Genome re-annotation: a wiki solution?

The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution.     

Rapid-response vaccines--does DNA offer a solution?

In responding to future influenza pandemics and other infectious agents, plasmid DNA overcomes many of the limitations of conventional vaccine production approaches.     

Dimerization of helical β-peptides in solution

Molecular simulations are used to examine the aggregation behavior of several β-peptides in explicit water. The particular peptides considered here adopt a helical, rodlike conformation in aqueous solution. Four distinct molecular sequences are considered. Earlier experimental studies have revealed the formation of ordered and disordered aggregates for such molecules, depending on sequence. The simulations reported here, which are conducted by resorting to metadynamics techniques, lead to free energy surfaces for dimerization of the peptides in water as a function of separation and relative orientation. Such surfaces are used to identify the molecular origins for the behaviors observed in the experiments.     

Facultative placentotrophy: half-way house or strategic solution?

While yolk is generally the primary source of embryo nutrients in squamates, numerous species supplement this with facultative placentotrophy. We argue that facultative placentotrophy should have selective importance relevant to offspring fitness. In the skink Niveoscincus metallicus, the size of ovulated eggs is unrelated to maternal size but large females produce offspring that are larger than is necessary for survival, providing evidence for facultative placentotrophy. We discuss the circumstances in which facultative placentotrophy might be used to supplement the nutritional support provided by yolk and obligate placentotrophy in this species, and present summary data from experiments designed to investigate these circumstances. Clutch reduction by oviduct removal had no effect on neonate mass or snout-vent length, indicating that the number of embryos does not influence allocation of maternal resources once gestation has commenced. Manipulation of maternal basking opportunity in combination with food intake during pregnancy suggested that an important role of facultative placentotrophy is the optimization of embryonic fat reserves. This hypothesis was supported by the observation that larger neonates have larger abdominal fat bodies. These reserves presumably facilitate survival in the relatively short pre-hibernatory period available to newborn animals. Our data indicate that they also play a vital role in maintaining pre-natal condition if birth is delayed by adverse weather, a common circumstance in this species. In such circumstances the yolk has been used up and the placental membranes have degenerated. Experimental induction of premature ovulation of eggs with reduced yolk, achieved by injecting females with FSH, was followed by fertilization using stored sperm. Gestation length was greatly reduced and the resulting neonates were all < or =75% normal birth mass, with two of the six births being stillborn. Thus facultative placentotrophy does not appear to be a means of compensating for a poor yolk supply. We suggest that facultative placentotrophy in N. metallicus is not a transitional stage en route to greater reliance on obligate placentotrophy, but a uniquely squamate adaptation that provides flexibility in embryonic nutrition, and optimizes offspring fitness in an unpredictable temperate climate.     

Obsolescence in LCA–methodological challenges and solution approaches

Purpose

Obsolescence, as premature end of use, increases the overall number of products produced and consumed, and thereby can increase the environmental impact. Measures to decrease the effects of obsolescence by altering the product or service design have the potential to increase use time (defined as the realized active service life) of devices, but can themselves have (environmental) drawbacks, for example, because the amount of material required for production increases. As such, paying special attention to methodological choices when assessing such measures and strategies using life cycle assessment (LCA) needs is crucial.

Methods

Open questions and key aspects of obsolescence, including the analysis of its effects and preventative measures, are discussed against the backdrop of the principles and framework for LCA given in ISO 14040/44, which includes guidance on how to define a useful functional unit and reference flow in the context of real-life use time.

Results and discussion

The open and foundational requirements of ISO 14040/14044 already form an excellent basis for analysis of the phenomenon obsolescence and its environmental impact in product comparisons. However, any analysis presumes clear definition of the goal and scope phase with special attention paid to aspects relevant to obsolescence: the target product and user group needs to be placed into context with the analysed “anti-obsolescence” measures. The reference flow needs to reflect a realized use time (and not solely a technical lifetime when not relevant for the product under study). System boundaries and types of data need to be chosen also in context of the anti-obsolescence measure to include, for example, the production of spare parts to reflect repairable design and/or manufacturer-specific yields to reflect high-quality manufacturing.

Conclusions

Understanding the relevant obsolescence conditions for the product system under study and how these may differ across the market segment or user types is crucial for a fair and useful comparison and the evaluation of anti-obsolescence measures.

     

Calcium in bacteria: a solution to which problem?

Calcium and calcium-binding proteins including those resembling calmodulin are implicated in numerous diverse processes in bacteria. These processes include chemotaxis, sporulation, virulence, the transport of sugars and proteins, phosphorylation, heat shock, the initiation of DNAS replication, septation, nucleoid structure, nuclease activity and recombination, the stability of the envelope, and phospholipids synthesis and configuration. That such varied processes should have a common factor, calcium, suggests major underlying principles of calcium metabolism metabolism which have yet to be discovered.     

α-Chymotrypsin-catalyzed synthesis of poly-l-cysteine in a frozen aqueous solution

Poly-l-cysteine (PLCys) is drawing attention as a potential sorbent of thiol (SH)-reactive toxic heavy metal ions in the wastewater and polluted soils. However, preparation of PLCys relies on chemically synthesized polymers, in which SH groups must be protected and deprotected prior to use. On the other hand, α-chymotrypsin polymerized l-cysteine ethyl ester in a frozen aqueous solution, provides PLCys with degree of polymerization from 6 to 11 without blocking of SH groups. Kinetic analyses suggested that the acylation of α-chymotrypsin with the initial substrate was a rate-limiting step in the enzymatic polymerization. The peptide yields reached 85% and 65% of SH groups in PLCys were assumed to be free forms. Although detail information on correlation between the state of SH groups and heavy metal adsorption properties of PLCys should be explored in further studies, the present study for the first time proposed an easy method for synthesis of PLCys requiring neither SH-protection nor -deprotection.     

Is ligation the only solution to the pyrophosphate problem?

Pyrophosphate linkages are easily formed during the nonenzymatic oligomerization of activated nucleotides. They often form caps which terminate an oligonucleotide with a 5-5 pyrophosphate. Owing to their structural resemblance to the intermediates in enzymatic ligation reactions, it has been suggested that pyrophosphate caps might have been capable of acting as activating groups in chain elongation processes. We argue that an alternative possibility would have been the specific hydrolysis of pyrophosphates.     

Plant individuality: a solution to the demographer’s dilemma

The problem of plant individuality is something which has vexed botanists throughout the ages, with fashion swinging back and forth from treating plants as communities of individuals (Darwin 1800; Braun and Stone 1853; Münch 1938) to treating them as organisms in their own right, and although the latter view has dominated mainstream thought most recently (Harper 1977; Cook 1985; Ariew and Lewontin 2004), a lively debate conducted mostly in Scandinavian journals proves that the issues are far from being resolved (Tuomi and Vuorisalo 1989b; Fagerström 1992; Pan and Price 2001). In this paper I settle the matter once and for all, by showing which elements of each side are correct.