Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean

Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.

Widespread microbial mercury methylation genes in the global ocean

Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.

Widespread microbial mercury methylation genes in the global ocean

Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.

Widespread microbial mercury methylation genes in the global ocean

Methylmercury is a neurotoxin that bioaccumulates from seawater to high concentrations in marine fish, putting human and ecosystem health at risk. High methylmercury levels have been found in the oxic subsurface waters of all oceans, but only anaerobic microorganisms have been shown to efficiently produce methylmercury in anoxic environments. The microaerophilic nitrite-oxidizing bacteria Nitrospina have previously been suggested as possible mercury methylating bacteria in Antarctic sea ice. However, the microorganisms responsible for processing inorganic mercury into methylmercury in oxic seawater remain unknown. Here, we show metagenomic and metatranscriptomic evidence that the genetic potential for microbial methylmercury production is widespread in oxic seawater. We find high abundance and expression of the key mercury methylating genes hgcAB across all ocean basins, corresponding to the taxonomic relatives of known mercury methylating bacteria from Deltaproteobacteria, Firmicutes and Chloroflexi. Our results identify Nitrospina as the predominant and widespread microorganism carrying and actively expressing hgcAB. The highest hgcAB abundance and expression occurs in the oxic subsurface waters of the global ocean where the highest MeHg concentrations are typically observed.

The Ocean Gene Atlas: exploring the biogeography of plankton genes online

The Ocean Gene Atlas is a web service to explore the biogeography of genes from marine planktonic organisms. It allows users to query protein or nucleotide sequences against global ocean reference gene catalogs. With just one click, the abundance and location of target sequences are visualized on world maps as well as their taxonomic distribution. Interactive results panels allow for adjusting cutoffs for alignment quality and displaying the abundances of genes in the context of environmental features (temperature, nutrients, etc.) measured at the time of sampling. The ease of use enables non-bioinformaticians to explore quantitative and contextualized information on genes of interest in the global ocean ecosystem. Currently the Ocean Gene Atlas is deployed with (i) the Ocean Microbial Reference Gene Catalog (OM-RGC) comprising 40 million non-redundant mostly prokaryotic gene sequences associated with both Tara Oceans and Global Ocean Sampling (GOS) gene abundances and (ii) the Marine Atlas of Tara Ocean Unigenes (MATOU) composed of >116 million eukaryote unigenes. Additional datasets will be added upon availability of further marine environmental datasets that provide the required complement of sequence assemblies, raw reads and contextual environmental parameters. Ocean Gene Atlas is a freely-available web service at: http://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.

Abstract GS2-04: Efficacy results from CIBOMA/2004-01_GEICAM/2003-11 study: A randomized phase III trial assessing adjuvant capecitabine after standard chemotherapy for patients with early triple negative breast cancer

Background: Triple negative breast cancers (TNBC) have a greater risk of relapse than non-TNBC. New therapeutic approaches are needed for these patients (pts). CIBOMA/2004-01_GEICAM/2003-11 is a multinational, randomized phase III trial exploring adjuvant capecitabine (X) after completion of standard treatment in early TNBC pts.

Materials and Methods: Patients with operable, node-positive (or node-negative with tumor size ≥ 1 cm), centrally confirmed hormone receptor-negative, HER2-negative early BC, who had received 6–8 cycles (cy) of standard anthracycline and/or taxane-containing chemotherapy or 4 cy of doxorubicin-cyclophosphamide (for node-negative disease) in the (neo)adjuvant setting, were eligible. Patients were randomized to either 8 cy of X (1,000 mg/m2 bid, days 1–14, every 3 weeks) or observation. Stratification factors included center, prior taxane-based therapy, number of involved axillary lymph nodes and phenotype (basal vs non-basal, according to cytokeratins 5/6 and/or EGFR positivity). The primary objective was to compare the disease-free survival (DFS) between both treatment arms, and secondary objectives included the comparison in terms of 5-year DFS, overall survival (OS) and safety. Assuming a 30% risk reduction in DFS rate at 5 years (from 64.7% to 73.7%, hazard ratio 0.70) with 80% power and a two-tailed log-rank test at 0.05, 834 evaluable pts were needed. 876 pts had to be finally enrolled considering a drop-out rate of 5%.

Results: Recruitment of 876 pts from 8 countries was completed in September 2011. Median age was 49 years; 68.5% of pts were postmenopausal, 55.5% were lymph node negative, 71.7% had a basal phenotype, 67.5% received chemotherapy based on anthracyclines and taxanes. Median follow-up was 7.3 years (range 0.0 to 11.1). DFS was not significantly prolonged with X vs observation (hazard ratio (HR) 0.82; 95% confidence interval (CI), 0.63 to 1.06; P=0.1353). Five-year DFS was 79.6% (95% CI, 75.8% to 83.4%) with X and 76.8% (95% CI, 72.7% to 80.9%) with observation. OS was not statistically different between treatment arms (HR 0.92; 95% CI, 0.66 to 1.28; P=0.6228). In subgroup analysis for DFS, we found no statistically significant interaction between X treatment and different subgroups, with the exception of basal vs non-basal phenotypes (basal HR 0.97, 95% CI 0.72 to 1.32, P=0.8620; non-basal HR 0.51, 95% CI, 0.31 to 0.86, P=0.0101; interaction P=0.0357). Similar results were found for OS (basal HR 1.20, 95% CI 0.81 to 1.77, P=0.3684; non-basal HR 0.48, 95% CI, 0.26 to 0.91, P=0.0205; interaction P=0.0155). 75.2% of pts completed 8 cy of X, with a median relative dose intensity of 86.3%. Grade (G) 3 or higher adverse events (AEs) were observed in 40.4% of pts in X arm. In 9.6% of pts the AEs were related with X. Hand-foot syndrome was the most common AE in X arm (G3 on 18.8% of pts).

