Biofuels are dead: long live biofuels(?) – Part one

Beleaguered by criticisms, and abused by politicians for ecological target-setting, biofuels are in their darkest hour. But their bringing to trial should remind us - yet again - of something else: the highly questionable sustainability of most of modern agriculture. Is this the end of biofuels? Probably not, but it is certainly the end of a cheap solution to the problem of sustainable portable fuels. Part one of this two-part article focuses on the political and agricultural dimensions of the topic.     

Large-scale production of diesel-like biofuels – process design as an inherent part of microorganism development

Industrial biotechnology is playing an important role in the transition to a bio-based economy. Currently, however, industrial implementation is still modest, despite the advances made in microorganism development. Given that the fuels and commodity chemicals sectors are characterized by tight economic margins, we propose to address overall process design and efficiency at the start of bioprocess development. While current microorganism development is targeted at product formation and product yield, addressing process design at the start of bioprocess development means that microorganism selection can also be extended to other critical targets for process technology and process scale implementation, such as enhancing cell separation or increasing cell robustness at operating conditions that favor the overall process. In this paper we follow this approach for the microbial production of diesel-like biofuels. We review current microbial routes with both oleaginous and engineered microorganisms. For the routes leading to extracellular production, we identify the process conditions for large scale operation. The process conditions identified are finally translated to microorganism development targets. We show that microorganism development should be directed at anaerobic production, increasing robustness at extreme process conditions and tailoring cell surface properties. All the same time, novel process configurations integrating fermentation and product recovery, cell reuse and low-cost technologies for product separation are mandatory. This review provides a state-of-the-art summary of the latest challenges in large-scale production of diesel-like biofuels.     

Starling circannual systems: are they arrested in long photoperiods?

Summary In the European starling,Sturnus vulgaris, circannual rhythms in gonadal size, molt and other related functions persist only in photoperiods close to 12 h, but are absent in longer or shorter daylengths. To find out whether the arrhythmia seen in long photoperiods results from an arrest of the underlying clock system, three groups of male starlings were held for 10, 14, or 20 months in a 13 h photoperiod and then transferred to a 12 h photoperiod. A control group was held in the 13 h photoperiod throughout the experiment for 28 months. During the initial exposure to the 13 h photoperiod, all birds went through a gonadal cycle, followed by a complete molt. Subsequently, the control birds retained small testes to the end of the experiment and there was no further molt. In contrast, most of the experimental birds re-initiated a testicular cycle, following transfer to the 12 h photoperiod and molted after its completion. The latency between the transfer to the 12 h photoperiod and the onset of testicular growth was not significantly different among the three groups, indicating that the underlying circannual clock had been arrested in the 13 h photoperiod and restarted in the 12 h photoperiod. The pattern of the second testicular cycle did, however, differ among groups. Particularly its amplitude decreased from group 1 to group 3, suggesting that the capacity of the birds to respond to a 12 h photoperiod decreased with increasing duration of exposure to the 13 h photoperiod.Dedicated to Prof. Dr. C.S. Pittendrigh on the occasion of his seventieth birthday.     

Diplochory: are two seed dispersers better than one?

Diplochory is seed dispersal by a sequence of two or more steps or phases, each involving a different dispersal agent. Here, we describe five forms of diplochory and derive general characteristics of each phase of seed dispersal. The first and second phases of diplochory offer different benefits to plants. Phase one dispersal often results in escape from density-dependent seed and seedling mortality near the parent plant and can result in the colonization of habitat patches far from the parent. Phase two dispersal often moves seeds to discrete and predictable microsites, where the probability of seedling establishment is disproportionately high (i.e. directed dispersal). Diplochory appears to have evolved because combining two means of seed dispersal can increase the benefits of seed dispersal whilst reducing the likelihood of seed mortality.     

Coherent phenomena in photosynthetic light harvesting: part two—observations in biological systems

Considerable debate surrounds the question of whether or not quantum mechanics plays a significant, non-trivial role in photosynthetic light harvesting. Many have proposed that quantum superpositions and/or quantum transport phenomena may be responsible for the efficiency and robustness of energy transport present in biological systems. The critical experimental observations comprise the observation of coherent oscillations or “quantum beats” via femtosecond laser spectroscopy, which have been observed in many different light harvesting systems. Part Two of this review aims to provide an overview of experimental observations of energy transfer in the most studied light harvesting systems. Length scales, derived from crystallographic studies, are combined with energy and time scales of the beats observed via spectroscopy. A consensus is emerging that most long-lived (hundreds of femtoseconds) coherent phenomena are of vibrational or vibronic origin, where the latter may result in coherent excitation transport within a protein complex. In contrast, energy transport between proteins is likely to be incoherent in nature. The question of whether evolution has selected for these non-trivial quantum phenomena may be an unanswerable question, as dense packings of chromophores will lead to strong coupling and hence non-trivial quantum phenomena. As such, one cannot discern whether evolution has optimised light harvesting systems for high chromophore density or for the ensuing quantum effects as these are inextricably linked and cannot be switched off.     

