a cascade of immunological events that involve both the components of the innate and adaptative immune responses. Alteration of the homeostatic balance of infected intestine results in an acute inflammatory ileitis in certain strains of inbred mice. Both the infected enterocytes as well as the CD4 T cells from the lamina propria produce chemokines and cytokines that are necessary to clear the parasite whereas CD8 intraepithelial lymphocytes secrete transforming growth factor beta that reduces the inflammation. In this review, we describe the salient features of this complex network of interactions among the different components of the gut-associated lymphoid tissue cell population that are induced after oral infection with T. gondii.     

Timing and abundance as key mechanisms affecting trophic interactions in variable environments

Climatic changes are disrupting otherwise tight trophic interactions between predator and prey. Most of the earlier studies have primarily focused on the temporal dimension of the relationship in the framework of the match–mismatch hypothesis. This hypothesis predicts that predator's recruitment will be high if the peak of the prey availability temporally matches the most energy‐demanding period of the predators breeding phenology. However, the match–mismatch hypothesis ignores the level of food abundance while this can compensate small mismatches. Using a novel time‐series model explicitly quantifying both the timing and the abundance component for trophic relationships, we here show that timing and abundance of food affect recruitment differently in a marine (cod/zooplankton), a marine–terrestrial (puffin/herring) and a terrestrial (sheep/vegetation) ecosystem. The quantification of the combined effect of abundance and timing of prey on predator dynamics enables us to come closer to the mechanisms by which environment variability may affect ecological systems.     

Mba1, a membrane-associated ribosome receptor in mitochondria

The genome of mitochondria encodes a small number of very hydrophobic polypeptides that are inserted into the inner membrane in a cotranslational reaction. The molecular process by which mitochondrial ribosomes are recruited to the membrane is poorly understood. Here, we show that the inner membrane protein Mba1 binds to the large subunit of mitochondrial ribosomes. It thereby cooperates with the C-terminal ribosome-binding domain of Oxa1, which is a central component of the insertion machinery of the inner membrane. In the absence of both Mba1 and the C-terminus of Oxa1, mitochondrial translation products fail to be properly inserted into the inner membrane and serve as substrates of the matrix chaperone Hsp70. We propose that Mba1 functions as a ribosome receptor that cooperates with Oxa1 in the positioning of the ribosome exit site to the insertion machinery of the inner membrane.     

Biogeochemical mass-balances (C, N, P, Si) in three large reservoirs of the Seine Basin (France)

Three major reservoirs (Marne, Seine and Aube), situated in the upstream basin of the river Seine represent a storage capacity of 800 10⁶ m³. In order to quantify the possible role of these reservoirs as a sink or source of nutrients and organic matter for the river system, an input/output mass-balance of suspended matter, organic carbon, inorganic nitrogen forms, phosphorus and reactive silica was established, providing reliable estimates of their retention/elimination and export. The study was carried out over 3 years (1993, 1994 and 1995) in differing hydrological conditions. The retention times varied from 0.3 to 0.8 year, depending on the reservoir and the year, but was longer in 1993 that was a drier year than 1994 and 1995, hydrologically quite similar.Regarding retention (or elimination) and export, the behaviour of the three studied reservoirs was similar. A clear loss or retention of nitrogen, phosphorus and silica was observed in the reservoirs and represented about 40% of the incoming flux of nitrate, 50% of silica, and 60% of phosphate. The retention was lower for total phosphorus than for phosphate. The reservoirs are also sites of suspended matter deposition except during the decennial drawdown, when suspended matter is exported. For inorganic nitrogen, the average amount of nitrate retained in the Seine basin reservoirs upstream from Paris is 5000 tonnes y^–1 that is almost equal to the estimated retention by deposition or denitrification in river channel sediments for the whole drainage network. The retention in the reservoirs represents about 12% of the total flux of nitrate at the outlet of the basin upstream from Paris, and 5% at the mouth of the Seine River.We also calculated inlake C, N, P, Si budgets on the basis of direct process measurements. Measurements of planktonic primary and bacterial activity production led to annual net production of 4200 and 580 tonnes of carbon, respectively. A reasonable value (450 tonnes of carbon) of grazing was calculated. Corresponding N, P, Si fluxes were drawn from appropriate C:N:P:Si ratios. Benthic fluxes were measured with bell jars. The retention of P and Si represents a small fraction of important internal fluxes of phytoplanktonic uptake and recycling, while inorganic nitrogen retention depends mostly on benthic denitrification. The behaviour of P and Si differs in that P is mainly recycled in the water column, while Si dissolution occurs at the sediment interface. Nitrogen is recycled in both the planktonic and the benthic phase.     