Conclusions: In our study, the addition of adjuvant X after standard (neo) adjuvant anthracycline and/or taxane-containing chemotherapy was not associated with a statistically significant improvement of DFS or OS compared to observation in pts with early TNBC. However, in a subgroup analysis a significant DFS and OS improvement was observed with X in pts with non-basal phenotype.

Sponsor: CIBOMA.

Citation Format: Martín M, Barrios CH, Torrecillas L, Ruiz-Borrego M, Bines J, Segalla J, Ruiz A, García-Sáenz JA, Torres R, de la Haba J, García E, Gómez HL, Llombart A, Rodríguez de la Borbolla M, Baena JM, Barnadas A, Calvo L, Pérez-Michel L, Ramos M, Castellanos J, Rodríguez-Lescure A, Cárdenas J, Vinholes J, Martínez de Dueñas E, Godes MJ, Seguí MA, Antón A, López-Álvarez P, Moncayo J, Amorim G, Villar E, Reyes S, Sampaio C, Cardemil B, Escudero MJ, Bezares S, Carrasco E, Lluch A. Efficacy results from CIBOMA/2004-01_GEICAM/2003-11 study: A randomized phase III trial assessing adjuvant capecitabine after standard chemotherapy for patients with early triple negative breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr GS2-04.

Improving survival in end-stage renal disease: A case study

Background: With the increase of life expectancy, *On behalf of the REIN registry. end-stage renal disease (ESRD) is affecting a growing number of people. Simultaneously, renal replacement therapies (RRTs) have considerably improved patient survival. We investigated the way current RRT practices would affect patients' survival.

Methods: We used a multi-state model to represent the transitions between RRTs and the transition to death. The concept of “crude probability of death” combined with this model allowed estimating the proportions of ESRD-related and ESRD-unrelated deaths. Estimating the ESRD-related death rate requires comparing the mortality rate between ESRD patients and the general population. Predicting patients' courses through RRTs and Death states could be obtained by solving a system of Kolmogorov differential equations. The impact of practice on patient survival was quantified using the restricted mean survival time (RMST) which was compared with that of healthy subjects with same characteristics.

Results: The crude probability of ESRD-unrelated death was nearly zero in the youngest patients (18–45 years) but was a sizeable part of deaths in the oldest (≥70 years). Moreover, in the oldest patients, the proportion of expected death was higher in patient without vs. with diabetes because the former live older. In men aged 75 years at first RRT, the predicted RMSTs in patients with and without diabetes were, respectively, 61% and 69% those of comparable healthy men.

Conclusion: Using the concept of “crude probability of death” with multi-state models is feasible and useful to assess the relative benefits of various treatments in ESRD and help patient long-term management.

Promoting healthy lives and well-being for all: The contribution of the International College of Person-Centered Medicine (ICPCM)

This article defines the scope of Person-Centered Medicine, traces its roots in ancient conceptions, explains the reasons for the revival of this perspective in our times, and highlights the contribution of the International College of Person-Centered Medicine (ICPCM) in the promotion of the personcentered perspective in health and disease. The value of communication is underlined with reference to both diagnosis and treatment. The concept of Health is considered historically and the inclusiveness, holistic vista and positive health orientation of the WHO definition of Health (1948) is underlined. It is emphasized that Mental Health Promotion is differentiated conceptually from Disease Prevention in that promotion deals with health and prevention deals with illness, the relationship of Health Promotion with Salutogenesis (Antonovsky 1996) is noted and it is pointed out that among the targets of health promotion, preservation of peace is also included (WHO, 2004). In line with this, the ICPCM has supported and co-signed the Athens Anti-War Declaration (2016). Evaluating the impact of Health Promotion efforts is a necessary but difficult task as it requires targeted research and there are many inherent confounding factors. The social or environmental contexts of health behaviors should be taken into account as well as the subjective indicators of health. In an attempt to resolve the difficulties arising from this issue, the ICPCM has developed a prototype "Person-centered Care Index" (Kirisci et al 2016). With reference to Education it is pointed out that it is necessary for the educators to speak with the students rather than speak to them. Concerning research, the ICPCM in its 2013 Geneva Declaration has identified the main research areas in the person-centered field. The importance of assuring healthy lives and well-being for ALL is underlined and the difficulties associated with the achievement of this goal are noted. Lastly, the need to apply the principles of Person-centered Medicine to victims of natural, human-made and economic disasters (Christodoulou et al 2016) is underlined, especially in view of the frequent occurrence of these disasters in our times. In conclusion, the contribution of the ICPCM during the ten years of its existence, with reference to the sensitization of health professionals in the Person-centered approach is noted. This contribution has been carried out in line with the principles of the ICPCM and with its Geneva Declarations.

A Simple Modeling-free Method Provides Accurate Estimates of Sensitivity and Specificity of Longitudinal Disease Biomarkers

Objective: To assess the time-dependent accuracy of a continuous longitudinal biomarker used as a test for early diagnosis or prognosis.

