BRCT domains: Easy as one,two, three

BRCA1 C-terminal (BRCT) domains are integral signaling modules in the DNA damage response (DDR). Aside from their established roles as phospho-peptide binding modules, BRCT domains have been implicated in phosphorylation-independent protein interactions, DNA binding and poly(ADP-ribose) (PAR) binding. These numerous functions can be attributed to the diversity in BRCT domain structure and architecture, where domains can exist as isolated single domains or assemble into higher order homo- or hetero-domain complexes. In this review, we incorporate recent structural and biochemical studies to demonstrate how structural features allow single and tandem BRCT domains to attain a high degree of functional diversity.Key words: BRCT domain, DNA repair, phosphorylation, phospho-peptide interaction, protein interaction, DNA binding, DNA damage response     

The efficiency of conversion of metabolisable protein into milk true protein over a range of metabolisable protein intakes

The aim of this work was to test the robustness of the 0.68 estimate of the efficiency of conversion of metabolisable protein into true milk protein (Agriculture and Food Research Council (AFRC), 1993) for protein-limiting diets and to determine whether a different value is appropriate for practical rationing. Seventy-two multiparous cows were blocked on the basis of milk energy output per unit of dry matter intake (DMI), and allocated at random to one of four treatments. Treatments supplied metabolisable energy (ME) at a fixed level to individuals within a block, but varied metabolisable protein (MP) supply from 25% below the estimated requirements, through -12.5% and +12.5% up to 25% above requirements for the average performance of animals within blocks at the start of the study. Cows were offered diets to meet their predicted ME requirements for each 3-week period with measurements performed in the last week of each period. Milk protein output was regressed against the estimated MP available for production for each cow and the efficiency of conversion of MP into milk true protein was calculated, assuming a maintenance requirement according to the MP system. The efficiency of conversion of MP into milk true protein decreased with the increasing supply of MP from 0.77 to 0.50. Using an iterative approach to determine the best fit of the data when supply matched requirement resulted in a range of efficiency values between 0.62 and 0.64 g of true milk protein per g of MP.     

Overexpression of trehalose synthase and accumulation of intracellular trehalose in 293H and 293FTetR:Hyg cells

A humanized clone containing the trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase (otsA/B) has been constructed. Using the Gateway Cloning System (Invitrogen, Inc.), the otsA/B genes have been placed under the control of the CMV promoter (pEXPcmv-otsA/B) or the CMV promoter and the tet operator (pEXP cmv TetO-otsA/B). The pEXPcmv-otsA/B clone has been introduced into 293H cells using LIPOFECTAMINE 2000 and the intracellular concentration of trehalose has been evaluated. The 293H cells accumulate 4-5 microg trehalose/mg dry weight and this concentration increases to 7-10 microg trehalose/mg dry weight if trehalose is included in the growth medium. The pEXPcmv TetO-otsA/B clone has been transfected into 293FTetR:Hyg cells which contain the tet repressor integrated into the genome. When these transfected cells are grown in the absence of tetracycline, no intracellular trehalose is detected. Inclusion of 0.3 microg/ml tetracycline in the growth medium results in the accumulation of 11-14 microg trehalose/mg dry weight, a value which increases to 19-20 microg trehalose/mg dry weight if trehalose is included in the growth medium. The data for the 293FTetR:Hyg cells indicate that intracellular trehalose accumulates in response to the addition of tetracycline. This system will allow us to manipulate the intracellular concentration of trehalose and to evaluate the desiccation tolerance of these cells as a function of intracellular trehalose concentration.     

Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves

The phyllosphere, which is defined as the parts of terrestrial plants above the ground, is a large habitat for different microorganisms that show a high extent of adaption to their environment. A number of hypotheses were generated by culture-independent functional genomics studies to explain the competitiveness of specialized bacteria in the phyllosphere. In contrast, in situ data at the metabolome level as a function of bacterial colonization are lacking. Here, we aimed to obtain new insights into the metabolic interplay between host and epiphytes upon colonization of Arabidopsis thaliana leaves in a controlled laboratory setting using environmental metabolomics approaches. Quantitative nuclear magnetic resonance (NMR) and imaging high-resolution mass spectrometry (IMS) methods were used to identify Arabidopsis leaf surface compounds and their possible involvement in the epiphytic lifestyle by relative changes in compound pools. The dominant carbohydrates on the leaf surfaces were sucrose, fructose and glucose. These sugars were significantly and specifically altered after epiphytic leaf colonization by the organoheterotroph Sphingomonas melonis or the phytopathogen Pseudomonas syringae pv. tomato, but only to a minor extent by the methylotroph Methylobacterium extorquens. In addition to carbohydrates, IMS revealed surprising alterations in arginine metabolism and phytoalexin biosynthesis that were dependent on the presence of bacteria, which might reflect the consequences of bacterial activity and the recognition of not only pathogens but also commensals by the plant. These results highlight the power of environmental metabolomics to aid in elucidating the molecular basis underlying plant–epiphyte interactions in situ.     