The impact of climate change on the distribution of two threatened Dipterocarp trees

Two ecologically and economically important, and threatened Dipterocarp trees Sal (Shorea robusta) and Garjan (Dipterocarpus turbinatus) form mono‐specific canopies in dry deciduous, moist deciduous, evergreen, and semievergreen forests across South Asia and continental parts of Southeast Asia. They provide valuable timber and play an important role in the economy of many Asian countries. However, both Dipterocarp trees are threatened by continuing forest clearing, habitat alteration, and global climate change. While climatic regimes in the Asian tropics are changing, research on climate change‐driven shifts in the distribution of tropical Asian trees is limited. We applied a bioclimatic modeling approach to these two Dipterocarp trees Sal and Garjan. We used presence‐only records for the tree species, five bioclimatic variables, and selected two climatic scenarios (RCP4.5: an optimistic scenario and RCP8.5: a pessimistic scenario) and three global climate models (GCMs) to encompass the full range of variation in the models. We modeled climate space suitability for both species, projected to 2070, using a climate envelope modeling tool “MaxEnt” (the maximum entropy algorithm). Annual precipitation was the key bioclimatic variable in all GCMs for explaining the current and future distributions of Sal and Garjan (Sal: 49.97 ± 1.33; Garjan: 37.63 ± 1.19). Our models predict that suitable climate space for Sal will decline by 24% and 34% (the mean of the three GCMs) by 2070 under RCP4.5 and RCP8.5, respectively. In contrast, the consequences of imminent climate change appear less severe for Garjan, with a decline of 17% and 27% under RCP4.5 and RCP8.5, respectively. The findings of this study can be used to set conservation guidelines for Sal and Garjan by identifying vulnerable habitats in the region. In addition, the natural habitats of Sal and Garjan can be categorized as low to high risk under changing climates where artificial regeneration should be undertaken for forest restoration.     

Mascot file parsing and quantification (MFPaQ), a new software to parse, validate, and quantify proteomics data generated by ICAT and SILAC mass spectrometric analyses: application to the proteomics study of membrane proteins from primary human endothelial cells

Proteomics strategies based on nanoflow (nano-) LC-MS/MS allow the identification of hundreds to thousands of proteins in complex mixtures. When combined with protein isotopic labeling, quantitative comparison of the proteome from different samples can be achieved using these approaches. However, bioinformatics analysis of the data remains a bottleneck in large scale quantitative proteomics studies. Here we present a new software named Mascot File Parsing and Quantification (MFPaQ) that easily processes the results of the Mascot search engine and performs protein quantification in the case of isotopic labeling experiments using either the ICAT or SILAC (stable isotope labeling with amino acids in cell culture) method. This new tool provides a convenient interface to retrieve Mascot protein lists; sort them according to Mascot scoring or to user-defined criteria based on the number, the score, and the rank of identified peptides; and to validate the results. Moreover the software extracts quantitative data from raw files obtained by nano-LC-MS/MS, calculates peptide ratios, and generates a non-redundant list of proteins identified in a multisearch experiment with their calculated averaged and normalized ratio. Here we apply this software to the proteomics analysis of membrane proteins from primary human endothelial cells (ECs), a cell type involved in many physiological and pathological processes including chronic inflammatory diseases such as rheumatoid arthritis. We analyzed the EC membrane proteome and set up methods for quantitative analysis of this proteome by ICAT labeling. EC microsomal proteins were fractionated and analyzed by nano-LC-MS/MS, and database searches were performed with Mascot. Data validation and clustering of proteins were performed with MFPaQ, which allowed identification of more than 600 unique proteins. The software was also successfully used in a quantitative differential proteomics analysis of the EC membrane proteome after stimulation with a combination of proinflammatory mediators (tumor necrosis factor-alpha, interferon-gamma, and lymphotoxin alpha/beta) that resulted in the identification of a full spectrum of EC membrane proteins regulated by inflammation.     

In vivo preclinical low field MRI monitoring of tumor growth following a suicide gene therapy in an orthotopic mice model of human glioblastoma

Purpose

The aim of this study was to monitor in vivo with low field MRI growth of a murine orthotopic glioma model following a suicide gene therapy.