Methods: A method for accuracy assessment is proposed taking into account the marker measurement time and the delay between marker measurement and outcome. It dealt with markers having interval-censored measurements and a detection threshold. The threshold crossing times were assessed by a Bayesian method. A numerical study was conducted to test the procedures that were later applied to PCR measurements for prediction of cytomegalovirus disease after renal transplantation.

Results: The Bayesian method corrected the bias induced by interval-censored measurements on sensitivity estimates, with corrections from 0.07 to 0.3. In the application to cytomegalovirus disease, the Bayesian method estimated the area under the ROC curve to be over 75% during the first 20 days after graft and within five days between marker measurement and disease onset. However, the accuracy decreased quickly as that delay increased and late after graft.

Conclusions: The proposed Bayesian method is easy to implement for assessing the time-dependent accuracy of a longitudinal biomarker and gives unbiased results under some conditions.

Abstract P3-07-14: Prosigna® intrinsic subtyping predicts response to neoadjuvant combination therapy in study that includes herceptin within HER2+ (IHC) patients

Background: The role of the HER2-enriched (HER2E) subtype determined by the Prosigna Assay in the neoadjuvant setting has remained largely uncharacterized. In this study, we examine whether Prosigna can identify a subgroup of HER2+ patients for whom combination neoadjuvant therapy that includes trastuzumab (Herceptin) is associated with a greater likelihood of pathological complete response (pCR). Methods: In this single-arm retrospective analysis, 75 patients determined to be HER2+ by IHC were treated with a neoadjuvant regimen (NAC) consisting of 8-12 cycles of anthracyclines and taxanes as well as Herceptin. The Prosigna Assay was performed on the NanoString nCounter® Dx Analysis System at HU Virgende la Victoria de Málaga/CIMES-UMA. pCR was used as the endpoint for this study and was determined using the Miller & Payne scoring criteria. Results: Mean patient age for this study population was 49 (±11.1yr) and all patients were determined to be HER2+ by IHC. The overall pCR rate in this patient population was 46.2%. Of the 75 patient samples analyzed for this study, 59 (78.6%) were HER2E, 4 (5.3%) were Luminal A and 12 (16.1%) were Luminal B, as identified by the Prosigna Assay. Of the 16 tumors classified as Luminal (A or B) by Prosigna within this HER2+ population, only 2 (12.5%) responders were observed. Categorical analysis revealed that Prosigna subtype predicted response to a NAC regimen combined with Herceptin (Odds ratio [Her2E vs. non-Her2E]=6.4, p=0.023). Further analysis of the Her2E subtype revealed that tumors with profile expression that correlated well with the prototypical Her2E centroid were significantly more likely to respond to combination NAC and Herceptin (Odds ratio [Unit increase of 1 in Her2E correlation]=88.2, p=0.004). Conclusions: The results of this study indicate that HER2+ patients with greater correlations to the HER2E subtype have an increased likelihood of response to combination neoadjuvant regimens that included HER2-targeted therapy.

Citation Format: Santonja Á, Ribelles N, Jiménez-Rodríguez B, Sánchez Rovira P, Álvarez M, Vicioso L, Isabel Fernandez A, de Luque V, Fernández de Sousa C, Villar E, Zarcos I, Ramírez C, González-Hermoso C, Jeiranian A, Dowidar N, Schaper C, Buckingham W, Ferree S, Jiménez A, Prat A, Alba E. Prosigna® intrinsic subtyping predicts response to neoadjuvant combination therapy in study that includes herceptin within HER2+ (IHC) patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-14.

Ocean plankton. Environmental characteristics of Agulhas rings affect interocean plankton transport

Agulhas rings provide the principal route for ocean waters to circulate from the Indo-Pacific to the Atlantic basin. Their influence on global ocean circulation is well known, but their role in plankton transport is largely unexplored. We show that, although the coarse taxonomic structure of plankton communities is continuous across the Agulhas choke point, South Atlantic plankton diversity is altered compared with Indian Ocean source populations. Modeling and in situ sampling of a young Agulhas ring indicate that strong vertical mixing drives complex nitrogen cycling, shaping community metabolism and biogeochemical signatures as the ring and associated plankton transit westward. The peculiar local environment inside Agulhas rings may provide a selective mechanism contributing to the limited dispersal of Indian Ocean plankton populations into the Atlantic.

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.

Individual and regional factors of access to the renal transplant waiting list in france in a cohort of dialyzed patients

Several studies have investigated geographical variations in access to renal transplant waiting lists, but none has assessed the impact on these variations of factors at both the patient and geographic levels. The objective of our study was to identify medical and non-medical factors at both these levels associated with these geographical variations in waiting-list placement in France. We included all incident patients aged 18-80 years in 11 French regions who started dialysis between January 1, 2006, and December 31, 2008. Both a multilevel Cox model with shared frailty and a competing risks model were used for the analyses. At the patient level, old age, comorbidities, diabetic nephropathy, non-autonomous first dialysis, and female gender were the major determinants of a lower probability of being waitlisted. At the regional level, the only factor associated with this probability was an increase in the number of patients on the waiting list from 2005 to 2009. This finding supports a slight but significant impact of a regional organ shortage on waitlisting practices. Our findings demonstrate that patients' age has a major impact on waitlisting practices, even for patients with no comorbidity or disability, whose survival would likely be improved by transplantation compared with dialysis.

