Dynamin recruitment by clathrin coats: a physical step?

Recent structural findings have shown that dynamin, a cytosol protein playing a key-role in clathrin-mediated endocytosis, inserts partly within the lipid bilayer and tends to self-assemble around lipid tubules. Taking into account these observations, we make the hypothesis that individual membrane-inserted dynamins imprint a local cylindrical curvature to the membrane. This imprint may give rise to long-range mechanical forces mediated by the elasticity of the membrane. Calculating the resulting many-body interaction between a collection of inserted dynamins and a membrane bud, we find a regime in which the dynamins are elastically recruited by the bud to form a collar around its neck, which is reminiscent of the actual process preempting vesicle scission. This physical mechanism might therefore be implied in the recruitment of dynamins by clathrin coats.     

The next step in biology: a periodic table?

Systems biology is an approach to explain the behaviour of a system in relation to its individual components. Synthetic biology uses key hierarchical and modular concepts of systems biology to engineer novel biological systems. In my opinion the next step in biology is to use molecule-to-phenotype data using these approaches and integrate them in the form a periodic table. A periodic table in biology would provide chassis to classify, systematize and compare diversity of component properties vis-a-vis system behaviour. Using periodic table it could be possible to compute higher- level interactions from component properties. This paper examines the concept of building a bio-periodic table using protein fold as the fundamental unit.     

Autophagy and self-preservation: a step ahead from cell plasticity?

Silencing the SPINK-related gene Kazal1 in hydra gland cells induces an excessive autophagy of both gland and digestive cells, leading to animal death. Moreover, during regeneration, autophagosomes are immediately detected in regenerating tips, where Kazal1 expression is lowered. When Kazal1 is completely silenced, hydra no longer survive the amputation stress (Chera S, de Rosa R, Miljkovic-Licina M, Dobretz K, Ghila L, Kaloulis K, Galliot B. Silencing of the hydra serine protease inhibitor Kazal1 gene mimics the human Spink1 pancreatic phenotype. J Cell Sci 2006; 119:846-57). These results highlight the essential digestive and cytoprotective functions played by Kazal1 in hydra. In mammals, autophagy of exocrine pancreatic cells is also induced upon SPINK1/Spink3 inactivation, whereas Spink3 is activated in injured pancreatic cells. Hence SPINKs, by preventing an excessive autophagy, appear to act as key players of the stress-induced self-preservation program. In hydra, this program is a prerequisite to the early cellular transition, whereby digestive cells of the regenerating tips transform into a head-organizer center. Enhancing the self-preservation program in injured tissues might therefore be the condition for unmasking their potential cell and/or developmental plasticity.     

Ethanol-inducible gene expression: first step towards a new green revolution?

The introduction of dwarf varieties of cereals was fundamental to the green revolution, but in the post-genomic era, the manipulation of plant morphology could be more sophisticated. A recent publication by Tahar Ait-ali et al. describes the use of the ethanol-inducible transgene expression system to re-examine plant architecture, and the genes that determine it. Their findings have implications for the manipulation of plant height and yield, and demonstrate the efficacy of regulated transgene expression for functional genomics.     

Improving cardiac regeneration after injury: Are we a step closer?

During regeneration, lost functional tissue can, in general, be replaced by different mechanisms, including proliferation of terminally differentiated cells or through differentiation of resident stem cells. It is a well-accepted dogma that the mammalian heart cannot efficiently regenerate upon injury as a consequence of insufficient oxygen supply. This is in sharp contrast to the hearts of adult zebrafish or newts that are able to replace lost ventricular tissue. Novel data indicate that the young murine heart also has the ability to regenerate within the first week after birth using mechanisms apparently quite similar to those observed in fish. This now provides us with a good starting point to identify the molecular mechanisms that led to the loss of the regenerative capacity of the adult mammalian heart. These future studies will also indicate whether it will be possible to reawaken the regenerative capability of cardiomyocytes in the human heart by treatment with selected pharmaceuticals.     

Postural preparation to making a step: is there a 'motor program' for postural preparation?

We tested the hypothesis that a sequence of mechanical events occurs preceding a step that scales in time and magnitude as a whole in a task-specific manner, and is a reflection of a "motor program." Young subjects made a step under three speed instructions and four tasks: stepping straight ahead, down a stair, up a stair, and over an obstacle. Larger center-of-pressure (COP) and force adjustments in the anterior-posterior direction and smaller COP and force adjustments in the mediolateral direction were seen during stepping forward and down a stair, as compared with the tasks of stepping up a stair and over an obstacle. These differences were accentuated during stepping under the simple reaction time instruction. These results speak against the hypothesis of a single motor program that would underlie postural preparation to stepping. They are more compatible with the reference configuration hypothesis of whole-body actions.     

