Chasing the elusive mammalian microautophagy

Different mechanisms for delivery of intracellular components (proteins and organelles) to lysosomes and late endosomes for degradation co-exist in almost all cells and set the basis for distinct autophagic pathways. Cargo can be sequestered inside double-membrane vesicles (or autophagosomes) and reach the lysosomal compartment upon fusion of these vesicles to lysosomes through macroautophagy. In a different type of autophagy, known as chaperone-mediated autophagy (CMA), single individual soluble proteins can be targeted one by one to the lysosomal membrane and translocated into the lumen for degradation. Direct sequestration of proteins and organelles by invaginations at the lysosomal membrane that pinch off into the lumen has also been proposed. This process, known as microautophagy, remains poorly understood in mammalian cells. In our recent work, we demonstrate the occurrence of both in bulk and selective internalization of cytosolic components in late endosomes and identify some of the molecular players of this process that we have named endosomalmicroautophagy (e-MI) due to its resemblance to microautophagy.     

Chasing coccidia--new tools enter the race

The 8th International Coccidiosis Conference, held on 9--13 July 2001 in Palm Cove, Australia, was a showcase of the latest studies on widely known coccidia, including Eimeria and Toxoplasma in addition to the emerging or re-emerging parasites such as Neospora, Cryptosporidium and Cyclospora. This meeting was staged in conjunction with the Annual Scientific Meeting of the Australian Society for Parasitology.     

Chasing the dream: plant EST microarrays

DNA microarray technology is poised to make an important contribution to the field of plant biology. Stimulated by recent funding programs, expressed sequence tag sequencing and microarray production either has begun or is being contemplated for most economically important plant species. Although the DNA microarray technology is still being refined, the basic methods are well established. The real challenges lie in data analysis and data management. To fully realize the value of this technology, centralized databases that are capable of storing microarray expression data and managing information from a variety of sources will be needed. These information resources are under development and will help usher in a new era in plant functional genomics.     

Chasing behaviour genes into the next millennium

Both linkage and association strategies are appropriate for the characterization of genes implicated in human behavioural dimensions and disorders. For the foreseeable future, association studies involving whole-genome scanning will combine strategies using both single-nucleotide and simple-sequence-repeat polymorphisms.     

Chasing long-range evolutionary couplings in the AlphaFold era

Coevolution between protein residues is normally interpreted as direct contact. However, the evolutionary record of a protein sequence contains rich information that may include long-range functional couplings, couplings that report on homo-oligomeric states or even conformational changes. Due to the complexity of the sequence space and the lack of structural information on various members of a protein family, it has been difficult to effectively mine the additional information encoded in a multiple sequence alignment (MSA). Here, taking advantage of the recent release of the AlphaFold (AF) database we attempt to identify coevolutionary couplings that cannot be explained simply by spatial proximity. We propose a simple computational method that performs direct coupling analysis on a MSA and searches for couplings that are not satisfied in any of the AF models of members of the identified protein family. Application of this method on 2012 protein families suggests that ~12% of the total identified coevolving residue pairs are spatially distant and more likely to be disordered than their contacting counterparts. We expect that this analysis will help improve the quality of coevolutionary distance restraints used for structure determination and will be useful in identifying potentially functional/allosteric cross-talk between distant residues.     

News on hypomethylating agents: Chasing the FOX

Comment on: Thépot S, et al. Cell Cycle 2011; 10:2323-30.     

Cytotoxic immune cells with specificity for defined soluble antigens. II. Chasing the killing cells

Cells from mice immune against soluble antigens were tested for their in vitro cytotoxicity against chicken red blood cells (CRBC) coated with these antigens. In parallel, cells from mice immune against allogeneic P815 mastocytoma cells were tested for their in -vitro cytotoxicity against P815 cells. Before the cytotoxicity test, the immune cell populations were fractionated, using four different types of techniques, to check the impact of the removal of given subpopulations of cells on cytotoxic activity.Fractionation on anti-immunoglobulin coated columns did not affect the anti P815 cytotoxicity, but markedly decreased the cytotoxicity against antigen-coated CRBC. The same results were obtained by incubation on a plastic surface and/or an “ironplus-magnet” technique. Preincubation of the cytotoxic cell populations with homologous anti-θ or heterologous anti-T antiserum, plus complement, abolished both types of cytotoxicity. However, preincubation with anti-θ or anti-T antiserum alone, without complement, also blocked the cytotoxicity against antigen-coated CRBC, but not the anti P815 cytotoxicity. In vivo injection of heterologous anti-lymphocyte gammaglobulin completely abolished the anti P815 cytotoxicity, but not the cytotoxicity against antigen-coated CRBC.These results confirm that T cells (thymus-processed lymphocytes) can kill autonomously in the anti P815 system. They also suggest that, in the cytotoxicity against antigen-coated CRBC, as effector cells, (1) non-T cells are involved, (2) T cells might not be involved.