Description of the pig production systems, biosecurity practices and herd health providers in two provinces with high swine density in the Philippines

A cross-sectional study was conducted between October 2011 and March 2012 in two major pig producing provinces in the Philippines. Four hundred and seventy one pig farms slaughtering finisher pigs at government operated abattoirs participated in this study. The objectives of this study were to group: (a) smallholder (S) and commercial (C) production systems into patterns according to their herd health providers (HHPs), and obtain descriptive information about the grouped S and C production systems; and (b) identify key HHPs within each production system using social network analysis. On-farm veterinarians, private consultants, pharmaceutical company representatives, government veterinarians, livestock and agricultural technicians, and agricultural supply stores were found to be actively interacting with pig farmers. Four clusters were identified based on production system and their choice of HHPs. Differences in management and biosecurity practices were found between S and C clusters. Private HHPs provided a service to larger C and some larger S farms, and have little or no interaction with the other HHPs. Government HHPs provided herd health service mainly to S farms and small C farms. Agricultural supply stores were identified as a dominant solitary HHP and provided herd health services to the majority of farmers. Increased knowledge of the routine management and biosecurity practices of S and C farmers and the key HHPs that are likely to be associated with those practices would be of value as this information could be used to inform a risk-based approach to disease surveillance and control.

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 10⁴–10⁵ genomes ml⁻¹ for the samples from the photic zone and 10²–10³ genomes ml⁻¹ for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.

East African cassava mosaic-like viruses from Africa to Indian ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus

BACKGROUND

Cassava (Manihot esculenta) is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD). Caused by a complex of bipartite cassava mosaic geminiviruses (CMG) species (Family: Geminivirideae; Genus: Begomovirus) CMD has been widely described throughout Africa and it is apparent that CMG's are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO) islands.

RESULTS

The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV). Phylogeographic analyses suggest that CMG's presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. While only two recombination events characteristic of SWIO islands isolates were identified, numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components.

CONCLUSIONS

Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain both their propensity to exchange components and the absence of recombination with non-CMG begomoviruses. Our results suggest an important role of anthropic factors in CMGs spread as the principal axes of viral migration correspond with major routes of human movement and commercial trade. Finer-scale temporal analyses of CMGs to precisely scale the relative contributions of human and insect transmission to their movement dynamics will require further extensive sampling in the SWIO region.

Proteomic plasticity of two Eucalyptus genotypes under contrasted water regimes in the field

Water deficit affects tree growth and limits wood production. In an attempt to identify the molecular triggers of adaptation mechanisms to water deficit in Eucalyptus, we investigated protein expression patterns of two ecophysiologically contrasted Eucalyptus genotypes. They were grown in the field in either natural conditions or irrigated for 7 weeks during the dry season in the Republic of Congo. At the phenotypic level, genotype (G), treatment (T) and/or G × T interaction effects were observed for above- and below-ground biomass-related traits. At the molecular level, changes in protein abundance were recorded in leaves (acidic pH 4-7, and basic pH 7-11, proteomes) and stems (acidic proteome) using two-dimensional gel electrophoresis (2-DE). One third of the detected protein spots displayed significant G, T and/or G × T effects, and 158 of them were identified by tandem mass spectrometry (LC-MS/MS) analysis. Thus, several proteins whose molecular plasticity was genetically controlled (i.e. G × T effect) were revealed, highlighting adaptive mechanisms to water deficit specific to each genotype, namely cell wall modification, cell detoxification and osmoregulation. Transcript abundances corresponding to G × T proteins were also investigated by quantitative RT-PCR. These proteins represent relevant targets to improve drought resistance in this ecologically and economically important forest tree genus.

RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus

BACKGROUND

In a context of climate change, phenotypic plasticity provides long-lived species, such as trees, with the means to adapt to environmental variations occurring within a single generation. In eucalyptus plantations, water availability is a key factor limiting productivity. However, the molecular mechanisms underlying the adaptation of eucalyptus to water shortage remain unclear. In this study, we compared the molecular responses of two commercial eucalyptus hybrids during the dry season. Both hybrids differ in productivity when grown under water deficit.

RESULTS

Pyrosequencing of RNA extracted from shoot apices provided extensive transcriptome coverage - a catalog of 129,993 unigenes (49,748 contigs and 80,245 singletons) was generated from 398 million base pairs, or 1.14 million reads. The pyrosequencing data enriched considerably existing Eucalyptus EST collections, adding 36,985 unigenes not previously represented. Digital analysis of read abundance in 14,460 contigs identified 1,280 that were differentially expressed between the two genotypes, 155 contigs showing differential expression between treatments (irrigated vs. non irrigated conditions during the dry season), and 274 contigs with significant genotype-by-treatment interaction. The more productive genotype displayed a larger set of genes responding to water stress. Moreover, stress signal transduction seemed to involve different pathways in the two genotypes, suggesting that water shortage induces distinct cellular stress cascades. Similarly, the response of functional proteins also varied widely between genotypes: the most productive genotype decreased expression of genes related to photosystem, transport and secondary metabolism, whereas genes related to primary metabolism and cell organisation were over-expressed.

CONCLUSIONS

For the most productive genotype, the ability to express a broader set of genes in response to water availability appears to be a key characteristic in the maintenance of biomass growth during the dry season. Its strategy may involve a decrease of photosynthetic activity during the dry season associated with resources reallocation through major changes in the expression of primary metabolism associated genes. Further efforts will be needed to assess the adaptive nature of the genes highlighted in this study.