Alpha-tectorin involvement in hearing disabilities: one gene – two phenotypes

The human alpha-tectorin (TECTA) gene has recently been cloned and proposed to be involved in autosomal dominant non-syndromic hearing impairment (NSHI) in two families linked to the DFNA12 locus. We have studied a Swedish pedigree with autosomal dominant NSHI with possible digenic inheritance of the disease, involving locus DFNA12 in chromosome 11 and locus DFNA2 in chromosome 1. Mutation analysis of the TECTA gene in this family has identified eight nucleotide substitutions indicating that TECTA is highly polymorphic. One of the changes results in a cysteine to serine (C 1057 S) mutation, in the zonadhesin domain of TECTA; this segregates with the disease haplotype on chromosome 11 and is not present in a control population. The mutation results in the replacement of a cysteine in one of the repeats of the zonadhesin/Von Willebrand domain of the protein and might cause a change in the crosslinking of the polypeptide. These findings add support to the involvement of TECTA in hearing disabilities. However, the three families carrying different TECTA mutations also show phenotypic differences: the hearing loss ranges from prelingual to progressive with late onset. The explanation for the different phenotypes and some clues regarding the functions of TECTA may lie in the localization of the mutations in the different modules of the protein. Another possibility is that the phenotype in the Swedish family is the result of two defective genes.     

Human disease glycomics: technology advances enabling protein glycosylation analysis – part 1

Introduction: Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics). The technologies currently available for glycomics are becoming streamlined and standardized and many features of protein glycosylation can now be determined using instruments available in most protein analytical laboratories.

Areas covered: This review focuses on the current glycomics technologies being commonly used for the analysis of the microheterogeneity of monosaccharide composition, sequence, branching and linkage of released N- and O-linked glycans that enable the determination of precise glycan structural determinants presented on secreted proteins and on the surface of all cells.

Expert commentary: Several emerging advances in these technologies enabling glycomics analysis are discussed. The technological and bioinformatics requirements to be able to accurately assign these precise glycan features at biological levels in a disease context are assessed.     

Pelagic occurrence of the sympagic amphipod Gammarus wilkitzkii in ice-free waters of the Greenland Sea – dead end or part of life-cycle?

The sympagic (=ice-associated) amphipod Gammarus wilkitzkii usually lives attached to the underside of Arctic sea ice. During an expedition to the Greenland Sea in May/June 1997, high numbers of this species were found in pelagic Rectangular Midwater Trawl catches (0–500 m water depth) in an ice-free area, 35–42 km away from the ice edge. The amphipods seemed to have maintained position in the water column for at least 4 days. Mean biomass data (length: 2.9 cm, organic content: 73% dry mass), gut fullness (>50% in 85% of specimens) and sex ratio (females:males = 1:1.5) of these amphipods were very similar to values for under-ice populations. Due to their relatively high body density (mean: 1.134 g cm⁻³), the energy demand for swimming was assumed to be high. Measurements of oxygen consumption of swimming and resting amphipods (8.8 and 4.0 J g wet mass⁻¹ day⁻¹, respectively) suggested that, from an energetic point of view, G. wilkitzkii would maintain position in an ice-free water column for the time period. Accepted: 11 January 1999     

Masting,mixtures and modes: are two models better than one?

A key hypothesis in population ecology is that synchronous and intermittent seed production, known as mast seeding, is driven by the alternating allocation of carbohydrates and mineral nutrients between growth and reproduction in different years, i.e. ‘resource switching’. Such behaviour may ultimately generate bimodal distributions of long‐term flower and seed production, and evidence of these patterns has been taken to support the resource switching hypothesis. Here, we show how a widely‐used statistical test of bimodality applied by many studies in different ecological contexts may fail to reject the null hypothesis that focal probability distributions are unimodal. Using data from five tussock grass species in South Island, New Zealand, we find clear evidence of bimodality only when flowering patterns are analyzed with probabilistic mixture models. Mixture models provide a theory oriented framework for testing hypotheses of mast seeding patterns, enabling the different responses underlying medium‐ and high‐ versus non‐ and low‐flowering years to be modelled more realistically by associating these with distinct probability distributions. Coupling theoretical expectations with more rigorous statistical approaches will empower ecologists to reject null hypotheses more often.     

