Protein Rou. A human IgA hybrid

Protein Rou is a human IgA2 myeloma protein that carries the isoallotype marker n A2m(2). Partial amino acid sequence of its H chain (alpha) shows that the hinge region and the CH2 domain are homologous to alpha 2-chain and the CH1 and the CH3 domains homologous to alpha 1. Moreover, the CH1 domain contains the H-L disulfide bond identical to alpha 1. It is concluded that Rou H chain is a hybrid molecule caused by a recombination between alpha 1 and alpha 2 genes. The recombination event occurred between alpha 1-exon 1 and alpha 2-exon hinge and corresponds to position 222-223 of the alpha-chain.     

An excision event that may depend on patchy homology for site specificity.

In mouse cells transformed by a mutant polyomavirus genome, recombination between integrated viral DNA and flanking cellular DNA resulted in the excision of two readily amplifiable chimeras, designated RmI and RmII. The crossing-over that generated RmII was unique in that it involved a simple cellular sequence in which the triplet 5'-CTG-3' was repeated many times. We show that the sequence across the junction resulting from excision was identical in several molecules of RmII, as if the cross-over generating this junction always involved exactly the same two sites on the viral and cellular DNA. We also show that the cellular site mapped where the replacement of a G by an A in one of many successive 5'-CTG-3' triplets generated a homology of five nucleotides (5'-CTACT-3') with the viral site. Oligonucleotides on both sides of these sites are probably involved in matching the two DNAs prior to recombination.     

Diel emergence patterns of drifting chironomid (Diptera) pupal exuviae in the Aude River (Eastern Pyrenees,France)

Two diel emergence patterns (April and October 1990) of chironomids from a hyporhithral site (4th–5th order) in the Aude River are described. In April, 62 species were collected with a mean hourly richness of 31 (±4). The Orthocladiinae (91%) largely dominated the emergence. The total number of exuviae captured by one drift-net varied from 1300 to 11600 per one hour period. There was a clear bimodal pattern with peaks post dawn (07.00–09.00 hrs) and around sunset (18.00 hrs).In October, the total number of exuviae captured was much lower and varied from 150 to 540 per one hour period with post dawn (06.00–08.00 hrs) and post sunset (18.00 hrs) peaks. Nevertheless, the total species richness (65) was higher as was the mean hourly richness (37±4). The Orthocladiinae (68%) dominated less because of increases in the Tanytarsini (15%) and Chiromini (14%). A diel rhythm appeared in autumn emergence. Most of the Orthocladiinae exuviae were collected during daylight hours, whereas most of the Chironomini and Tanytarsini were sampled during darkness. A majority of the exuviae with a length below 3 mm emerged during daylight, but most of the exuviae above 5 mm length emerged during darkness. The exuviae with an intermediate length (3–5 mm) had an amodal diel emergence pattern. In spring and autumn, the majority of species had a bimodal emergence pattern either by day (Orthocladiinae) or by night (Chironominae). But the smallest species had either an unimodal (Thiennemaniella vittata) or bimodal (Neozavrelia fuldensis) daytime emergence. The diel emergence patterns of 10 of the most frequently recorded species are presented.     

Fine-Scale Population Structure of Blue Whale Wintering Aggregations in the Gulf of California

Population differentiation in environments without well-defined geographical barriers represents a challenge for wildlife management. Based on a comprehensive database of individual sighting records (1988–2009) of blue whales from the winter/calving Gulf of California, we assessed the fine-scale genetic and spatial structure of the population using individual-based approaches. Skin samples of 187 individuals were analyzed for nine microsatellite loci. A single population with no divergence among years and months and no isolation by distance (Rxy = 0.1–0.001, p>0.05) were found. We ran two Bayesian clustering methods using Structure and Geneland softwares in two different ways: 1) a general analysis including all individuals in which a single cluster was identified with both softwares; 2) a specific analysis of females only in which two main clusters (Loreto Bay and northern areas, and San Jose-La Paz Bay area) were revealed by Geneland program. This study provides information indicating that blue whales wintering in the Gulf of California are part of a single population unit and showed a fine-scale structure among females, possibly associated with their high site fidelity, particularly when attending calves. It is likely that the loss of genetic variation is minimized by male mediated gene flow, which may reduce the genetic drift effect. Opportunities for kin selection may also influence calf survival and, in consequence, have a positive impact on population demography in this small and endangered population.     

P2Y2 receptor promotes intestinal microtubule stabilization and mucosal re‐epithelization in experimental colitis

P2Y₂ receptor expression is increased in intestinal epithelial cells (IECs) during inflammatory bowel diseases (IBDs). In this context, P2Y₂ stimulates PGE₂ release by IECs, suggesting a role in wound healing. For this study, we have used the non‐cancerous IEC‐6 cell line. IEC‐6 cell migration was determined using Boyden chambers and the single‐edged razor blade model of wounding. The receptor was activated using ATP, UTP, or 2‐thioUTP. Pharmacological inhibitors, a blocking peptide, a neutralizing antibody and interfering RNAs were used to characterize the signaling events. Focal adhesions and microtubule (MT) dynamics were determined by immunofluorescence using anti‐vinculin and anti‐acetylated‐α‐tubulin antibodies, respectively. In vivo, the dextran sodium sulfate mouse model of colitis was used to characterize the effects of P2Y₂ agonist 2‐thioUTP on remission. We showed that P2Y₂ increased cell migration and wound closure by recruiting Go protein with the cooperation of integrin α_v. Following P2Y₂ activation, we demonstrated that GSK3β activity was inhibited in response to Akt activation. This leads to MT stabilization and increased number of focal adhesions. In vivo, P2Y₂ activation stimulates remission, as illustrated by a reduction in the disease activity index values and histological scores as compared to control mice. These findings highlight a novel function for this receptor in IECs. They also illustrate that P2Y receptors could be targeted for the development of innovative therapies for the treatment of IBDs. J. Cell. Physiol. 228: 99–109, 2013. © 2012 Wiley Periodicals, Inc.     