The immediate effects of diacutaneous fibrolysis on pain and mobility in patients suffering from painful shoulder: a randomized placebo-controlled pilot study

OBJECTIVES

To describe the immediate effects of diacutaneous fibrolysis on pain and mobility in patients suffering from painful shoulder, and to assess the ability of the placebo technique to blind participants to group allocation.

DESIGN

A double-blind before-after randomized placebo-controlled pilot study.

SETTING

Two public centres of Primary Health Care of the Spanish National Health System.

PARTICIPANTS

Fifty patients (29 women, 21 men) with a diagnosis of painful shoulder of subacromial origin were included.

INTERVENTION

Participants were randomly allocated to one of two groups. The intervention group (N = 25) was actually treated with diacutaneous fibrolysis, while the placebo group (N = 25) was treated with placebo diacutaneous fibrolysis.

MEASUREMENTS

Active range of motion (flexion, abduction, extension, external and internal rotation) and pain intensity in the hand-behind-back position were measured. Participants were also asked about their perception in terms of comfort of the technique and results obtained.

RESULTS

Between-groups differences were significant in flexion (mean 11.4 degrees; 95% confidence interval (CI) 5.7-17.1), abduction (mean 7.2 degrees; 95% CI 2.0-12.5) and internal rotation movements (mean 3.1 cm; 95% CI 0.1-6.1). There were no significant differences between groups in pain intensity, extension or external rotation movements. The placebo technique showed its ability to blind participants to group allocation. None of the participants suffered any adverse effects from diacutaneous fibrolysis.

CONCLUSION

Diacutaneous fibrolysis may be an effective and safe therapeutic option to improve active range of motion in patients suffering from painful shoulder.

Simultaneous detection of anti-C1q and anti-double stranded DNA autoantibodies in lupus nephritis: predictive value for renal flares

Clinical difficulties in predicting systemic lupus erythematosus (SLE) renal flares are still encountered. Biological markers such as autoantibodies (aAbs) may be of major interest for clinicians in the follow-up of SLE patients. The aim of our study was to investigate the clinical utility of one of these biological markers, anti-C1q aAbs, in predicting renal flares of SLE nephritis in comparison with the 'gold standard' anti-double stranded DNA (anti-dsDNA) aAbs. Anti-C1q aAbs and anti-dsDNA aAbs were analysed through a longitudinal retrospective study of 23 SLE patients presenting with one or more renal flares. Anti-C1q and/or anti-dsDNA aAbs were found in 20 (87%) of 23 patients, of whom 16 (69%) displayed both. Thirty-three renal flares occurred during the course of the study, and anti-C1q aAbs and anti-dsDNA aAbs were positive in 25 (76%) and 24 (73%) of these flares respectively. The sensitivity of anti-C1q and/or anti-dsDNA aAbs in predicting renal flares reached 85%. The specificity of anti-C1q aAbs was 84%, of anti-dsDNA aAbs 77% and of both aAbs 97%. Positive and negative predictive values were as follows: 56% and 70% for anti-C1q aAbs, 53% and 72% for anti-dsDNA aAbs. The combination of both aAbs had the highest positive predictive value (69%), whereas absence of both aAbs was associated with the highest negative predictive value (74%). In conclusion, our results confirm that anti-C1q aAbs are present in a significant percentage of SLE patients with active renal involvement, suggesting that these aAbs could be a useful additional marker. The presence of anti-C1q and anti-dsDNA aAbs was associated with a high risk of renal flare, whereas the absence of both aAbs excluded such an event. These data confirm that systematic detection of anti-C1q and anti-dsDNA aAbs is of interest for the follow-up in SLE patients with renal involvement.

Effect of type 2 diabetes on mortality risk associated with end-stage kidney disease

AIMS/HYPOTHESIS

Patients with end-stage kidney disease (ESKD) and patients with diabetes mellitus experience higher mortality rates than the general population. Whether ESKD imparts the same excess in mortality risk for those with diabetes as it does for those without diabetes is unknown.

METHODS

Included in the study were all white patients aged > or =25 years with incident ESKD and type 2 diabetes (n = 4,141) or with incident ESKD but without diabetes (n = 13,289) in Australia from 1991 to 2005, and all the individuals aged > or =25 years without ESKD and with type 2 diabetes (n = 909) or without ESKD without diabetes (n = 10,302) enrolled in the AusDiab Study--a nationwide Australian representative cohort--from 1999 to 2005. Excess mortality was analysed in patients with ESKD by diabetes status, using age-, sex- and diabetes-status-specific standardised mortality ratios (SMRs) in the first 8 years after first renal replacement therapy among ANZDATA patients relative to AusDiab participants.

RESULTS

The SMRs in patients with ESKD were, in non-diabetic patients and in those with type 2 diabetes, respectively: 14.2 (95% CI 13.9-14.6) and 10.8 (95% CI 10.4-11.2) (p < 0.01); in people aged <60 years, 28.7 (95% CI 27.2-30.4) and 18.6 (95% CI 17.1-20.4) (p < 0.01); in people aged > or =60 years, 12.5 (95% CI 12.1-12.9) vs 9.7 (95% CI 9.3-10.1) (p < 0.01); in men, 11.0 (95% CI 10.7-11.4) vs 8.9 (95% CI 8.4-9.3) (p < 0.01); and in women, 23.4 (95% CI 22.5-24.3) vs 16.2 (95% CI 15.2-17.3) (p < 0.01).

