The post-genomic era for a select few

A report of the 4th Colmar Scientific Symposium 'Biology in the Post-genomic Era', Colmar, France, 16-17 October 2003.     

几个容易混淆的概念

在教学中,教师和学生对一些生物学概念通常存在含混不清的情况。为了便于教师开展教学活动,笔者针对神经纤维、动物的雄性生殖器官、鸡卵等常见生物学概念进行了辨析。以为教学提供参考。     

A few good genes

Comment on: Alizadeh AA, et al. Blood. 2011; 118:1350-8.     

A few standing for many: embryo receptor-like kinases

Development of plant embryos is a complex and highly organized process, and experimental evidence indicates that intercellular signaling plays a major role. The recent identification of Receptor-Like Kinases (RLKs) and related Receptor-Like Cytoplasmic Kinases (RLCKs) with specific roles in Arabidopsis thaliana embryo development suggest important functions of intercellular signaling during embryogenesis. Despite the characterization of only a few RLKs and RLCKs with embryonic roles, expression data indicate that many RLKs and RLCKs with either post-embryonic functions or unknown functions are transcribed in Arabidopsis embryos. The functional characterization of a few members of this large kinase family is likely to represent only the tip of the iceberg, and we predict that many RLKs and RLCKs play major roles throughout embryo development.     

A few immobilized thrombins are sufficient for platelet spreading

Eukaryotic cells respond to signaling molecules with picomolar to nanomolar sensitivities. However, molar concentrations give no suggestion of the sufficient number of molecules per cell and are confusing when referring to physiological situations in which signaling molecules act in an immobilized state. Here, we studied platelet adhesion by thrombin, a key step in normal hemostasis and pathological arterial thrombosis. We generated a biofunctional nanosheet surface to mimic the in vivo solid-state interaction between platelets and thrombin at sites of injured tissues. We observed that <10 molecules readily activate platelets with high specificity, resulting in platelet adhesion and spreading. This number is much lower than expected from previous experiments in solution, in which the sole activation of platelets required a >1000-fold stoichiometric excess of thrombin. We conclude that immobilizing thrombin apposed to the membrane receptor allows platelets to respond with very high sensitivity. Moreover, we propose that irreversible cell activation may require several ligands to avoid activation by single, mislocalized signaling molecules.     

Efficient peptide-MHC-I binding prediction for alleles with few known binders

MOTIVATION: In silico methods for the prediction of antigenic peptides binding to MHC class I molecules play an increasingly important role in the identification of T-cell epitopes. Statistical and machine learning methods in particular are widely used to score candidate binders based on their similarity with known binders and non-binders. The genes coding for the MHC molecules, however, are highly polymorphic, and statistical methods have difficulties building models for alleles with few known binders. In this context, recent work has demonstrated the utility of leveraging information across alleles to improve the performance of the prediction. RESULTS: We design a support vector machine algorithm that is able to learn peptide-MHC-I binding models for many alleles simultaneously, by sharing binding information across alleles. The sharing of information is controlled by a user-defined measure of similarity between alleles. We show that this similarity can be defined in terms of supertypes, or more directly by comparing key residues known to play a role in the peptide-MHC binding. We illustrate the potential of this approach on various benchmark experiments where it outperforms other state-of-the-art methods. AVAILABILITY: The method is implemented on a web server: http://cbio.ensmp.fr/kiss. All data and codes are freely and publicly available from the authors.     

Quite a few reasons for calling carnivores 'the most wonderful plants in the world'

Background

A plant is considered carnivorous if it receives any noticeable benefit from catching small animals. The morphological and physiological adaptations to carnivorous existence is most complex in plants, thanks to which carnivorous plants have been cited by Darwin as ‘the most wonderful plants in the world’. When considering the range of these adaptations, one realizes that the carnivory is a result of a multitude of different features.

Scope

This review discusses a selection of relevant articles, culled from a wide array of research topics on plant carnivory, and focuses in particular on physiological processes associated with active trapping and digestion of prey. Carnivory offers the plants special advantages in habitats where nutrient supply is scarce. Counterbalancing costs are the investments in synthesis and the maintenance of trapping organs and hydrolysing enzymes. With the progress in genetic, molecular and microscopic techniques, we are well on the way to a full appreciation of various aspects of plant carnivory.

Conclusions

Sufficiently complex to be of scientific interest and finite enough to allow conclusive appraisal, carnivorous plants can be viewed as unique models for the examination of rapid organ movements, plant excitability, enzyme secretion, nutrient absorption, food-web relationships, phylogenetic and intergeneric relationships or structural and mineral investment in carnivory.     

A few remarks on the morphogenesis of the larynx.

After having reviewed the principal theories regarding the development of the larynx the authors performed a study on the morphogenesis of the above structure using four horizontally- and sagitally-sectioned human embryos. The conclusion of a study of these sections is that the LC constitutes the primordium of the laryngeal vestibule. From its lateral margin, caudally (Stage 19, Carnegie System), the primitive ventricles begin to form, while in the final stages the EL extends caudally enclosing a small cephalic infraglottic area and therefore completely separating the IG from the LC. Such findings in our opinion would confirm a different embryological derivation of the laryngeal cavity above and below the glottis.