Glucose transporter 2 expression is down regulated following P2X7 activation in enterocytes

With the diabetes epidemic affecting the world population, there is an increasing demand for means to regulate glycemia. Dietary glucose is first absorbed by the intestine before entering the blood stream. Thus, the regulation of glucose absorption by intestinal epithelial cells (IECs) could represent a way to regulate glycemia. Among the molecules involved in glycemia homeostasis, extracellular ATP, a paracrine signaling molecule, was reported to induce insulin secretion from pancreatic β cells by activating P2Y and P2X receptors. In rat's jejunum, P2X7 expression was previously immunolocalized to the apex of villi, where it has been suspected to play a role in apoptosis. However, using an antibody recognizing the receptor extracellular domain and thus most of the P2X7 isoforms, we showed that expression of this receptor is apparent in the top two‐thirds of villi. These data suggest a different role for this receptor in IECs. Using the non‐cancerous IEC‐6 cells and differentiated Caco‐2 cells, glucose transport was reduced by more than 30% following P2X7 stimulation. This effect on glucose transport was not due to P2X7‐induced cell apoptosis, but rather was the consequence of glucose transporter 2 (Glut2)'s internalization. The signaling pathway leading to P2X7‐dependent Glut2 internalization involved the calcium‐independent activation of phospholipase Cγ1 (PLCγ1), PKCδ, and PKD1. Although the complete mechanism regulating Glut2 internalization following P2X7 activation is not fully understood, modulation of P2X7 receptor activation could represent an interesting approach to regulate intestinal glucose absorption. J. Cell. Physiol. 228: 120–129, 2013. © 2012 Wiley Periodicals, Inc.     

Coral microbiome diversity reflects mass coral bleaching susceptibility during the 2016 El Niño heat wave

Repeat marine heat wave‐induced mass coral bleaching has decimated reefs in Seychelles for 35 years, but how coral‐associated microbial diversity (microalgal endosymbionts of the family Symbiodiniaceae and bacterial communities) potentially underpins broad‐scale bleaching dynamics remains unknown. We assessed microbiome composition during the 2016 heat wave peak at two contrasting reef sites (clear vs. turbid) in Seychelles, for key coral species considered bleaching sensitive (Acropora muricata, Acropora gemmifera) or tolerant (Porites lutea, Coelastrea aspera). For all species and sites, we sampled bleached versus unbleached colonies to examine how microbiomes align with heat stress susceptibility. Over 30% of all corals bleached in 2016, half of which were from Acropora sp. and Pocillopora sp. mass bleaching that largely transitioned to mortality by 2017. Symbiodiniaceae ITS2‐sequencing revealed that the two Acropora sp. and P. lutea generally associated with C3z/C3 and C15 types, respectively, whereas C. aspera exhibited a plastic association with multiple D types and two C3z types. 16S rRNA gene sequencing revealed that bacterial communities were coral host‐specific, largely through differences in the most abundant families, Hahellaceae (comprising Endozoicomonas), Rhodospirillaceae, and Rhodobacteraceae. Both Acropora sp. exhibited lower bacterial diversity, species richness, and community evenness compared to more bleaching‐resistant P. lutea and C. aspera. Different bleaching susceptibility among coral species was thus consistent with distinct microbiome community profiles. These profiles were conserved across bleached and unbleached colonies of all coral species. As this pattern could also reflect a parallel response of the microbiome to environmental changes, the detailed functional associations will need to be determined in future studies. Further understanding such microbiome‐environmental interactions is likely critical to target more effective management within oceanically isolated reefs of Seychelles.     

Quantitative analysis of nucleic acid three-dimensional structures

A new computer program to annotate DNA and RNA three-dimensional structures, MC-Annotate, is introduced. The goals of annotation are to efficiently extract and manipulate structural information, to simplify further structural analyses and searches, and to objectively represent structural knowledge. The input of MC-Annotate is a PDB formatted DNA or RNA three-dimensional structure. The output of MC-Annotate is composed of a structural graph that contains the annotations, and a series of HTML documents, one for each nucleotide conformation and base-base interaction present in the input structure. The atomic coordinates of all nucleotides and the homogeneous transformation matrices of all base-base interactions are stored in the structural graph. Symbolic classifications of nucleotide conformations, using sugar puckering modes and nitrogen base orientations around the glycosyl bond, and base-base interactions, using stacking and hydrogen bonding information, are introduced. Peculiarity factors of nucleotide conformations and base-base interactions are defined to indicate their marginalities with all other examples. The peculiarity factors allow us to identify irregular regions and possible stereochemical errors in 3-D structures without interactive visualization. The annotations attached to each nucleotide conformation include its class, its torsion angles, a distribution of the root-mean-square deviations with examples of the same class, the list of examples of the same class, and its peculiarity value. The annotations attached to each base-base interaction include its class, a distribution of distances with examples of the same class, the list of examples of the same class, and its peculiarity value. The distance between two homogeneous transformation matrices is evaluated using a new metric that distinguishes between the rotation and the translation of a transformation matrix in the context of nitrogen bases. MC-Annotate was used to build databases of nucleotide conformations and base-base interactions. It was applied to the ribosomal RNA fragment that binds to protein L11, which annotations revealed peculiar nucleotide conformations and base-base interactions in the regions where the RNA contacts the protein. The question of whether the current database of RNA three-dimensional structures is complete is addressed.