Sources of exposure to lead in Arctic and subarctic regions: a scoping review

Understanding lead exposure pathways is a priority because of its ubiquitous presence in the environment as well as the potential health risks. We aimed to identify potential lead sources and pathways of lead exposure, including long-range transport, and the magnitude of exposure in Arctic and subarctic communities. A scoping review strategy and screening approach was used to search literature from January 2000 to December 2020. A total of 228 academic and grey literature references were synthesised. The majority of these studies (54%) were from Canada. Indigenous people in Arctic and subarctic communities in Canada had higher levels of lead than the rest of Canada. The majority of studies in all Arctic countries reported at least some individuals above the level of concern. Lead levels were influenced by a number of factors including using lead ammunition to harvest traditional food and living in close proximity to mines. Lead levels in water, soil, and sediment were generally low. Literature showed the possibility of long-range transport via migratory birds. Household lead sources included lead-based paint, dust, or tap water. This literature review will help to inform management strategies for communities, researchers, and governments, with the aim of decreasing lead exposure in northern regions.

Microbial degradation of naphthenic acids using constructed wetland treatment systems: metabolic and genomic insights for improved bioremediation of process-affected water

Naphthenic acids (NAs) are a complex mixture of organic compounds released during bitumen extraction from mined oil sands that are important contaminants of oil sands process-affected water (OSPW). NAs can be toxic to aquatic organisms and, therefore, are a main target compound for OSPW. The ability of microorganisms to degrade NAs can be exploited for bioremediation of OSPW using constructed wetland treatment systems (CWTS), which represent a possible low energy and low-cost option for scalable in situ NA removal. Recent advances in genomics and analytical chemistry have provided insights into a better understanding of the metabolic pathways and genes involved in NA degradation. Here, we discuss the ecology of microbial NA degradation with a focus on CWTS and summarize the current knowledge related to the metabolic pathways and genes used by microorganisms to degrade NAs. Evidence to date suggests that NAs are mostly degraded aerobically through ring cleavage via the beta-oxidation pathway, which can be combined with other steps such as aromatization, alpha-oxidation, omega-oxidation, or activation as coenzyme A (CoA) thioesters. Anaerobic NA degradation has also been reported via the production of benzoyl-CoA as an intermediate and/or through the involvement of methanogens or nitrate, sulfate, and iron reducers. Furthermore, we discuss how genomic, statistical, and modeling tools can assist in the development of improved bioremediation practices.

Rapid on-site detection of harmful algal blooms: real-time cyanobacteria identification using Oxford Nanopore sequencing

With the increasing occurrence and severity of cyanobacterial harmful algal blooms (cHAB) at the global scale, there is an urgent need for rapid, accurate, accessible, and cost-effective detection tools. Here, we detail the RosHAB workflow, an innovative, in-the-field applicable genomics approach for real-time, early detection of cHAB outbreaks. We present how the proposed workflow offers consistent taxonomic identification of water samples in comparison to traditional microscopic analyses in a few hours and discuss how the generated data can be used to deepen our understanding on cyanobacteria ecology and forecast HABs events. In parallel, processed water samples will be used to iteratively build the International cyanobacterial toxin database (ICYATOX; http://icyatox.ibis.ulaval.ca) containing the analysis of novel cyanobacterial genomes, including phenomics and genomics metadata. Ultimately, RosHAB will (1) improve the accuracy of on-site rapid diagnostics, (2) standardize genomic procedures in the field, (3) facilitate these genomics procedures for non-scientific personnel, and (4) identify prognostic markers for evidence-based decisions in HABs surveillance.

Spatio-temporal connectivity of the aquatic microbiome associated with cyanobacterial blooms along a Great Lake riverine-lacustrine continuum

Lake Erie is subject to recurring events of cyanobacterial harmful algal blooms (cHABs), but measures of nutrients and total phytoplankton biomass seem to be poor predictors of cHABs when taken individually. A more integrated approach at the watershed scale may improve our understanding of the conditions that lead to bloom formation, such as assessing the physico-chemical and biological factors that influence the lake microbial community, as well as identifying the linkages between Lake Erie and the surrounding watershed. Within the scope of the Government of Canada's Genomics Research and Development Initiative (GRDI) Ecobiomics project, we used high-throughput sequencing of the 16S rRNA gene to characterize the spatio-temporal variability of the aquatic microbiome in the Thames River-Lake St. Clair-Detroit River-Lake Erie aquatic corridor. We found that the aquatic microbiome was structured along the flow path and influenced mainly by higher nutrient concentrations in the Thames River, and higher temperature and pH downstream in Lake St. Clair and Lake Erie. The same dominant bacterial phyla were detected along the water continuum, changing only in relative abundance. At finer taxonomical level, however, there was a clear shift in the cyanobacterial community, with Planktothrix dominating in the Thames River and Microcystis and Synechococcus in Lake St. Clair and Lake Erie. Mantel correlations highlighted the importance of geographic distance in shaping the microbial community structure. The fact that a high proportion of microbial sequences found in the Western Basin of Lake Erie were also identified in the Thames River, indicated a high degree of connectivity and dispersal within the system, where mass effect induced by passive transport play an important role in microbial community assembly. Nevertheless, some cyanobacterial amplicon sequence variants (ASVs) related to Microcystis, representing less than 0.1% of relative abundance in the upstream Thames River, became dominant in Lake St. Clair and Erie, suggesting selection of those ASVs based on the lake conditions. Their extremely low relative abundances in the Thames suggest additional sources are likely to contribute to the rapid development of summer and fall blooms in the Western Basin of Lake Erie. Collectively, these results, which can be applied to other watersheds, improve our understanding of the factors influencing aquatic microbial community assembly and provide new perspectives on how to better understand the occurrence of cHABs in Lake Erie and elsewhere.