CONCLUSIONS/INTERPRETATION

ESKD was associated with a greater relative increase in mortality in the non-diabetic study populations than in the type 2 diabetes population. Excess mortality was greater among younger people and women.

Conservative treatment with transurethral resection, neoadjuvant chemotherapy followed by radiochemotherapy in stage T2-3 transitional bladder cancer

PURPOSE

Organ preservation has been investigated in patients (p) with infiltrating transitional cell carcinoma (TCC) of the bladder over the past decade as an alternative to radical cystectomy. This is a trimodal schedule study, including transurethral resection of bladder tumor (TURB), neoadjuvant chemotherapy and concomitant radiochemotherapy (RTC).

PATIENTS AND METHODS

From April 1996 until August 2005, 29 evaluable patients (p) with T2-T3NXM0 bladder cancer were enrolled. After a transurethral resection of bladder tumor (TURB), we administered 2 cycles of induction chemotherapy with CMV (15 p) or Gemcitabine-Cisplatin (14 p) followed by radiotherapy 45 Gy 1.8 Gy/fraction and two cycles of concomitant cisplatin 70 mg/m(2). 2-3 weeks later, a cystoscopy with tumor-site biopsy was performed. If complete histological response, p were treated with consolidation radiotherapy until 64.8 Gy. For p with residual or recurrent tumor, cystectomy was performed.

RESULTS

We included 28 men and 1 women (median age 63, range 39-72 years) with PS (ECOG) 0-1. The stage was: 21 p T2; 6 p T3a; and 2 p T3b. Toxicity was higher in CMV compared with Gem- Cis: grade (3/4) neutropenia 4/15 (26%) vs 1/14 (7%); febrile neutropenia 3/15 (20%) vs 1/14 (7%); grade (3/4) trombocytopenia 2/15 (13%) vs 1/14 (7%). Toxicities with concomitant RCT were low-moderate: urocystitis (26%) and enteritis (18%).

RESPONSE

microscopically complete TURB was obtained in 20 p (69%), but not in 9 p (31%) (7 microscopic, and 2 macroscopic residual tumor). We found a complete histologic response after induction RCT in 25 p (86%). After a median follow-up of 69.4 months (m) (range: 8-97.7), there were 8 deaths, with a overall survival of 72%. Furthermore 14 of 29 p (48%) were alive with intact bladder, and median survival time with intact bladder was 63.6 m (50.1-77.2); were predictive of best outcome T2 stage vs T3 (p < 0.0001), and complete histologic resection in initial TURB vs residual tumor (p = 0.0004).

CONCLUSIONS

Combined treatment provide high response rates and can be offered as an alternative option to radical cystectomy in selected patients with TCC. Patients with T2 stage and complete histologic resection in initial TURB had the best outcome.

Chapitre B - Insuffisance rénale et vessie neurologique

Historically, impaired renal function was the leading cause of death in spinal cord injury patients. Although the management of these patients has considerably improved due to progress in functional rehabilitation and neurourology, renal failure remains a significant cause of morbidity in this population. In this article, the authors review and classify the diagnostic tools able to detect urological changes likely to induce irreversible impairment of renal function. Based on a review of the recent literature, they define the incidence of renal impairment (morphological or function) in spinal cord injury patients and describe the main risk factors for deterioration of renal function in these patients.

Prediction of relapse by day 100 BCR-ABL quantification after allogeneic stem cell transplantation for chronic myeloid leukemia

Chronic myeloid leukemia (CML) relapse after allogeneic stem cell transplantation (SCT) is a relatively frequent situation, which is correlated to disease status, time from diagnosis to transplant and T-cell depletion. We evaluated the potential for early minimal residual disease (MRD) BCR-ABL quantification to predict relapse of CML patients receiving allogeneic SCT. Minimal residual disease was analyzed by real-time quantitative reverse transcriptase-polymerase chain reaction (RQ-PCR) at day 100 (d100) in 38 patients with >1 year follow-up after conventional non-T-cell-depleted SCT. Normal ABL control values from 1724 follow-up blood samples were used to define an RQ-PCR amplifiability index and the limits of reliable use of BCR-ABL ratios. We then compared the 14 patients with a high-level d100 BCR-ABL/ABL ratio (> or = 10(-4)) to that of the 24 patients with a negative/low-level ratio (<10(-4)). Despite being comparable for all classical parameters, the incidence of relapse was significantly higher in the high MRD group (11/14 (79%)) compared to that of the low/negative MRD group (7/24 (29%)) (P = 0.009), with d100 MRD values representing an independent risk factor of relapse and disease-free survival, but not of overall survival, in multivariate analysis. These data should facilitate risk-adapted post-transplant immunosuppression and/or tyrosine kinase inhibitor therapy based on an early evaluation of MRD.

