Mapping of antigenic domains on phytochrome from etiolated Avena sativa L. by immunoblot analysis of proteolytically derived peptides

Several monoclonal antibodies to phytochrome that interact with putative functionally important domains have been previously identified. The locations of some of these domains are determined here by epitope mapping experiments that utilize immunoblot analyses of proteolytically degraded phytochrome. Seven independent epitopes are identified. An epitope that is recognized by monoclonal antibody Oat-25 is confirmed to be wholly located near the N terminus of phytochrome. This domain undergoes a conformational change when phytochrome is interconverted between its red- and far-red-absorbing forms and is recognized by Oat-25 better in the red-absorbing form. A second domain that also undergoes a photointerconvertible conformation change and that contains the epitope for Oat-16 is localized near the site of chromophore attachment, which is about 36 kDa from the N terminus. A third domain, which contains the most highly conserved epitope on phytochrome that has so far been identified, is recognized by Pea-25 and is located about 85 kDa from the N terminus. Other epitopes and their approximate distances from the N terminus are those recognized by Oat-22 (36 kDa), Oat-13 (65 kDa), and Oat-8 and Oat-28 (70-75 kDa). Even though epitopes for Oat-16 and Oat-22, as well as for Oat-8 and Oat-28, are close together, competitive binding assays indicate that they are different. Immunoblot analyses also indicate that the epitope for Oat-28 is further from the N terminus of phytochrome than is that for Oat-8.     

Tree Size Inequality Reduces Forest Productivity: An Analysis Combining Inventory Data for Ten European Species and a Light Competition Model

Plant structural diversity is usually considered as beneficial for ecosystem functioning. For instance, numerous studies have reported positive species diversity-productivity relationships in plant communities. However, other aspects of structural diversity such as individual size inequality have been far less investigated. In forests, tree size inequality impacts directly tree growth and asymmetric competition, but consequences on forest productivity are still indeterminate. In addition, the effect of tree size inequality on productivity is likely to vary with species shade-tolerance, a key ecological characteristic controlling asymmetric competition and light resource acquisition. Using plot data from the French National Geographic Agency, we studied the response of stand productivity to size inequality for ten forest species differing in shade tolerance. We fitted a basal area stand production model that included abiotic factors, stand density, stand development stage and a tree size inequality index. Then, using a forest dynamics model we explored whether mechanisms of light interception and light use efficiency could explain the tree size inequality effect observed for three of the ten species studied. Size inequality negatively affected basal area increment for seven out of the ten species investigated. However, this effect was not related to the shade tolerance of these species. According to the model simulations, the negative tree size inequality effect could result both from reduced total stand light interception and reduced light use efficiency. Our results demonstrate that negative relationships between size inequality and productivity may be the rule in tree populations. The lack of effect of shade tolerance indicates compensatory mechanisms between effect on light availability and response to light availability. Such a pattern deserves further investigations for mixed forests where complementarity effects between species are involved. When studying the effect of structural diversity on ecosystem productivity, tree size inequality is a major facet that should be taken into account.     

Role of the ubiquitin-binding domain of Polη in Rad18-independent translesion DNA synthesis in human cell extracts

In eukaryotic cells, the Rad6/Rad18-dependent monoubiquitination of the proliferating cell nuclear antigen (PCNA) plays an essential role in the switching between replication and translesion DNA synthesis (TLS). The DNA polymerase Polη binds to PCNA via a consensus C-terminal PCNA-interacting protein (PIP) motif. It also specifically interacts with monoubiquitinated PCNA thanks to a recently identified ubiquitin-binding domain (UBZ). To investigate whether the TLS activity of Polη is always coupled to PCNA monoubiquitination, we monitor the ability of cell-free extracts to perform DNA synthesis across different types of lesions. We observe that a cis-syn cyclobutane thymine dimer (TT-CPD), but not a N-2-acetylaminofluorene-guanine (G-AAF) adduct, is efficiently bypassed in extracts from Rad18-deficient cells, thus demonstrating the existence of a Polη-dependent and Rad18-independent TLS pathway. In addition, by complementing Polη-deficient cells with PIP and UBZ mutants, we show that each of these domains contributes to Polη activity. The finding that the bypass of a CPD lesion in vitro does not require Ub-PCNA but nevertheless depends on the UBZ domain of Polη, reveals that this domain may play a novel role in the TLS process that is not related to the monoubiquitination status of PCNA.     

