Publications

Chronic renal allograft injury is reflected by interstitial fibrosis and tubular atrophy (IF/TA) and by the accumulation of extracellular matrix (ECM). Metalloproteinases (MMPs) are renal physiologic regulators of ECM degradation. Changes in MMPs expression or activity may disturb ECM turnover leading to glomerular scarring and worsening renal function. Our goal was to investigate intragraft MMP2 and MMP9 activities and their correlation with renal dysfunction. Plasma MMP2 and MMP9 activities were analyzed as noninvasive markers of renal allograft deterioration. Transplanted patients were biopsied and histopathologically characterized as IF/TA+ or IF/TA-. Renal function was evaluated by serum creatinine, glomerular filtration rate (GFR) estimated by Modification of Diet in Renal Disease equation and urinary protein/creatinine ratio. Kidney and plasma MMP2 and MMP9 activities were analyzed by zymography. A significant renal dysfunction was observed in IF/TA+ patients. Intragraft proMMP9 showed a significant higher activity in IF/TA+ than in IF/TA- samples and was inversely correlated with the GFR. Intragraft proMMP2 activity tended to increase in IF/TA+ samples, although no statistic significance was reached. Circulating proMMP2 and proMMP9 activities did not show significant differences between groups. Our data provide evidence that correlates intragraft proMMP9 activity with the fibrotic changes and renal dysfunction observed in IF/TA.

The simulated presence of conspecifics has been proposed to attract territorial songbirds to protect nesting areas when the habitat is being disturbed by human activities. We studied the effects of conspecifics on the nest-site selection of the Thorn-tailed Rayadito (Aphrastura spinicauda; Furnariidae), a forest songbird that depends on cavities for nesting.Plantations represent usable habitat for foraging, but the scarcity of cavities restricts their use during the breeding period. The use of nest boxes is a documented measure to mitigate the negative effect of plantations on cavity users. We installed nest boxes in a plantation ofPinus radiata in south-central Chile, using the simulated presence of conspecifics as a potential tool to attract rayaditos to new available sites to nest. We simulated the presence of conspecifics through playback during 45 days prior nest building. Our results showed two contrasting outcomes. Firstly, conspecific simulation attracts rayaditos, by increasing their density before playback experiments by 75%. Secondly, rayaditos tended to avoid playback treatment sites as nesting started. The establishment of nests occurred 71%of the time and started 20 days earlier in control sites compared to playback treatment. Other secondary cavity-nesting birds, such as the House Wren (Troglodytes aedon;Troglodytidae) andWhite-throated Tree runner (Pygarrhichas albogularis; Furnariidae), also avoided playback plots as nesting sites. The scarcity of cavities in pine plantations may increase the aggressive defense of breeding territories, making cavity-nesting birds move to other previously known vacant sites to nest when they listen other birds in the nesting site. It is highly recommended to assess the behavioral response to conspecific and heterospecific birds before the establishment of a management measure aiming to attract or discourage the presence of a target species.

Ribosomal DNA is commonly used as a marker for protist phylogeny and taxonomy because of its ubiquity and its expected species specificity thanks to the mechanism of concerted evolution. However, numerous studies reported the occurrence of intragenomic (intra-individual) polymorphism in various protists and particularly in Foraminifera. To infer to what extent the SSU rDNA intragenomic variability occurs in Foraminifera, we studied 16 foraminiferal species belonging to single-chambered monothalamids and multi-chambered Globothalamea, with one to six individuals per species. We performed single-cell DNA extractions and PCRs of a 600bp fragment of SSU rDNA, and sequenced 9 to 23 clones per individual for a total of 818 sequences. We found intragenomic variability in almost all species, even after excluding singleton mutations. Intra-individual sequence divergence ranged from 0 to 5.15% and was higher than 1% in 11 species. Variability was usually located at the end of stem-loop structures and included compensatory single nucleotide polymorphisms and expansion segments polymorphisms. However, the polymorphisms did not change the secondary structure of the rRNA. Our results suggest a non-concerted evolution of rRNA genes in Foraminifera. The origin of this variability and its implications for species identification in environmental DNA studies are discussed.

Following their duplications at the base of the vertebrate clade, Hox gene clusters underwent remarkable sub- and neo-functionalization events. Many of these evolutionary innovations can be associated with changes in the transcriptional regulation of their genes, where an intricate relationship between the structure of the gene cluster and the architecture of the surrounding genomic landscape is at play. Here, we report on a portfolio of in vivo genome engineering strategies in mice, which have been used to probe and decipher the genetic and molecular underpinnings of the complex regulatory mechanisms implemented at these loci.

How transcription is controlled by distally located cis-regulatory elements is an active area of research in biology. As such, there have been many techniques developed to probe these long-distance chromatin interactions. Here, we focus on one such method, called DamID (van Steensel and Henikoff, Nat Biotechnol 18(4):424-428, 2000). While other methods like 3C (Dekker et al., Science 295(5558):1306-1311, 2002), 4C (Simonis et al., Nat Genet 38(11):1348-1354, 2006; Zhao et al., Nat Genet 38(11):1341-1347, 2006), and 5C (Dostie et al., Genome Res 16(10):1299-1309, 2006) are undoubtedly powerful, the DamID method can offer some advantages over these methods if the genetic locus can be easily modified. The lack of tissue fixation, the low amounts of starting material required to perform the experiment, and the relatively modest hardware requirements make DamID experiments an interesting alternative to consider when examining long-distance chromatin interactions.