Does the neurotropic action of adrenocorticotrophic hormone involve a lipolytic step?

The stimulatory effect of adrenocorticotrophic hormone (ACTH)-related synthetic peptides on the hydrolysis of emulsified trioleoylglycerol by a rat brain lipase was studied. The ACTH effect was related to the net positive charge associated with the basic amino acid residues at position 15-18 in the ACTH sequence, as well as to the presence of the NH2-terminal amino acid residues at position 1-2. The ACTH effect on lipolysis was markedly reduced when lipids were partially removed from the enzyme preparation by extraction with chloroform/acetone. Full restoration of the stimulatory effect was obtained upon addition of phosphatidylcholine (2 mg/ml) to the lipolytic medium. Striking similarities between the structure-activity pattern for the stimulatory effect of ACTH on brain lipase and that described for the receptor-mediated actions of ACTH on adrenal and fat cells suggest that the ACTH effect might involve recognition of a binding site associated with the brain enzyme. Complete log concentration response curves obtained with four ACTH analogs may also be regarded as simulating hormone-receptor interaction. These findings are discussed in relation to the possibility that ACTH may have a neurohormonal role via lipase-catalyzed changes in the lipid matrix of membranes.     

Is there a rate-limiting step before GTP cleavage by H-ras p21?

A slow fluorescence change of the complex between ras p21 and the fluorescent GTP analogue 2'(3')-O-(N-methylanthraniloyl)guanosine 5'-triphosphate (mGTP) has been postulated to be a signal arising from a step which is rate limiting and precedes the actual GTP hydrolysis reaction [Neal, S. E., Eccleston, J. F., & Webb, M. R. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 3562-3565]. We have now shown that the rate of the fluorescence change is accelerated by GTPase-activating protein (GAP) in the same manner as that of the GTP cleavage reaction. In contrast, a faster fluorescence change of smaller amplitude seen in the complex between p21 and the uncleavable 2'(3')-O-(N-methylanthraniloyl)guanosine 5'-O-(beta,gamma-imidotriphosphate) (mGppNHp) is not affected by GAP. The corresponding fluorescent derivative of guanosine 5'-O-(gamma-thiotriphosphate) (mGTP gamma S) shows a very slow fluorescence change after binding to p21, and this rate is also accelerated significantly by GAP. Hydrolysis of GTP gamma S is similarly slow, and it is accelerated by GAP in a similar manner to the fluorescence change. The results are interpreted to indicate that the fluorescence change occurs either at the hydrolysis step or on release of inorganic phosphate or thiophosphate but does not occur in a rate-limiting step preceding hydrolysis.     

Measuring metacarpal cortical bone by digital x-ray radiogrammetry: a step forward?

Changes in metacarpal cortical bone mineral density (BMD) using digital x-ray radiogrammetry were studied in patients with early rheumatoid arthritis. After 1, 2, and 5 years, large BMD losses were found: -1.7%, -2.8%, and -5.6%, respectively. Elevated erythrocyte sedimentation rate and anti-cyclic citrullinated peptide levels were independent predictors of bone loss, indicating that the largest amount of bone loss was found in patients with severe inflammation and high production of auto-antibodies, who are known to be at the highest risk of developing radiological bone damage. Studies are needed about the spatial and time relationship between erosions and juxta-articular and metacarpal bone loss.     

A-type lamin complexes and regenerative potential: a step towards understanding laminopathic diseases?

The lamins are nuclear intermediate filament-type proteins forming the nuclear lamina meshwork at the inner nuclear membrane as well as complexes in the nucleoplasm. The recent discoveries that mutated A-type lamins and lamin-binding nuclear membrane proteins can be linked to numerous rare human diseases (laminopathies) affecting a multitude of tissues has changed the cell biologist’s view of lamins as mere structural nuclear scaffold proteins. It is still unclear how mutations in these ubiquitously expressed proteins give rise to tissue-restricted pathological phenotypes. Potential disease models include mutation-caused defects in lamin structure and stability, the deregulation of gene expression, and impaired cell cycle control. This review brings together various previously proposed ideas and suggests a novel, more general, disease model based on an impairment of adult stem cell function and thus compromised tissue regeneration in laminopathic diseases.     

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species >15 kb and the remaining >10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.     