Structural shifts in sea ice prokaryotic communities across a salinity gradient in the subarctic

Current knowledge of the processes that shape prokaryotic community assembly in sea ice across polar ecosystems is scarce. Here, we coupled culture-dependent (bacterial isolation on R2A medium) and culture-independent (high-throughput 16S rRNA gene sequencing) approaches to provide the first comprehensive assessment of prokaryotic communities in the late winter ice and its underlying water along a natural salinity gradient in coastal Hudson Bay, an iconic cryo-environment that marks the ecological transition between Canadian Subarctic and Arctic biomes. We found that prokaryotic community assembly processes in the ice were less selective at low salinity since typical freshwater taxa such as Frankiales, Burkholderiales, and Chitinophagales dominated both the ice and its underlying water. In contrast, there were sharp shifts in community structure between the ice and underlying water samples at sites with higher salinity, with the orders Alteromonadales and Flavobacteriales dominating the ice, while the abovementioned freshwater taxa dominated the underlying water communities. Moreover, primary producers including Cyanobium (Cyanobacteria, Synechococcales) may play a role in shaping the ice communities and were accompanied by known Planctomycetes and Verrucomicrobiae taxa. Culture-dependent analyses showed that the ice contained pigment-producing psychrotolerant or psychrophilic bacteria from the phyla Proteobacteria, Actinobacteriota, and Bacteroidota, likely favored by the combination of low temperatures and the seasonal increase in sunlight. Our findings suggest that salinity, photosynthesis and dissolved organic matter are the main drivers of prokaryotic community structure in the late winter ice of coastal Hudson Bay, the ecosystem with the fastest sea ice loss rate in the Canadian North.

Frogs Respond to Commercial Formulations of the Biopesticide Bacillus thuringiensis var. israelensis, Especially Their Intestine Microbiota

It is generally believed that Bacillus thuringiensis var. israelensis (Bti) biopesticides are harmless to non-target organisms; however, new research shows controversial results. We exposed acutely and chronicallyLithobates sylvaticusandAnaxyrus americanus tadpoles until metamorphic climax to VectoBac 200G (granules) and VectoBac 1200L (aqueous suspension) at 300-20,000 ITU/L covering field-relevant concentrations and higher. The data show that the exposure parameters tested did not affect significantly the survival, total length, total weight, hepatosomatic index, gonadosomatic index, the expression of genes of interest (i.e., related to xenobiotic exposure, oxidative stress, and metamorphosis), and the intestine tissue layer detachment ofL. sylvaticusandA. americanus in a concentration-response pattern. In contrast, VectoBac 200G significantly increased the median time to metamorphosis ofL. sylvaticus tadpoles by up to 3.5 days and decreased the median by up to 1 day inA. americanus. VectoBac 1200L significantly increased the median time to metamorphosis ofL. sylvaticusandA. americanustadpoles by up to 4.5 days. Also, the exposure to VectoBac 200G and 1200L altered the intestine bacterial community composition inA. americanus at application rates recommended by the manufacturer, which led to an increase in the relative abundance of Verrucomicrobia, Firmicutes, Bacteroidetes, and Actinobacteria. Changes in the intestine microbiota might impact the fitness of individuals, including the susceptibility to parasitic infections. Our results indicate that the effect of Bti commercial products is limited; however, we recommend that Bti-spraying activities in amphibian-rich ecosystems should be kept minimal until there is more conclusive research to assess if the changes in the time to metamorphosis and microbiota can lead to negative outcomes in amphibian populations and, eventually, the functioning of ecosystems.

The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada

Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.

Data driven optimization of sexual assault case processing

In recent years, several forensic laboratories have noted an increase in the number of sexual assault cases submitted for testing, often leading to longer turnaround times. In that context, forensic laboratories may be interested in reviewing their procedures to increase productivity. Here, we present two different strategies that were put in place in our laboratory. First, we changed the way sexual assault evidence kits (SAEK) are processed by implementing an optimized workflow that prioritizes the internal samples (vaginal, anal, and oral). This new procedure allowed for a drastic decrease in turnaround time, while maintaining a similar investigative power.

Secondly, we used data from casework to target cases and samples that were likely to yield biological material from the perpetrator, in an attempt to avoid dedicating time and effort to cases for which there is a very low probability of obtaining foreign DNA evidence. Among other things, we looked at the likelihood of obtaining DNA from the perpetrator when the complainant reported the use of a condom, has showered after the assault or when the complainant has no memory of the assault. Results show that those circumstances do not dramatically decrease the probability of finding DNA from the perpetrator.

The characterization of radioactive waste: a critical review of techniques implemented or under development at CEA, France

This review paper describes the destructive and non-destructive measurements implemented or under development at CEA, in view to perform the most complete radioactive waste characterization. First, high-energy photon imaging (radiography, tomography) brings essential information on the waste packages, such as density, position and shape of the waste inside the container and in the possible binder, quality of coating and blocking matrices, presence of internal shields or structures, presence of cracks, voids, or other defects in the container or in the matrix, liquids or other forbidden materials, etc. Radiological assessment is then performed using a series of non-destructive techniques such as gamma-ray spectroscopy, which allows characterizing a wide range of radioactive and nuclear materials, passive neutron coincidence counting and active neutron interrogation with the differential die-away technique, or active photon interrogation with high-energy photons (photofission), to measure nuclear materials. Prompt gamma neutron activation analysis (PGNAA) can also be employed to detect toxic chemicals or elements which can greatly influence the above measurements, such as neutron moderators or absorbers. Digital auto-radiography can also be used to detect alpha and beta contaminated waste. These non-destructive assessments can be completed by gas measurements, to quantify the radioactive and radiolysis gas releases, and by destructive examinations such as coring homogeneous waste packages or cutting the heterogeneous ones, in view to perform visual examination and a series of physical, chemical, and radiochemical analyses on samples. These last allow for instance to check the mechanical and containment properties of the package envelop, or of the waste binder, to measure toxic chemicals, to assess the activity of long-lived radionuclides or pure beta emitters, to determine the isotopic composition of nuclear materials, etc.