Keratinocyte migration, proliferation, and differentiation in chronic ulcers from patients with diabetes and normal wounds.

Epithelialization of normal acute wounds occurs by an orderly series of events whereby keratinocytes migrate, proliferate, and differentiate to restore barrier function. The keratinocytes in the epidermis of chronic ulcers fail to execute this series of events. To better understand the epithelial dynamics of chronic ulcers, we used immunohistochemistry to evaluate proliferation, differentiation, adhesion, and migration in keratinocytes along the margin of chronic ulcers from patients with diabetes mellitus. We compared these features with keratinocytes from the migrating epithelial tongues of acute incisional and excisional wounds from normal volunteers. Keratinocytes at the chronic ulcer edge are highly proliferative (Ki67 proliferation marker), have an activated phenotype (K16), do not stain for keratins involved in epidermal differentiation (K10 and K2), and show a reduced expression of LM-3A32 (uncleaved, precursor of the alpha3 chain of laminin 5), a key molecule present on migrating epithelium. In contrast, keratinocytes in normal acute wound migrating epithelium do not express the proliferation marker Ki67 but do express K10, K2, and LM-3A32. A better understanding of molecular mechanisms involved in keratinocyte migration may lead to molecular targets for therapies for impaired wound healing.     

Identification of genes differentially expressed in dorsal and ventral chick midbrain during early Development

Background  

During the development of the central nervous system (CNS), patterning processes along the dorsoventral (DV) axis of the neural tube generate different neuronal subtypes. As development progresses these neurons are arranged into functional units with varying cytoarchitecture, such as laminae or nuclei for efficient relaying of information. Early in development ventral and dorsal regions are similar in size and structure. Different proliferation rates and cell migration patterns are likely to result in the formation of laminae or nuclei, eventually. However, the underlying molecular mechanisms that establish these different structural arrangements are not well understood.     

The fractionation of adenosine-rich oligoribonucleotides on polyethyleneimine-cellulose

After combined pancreatic and T(1) ribonuclease treatment of RNA, a characteristic series of products of the type A(n)N are obtained, where N can be any of the four ribonucleosides. Depending on whether phosphatase treatment is used before the addition of labelled phosphate at the 5'-terminus with bacteriophage phosphokinase, the labelled oligonucleotides obtained may or may not possess a phosphate group at the 3'- as well as the 5'-end. The behaviour of these characteristic products after electrophoresis on cellulose acetate strips followed by chromatography on polyethyleneimine-cellulose thin-layer plates was examined.     

Genetic Analysis of Orbiviruses by Using RNase T(1) Oligonucleotide Fingerprints

Corresponding double-stranded RNA segments of the related orbiviruses Wallal and Mudjinbarry produced distinctly different RNase T₁ fingerprint patterns. No extensive sequence reiteration was observed between segments of Mudjinbarry virus. Fingerprint analysis of the genome of recombinant orbiviruses confirmed segment reassortment as a mechanism of interchange of genetic information. When temperature-sensitive mutants of each virus were crossed in mixed infection, a consistent pattern of segment reassortment was correlated with generation of the wild-type phenotype. Thus, the temperature-sensitive lesion of group II Wallal serogroup mutants was mapped to segment 1. The group I mutant lesion appears to be located in segment 2.     

Efficient four fragment cloning for the construction of vectors for targeted gene replacement in filamentous fungi

Background  

The rapid increase in whole genome fungal sequence information allows large scale functional analyses of target genes. Efficient transformation methods to obtain site-directed gene replacement, targeted over-expression by promoter replacement, in-frame epitope tagging or fusion of coding sequences with fluorescent markers such as GFP are essential for this process. Construction of vectors for these experiments depends on the directional cloning of two homologous recombination sequences on each side of a selection marker gene.