Laboratory of Molecular Biology

About: Laboratory of Molecular Biology is a facility organization based out in Cambridge, Cambridgeshire, United Kingdom. It is known for research contribution in the topics: Gene & RNA. The organization has 19395 authors who have published 24236 publications receiving 2101480 citations.

Mutations affecting programmed cell deaths in the nematode Caenorhabditis elegans.

Abstract: Mutations in two nonessential genes specifically block the phagocytosis of cells programmed to die during development. With few exceptions, these cells still die, suggesting that, in nematodes, engulfment is not necessary for most programmed deaths. Instead, these deaths appear to occur by cell suicide.

Combinatorial infection and in vivo recombination: a strategy for making large phage antibody repertoires.

Abstract: Antibody fragments, comprising paired heavy (VH) and light (VL) chain variable domains, can be displayed on the surface of filamentous bacteriophage, and rare phage (encoding antigen binding activities) selected by binding to antigen (1). The process mimics immune selection and has been used to make human antibody fragments in bacteria, without immunisation, by random combinatorial linkage (2) of diverse repertoires of VH and VL genes from lymphocytes (3, 4). Fragments with a range of binding specificities have been isolated with binding affinities in the range 10 M~'-10 M\" (for reviews see (5, 6)). However larger 'primary' repertoires of phage antibodies should allow higher affinity fragments to be isolated (7, 8). The size of phage antibody repertoires (10) is limited by the efficiency of transformation of E.coli. In principle, larger repertoires could be made by combinatorial infection, for example by transforming E. coli with a repertoire of heavy chains (encoded on plasmids) then infecting with a repertoire of light chains (encoded on phage) (9). Since infection is extremely efficient, and most E.coli cells in an exponential culture can be infected, the combinatorial diversity of Fab fragments displayed on phage could be as large as the number of E.coli in culture (10 per litre). However the heavy and light chain genes would not be packaged together within the same phage particle, and so could not be simultaneously co-selected. Here we describe a model system, involving the lox-Cre site-specific recombination system of bacteriophage PI, to lock together the heavy and light chain genes from two different replicons within an infected bacterium.

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

Abstract: Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. Moreover, using principal component analysis on the relative orientations of the bodies over all particle images in the data set, we generate movies that describe the most important motions in the data. Our results on two test cases, a cytoplasmic ribosome from Plasmodium falciparum, and the spliceosomal B-complex from yeast, illustrate how multi-body refinement can be useful to gain unique insights into the structure and dynamics of large and flexible macromolecular complexes.

Nucleotide-dependent conformational changes in dynamin: evidence for a mechanochemical molecular spring.

Abstract: Nucleotide-dependent conformational changes in dynamin: evidence for a mechanochemical molecular spring

A directory of human germ-line Vχ segments reveals a strong bias in their usage

Abstract: From the genomic DNA of a single individual, we have amplified, cloned and sequenced 37 human germ-line V kappa segments. Four of these segments were new. We then compiled a comprehensive directory of all germ-line V kappa segments and identified 50 different sequences with open reading frames. Comparison with 236 rearranged sequences revealed that no more than 24 of these germ-line sequences could be assigned rearranged counterparts, that some of these were rarely used, and that only about 11 sequences are used frequently. This suggests that the expressed V kappa repertoire is mainly derived from a limited number of segments. Most surprisingly, the J kappa-distal region of the locus appears to be rarely used: we could unambiguously assign 162 rearranged sequences to V kappa segments of the J kappa-proximal region, but only 5 to segments of the J kappa-distal region.