Diversity and potential activity of methanotrophs in high methane-emitting permafrost thaw ponds

Lakes and ponds derived from thawing permafrost are strong emitters of carbon dioxide and methane to the atmosphere, but little is known about the methane oxidation processes in these waters. Here we investigated the distribution and potential activity of aerobic methanotrophic bacteria in thaw ponds in two types of eroding permafrost landscapes in subarctic Québec: peatlands and mineral soils. We hypothesized that methanotrophic community composition and potential activity differ regionally as a function of the landscape type and permafrost degradation stage, and locally as a function of depth-dependent oxygen conditions. Our analysis of pmoA transcripts by Illumina amplicon sequencing and quantitative PCR showed that the communities were composed of diverse and potentially active lineages. Type I methanotrophs, particularly Methylobacter, dominated all communities, however there was a clear taxonomic separation between the two landscape types, consistent with environmental control of community structure. In contrast, methanotrophic potential activity, measured by pmoA transcript concentrations, did not vary with landscape type, but correlated with conductivity, phosphorus and total suspended solids. Methanotrophic potential activity was also detected in low-oxygen bottom waters, where it was inversely correlated with methane concentrations, suggesting methane depletion by methanotrophs. Methanotrophs were present and potentially active throughout the water column regardless of oxygen concentration, and may therefore be resilient to future mixing and oxygenation regimes in the warming subarctic.

Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin

Some bacteria can be preserved over time in deep sediments where they persist either in dormant or slow-growing vegetative stages. Here, we hypothesized that such cells can be revived when exposed to environmental conditions similar to those before they were buried in the sediments. To test this hypothesis, we collected bacteria from sediment samples of different ages (140-8500 calibrated years before present, cal BP) from three lakes that differed in the timing of their physical isolation from the Baltic Sea following postglacial uplift. After these bacterial communities were grown in sterile water from the Baltic Sea, we determined the proportion of 16S rRNA sequence reads associated with marine habitats by extracting the environment descriptive terms of homologous sequences retrieved from public databases. We found that the proportion of reads associated with marine descriptive term was significantly higher in cultures inoculated with sediment layers formed under Baltic conditions and where salinities were expected to be similar to current levels. Moreover, a similar pattern was found in the original sediment layers. Our study, therefore, suggests that remnants of marine bacterial communities can be preserved in sediments over thousands of years and can be revived from deep sediments in lakes of marine origin.

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities

Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted.

Bacterial community structure across environmental gradients in permafrost thaw ponds: methanotroph-rich ecosystems

Permafrost thawing leads to the formation of thermokarst ponds that potentially emit CO₂ and CH₄ to the atmosphere. In the Nunavik subarctic region (northern Québec, Canada), these numerous, shallow ponds become well-stratified during summer. This creates a physico-chemical gradient of temperature and oxygen, with an upper oxic layer and a bottom low oxygen or anoxic layer. Our objective was to determine the influence of stratification and related limnological and landscape properties on the community structure of potentially active bacteria in these waters. Samples for RNA analysis were taken from ponds in three contrasting valleys across a gradient of permafrost degradation. A total of 1296 operational taxonomic units were identified by high throughput amplicon sequencing, targeting bacterial 16S rRNA that was reverse transcribed to cDNA. β-proteobacteria were the dominant group in all ponds, with highest representation by the genera Variovorax and Polynucleobacter. Methanotrophs were also among the most abundant sequences at most sites. They accounted for up to 27% of the total sequences (median of 4.9% for all samples), indicating the importance of methane as a bacterial energy source in these waters. Both oxygenic (cyanobacteria) and anoxygenic (Chlorobi) phototrophs were also well-represented, the latter in the low oxygen bottom waters. Ordination analyses showed that the communities clustered according to valley and depth, with significant effects attributed to dissolved oxygen, pH, dissolved organic carbon, and total suspended solids. These results indicate that the bacterial assemblages of permafrost thaw ponds are filtered by environmental gradients, and are complex consortia of functionally diverse taxa that likely affect the composition as well as magnitude of greenhouse gas emissions from these abundant waters.

Total and methylated mercury in Arctic multiyear sea ice

Mercury is one of the primary contaminants of concern in the Arctic marine ecosystem. While considerable efforts have been directed toward understanding mercury cycling in the Arctic, little is known about mercury dynamics within Arctic multiyear sea ice, which is being rapidly replaced with first-year ice. Here we report the first study on the distribution and potential methylation of mercury in Arctic multiyear sea ice. Based on three multiyear ice cores taken from the eastern Beaufort Sea and McClure Strait, total mercury concentrations ranged from 0.65 to 60.8 pM in bulk ice, with the highest values occurring in the topmost layer (∼40 cm) which is attributed to the dynamics of particulate matter. Methylated mercury concentrations ranged from below the method detection limit (<0.1 pM) to as high as 2.64 pM. The ratio of methylated to total mercury peaked, up to ∼40%, in the mid to bottom sections of the ice, suggesting the potential occurrence of in situ mercury methylation. The annual fluxes of total and methylated mercury into the Arctic Ocean via melt of multiyear ice are estimated to be 420 and 42 kg yr(-1), respectively, representing an important and changing source of mercury and methylmercury into the Arctic Ocean marine ecosystem.