Chronic renal failure and end-stage renal disease are associated with a high rate of mortality after heart transplantation

The aim of the study was to analyze the etiology, the factors for progression of chronic renal failure to end-stage-renal disease (ESRD), and the influence of ESRD on the survival rate among a cohort of 59 heart transplant patients (HTP) referred for the management of chronic renal failure (CRF). At the time of the first nephrology consultation (6 +/- 4.25 years after cardiac transplantation) the mean creatininemia was 261.5 +/- 99 micromol/L and mean creatinine clearance (Cockcroft formula) was 32 +/- 15 mL/min. The cause of CRF were calcineurin inhibitor toxicity in 38.9% of patients, vascular events in 15.2%, hemolytic uremic syndrome in 5%, membranous glomerulopathy in 3.3%, diabetes in two patients, focal/segmental glomerulosclerosis in 3.3%, renal hypoplasia in 1.7%, and unknown in 27%. Evolution to ESRD occurred in 38.9% of patients: 17 patients started hemodialysis, three peritoneal dialysis, and two received a preemptive kidney transplantation. Creatininemia (micromol/L) at the time of nephrology referral was 229.2 +/- 72.6 versus 315.8 +/- 113.4 (P < .001) and creatinine clearance (mL/min) was 34.9 +/- 15.1 versus 27.3 +/- 13.7 (P = .049) for patients with CRF versus ESRD, respectively. Both proteinuria (g/24 hours) of 1 +/- 2.2 versus 2.3 +/- 1.8 (P = .02) and tobacco use in 35.1% versus 54.4% (P = .045) were significantly associated with progression of CRF, while age at the time of heart transplantation, cause of cardiac failure and renal failure, high blood pressure, type 2 diabetes, dyslipidemia, alcoholism, cirrhosis, and cerebral vascular accident were not. Death occurred in 18 HTP: 50% of patients with ESRD and 18.5% of patients with CRF-a 2.6 relative risk of of death in HTP patients with ESRD compared with HTP with CRF only (P < .01).

Weekly Irinotecan (CPT-11) in 5-FU Heavily Pretreated and Poor-Performance-Status Patients with Advanced Colorectal Cancer

Irinotecan (CPT-11) is an effective drug in patients with advanced colorectal cancer (CRC). Little is known about its efficacy and safety in previously treated patients with poor performance status. We prospectively evaluated the antitumor efficacy and safety of CPT-11 monotherapy in this setting. Thirty-four patients with poor performance status (Karnofsky score between 60 and 80) and/or progressing on one or more previous 5-FU-based chemotherapy lines for advanced colorectal adenocarcinoma were enrolled in this study. Treatment consisted of irinotecan (CPT-11) at 100 mg/m(2) administered as a 60-min iv infusion every week for four consecutive weeks followed by a 2-wk rest period until disease progression or unacceptable toxicity. The overall objective response rate (WHO criteria) for the 34 patients included was 20.6% [95% confidence interval (CI): 6.3%-34.9%]. Stable disease was obtained in 13 patients (38.2%) and 14 patients (41.2%) progressed. The median time to disease progression was 5.5 mo (range: 0.9-17.5) and the median survival was 8.3 mo (95% CI: 1.7-16.9). Overall, weekly CPT-11 was well tolerated with grade 3/4 neutropenia as the main hematological toxicity (11 patients: 32.4%; 14 infusions: 3.3%), and delayed diarrhea (10 patients: 29.4%; 16 infusions: 3.8%) as the main grade 3/4 non-hematological toxicity. In conclusion, weekly CPT-11 at 100 mg/m(2) for four consecutive weeks followed by a 2-wk rest period showed antitumor efficacy and may be safely administered to heavily pretreated patients with advanced colorectal cancer and a poor performance status. Weekly CPT-11 monotherapy may be considered as a therapeutic option for this population of patients.

[A tool to predict the resources necessary for the whole hemodialysis population]

Predicting the resources necessary for the treatment of terminal renal insufficiency requires an understanding of the needs of the whole dialysis population. This study evaluates the advantages of a complete evaluation grid for care needs (CG, 47 items) compared with a simplified version (SG) and with the data obtained from REIN (R) as a tool for predicting the required resources. Compared to CG, the two other classifications under-estimate the level of care needed and the prevalence of patients who have at least one condition resulting in an 'excess' of needs. In a system with three types of structures, the theoretical distribution of patients according to the CG is: in structure A (permanent medical presence): 43.4% (vs 39 for SG and 21% for R); in structure B (intermediate): 34% (vs 31.5 and 24.7% respectively); and in structure C (independent): 22.3% (vs 29.5 and 53.5%) of patients. The care needs scores of populations assigned by R to home dialysis are incompatible with the resources allocated to it. With a certain number of adjustments and qualifications, a population study using a simplified needs grid could enable a prediction of the resources which need to be provided. The patients' records which take precedence in the future REIN should be modified in order to make possible a regular evaluation of the appropriateness of the resources allocated.

Expression of bax and p53 proteins in the tumorigenesis and progression of breast carcinomas

OBJECTIVES

Dysregulation of normal programmed cell death mechanisms plays an important role in the pathogenesis of breast cancer. The purpose of this study was to investigate the role of bax and p53 expression in tumorigenesis and progression of breast carcinoma as well as their relationship with proliferative and apoptotic activity.

METHODS

We used immunohistochemical methods and in situ detection of apoptotic cells to examine 30 carcinomas in situ (CIS), 131 invasive breast carcinomas and 45 lymph node metastases.

RESULTS

In 25% (33 of 131) of invasive breast carcinomas examined, bax expression was absent, while p53 accumulation was present in 37% (49 of 131). Interestingly, p53 accumulation and loss of bax expression occur in breast CIS as frequently as in invasive breast carcinoma. Thus, in 17% (5 of 30) of CIS bax expression was absent, and 30% (9 of 30) presented nuclear expression of p53. p53 accumulation was related to apoptosis and proliferative activity. However, the protein level of bax was unrelated to all parameters studied, including proliferation and apoptosis of tumor cells. A multivariate analysis of disease-free survival demonstrated that p53 accumulation and bax expression are not significant independent indicators of prognosis in operable breast carcinoma. Our results also show that the proportion of bax- and p53-positive cells does not vary between primary and metastatic tumors.