Methods

The gene therapy consisted in the stereotactic injection in the mice brain of a modified vaccinia virus Ankara (MVA) vector encoding for a suicide gene (FCU1) that transforms a non toxic prodrug 5-fluorocytosine (5-FC) to its highly cytotoxic derivatives 5-fluorouracil (5-FU) and 5’-fluorouridine-5’monophosphate (5’-FUMP). Using a warmed-up imaging cell, sequential 3D T1 and T2 0.1T MRI brain examinations were performed on 16 Swiss female nu/nu mice bearing orthotopic human glioblastoma (U87-MG cells). The 6-week in vivo MRI follow-up consisted in a weekly measurement of the intracerebral tumor volume leading to a total of 65 examinations. Mice were divided in four groups: sham group (n = 4), sham group treated with 5-FC only (n = 4), sham group with injection of MVA-FCU1 vector only (n = 4), therapy group administered with MVA-FCU1 vector and 5-FC (n = 4). Measurements of tumor volumes were obtained after manual segmentation of T1- and T2-weighted images.

Results

Intra-observer and inter-observer tumor volume measurements show no significant differences. No differences were found between T1 and T2 volume tumor doubling times between the three sham groups. A significant statistical difference (p < 0.05) in T1 and T2 volume tumor doubling times between the three sham groups and the animals treated with the intratumoral injection of MVA-FCU1 vector in combination with 2 weeks per os 5-FC administration was demonstrated.

Conclusion

Preclinical low field MRI was able to monitor efficacy of suicide gene therapy in delaying the tumor growth in an in vivo mouse model of orthotopic glioblastoma.     

Detection of gaps in the spatial coverage of coral reef monitoring projects in the US Caribbean and Gulf of Mexico

As part of the US Coral Reef Task Force's National Program to Map, Assess, Inventory, and Monitor US Coral Reef Ecosystems, a comprehensive survey of projects/programs monitoring coral reef ecosystems and related habitats (i.e., seagrass beds and mangroves) in the US Caribbean and Pacific was undertaken. Information was gathered on a total of 296 monitoring and assessment projects conducted since 1990 in the US Caribbean and the Gulf of Mexico. Substantial gaps in monitoring coverage of US coral reef ecosystems were revealed through geographic information system (GIS) analysis of survey metadata. Although southern Florida contains approximately two-thirds of all marine monitoring projects found in the US Caribbean and Gulf of Mexico, we were unable to identify any ongoing projects that monitor coral reefs along Florida's western coast and off of the Florida Middle Grounds. Additionally, Florida is covered by approximately 1 900 km2 of mangroves, yet there were only four ongoing projects that monitor this ecosystem, leaving gaps in coverage in the Lower and Middle Keys and along the eastern and western coasts. The Flower Garden Banks National Marine Sanctuary, located offshore of the Texas/Louisiana border, has an integral long-term monitoring program, but lacks a monitoring project that gathers long-term, quantitative data on reef lish abundance and certain water quality parameters. Numerous coral reef monitoring projects in Puerto Rico are concentrated on the island's southwestern coast surrounding La Parguera, while far fewer monitoring projects are conducted along the northern and southeastern coasts and around Vieques Island. In the US Virgin Islands, the paucity of monitoring projects in large areas of St. Croix and St. Thomas contrasts with monitoring activity in three marine protected areas (MPAs), where 66% of the US Virgin Islands' coral reef monitoring sites were found. Only a series of assessments have been conducted at Navassa, a small, uninhabited island located 55 km west of Haiti and 137 km northeast of Jamaica. In order to better understand changes in coral reef communities and to produce a series of biennial reports on the status of US coral reef ecosystems, the National Oceanic and Atmospheric Administration (NOAA) is developing a national coral reef monitoring network. This network has already begun to fill some of these gaps in monitoring coverage through issuing cooperative grants to states and territories to build long-term monitoring capacity.     

Quantitative evaluation of siRNA delivery in vivo

Effective small interfering RNA (siRNA)-mediated therapeutics require the siRNA to be delivered into the cellular RNA-induced silencing complex (RISC). Quantitative information of this essential delivery step is currently inferred from the efficacy of gene silencing and siRNA uptake in the tissue. Here we report an approach to directly quantify siRNA in the RISC in rodents and monkey. This is achieved by specific immunoprecipitation of the RISC from tissue lysates and quantification of small RNAs in the immunoprecipitates by stem-loop PCR. The method, expected to be independent of delivery vehicle and target, is label-free, and the throughput is acceptable for preclinical animal studies. We characterized a lipid-formulated siRNA by integrating these approaches and obtained a quantitative perspective on siRNA tissue accumulation, RISC loading, and gene silencing. The described methodologies have utility for the study of silencing mechanism, the development of siRNA therapeutics, and clinical trial design.