Links between metabolic plasticity and functional redundancy in freshwater bacterioplankton communities

Metabolic plasticity and functional redundancy are fundamental properties of microbial communities, which shape their response to environmental forcing, and also mediate the relationship between community composition and function. Yet, the actual quantification of these emergent community properties has been elusive, and we thus do not know how they vary across bacterial communities, and their relationship to environmental gradients and to each other. Here we present an experimental framework that allows us to simultaneously quantify metabolic plasticity and functional redundancy in freshwater bacterioplankton communities, and to explore connections that may exists between them. We define metabolic plasticity as the rate of change in single-cell properties (cell wall integrity, cell size, single-cell activity) relative to changes in community composition. Likewise, we define functional redundancy as the rate of change in carbon substrate uptake capacities relative to changes in community composition. We assessed these two key community attributes in transplant experiments where bacterioplankton from various aquatic habitats within the same watershed were transplanted from their original water to waters from other systems that differ in their main resources. Our results show that metabolic plasticity is an intrinsic property of bacterial communities, whereas the expression of functional redundancy appears to be more dependent on environmental factors. Furthermore, there was an overall strong positive relationship between the level of functional redundancy and of metabolic plasticity, suggesting no trade-offs between these community attributes but rather a possible co-selection. The apparent continuum in the expression of both functional redundancy and plasticity among bacterial communities and the link between them, in turn suggest that the link between community diversity and function may also vary along a continuum, from being very tight, to being weak, or absent.

Composition influences the pathway but not the outcome of the metabolic response of bacterioplankton to resource shifts

Bacterioplankton community metabolism is central to the functioning of aquatic ecosystems, and strongly reactive to changes in the environment, yet the processes underlying this response remain unclear. Here we explore the role that community composition plays in shaping the bacterial metabolic response to resource gradients that occur along aquatic ecotones in a complex watershed in Québec. Our results show that the response is mediated by complex shifts in community structure, and structural equation analysis confirmed two main pathways, one involving adjustments in the level of activity of existing phylotypes, and the other the replacement of the dominant phylotypes. These contrasting response pathways were not determined by the type or the intensity of the gradients involved, as we had hypothesized, but rather it would appear that some compositional configurations may be intrinsically more plastic than others. Our results suggest that community composition determines this overall level of community plasticity, but that composition itself may be driven by factors independent of the environmental gradients themselves, such that the response of bacterial communities to a given type of gradient may alternate between the adjustment and replacement pathways. We conclude that community composition influences the pathways of response in these bacterial communities, but not the metabolic outcome itself, which is driven by the environment, and which can be attained through multiple alternative configurations.

Seasonal variations of phage life strategies and bacterial physiological states in three northern temperate lakes

The current consensus concerning the prevalence of lytic and lysogenic phage life cycles in aquatic systems is that the host physiological state may influence viral strategies, lysogeny being favoured when hosts have reduced metabolic rates. We explored this hypothesis, by following phage cycle dynamics, host physiological state and metabolic activity over an annual cycle in three lakes subjected to strong seasonal fluctuations, including 4-5 months of ice cover. We observed marked seasonal dynamics of viral and bacterial communities, with low bulk and cell-specific bacterial metabolism in winter, and a dramatic increase in injured bacteria under the ice cover in all lakes. This period was accompanied by contrasting patterns in the proportion of lysogenic cells. In the eutrophic lake, times of low bacterial metabolic rates and high proportion of damaged cells corresponded to highest levels of lysogeny, supporting the notion that hosts are a 'refuge' for viruses. In the two unproductive lakes, peaks of injured cells corresponded to a minimum of lysogeny, suggesting an 'abandon the sinking ship' response, where the prophage replicates before the loss of genome. We suggest that these diverging responses to the host physiological state are not contradictory, but rather that there may be thresholds of cell stress and metabolic activity leading to one or the other response.

Links between resources, C metabolism and the major components of bacterioplankton community structure across a range of freshwater ecosystems

We explored the patterns in bacterioplankton community metabolism (BCM) and four components of community structure [composition (BCC), metabolic capacities (MC), physiological structure (PS) and single-cell characteristics (SCC)], between lakes, rivers and marshes within a watershed in Québec, to assess the connections that exist between them and with the main resources (organic matter, nutrients). Habitat types were well segregated by both resources and BCM and their corresponding dissimilarity matrices were significantly correlated, suggesting that BCM tracks resource conditions in a consistent manner across ecosystem types. MC also segregated the various habitats and was correlated to BCM but less so to resources, whereas BCC at times resulted in a clear separation of habitats, but was rarely correlated to resources and never to BCM, suggesting a higher degree of ecosystem specificity at this particular level. Finally, there was no clear separation of habitats in terms of PS and SCC, and none covaried with resources or BCM. The habitat patterns based on these different components of structure were rarely correlated to each other, indicating weak deterministic connections between them. MC appears to mediate the link between resources and BCM more directly and consistently across systems; BCC appears to be more influenced by ecosystem-specific factors that weaken its overall connection to both resources and BCM, whereas PS and SCC show no discernible patterns. Our results thus suggest that the bottom-up regulation of BCM by resources is mediated by complex shifts within components of community structure that can be directional, ecosystem-specific or apparently random, which combined nevertheless result in a systematic overall response to resources in terms of C metabolism.

