Blocking hedgehog signaling after ablation of the dorsal neural tube allows regeneration of the cardiac neural crest and rescue of outflow tract septation

Cardiac neural crest cells (CNCC) migrate into the caudal pharynx and arterial pole of the heart to form the outflow septum. Ablation of the CNCC results in arterial pole malalignment and failure of outflow septation, resulting in a common trunk overriding the right ventricle. Unlike preotic cranial crest, the postotic CNCC do not normally regenerate. We applied the hedgehog signaling inhibitor, cyclopamine (Cyc), to chick embryos after CNCC ablation and found normal heart development at day 9 suggesting that the CNCC population was reconstituted. We ablated the CNCC, and labeled the remaining neural tube with DiI/CSRE and applied cyclopamine. Cells migrated from the neural tube in the CNCC-ablated, cyclopamine-treated embryos but not in untreated CNCC-ablated embryos. The newly generated cells followed the CNCC migration pathways, expressed neural crest markers and supported normal heart development. Finally, we tested whether reducing hedgehog signaling caused redeployment of the dorsal–ventral axis of the injured neural tube, allowing generation of new neural crest-like cells. The dorsal neural tube marker, Pax7, was maintained 12 h after CNCC ablation with Cyc treatment but not in the CNCC-ablated alone. This disruption of dorsal–ventral neural patterning permits a new wave of migratory cardiac neural crest-like cells.     

Exceptional carbon uptake in European forests during the warm spring of 2007: a data–model analysis

Temperate and boreal forests undergo drastic functional changes in the springtime, shifting within a few weeks from net carbon (C) sources to net C sinks. Most of these changes are mediated by temperature. The autumn 2006–winter 2007 record warm period was followed by an exceptionally warm spring in Europe, making spring 2007 a good candidate for advances in the onset of the photosynthetically active period. An analysis of a decade of eddy covariance data from six European forests stands, which encompass a wide range of functional types (broadleaf evergreen, broadleaf deciduous, needleleaf evergreen) and a wide latitudinal band (from 44° to 62°N), revealed exceptional fluxes during spring 2007. Gross primary productivity (GPP) of spring 2007 was the maximum recorded in the decade examined for all sites but a Mediterranean evergreen forest (with a +40 to +130 gC m^?2 anomaly compared with the decadal mean over the January–May period). Total ecosystem respiration (TER) was also promoted during spring 2007, though less anomalous than GPP (with a +17 to +93 gC m^?2 anomaly over 5 months), leading to higher net uptake than the long‐term mean at all sites (+12 to +79 gC m^?2 anomaly over 5 months). A correlative analysis relating springtime C fluxes to simple phenological indices suggested spring C uptake and temperatures to be related. The CASTANEA process‐based model was used to disentangle the seasonality of climatic drivers (incoming radiation, air and soil temperatures) and biological drivers (canopy dynamics, thermal acclimation of photosynthesis to low temperatures) on spring C fluxes along the latitudinal gradient. A sensitivity analysis of model simulations evidenced the roles of (i) an exceptional early budburst combined with elevated air temperature in deciduous sites, and (ii) an early relief of winter thermal acclimation in coniferous sites for the promotion of 2007 spring assimilation.     

Understanding Fluctuations in Bobcat Harvest at the Northern Limit of Their Range

ABSTRACT In Quebec, Canada, harvest of bobcats (Lynx rufus) started to decline in 1985 and by 1991, harvest seasons were closed due to concerns of a perceived population decline. Since the closing of harvest season in 1991, the average temperature has increased, snow quantity has decreased, and important changes in agriculture and forest management have occurred. In light of changing conditions, the situation of Quebec bobcats needed reassessment. Thus, we analyzed harvest data to clarify the current status of bobcat populations in Quebec. From 1980 to 1991, bobcat harvest in Quebec was strongly correlated with bobcat harvest in Maine (USA), Nova Scotia (Canada), Ontario (Canada), and Vermont (USA). Extrapolations of harvest in Quebec relative to harvest in Maine, Ontario, Vermont, and Nova Scotia suggested an increase in number of bobcats after 1991. Mass of male and female bobcats before 1991 was less than mass of animals captured after 1991. Percentage of juveniles in the reported harvest before 1991 was higher than after 1991. However, percentage of males and litter sizes in the harvest did not differ before and after 1991. The geographic distribution of bobcats captured has gradually expanded after the closure of the harvest season. Our findings suggest that bobcat populations in Quebec have recovered from the 1985–1991 decline, and that the harvest season for this species could resume. This study also illustrates how managers can rely on data from neighboring jurisdiction to manage species when local harvest data is unavailable.     