Early teratogen effect of neutral desoxyribonuclase on young chick embryo]

Neutral DNA-ase acts as a general teratogen when given to young chicken blastoderms. The rate of the differents abnormalities varies according to the dose given and the embryos' stage. The frequency of the different defects reaches a maximum value with increasing doses it falls generally down with more important doses. DMSO added to the enzyme solution changes the susceptibility of the embryos.     

Proteomic Analysis of DNA Synthesis on a Structured DNA Template in Human Cellular Extracts: Interplay Between NHEJ and Replication‐Associated Proteins

It is established that short inverted repeats trigger base substitution mutagenesis in human cells. However, how the replication machinery deals with structured DNA is unknown. It has been previously reported that in human cell‐free extracts, DNA primer extension using a structured single‐stranded template is transiently blocked at DNA hairpins. Here, the proteomic analysis of proteins bound to the DNA template is reported and evidence that the DNA‐PK complex (DNA‐PKcs and the Ku heterodimer) recognizes, and is activated by, structured single‐stranded DNA is provided. Hijacking the DNA‐PK complex by double‐stranded oligonucleotides results in a large removal of the pausing sites and an elevated DNA extension efficiency. Conversely, DNA‐PKcs inhibition results in its stabilization on the template, along with other proteins acting downstream in the Non‐Homologous End‐Joining (NHEJ) pathway, especially the XRCC4‐DNA ligase 4 complex and the cofactor PAXX. Retention of NHEJ factors to the DNA in the absence of DNA‐PKcs activity correlates with additional halts of primer extension, suggesting that these proteins hinder the progression of the DNA synthesis at these sites. Overall these results raise the possibility that, upon binding to hairpins formed onto ssDNA during fork progression, the DNA‐PK complex interferes with replication fork dynamics in vivo.     

On-line identification of parameters in a fermentation process

In a fermentation process, the establishment of gas mass balances provides valuable information and allows both measurements concerning the characteristics of the biomass itself and the monitoring of a cultivation process. If the quantity and oxidation level of substances excreted into the fermentation broth are known or constant, the yield factor and the dry cell-weight production are stoichiometrically related to the quantity of CO₂ evolved and to the quantity of O₂ consumed. Where frequent measurements of both yield factor and dry cell-weight production are desirable or where rapid adjustment of the parameters is necessary, on-line identification of these parameters is required, An algorithm allowing the identification of the specific growth rate is presented. Moreover, this technique allows one to estimate the percent protein in the biomass during continuous culture.     

The number of Great Tit mobbers influences the mobbing response of heterospecific birds

Many species mob predators to drive them away. Mobbing carries personal risk, but the risk of injury or death declines and the likelihood of repelling the predator increases in larger groups. The capacity to evaluate the number of mobbers before joining a mobbing group may be highly beneficial for individuals when deciding to join. Although recent studies have found that birds can use individual vocal discrimination to assess the number of conspecifics involved in initiating mobbing events, it is little known whether birds are able to evaluate the number of heterospecific mobbers. In this study, we investigated whether the number of heterospecifics responding to mobbing calls of Great Tits Parus major was influenced by the number of callers (a mix of Great Tit callers simulated by playbacks and live Great Tits attracted to playbacks, range one to seven callers). The total number of responding heterospecific individuals and species was positively influenced by the total number of callers, with heterospecifics responding more to larger than smaller Great Tit groups. However, these results may be driven by the total number of calls, call overlap and increased noise generated by the additional mobbers, and not the number per se. These findings therefore allow us to assess whether birds are more inclined to join a mobbing group when it consists of more heterospecific callers, but we cannot tell whether birds use individual vocal discrimination to assess the number of heterospecific callers.