Microbial community structure and dynamics in the largest natural French lake (Lake Bourget)

We investigated the dynamics and diversity of heterotrophic bacteria, autotrophic and heterotrophic flagellates, and ciliates from March to July 2002 in the surface waters (0-50 m) of Lake Bourget. The heterotrophic bacteria consisted mainly of "small" cocci, but filaments (>2 microm), commonly considered to be grazing-resistant forms under increased nanoflagellate grazing, were also detected. These elongated cells mainly belonged to the Cytophaga-Flavobacterium (CF) cluster, and were most abundant during spring and early summer, when mixotrophic or heterotrophic flagellates were the main bacterial predators. The CF group strongly dominated fluorescent in situ hybridization-detected cells from March to June, whereas clear changes were observed in early summer when Beta-proteobacteria and Alpha-proteobacteria increased concomitantly with maximal protist grazing pressures. The analysis of protist community structure revealed that the flagellates consisted mainly of cryptomonad forms. The dynamics of Cryptomonas sp. and Dinobryon sp. suggested the potential importance of mixotrophs as consumers of bacteria. This point was verified by an experimental approach based on fluorescent microbeads to assess the potential grazing impact of all protist taxa in the epilimnion. From the results, three distinct periods in the functioning of the epilimnetic microbial loop were identified. In early spring, mixotrophic and heterotrophic flagellates constituted the main bacterivores, and were regulated by the availability of their resources mainly during April (phase 1). Once the "clear water phase" was established, the predation pressure of metazooplankton represented a strong top-down force on all microbial compartments. During this period only mixotrophic flagellates occasionally exerted a significant bacterivory pressure (phase 2). Finally, the early summer was characterized by the highest protozoan grazing impact and by a rapid shift in the carbon pathway transfer, with a fast change-over of the main predators contribution, i.e., mixotrophic, heterotrophic flagellates and ciliates in bacterial mortality. The high abundance of ciliates during this period was consistent with the high densities of resources (heterotrophic nanoflagellates, algae, bacteria) in deep layers containing the most chlorophyll. Bacteria, as ciliates, responded clearly to increasing phytoplankton abundance, and although bacterial grazing impact could vary largely, bacterial abundance seemed to be primarily bottom-up regulated (phase 3).

Impact on treatment outcome and late effects of customized treatment planning in cervix carcinomas: baseline results to compare new strategies

PURPOSE

The aim of the study was to determine the predictive factors of complications, to evaluate the impact of customized treatment planning on late normal tissue effects per stage, and to report disease-free survival (DFS) and local control (LC) rates.

METHODS AND MATERIALS

From 1970 to 1994, 642 patients were treated with radiotherapy alone for carcinoma of the intact uterine cervix. According to the International Federation of Gynecology and Obstetrics (FIGO) substaging, 34% were Stage I, 39% Stage II, and 27% Stage III. The analysis was divided into three periods: 1970-1978 (use of standard prescriptions),1979-1984 (implementation of individual adjustments), 1985-1994 (systematic individual adjustments). Five-year DFS, LC, and complications rates were calculated using the Kaplan-Meier method. Predictive factors of complications were determined by univariate analysis using frequency tables and nonparametric t-tests. Multivariate analysis consisted of a polychotomous stepwise regression.

RESULTS

The comparison of the three time periods showed a significant reduction of the external radiation dose (dose above 40 Gy in 47% of patients before 1979 vs. 36% after 1984), of the use of parametrial boost (55% vs. 39%), of the use of vaginal cylinder (28% vs. 11.5%), and of the HWT volume (combined intracavitary and external irradiation) (842 cc vs. 503 cc on average). The total sequelae/complications rate, all toxicity grades, all stages, all organs was 51%. Five-year actuarial rate per toxicity grade was: G1, 42%; G2, 23.5%; G3, 10%; G4, 3%. The three main predictive factors for rectal and bladder sequelae/complications (all toxicity grades) taking into account time period were: the increase of external radiation dose, the high dose rate at reference points, and the whole vagina brachytherapy. No G4 occurred in the third period. The rate of G3 complications dropped from 16% to 6% over time: from 5% during the first period to 0% during the third period in Stage I, from 8% to 6% in Stage II, and from 23% to 12% in Stage III. G3 currently describes a variety of clinical situations with a different impact on quality of life which justifies further refinements of definitions of late effects. In our experience the severity of G3 markedly decreased: less than one-third of G3 had a real impact on quality of life in the last period compared to more than two-thirds in the first period. Meanwhile, 5-year LC rates remained stable in Stages I and II, 91% and 85% respectively. Conversely they fell from 75% to 55% in Stage III, thus raising the problem of underdosage and/or more accurate staging with time.

CONCLUSIONS

Customized treatment planning eradicated lethal complications and provided a significant decrease of G3 in all stages while maintaining high cure rates in early stages. Dose reduction should be considered with caution in Stage III.

Triple helix assembly and processing of human collagen produced in transgenic tobacco plants

The use of tobacco plants as a novel expression system for the production of human homotrimeric collagen I is presented in this report. Constructs were engineered from cDNA encoding the human proalpha1(I) chain to generate transgenic tobacco plants expressing collagen I. The recombinant proalpha1(I) chains were expressed as disulfide-bonded trimers and were shown to fold into a stable homotrimeric triple helix. Moreover, the recombinant procollagen was subsequently processed to collagen as it occurs in animals. Large amounts of recombinant collagen were purified from field grown plant material. The data suggest that plants are a valuable alternative for the recombinant production of collagen for various medical and scientific purposes.