CONCLUSIONS

p53 accumulation and loss of bax expression influence the acquisition of a malignant phenotype but seem to have no further impact on tumor progression.

Mode of action of two inhibitory peptides from heptad repeat domains of the fusion protein of Newcastle disease virus

Peptides derived from heptad repeat (HR) sequences of viral fusion proteins from several enveloped viruses have been shown to inhibit virus-mediated membrane fusion but the mechanism remains unknown. To further investigate this, the inhibition mechanism of two HR-derived peptides from the fusion protein of the paramyxovirus Newcastle disease virus (NDV) was investigated. Peptide N24 (residues 145-168) derived from HR1 was found to be 145-fold more inhibitory in a syncytium assay than peptide C24 (residues 474-496), derived from HR2. Both peptides failed to block lipid-mixing between R18-labeled virus and cells. None of the peptides interfered with the binding of hemagglutinin-neuraminidase (HN) protein to the target cells, as demonstrated by hemagglutining assays. When both peptides were mixed at equimolar concentrations, their inhibitory effect was abolished. In addition, both peptides induced the aggregation of negatively charged and zwitterionic phospholipid membranes. The ability of the peptides to interact with each other in solution suggests that these peptides may bind to the opposite HR region on the protein whereas their ability to interact with membranes as well as their failure to block lipid transfer suggest a second binding site. Taken together these results, suggest a mode of action for C24 and N24 in which both peptides have two different targets on the F protein: the opposite HR sequence and their corresponding domains.

Fusogenic activity of reconstituted newcastle disease virus envelopes: a role for the hemagglutinin-neuraminidase protein in the fusion process

Enveloped viruses, such as newcastle disease virus (NDV), make their entry into the host cell by membrane fusion. In the case of NDV, the fusion step requires both transmembrane hemagglutinin-neuraminidase (HN) and fusion (F) viral envelope glycoproteins. The HN protein should show fusion promotion activity. To date, the nature of HN-F interactions is a controversial issue. In this work, we aim to clarify the role of the HN glycoprotein in the membrane fusion step. Four types of reconstituted detergent-free NDV envelopes were used, on differing in their envelope protein contents. Fusion of the different virosomes and erythrocyte ghosts was monitored using the octadecyl rhodamine B chloride assay. Only the reconstituted envelopes having the F protein, even in the absence of HN protein, displayed residual fusion activity. Treatment of such virosomes with denaturing agents affecting the F protein abolished fusion, indicating that the fusion detected was viral protein-dependent. Interestingly, the rate of fusion in the reconstituted systems was similar to that of intact viruses in the presence of the inhibitor of HN sialidase activity 2,3-dehydro-2-deoxy-N-acetylneuraminic acid. The results show that the residual fusion activity detected in the reconstituted systems was exclusively due to F protein activity, with no contribution from the fusion promotion activity of HN protein.

Abnormal expression of acid glycosidases in seminal plasma and spermatozoa from infertile men with varicocele

The activities of acid beta-glucuronidase, alpha-mannosidase, alpha-glucosidase, alpha-galactosidase, beta-galactosidase and beta-N-acetylglucosaminidase were analysed in seminal plasma and spermatozoa from 26 infertile men with varicocele and from 36 men of normal fertility. Semen samples from ten men with non-obstructive azoospermia were used as control specimens that contained the other components of semen. Spermatozoa were solubilized by both physical (homogenization) and chemical (Triton-X100) methods to obtain the soluble and non-soluble fractions. The activities of several glycosidases measured both in seminal plasma and spermatozoa were directly correlated with the numbers of spermatozoa and sperm motility, confirming previous studies. As some infertile patients with varicocele have normal semen parameters, whereas others have low numbers of spermatozoa and low sperm motility, the varicocele patients were prospectively divided into two groups: one (n = 15) with normal spermiograms and the other (n = 11) with abnormal spermiograms. The activities (expressed in mU ml(-1)) of alpha-mannosidase, beta-galactosidase and beta-N-acetylglucosaminidase in seminal plasma of normozoospermic infertile patients with varicocele were significantly higher than those of fertile controls, but not when expressed in U per 10(8) spermatozoa. The activities of beta-glucuronidase, alpha-mannosidase, beta-galactosidase and beta-N-acetylglucosaminidase in seminal plasma when expressed in U per 10(8) spermatozoa in varicocele patients with abnormal spermiograms were significantly higher than in those of men of normal fertility. The activity of alpha-mannosidase in the soluble fraction of sperm homogenates, expressed as U per 10(8) spermatozoa, was significantly higher in infertile patients with varicocele and abnormal spermiograms than in controls. In the non-soluble fraction of spermatozoa from infertile patients with varicocele, there was an increase in the expression of beta-galactosidase and beta-N-acetylglucosaminidase activities compared with the fraction of spermatozoa from fertile subjects. In summary, infertile patients with varicocele displayed an overexpression of acid alpha-mannosidase, beta-galactosidase and beta-N-acetylglucosaminidase activities in seminal plasma and spermatozoa that may be associated with functional defects in spermatozoa as these glycosidases play an important role in mammalian fertilization.