The Millennial model: in search of measurable pools and transformations for modeling soil carbon in the new century

Soil organic carbon (SOC) can be defined by measurable chemical and physical pools, such as mineral-associated carbon, carbon physically entrapped in aggregates, dissolved carbon, and fragments of plant detritus. Yet, most soil models use conceptual rather than measurable SOC pools. What would the traditional pool-based soil model look like if it were built today, reflecting the latest understanding of biological, chemical, and physical transformations in soils? We propose a conceptual model—the Millennial model—that defines pools as measurable entities. First, we discuss relevant pool definitions conceptually and in terms of the measurements that can be used to quantify pool size, formation, and destabilization. Then, we develop a numerical model following the Millennial model conceptual framework to evaluate against the Century model, a widely-used standard for estimating SOC stocks across space and through time. The Millennial model predicts qualitatively similar changes in total SOC in response to single factor perturbations when compared to Century, but different responses to multiple factor perturbations. We review important conceptual and behavioral differences between the Millennial and Century modeling approaches, and the field and lab measurements needed to constrain parameter values. We propose the Millennial model as a simple but comprehensive framework to model SOC pools and guide measurements for further model development.     

Germline genomic structure of the B10.A mouseTcra-V2 gene subfamily

 The number of mouse Tcra-V gene segments varies from one individual to another and is estimated to be about 100. Southern blot analysis revealed that most of the Tcra-V are organized in clusters composed of copies of Tcra-V belonging to different subfamilies. We analyzed in detail a Tcra-V subfamily and looked for new Tcra-V in order to improve the knowledge of the mouse Tcra locus organization. A series of genomic clones derived from the B10.A mouse strain enclosing these clusters was used to determined the structure of all the Tcra-V2. We were able to identify ten Tcra-V2. This study showed that the Tcra-V2 can be organized into three structural subgroups. The distribution of the genes along the Tcra locus, plus their structural organization, indicates that successive duplications occurred during the processes of expansion and contraction of the Tcra-V gene subfamilies. Several Tcra-V2 are also identical, indicating recent duplications. The most divergent Tcra-V2 differ by 7.4% nucleotides, leading to 5.2% differences in amino acid contents. Received: 8 August 1995 / Revised: 24 April 1996     

Evaluation of regioselectivity of lipases based on synthesis reaction conducted with propyl alcohol, isopropyl alcohol and propylene glycol

Preliminary investigations on the regioselectiviy of various lipases were performed. Ten commercial lipases from different origins, including three immobilized lipases, were tested by esterification reaction between caprylic acid and propyl or isopropyl alcohol in n-hexane. Reaction products were analyzed with a gas chromatograph. Best yields were obtained with immobilized lipase IM60 from Rhizomucor miehei. Therefore, this enzyme was chosen as biocatalyst for a second step of regioselectiviy study with propylene glycol which bears primary and secondary alcohol groups. It was shown, by using several solvents, that polarity could influence the product profile in situations in which multiple products of various polarities can be formed. Furthermore, the major role of silica gel in reaction mixture was established.     

Local and landscape determinants of pollen beetle abundance in overwintering habitats

• 1 The development of integrated pest management strategies requires that the semi‐natural habitats scattered across the landscape are taken into account. Particular determinants of insect pest abundance in overwintering habitats just before they migrate onto crops appear to be poorly known and of crucial importance for understanding patterns of crop colonization and pest population dynamics at the landscape scale.
• 2 The emergence of pollen beetle Meligethes aeneus F. was studied in grassland, woodland edge and woodland interior over a 3‐year survey in France using macro‐emergence traps. A suite of variables at the local and the landscape scale was assessed for each trap, aiming to identify potential relevant habitat indicators. The effects of habitat characteristics were evaluated using partial least square regressions.
• 3 It was found that M. aeneus can overwinter in all types of habitat but that particular habitat characteristics at the local and landscape scales may explain their abundance in overwintering sites more than the types of habitat: relative altitude, litter thickness, soil moisture and proximity to the previous year's oilseed rape fields appear to be positively correlated with abundance of adults over the 3 years.
• 4 Hence, the abundance of emerged pollen beetles depends on both the landscape configuration of the previous year's oilseed rape fields around overwintering sites and local habitat characteristics. Landscape configuration may determine population flow towards overwintering sites in the late summer, and local habitat characteristics may influence survival rates during the winter. The findings of the present study provide valuable insight into the role of semi‐natural habitats as a source of pests, patterns of crop colonization in the spring, and the influence of landscape on pollen beetle abundance.

     

Plant biomechanical strategies in response to frequent disturbance: uprooting of Phyllostachys nidularia (Poaceae) growing on landslide-prone slopes in Sichuan, China

Bamboo is considered useful for controlling landslides, but we observed numerous shallow-slope failures in forests of big node bamboo (Phyllostachys nidularia) in Sichuan, China. Therefore, we inventoried landslide occurrence and vegetation type along one valley. To quantify bamboo root anchorage, we performed uprooting tests and measured plant morphological characteristics. Landslide occurrence was greatest at sites with bamboo and young trees. Culm failure was common because of the high length to diameter ratio (242 ± 6). Uprooting tests showed that the maximal force to cause failure was small (1615 ± 195 N). Uprooting force was strongly and positively regressed with a combination of the predictors lateral root number and volume (R(2) = 0.92), and root systems were highly superficial (depth = 0.15 ± 0.12 m), contributing little to slope stability. In P. nidularia, which grows on landslide-prone slopes, surprisingly few resources have been allocated to anchorage. We suggest that this strategy puts this pioneer at an advantage on steep slopes, where it contributes little to slope stability and colonizes frequently formed gaps through vegetative regeneration. Fewer disturbances would result in subsequent secondary succession and dying back of this shade intolerant species.     

A specific protein disorder catalyzer of HIV-1 Nef

The HIV-1 auxiliary protein Nef is required for the onset and progression of AIDS in HIV-1-infected persons. Here, we have deciphered the mode of action of a second-generation inhibitor of Nef, DLC27-14, presenting a competitive IC(50) of ～16 μM measured by MALDI-TOF experiments. Thermal protein denaturation experiments revealed a negative effect on stability of Nef in the presence of a saturating concentration of the inhibitor. The destabilizing action of DLC27-14 was confirmed by a HIV protease-based experiment, in which the protease sensitivity of DLC27-14-bound Nef was three times as high as that of apo Nef. The only compatible docking modes of action for DLC27-14 suggest that DLC27-14 promotes an opening of two α-helices that would destabilize the Nef core domain. DLC27-14 thus acts as a specific protein disorder catalyzer that destabilizes the folded conformation of the protein. Our results open novel avenues toward the development of next-generation Nef inhibitors.     

Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic

Based on the discrete definition of biological regulatory networks developed by René Thomas, we provide a computer science formal approach to treat temporal properties of biological regulatory networks, expressed in computational tree logic. It is then possible to build all the models satisfying a set of given temporal properties. Our approach is illustrated with the mucus production in Pseudomonas aeruginosa. This application of formal methods from computer science to biological regulatory networks should open the way to many other fruitful applications.