Organ preservation in cervix cancer

From 1970 to 1994, 642 patients with carcinomas of intact uterine cervix were treated with radiotherapy alone Univariate and multivariate analysis was carried out of predictive factors for: 1) pelvic control and survival rates; 2) complications using French-Italian Syllabus, combined with an evaluation of the impact of customized treatment planning policy (CTP) on G3-G4. According to Figo substaging 30% of patients were stage I, 42% stage II and 28% stage III/IV. Diameter of cervical disease was 3-5 cm in 38% of cases and > 5 cm in 15%. Nodal involvement from lymphangiogram was 21%. The distribution of sequelae and complications was: G1 23%, G2 18%, G3 6%, G4 2.5%. The distribution of G3-G4 per organ was: genitalia 6% (no G4), rectum 4%, colon 1.5%, bladder 1.2%, soft tissues 1%, small bowel 0.5%. Stage (RR ranging from 1.5 for stage IIb to 5 for stage III/IV), tumor size (RR = 1.5), nodal involvement (RR = 2) were significant predictive factors for survival and pelvic control rates (p < 0.0001). In univariate analysis the main factors influencing the risk of G3-G4 complications were: Figo substaging, external radiation dose over 40 Gy (ED), parametrium boost (PB), use of brachytherapy vaginal cylinders applicator (CA), high HWT and mean rectal dose rate for rectal complications. In multivariate analysis, CA remained the only predictive factor for G3-G4 bladder events (odds ratio OR = 10.8) while the increase of mean dose rate (OR = 1.1), use of CA (OR = 4.2) and ED > 40 Gy (OR = 4.4) were predictive of severe rectal sequelae. Prevention of complications based upon individual changes of treatment planning according to dosimetry parameters led to a sharp decrease in severe complications with time. No G4 occurred after 1983. G3 rates dropped from 5% before 1978 to 0% after 1983 in stage I, from 10% to 6% in stage II and from 23% to 12% in stages III/IV. Meanwhile 5-year LC rates remained stable in early stages, about 91% in stage I and 85% in stage II, conversely they fell from 75% to 55% in stages III/IV, thus raising the problem of underdosage and/or more reliable staging with time. It is concluded that radiotherapy prescriptions based upon tumor diameter per stage and delivered using CTP led to an eradication of lethal complications and provided significant decrease of G3 in all cases while maintaining high cure rates in early stages. Dose reduction should be considered with caution in stages III/IV.

Structural requirements for alpha 1 beta 1 and alpha 2 beta 1 integrin mediated cell adhesion to collagen V

A large variety of cells adhere to and spread on specific regions within the triple helix of collagens, mainly via alpha 1 beta 1 and alpha 2 beta 1 integrins. Disruption of collagen triple helical integrity generally affects the efficiency of cell adhesion on different collagens including collagen V. This report addresses the question of the importance of the linear sequence of the constitutive alpha-chains versus the triple helical conformation in the recognition of collagen V binding sites. To investigate this question, in vitro renaturation of the isolated alpha 1 (V) and alpha 2 (V) chains was performed according to the annealing procedure and formation of the triple helix was monitored by rotary shadowing and by mild trypsin digestion followed by electrophoretic analysis. The results indicate that the alpha 1 (V) and alpha 2 (V) homotrimeric reassociation can occur up to a full-length triple helix but intermediate forms of 50–200 nm long rod-like segments are also observed. We have previously shown that alpha 1 beta 1 and alpha 2 beta 1 integrins, the major collagen receptors, are also involved in cell adhesion to native collagen V. Therefore we chose the following two different cell lines for this study: HT1080 (a human fibrosarcoma cell line) expressing alpha 2 beta 1 and HBL100 (a human mammary epithelial cell line) containing significant amounts of alpha 1 beta 1 and alpha 2 beta 1 integrins. We showed that both alpha 1 (V) and alpha 2(V) homotrimers induced cell adhesion but refolded alpha2(V) chains were more efficient and promoted cell adhesion as well as native collagen V. Thermal stability of refolded alpha-chains was monitored by adhesion promoting activity and showed that cell adhesion was dependent on triple helical conformation of the substrates. Adhesion in all cases was strongly Mg2+ and Mn(2+)-dependent and Ca2+ ions alone were ineffective. Antibodies against alpha 2 and beta 1 integrin subunits completely inhibited HT1080 cell adhesion to all substrates. Moreover, addition of cyclic RGD peptides, which had been shown to interact with alpha 2 beta 1, dramatically affected HT1080 cell adhesion to native collagen V and to the refolded alpha-chains. Antibody to beta 1 subunits abolished HBL100 cell adhesion to all substrates. A complete inhibition of HBL100 cell adhesion to native collagen V was achieved only by simultaneous addition of function-blocking specific monoclonal antibodies against alpha 1 and alpha 2 integrin subunits. However, only alpha 2 beta 1 was engaged obviously in HBL100 cell adhesion to refolded alpha-chains. These data indicate that triple helical conformation is particularly critical for alpha 2 beta 1- and alpha 1 beta 1-dependent adhesion and that the integrin alpha 2 beta 1 is a dominant functional receptor for refolded alpha-chains. We conclude that alpha 2 beta 1-dependent adhesion seems to involve multiple different conformational binding sites while alpha 1 beta 1-dependent adhesion is more restricted to the heterotrimeric native form of the molecule.