What are the maximum size and live body coloration of opah (Teleostei: Lampridae: Lampris species)?

Validity of the largest size accounts is not well documented and most published accounts of body coloration describe dead specimens lacking scales instead of the color of freshly caught opah. Maximum length is at least 163?cm fork length and maximum weight about 89?kg. The body color of fresh specimens is vermilion with white spots.     

Eight human OPA1 isoforms,long and short: What are they for?

OPA1 is a dynamin-related GTPase that controls mitochondrial dynamics, cristae integrity, energetics and mtDNA maintenance. The exceptional complexity of this protein is determined by the presence, in humans, of eight different isoforms that, in turn, are proteolytically cleaved into combinations of membrane-anchored long forms and soluble short forms. Recent advances highlight how each OPA1 isoform is able to fulfill “essential” mitochondrial functions, whereas only some variants carry out “specialized” features. Long forms determine fusion, long or short forms alone build cristae, whereas long and short forms together tune mitochondrial morphology. These findings offer novel challenging therapeutic potential to gene therapy.     

A tale of two tails: why are terminal residues of proteins exposed?

MOTIVATION: It is widely known that terminal residues of proteins (i.e. the N- and C-termini) are predominantly located on the surface of proteins and exposed to the solvent. However, there is no good explanation as to the forces driving this phenomenon. The common explanation that terminal residues are charged, and charged residues prefer to be on the surface, cannot explain the magnitude of the phenomenon. Here, we survey a large number of proteins from the PDB in order to explore, quantitatively, this phenomenon, and then we use a lattice model to study the mechanisms involved. RESULTS: The location of the termini was examined for 425 small monomeric proteins (50-200 amino acids) and it was found that the average solvent accessibility of termini residues is 87.1% compared with 49.2% of charged residues and 35.9% of all residues. Using a cutoff of 50% of the maximal possible exposure, 80.3% of the N-terminal and 86.1% of the C-terminal residues are exposed compared to 32% for all residues. In addition, terminal residues are much more distant from the center of mass of their proteins than other residues. Using a 2D lattice, a large population of model proteins was studied on three levels: structural selection of compact structures, thermodynamic selection of conformations with a pronounced energy gap and kinetic selection of fast folding proteins using Monte-Carlo simulations. Progressively, each selection raises the proportion of proteins with termini on the surface, resulting in similar proportions to those observed for real proteins.     

Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home?

In recent years, the increased sampling of protein-coding genes from diverse eukaryotes has revealed that many aspects of each gene tree are at odds with other phylogenies. This has led to the belief that each gene tree has unique strengths and weaknesses, suggesting that an accurate picture of eukaryotic relationships will be achieved only through comparative phylogeny using several different genes. To this end, actin genes were characterized from two genera of chlorarachniophytes, Chlorarachnion and Lotharella, and three species of the cercomonad flagellate Cercomonas: Phylogenetic trees including these new actin genes confirm the recently proposed relationship between chlorarachniophytes and cercomonads (Cercozoa) and, more importantly, also show a close relationship between Cercozoa and Foraminifera. Both of these are major eukaryotic groups encompassing extremely diverse organisms, yet there is no strong evidence for the evolutionary position of either from morphological or molecular data. The union of Cercozoa and Foraminifera suggested by actin phylogeny represents a novel step in the long process of determining the broad relationships between all major eukaryotic groups.     

Festuca inops and Festuca gracilior (Poaceae): are they two different species?

According to current systematics, Festuca inops and F. gracilior are two distinct species. However, they are hardly distinguishable from each other on the basis of their morphological characters. Festuca inops is considered a diploid species endemic to Italy, while F. gracilior has a discontinuous distribution area, apparently related to chromosomal levels: diploid populations in Italy and south-east France, tetraploid populations in north-east Spain. The diploid populations of both taxa from Italy and south-east France are investigated in the present study. Nearly 1000 exsiccata were examined and morphometric analysis was carried out on macro- and micromorphological features of 119 specimens (including type-specimens) and on 20 natural populations (including loci classici ). All these data showed that the two species should be referred to a single taxon, for which the rank of species seems to be appropriate. This result is supported by karyological, ecological and chorological data and was confirmed by the results of ISSR analysis. According to nomenclatural rules, the legitimate name for the species is Festuca inops De Not.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 239–258.