Role of autophagy in the clearance of mutant huntingtin: a step towards therapy?

Macroautophagy (henceforth referred to simply as autophagy) is a bulk degradation process involved in the clearance of long-lived proteins, protein complexes and organelles. A portion of the cytosol, with its contents to be degraded, is enclosed by double-membrane structures called autophagosomes/autophagic vacuoles, which ultimately fuse with lysosomes where their contents are degraded. In this review, we will describe how induction of autophagy is protective against toxic intracytosolic aggregate-prone proteins that cause a range of neurodegenerative diseases. Autophagy is a key clearance pathway involved in the removal of such proteins, including mutant huntingtin (that causes Huntington’s disease), mutant ataxin-3 (that causes spinocerebellar ataxia type 3), forms of tau that cause tauopathies, and forms of alpha-synuclein that cause familial Parkinson’s disease. Induction of autophagy enhances the clearance of both soluble and aggregated forms of such proteins, and protects against toxicity of a range of these mutations in cell and animal models. Interestingly, the aggregates formed by mutant huntingtin sequester and inactivate the mammalian target of rapamycin (mTOR), a key negative regulator of autophagy. This results in induction of autophagy in cells with these aggregates.     

Identifying conversion efficiency as a key mechanism underlying food webs adaptive evolution: a step forward,or backward?

Body size or mass is one of the main factors underlying food webs structure. A large number of evolutionary models have shown that indeed, the adaptive evolution of body size (or mass) can give rise to hierarchically organised trophic levels with complex between and within trophic interactions. However, these models generally make strong arbitrary assumptions on how traits evolve, casting doubts on their robustness. In particular, biomass conversion efficiency is always considered independent of the predator and prey size, which contradicts with the literature. In this paper, we propose a general model encompassing most previous models which allows to show that relaxing arbitrary assumptions gives rise to unrealistic food webs. We then show that considering biomass conversion efficiency dependent on species size is certainly key for food webs adaptive evolution because realistic food webs can evolve, making obsolete the need of arbitrary constraints on traits' evolution. We finally conclude that, on the one hand, ecologists should pay attention to how biomass flows into food webs in models. On the other hand, we question more generally the robustness of evolutionary models for the study of food webs.     

Is there a rate-limiting step in the catalytic cycle of [Ni-Fe] hydrogenases?

The question of the existence of a rate-limiting step in the catalytic cycle of Ni-Fe hydrogenases was taken up by using the sets of data available in the case of two specific enzymes: the hydrogenase from Thiocapsa roseopercisina, in which isotope effects have been systematically investigated over a wide pH range, and the enzyme from Desulfovibrio fructosovorans, for which the activities and the redox properties have been studied in two different forms, the wild type and the P238C mutant. When these data are analyzed in the light of appropriate kinetic models, it is concluded that electron transfer and proton transfer are rate limiting in the H2 uptake and H2 evolution reactions, respectively. This proposal is consistent with the data available from other Ni-Fe enzymes.     

Development of a highly regenerable elite Acala cotton (Gossypium hirsutum cv. Maxxa) – a step towards genotype-independent regeneration

A step towards genotype-independent regeneration of cotton (Gossypium hirsutum L.) was achieved by selection for regeneration potential (RG) in commercial seed of elite cultivars. A callus induction medium (MCIM) empirically determined for the cultivar `Maxxa' paved the way for RG selection among individual genotypic variants within a cultivar. MCIM consists of a basal Murashige-Skoog medium, supplemented with a unique combination of two synthetic auxins. Hypocotyl explants of `Coker 312', `Maxxa' and `Riata' seedlings cultured on MCIM successfully produced a high quality, friable callus as defined by its color, texture, size, and organization. Based on the number of fertile plants regenerated on a per seedling basis, RG was estimated as 17.4%, 44.4% and 80% in Acala cotton cultivars `Maxxa', `Ultima', and `Riata', respectively. The high RG of the cultivar Riata, a Round-up Ready® transgenic cultivar in a Maxxa genetic background, is likely due to additional RG alleles introgressed from the transgenic parent. Genotypic differences between cultivars for RG was reflected by the need for supplemental kinetin to efficiently regenerate `Ultima' plantlets via somatic embryogenesis. RG selection pressure through two cycles of selection resulted in development of advanced highly regenerable `Max-R' lines in an elite genetic background with immediate potential as suitable germplasm for breeding and biotechnology applications. Based on the results presented here, strategies for genotype-independent transformation and regeneration of cotton are proposed that integrate selection and introgression of regeneration potential in improvement programs.