Composition and organization of the extracellular matrix of vein walls: collagen networks

As there are few recent reports concerning the structure and exact composition of the extracellular matrix from human normal and varicose veins, we carried out comparative immunohistochemical analysis of vessel wall using conventional and confocal laser scanning immunofluorescence techniques. The present report is a rapid review of the structure and function of the 19 known collagen types and our first results on the distribution of collagen types VI, XII and XIV and laminin (glycoprotein from basement membrane) in vein walls. Type VI collagen is concentrated in the sub-endothelium and widely distributed in the media and adventice. For the first time, we demonstrated that both FACIT (fibril-associated) collagens XII and XIV were present in the vein wall, but at different anatomic sites.

Preparation of highly phosphorylating mitochondria from the yeast Schizosaccharomyces pombe

Schizosaccharomyces pombe yeast cells grown on either fermentable or respiratory media were efficiently converted to stable spheroplasts by the alpha-(1-->3)-glucanase Novozym 234 in the presence of 1.2 M sorbitol. Lysis of spheroplasts by gentle homogenization in dilute sorbitol resulted in the preparation of mitochondria with a structure similar to that observed within the starting yeast cells. The isolated mitochondria exhibited high oxidation rates with various respiratory substrates, NADH being the most efficient. The mitochondria appeared well coupled since the second State 4 rate observed after ADP consumption was identical to the initial one. The State 3 rate in the presence of ADP was completely inhibited by low oligomycin concentrations, similarly to the concomitant ATP synthesis of 900 nmol/min x mg protein. These NADH oxidation and dependent ATP-synthesis activities are much higher than those previously described for mitochondria isolated from Schizosaccharomyces pombe, and similar to the highest values reported for Saccharomyces cerevisiae.

Cyclic GMP, cyclic AMP, glucose at birth, and maturation of rat liver mitochondria

The improvement in mitochondrial functions which normally occurs in newborn rat liver in vivo during the few hours following delivery is inhibited by a glucose injection at birth (Meister, R., Comte, J., Baggetto, L., G., Godinot, C. and Gautheron, D.C. (1983) Biochim. Biophys. Acta 722, 36-42). To test whether this improvement could be correlated to changes in cyclic nucleotides, the levels of cAMP and cGMP have been measured during the 2 h following birth. At birth, a short rise followed by a decrease of cAMP occurs, then a significant increase of cAMP level is observed between 45 min and 2 h. The cAMP level for animals injected at birth with glucose is lower than for control animals at each time studied. The cGMP level is not significantly affected in control animals, while in glucose-treated animals a significant decrease of cGMP is observed in the postnatal 2 h. The present work shows also that the glucose-induced inhibition of mitochondrial maturation is mimicked by injection at birth of either 8-Br-cGMP or nitroprusside. The latter transiently increases intracellular cGMP. In contrast, the glucose-induced inhibition is prevented by the injection at birth of either dbcAMP or alkylxanthines together with glucose (Comte, J., Meister, R., Baggetto, L.G., Godinot, C. and Gautheron, D.C. (1986) Biochem. Pharmacol. 35, 2411-2416). It is concluded that the postnatal improvement of mitochondrial functions is stimulated by cAMP and inhibited by cGMP, and that glucose-induced inhibition of the maturation is at least partly supported by a decrease in cAMP but not correlated to an increase in cGMP.

[Comparative effects of pentoxifylline and of HWA 285 on mitochondrial maturation and biosynthesis of proteins in rats in the perinatal period]

To improve our understanding of the beneficial effects of alkylxanthines in various disorders, two animal models were used. The biochemical modifications due to pentoxifylline and HWA 285 on mitochondrial maturation and protein biosynthesis during the neonatal period were determined simultaneously.

Reversal of glucose-induced inhibition of newborn rat liver mitochondrial maturation by administration of alkylxanthines at birth

A glucose injection given immediately after birth delays the maturation which normally occurs in rat liver mitochondria and which increases the rate of ATP synthesis coupled to succinate oxidation from a low value at birth to the adult value a few hours after birth [R. Meister, J. Comte, L. Baggetto, C. Godinot and D. C. Gautheron, Biochim. biophys. Acta 722, 36 (1983)]. Alkylxanthine (pentoxifylline, HWA 285) administration at birth has no effect on the maturation of mitochondria prepared from 2-hr-old rat livers while DBcAMP administration increases their RCR and their rate of ATP synthesis. On the contrary, both alkylxanthines and DBcAMP reverse the glucose-induced inhibition of mitochondrial maturation. This DBcAMP effect cannot be mimicked by butyrate and is therefore related to cAMP. The cAMP content of rat liver increases during this postnatal period in both control and glucose-treated rats, although glucose administration tends to decrease the level of cAMP. Alkylxanthine administration restores after 2 hr the cAMP level in glucose-treated animals. The variations of RCR could not be completely correlated with the level of cAMP. The possible involvement of other factors in the mitochondrial maturation and the glucose effect is discussed.