Genetic control of chicken heterophil function in advanced intercross lines: associations with novel and with known <Emphasis Type="Italic">Salmonella</Emphasis> resistance loci and a likely mechanism for cell death in extracellular trap production

Heterophils, the avian polymorphonuclear leukocyte and the counterpart of mammalian neutrophils, generate the primary innate response to pathogens in chickens. Heterophil performance against pathogens is associated with host disease resistance, and heterophil gene expression and function are under genetic control. To characterize the genomic basis of heterophil function, heterophils from F₁₃ advanced intercross chicken lines (broiler × Leghorn and broiler × Fayoumi) were assayed for phagocytosis and killing of Salmonella enteritidis, oxidative burst, and extracellular trap production. A whole-genome association analysis of single nucleotide polymorphisms at 57,636 loci identified genomic locations controlling these functional phenotypes. Genomic analysis revealed a significant association of extracellular trap production with the SAL1 locus and the SLC11A1 gene, which have both been previously associated with resistance to S. enteritidis. Fine mapping supports SIVA1 as a candidate gene controlling SAL1-mediated resistance and indicates that the proposed cell-death mechanism associated with extracellular trap production, ETosis, likely functions through the CD27/Siva-1-mediated apoptotic pathway. The SLC11A1 gene was also associated with phagocytosis of S. enteritidis, suggesting that the Slc11a1 protein may play an additional role in immune response beyond depleting metal ions to inhibit intracellular bacterial growth. A region of chromosome 6 with no characterized genes was also associated with extracellular trap production. Further characterization of these novel genes in chickens and other species is needed to understand their role in polymorphonuclear leukocyte function and host resistance to disease.     

Relationship between photochemical reflectance index and leaf ecophysiological and biochemical parameters under two different water statuses: towards a rapid and efficient correction method using real‐time measurements

The use of the photochemical reflectance index (PRI) as a promising proxy of light use efficiency (LUE) has been extensively studied, and some issues have been identified, notably the sensitivity of PRI to leaf pigment composition and the variability in PRI response to LUE because of stress. In this study, we introduce a method that enables us to track the short‐term PRI response to LUE changes because of photosynthetically active radiation (PAR) changes. The analysis of these short‐term relationships between PRI and LUE throughout the growing season in two species (Quercus robur L. and Fagus sylvatica L.) under two different soil water statuses showed a clear change in PRI response to LUE, which is related to leaf pigment content. The use of an estimated or approximated PRI0, defined as the PRI of perfectly dark‐adapted leaves, allowed us to separate the PRI variability due to leaf pigment content changes and the physiologically related PRI variability over both daily (PAR‐related) and seasonal (soil water content‐related) scales. The corrected PRI obtained by subtracting PRI0 from the PRI measurements showed a good correlation with the LUE over both of the species, soil water statuses and over the entire growing season.     

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas

Background

Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question.

Results

We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events.

Conclusions

Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0432-0) contains supplementary material, which is available to authorized users.     

A QTL on distal Chromosome 3 that influences the severity of light-induced damage to mouse photoreceptors

C57BL/6J-c^2J (c2J) albino mice showed much less damage to their photoreceptors after exposure to prolonged light than BALB/c mice and seven other albino strains tested. There were no gender differences, and preliminary studies suggested that the c2J relative protective effect was a complex trait. A genome-wide scan using dinucleotide repeat markers was carried out for the analysis of 194 progeny of the backcross (c2J × BALB/c)F₁× c2J and the thickness of the outer nuclear layer (ONL) of the retina was the quantitative trait reflecting retinal damage. Our results revealed a strong and highly significant quantitative trait locus (QTL) on mouse Chromosome (Chr) 3 that contributes almost 50% of the c2J protective effect, and three other very weak but significant QTLs on Chrs 9, 12, and 14. Interestingly, the Chrs 9 and 12 QTLs corresponded to relative susceptibility alleles in c2J (or relative protection alleles in BALB/c), the opposite of the relative protective effect of the QTLs on Chrs 3 and 14. We mapped the Rpe65 gene to the apex of the Chr 3 QTL (LOD score = 19.3). Northern analysis showed no difference in retinal expression of Rpe65 message between c2J and BALB/c mice. However, sequencing of the Rpe65 message revealed a single base change in codon 450, predicting a methionine in c2J and a leucine in BALB/c. When the retinas of aging BALB/c and c2J mice reared in normal cyclic light were compared, the BALB/c retinas showed a small but significant loss of photoreceptor cells, while the c2J retinas did not. Finding light damage-modifying genes in the mouse may open avenues of study for understanding age-related macular degeneration and other retinal degenerations, since light exposures may contribute to the course of these diseases. Received: 14 December 1999 / Accepted: 18 February 2000