Although a small number of the vast array of animal long non-coding RNAs (lncRNAs) have known effects on cellular processes examined in vitro, the extent of their contributions to normal cell processes throughout development, differentiation and disease for the most part remains less clear. Phenotypes arising from deletion of an entire genomic locus cannot be unequivocally attributed either to the loss of the lncRNA per se or to the associated loss of other overlapping DNA regulatory elements. The distinction between cis- or trans-effects is also often problematic. We discuss the advantages and challenges associated with the current techniques for studying the in vivo function of lncRNAs in the light of different models of lncRNA molecular mechanism, and reflect on the design of experiments to mutate lncRNA loci. These considerations should assist in the further investigation of these transcriptional products of the genome.

Next generation sequencing (NGS) is currently being adapted by different biotechnological platforms to the standard typing method for HLA polymorphism, the huge diversity of which makes this initiative particularly challenging. Boosting the molecular characterization of the HLA genes through efficient, rapid, and low-cost technologies is expected to amplify the success of tissue transplantation by enabling us to find donor-recipient matching for rare phenotypes. But the application of NGS technologies to the molecular mapping of the MHC region also anticipates essential changes in population genetic studies. Huge amounts of HLA sequence data will be available in the next years for different populations, with the potential to change our understanding of HLA variation in humans. In this review, we first explain how HLA sequencing allows a better assessment of the HLA diversity in human populations, taking also into account the methodological difficulties it introduces at the statistical level; secondly, we show how analyzing HLA sequence variation may improve our comprehension of population genetic relationships by facilitating the identification of demographic events that marked human evolution; finally, we discuss the interest of both HLA and genome-wide sequencing and genotyping in detecting functionally significant SNPs in the MHC region, the latter having also contributed to the makeup of the HLA molecular diversity observed today.

Since its usage by Darwin (1859), the concept of “living fossil” has undergone multiple definitions and has been much discussed and criticized. Soon after its discovery in 1938, the coelacanth Latimeria was regarded as the iconic example of a “living fossil.” Several morphological studies have shown that the coelacanth lineage (Actinistia) has not displayed critical morphological transformation during its evolutionary history and molecular studies have revealed a low substitution rate for Latimeria, indicating a slow genetic evolution. This statement, however, has been recently questioned by arguing that the low substitution rate was not real, and that the slow morphological evolution of actinistians was not supported by paleontological evidence. The assessment of morphological transformation among three vertebrate lineages during a time interval of circa 400 million years shows that the morphological disparity of coelacanths is much more reduced than the morphological disparity of Actinopterygii and Tetrapoda. These results support the idea that living coelacanths are singular organisms among the living world.

The cytoplasm of four species of abyssal benthic foraminiferans from the Southern Ocean (around 51°S; 12°W and 50°S; 39°W) was analysed by High Performance Liquid Chromatography (HPLC) and found to contain large concentrations of algal pigments and their degradation products. The composition of the algal pigments in the foraminiferan cytoplasm reflected the plankton community at the surface. Some foraminiferans contained high ratios of chlorophyll a/degraded pigments because they were feeding on fresher phytodetritus. Other foraminiferans contained only degraded pigments which shows that they utilized degraded phytodetritus. The concentration of algal pigment and corresponding degradation products in the foraminiferan cytoplasm is much higher than in the surrounding sediment. It shows that the foraminiferans collect a diluted and sparse food resource and concentrate it as they build up their cytoplasm. This ability contributes to the understanding of the great quantitative success of foraminiferans in the deep sea. Benthic foraminiferans are a food source for many abyssal metazoans. They form a link between the degraded food resources, phytodetritus, back to the active metazoan food chains.

The impact of injury-induced immune responses on animal regenerative processes is highly variable, positive or negative depending on the context. This likely reflects the complexity of the innate immune system that behaves as a sentinel in the transition from injury to regeneration. Early-branching invertebrates with high regenerative potential as Hydra provide a unique framework to dissect how injury-induced immune responses impact regeneration. A series of early cellular events likely require an efficient immune response after amputation, as antimicrobial defence, epithelial cell stretching for wound closure, migration of interstitial progenitors toward the wound, cell death, phagocytosis of cell debris, or reconstruction of the extracellular matrix. The analysis of the injury-induced transcriptomic modulations of 2636 genes annotated as immune genes in Hydra identified 43 genes showing an immediate/early pulse regulation in all regenerative contexts examined. These regulations point to an enhanced cytoprotection via ROS signaling (Nrf, C/EBP, p62/SQSMT1-l2), TNFR and TLR signaling (TNFR16-like, TRAF2l, TRAF5l, jun, fos-related, SIK2, ATF1/CREB, LRRC28, LRRC40, LRRK2), proteasomal activity (p62/SQSMT1-l1, Ced6/Gulf, NEDD8-conjugating enzyme Ubc12), stress proteins (CRYAB1, CRYAB2, HSP16.2, DnaJB9, HSP90a1), all potentially regulating NF-κB activity. Other genes encoding immune-annotated proteins such as NPYR4, GTPases, Swap70, the antiproliferative BTG1, enzymes involved in lipid metabolism (5-lipoxygenase, ACSF4), secreted clotting factors, secreted peptidases are also pulse regulated upon bisection. By contrast, metalloproteinases and antimicrobial peptide genes largely follow a context-dependent regulation, whereas the protease inhibitor α2macroglobulin gene exhibits a sustained up-regulation. Hence a complex immune response to injury is linked to wound healing and regeneration in Hydra.