Topography of oligomycin sensitivity conferring protein in the mitochondrial adenosinetriphosphatase-ATP synthase

The topographical organization of oligomycin sensitivity conferring protein (OSCP) in the mitochondrial adenosinetriphosphatase (ATPase)-ATP synthase complex has been studied. The accessibility of OSCP to monoclonal antibodies has been qualitatively visualized by using the protein A-gold electron microscopy immunocytochemistry or quantitatively estimated by immunotitration of OSCP in depolymerized or intact membranes. Besides, OSCP cannot be labeled by 3-(trifluoromethyl)-3-(m-[125I]iodophenyl)diazirine ([125I]TID) which selectively labels the hydrophobic core of membrane proteins. These observations demonstrate an external location of OSCP on the inner face of the inner mitochondrial membrane. The position of OSCP relative to other peptides of the complex has been analyzed by cross-linking experiments using either zero length N-(ethoxycarbonyl)-2-ethoxydihydroquinoline or 11-A span dimethyl suberimidate cross-linkers in the ATPase-ATP synthase complex. The OSCP cross-linked products were identified either by immunocharacterization with anti-alpha, anti-beta, or anti-OSCP monoclonal antibodies or by their molecular weight. OSCP was cross-linked with either the alpha- or beta-subunits of F1 or to a subunit of Mr 24 000. Other types of cross-linking were obtained by the labeling of OSCP with [cysteamine-35S]-N-succinimidyl 3-[[2-((2-nitro-4-azidophenyl)amino)ethyl]dithio]propionate ([35S]SNAP) and reconstitution of SNAP-OSCP with F1 in urea-treated submitochondrial particles. Under these conditions, OSCP is found to be adjacent to two other peptides of molecular weight close to 30 000. A comparison is made between the topology and the organization of the b-subunit of Escherichia coli and OSCP, suggesting an analogy between OSCP and the hydrophilic part of the b-subunit.

High phosphate requirement for oxidative phosphorylation and low affinity for phosphate transport in newborn rat liver mitochondria

Rat liver mitochondria are not fully functional at birth. The relationship between this deficiency and the affinity for phosphate, in oxidative phosphorylation or in phosphate transport, have been studied. The phosphate concentration necessary to observe maximal rate of succinate oxidation in the presence of ADP was higher for newborn than for adult rat liver mitochondria. After preincubation of newborn rat liver mitochondria with ATP, the rate of succinate oxidation in the presence of ADP increased with phosphate concentration similarly for newborn and adult rat liver mitochondria. The maximal rate of phosphate-acetate exchange, which is an indirect measure of the rate of phosphate transport across the mitochondrial membrane, was not significantly different for adult and newborn rat liver mitochondria. On the contrary the apparent affinity for phosphate was about ten-fold lower for newborn than for adult mitochondria.

Inhibitory effect of glucose on the maturation of rat liver mitochondria at birth. Phospholipid and oxidative metabolism

(1) The rate of ATP synthesis coupled with succinate oxidation in rat liver mitochondria is low at birth and increases rapidly during the first postnatal hours (Nakazawa, T., Asami, K., Suzuki, H. and Yakawa, O. (1973) J. Biochem. 73, 397-406). A glucose injection given to newborn rats immediately after birth seemed to delay this maturation process. (2) Glucose administration specifically diminished the rate of 32Pi incorporation into phosphatidylcholine both in microsomes and in mitochondria while other phospholipids remained unaffected. (3) In newborn rat liver, 32Pi incorporation into phospholipids can be explained by de novo synthesis of phospholipids in microsomes followed by transfer to mitochondria with two exceptions phosphatidylserine and sphingomyelin. Indeed, after a 20-min incorporation of 32Pi into phospholipids, the specific radioactivity of phosphatidylserine and sphingomyelin was higher in mitochondria than in microsomes. (4) As far as phospholipid synthesis is concerned, no precursor-product relationship could be observed between light and heavy mitochondria.

Vesicular preparation of a highly coupled ATPase-ATP synthase complex from pig heart mitochondria

1. A method is described to prepare an ATPase-ATP synthase complex from pig heart mitochondria exhibiting a very high ATP-32Pi exchange activity (1.6 mumol/min per mag protein in optimal conditions). 2. The preparation is virtually devoid of nucleoside diphosphokinase and adenylate kinase activities. 3. Freeze-fracture studies show that the ATPase-ATP synthase complex is integrated in lipid vesicles of 400-600 A in diameter. 4. It contains the endogenous natural proteic inhibitor which seems to behave as a coupling factor. 5. The rate of ATP hydrolysis catalyzed by the ATPase-ATP synthase complex is competitively inhibited by ADP, while the presence of ADP increases the initial rate of 32Pi incorporation into ATP. 6. The 32Pi incorporation into ATP can occur at a rate almost equal to that of nucleoside triphosphate (NTP) hydrolysis provided that the rate of NTP hydrolysis is kept low and that the ADP concentration is high enough. In these conditions, a very high coupling between NTP hydrolysis and ATP synthesis can be demonstrated.

Lipid composition and protein profiles of outer and inner membranes from pig heart mitochondria. Comparison with microsomes

1. Mitochondria, inner and outer mitochondrial membranes and microsomes were isolated and purified from pig heart. Their lipid composition and protein components were studied. 2. The fatty acid distribution in the main phospholipids seemed specific rather of a given phospholipid and not of one type of membrane. 3. Inner mitochondrial membranes were characterized by a high content in cardiolipin and a very low level of triglycerides together with a high degree of unsaturation and C18 acids. Gel electrophoresis revealed 13 different polypeptide subunits of which 5 were major ranging in molecular weights from 10000 to 215000. 4. In outer mitochondrial membranes, total lipid, phosphatidylcholine, phosphatidylinositol, plasmologen and triglyceride contents were much higher than in inner membranes. Fatty acids of phospholipids were mostly saturated and the polypeptide pattern showed 12 components, of which 4 were major of mol. wt 75000, 60000, 20000 and below 10000. 5. Compared to outer membrane, microsomes exhibited a much higher cholesterol content and markedly different protein profiles. They contained significant amounts of cardiolipin and phosphatidylserine, this latter phospholipid being exclusively located in microsomes. However odd similarities were observed in some lipid components of microsomes and inner mitochondrial membranes, but fatty acids were more saturated in microsomes and electrophoretic profiles of protein components appeared very different and revealed components of high mol. wt.