Detection of in vivo protein-DNA interactions using DamID in mammalian cells

Understanding gene regulatory networks in mammalian cells requires detailed knowledge of protein-DNA interactions. Commonly used methods for genome-wide mapping of these interactions are based on chromatin immunoprecipitation. However, these methods have some drawbacks, such as the use of crosslinking reagents, the need for highly specific antibodies and relatively large amounts of starting material. We present DamID, an alternative technique to map genome-wide occupancy of interaction sites in vivo, that bypasses these limitations. DamID is based on the expression of a fusion protein consisting of a protein of interest and DNA adenine methyltransferase (Dam). This leads to methylation of adenines near sites where the protein of interest interacts with the DNA. These methylated sequences are subsequently amplified by a methylation-specific PCR protocol and identified by hybridization to microarrays. Using DamID, genome-wide maps of the binding of DNA-interacting proteins in mammalian cells can be constructed efficiently. Depending on the strategy used for expression of the Dam-fusion proteins, genome-wide binding maps can be obtained in as little as 2 weeks.     

Efficient and error-free fluorescent gene tagging in human organoids without double-strand DNA cleavage

CRISPR-associated nucleases are powerful tools for precise genome editing of model systems, including human organoids. Current methods describing fluorescent gene tagging in organoids rely on the generation of DNA double-strand breaks (DSBs) to stimulate homology-directed repair (HDR) or non-homologous end joining (NHEJ)-mediated integration of the desired knock-in. A major downside associated with DSB-mediated genome editing is the required clonal selection and expansion of candidate organoids to verify the genomic integrity of the targeted locus and to confirm the absence of off-target indels. By contrast, concurrent nicking of the genomic locus and targeting vector, known as in-trans paired nicking (ITPN), stimulates efficient HDR-mediated genome editing to generate large knock-ins without introducing DSBs. Here, we show that ITPN allows for fast, highly efficient, and indel-free fluorescent gene tagging in human normal and cancer organoids. Highlighting the ease and efficiency of ITPN, we generate triple fluorescent knock-in organoids where 3 genomic loci were simultaneously modified in a single round of targeting. In addition, we generated model systems with allele-specific readouts by differentially modifying maternal and paternal alleles in one step. ITPN using our palette of targeting vectors, publicly available from Addgene, is ideally suited for generating error-free heterozygous knock-ins in human organoids.

A major downside of double-strand break-mediated genome editing is the need to verify the genomic integrity of the targeted locus and confirm the absence of off-target indels. This study shows that in-trans paired nicking is a mutation-free CRISPR strategy to introduce precise knock-ins into human organoids; its genomic fidelity allows all knock-in cells to be pooled, accelerating the establishment of new organoid models.     

Effect of feeding program during rearing and age at first insemination on performances during subsequent reproduction in young rabbit does

An experiment was performed to study the effect of the feeding program and age at first mating on body growth, feed intake, reproductive performance, and culling of rabbit does over three parities, using 155 does of a strain of New Zealand white rabbits. Three treatments were applied. Ad libitum feeding until first insemination at 14.5 wk (AL-14.5) or 17.5 wk of age (AL-17.5), and restrictive feeding from five wk of age until first insemination at 17.5 wk of age (R-17.5). At first insemination, the BW of AL-14.5 and R-17.5 was similar (3 907 vs. 3 791 +/- 46 g, respectively), whereas AL-17.5 does were heavier (4 390 +/- 46 g, P < 0.001). During reproduction, performance of AL-17.5 was not improved compared to AL-14.5 and R-17.5 does. Al-17.5 does showed a lower feed intake during the first gestation (-25%) and first parity (-10%) than R- 17.5, resulting in weight loss (-6%) during the first gestation and decreased litter weights (-19%) and litter growth (-14%) in the first parity. Extended first mating by three wk (17.5 vs. 14.5 wk) but similar BW at first mating did not affect feed intake and BW development during the first three parities. However, the number of live born kits and weight at first kindling, and litter growth in the first parity were improved in R-17.5 (+23%, +18%, and +14%, respectively). Reproductive performance can be improved by restricted feeding during rearing and extended first insemination to 17.5 wk of age. However, the culling rate was not affected by the rearing strategy.     

Glucose delays seed germination in<Emphasis Type="Italic"> Arabidopsis thaliana</Emphasis>

Here we report that glucose delays germination of Arabidopsis thaliana (L.) Heynh. seeds at concentrations below those known to inhibit early seedling development. This inhibition acts on embryo growth and is independent of hexokinase (HXK) function. Hormones and hormone inhibitors were applied to the germination media and several hormone biosynthesis and signalling mutants were tested on glucose media to investigate a possible role of abscisic acid (ABA), gibberellin and ethylene in the glucose-induced germination delay. Results indicate that the germination inhibition by glucose cannot be antagonized by ethylene or gibberellin and is independent of the HXK1/ABA/ABI4 signalling cascade. These findings suggest that there is a separate regulatory pathway independent of ABI2/ABI4/ABI5. Thus, in a relatively short time frame sugars utilize different signalling cascades to inhibit germination and post-germination growth, underlining the complexity of sugar responses.Abbreviations ABA Abscisic acid - ABI ABA insensitive - ACC 1-Aminocyclopropane-1-carboxylic acid - BR Brassinosteroid - CAB Chlorophyll a/b-binding protein - FUS3 Fusca3 - GA Gibberellin - GA ₃ Gibberellic acid - HXK Hexokinase - LEC1 Leafy cotyledon1 - RBCS Ribulose-1,5-bisphosphate carboxylase small subunit - WT Wild type     

Production of tailor-made fructans in sugar beet by expression of onion fructosyltransferase genes

The consumption of fructans as a low caloric food ingredient or dietary fibre is rapidly increasing due to health benefits. Presently, the most important fructan source is chicory, but these fructans have a simple linear structure and are prone to degradation. Additional sources of high-quality tailor-made fructans would provide novel opportunities for their use as food ingredients. Sugar beet is a highly productive crop that does not normally synthesize fructans. We have introduced specific onion fructosyltransferases into sugar beet. This resulted in an efficient conversion of sucrose into complex, onion-type fructans, without the loss of storage carbohydrate content.     

The presence of promatrix metalloproteinase-3 and its relation with different categories of coal workers' pneumoconiosis

Extracellular matrix formation (ECM) and remodeling are critical events related to the pathogenesis of pulmonary fibrosis. Matrix metalloproteinases play an essential role in degrading and remodeling the ECM. In this study, we tried to show the presence and correlation of promatrix metalloproteinase-3 (proMMP-3) (the inactive form of metalloproteinase-3) levels in coal workers' pneumoconiosis (CWP) with different categories. The study population consisted of 44 coal miners with CWP (pos CWP). Coal miners without CWP (neg CWP, n = 24) and non-underground personnel (controls, n = 17) were taken as controls. All coal miners were stable and had no systemic infection or disease. Standard posterio-anterior chest radiographs and pulmonary function tests were performed to exclude any diseases other than CWP. Serum proMMP-3 was analysed using the sandwich enzyme-linked immunosorbent assay according to the manufacturer's instructions (The Binding Site, Birmingham, UK). Mean proMMP-3 values of the all three groups were compared and a significant statistical difference obtained (p < 0.001). In addition, a statistically significant difference was found between categories of the disease and proMMP-3 values (p < 0.05). The effects of age, exposure duration and cigarette smoking on proMMP-3 values in coal miners with CWP were investigated. There were no correlations between age, smoking and proMMP-3 values. However, a positive correlation was found between exposure duration and proMMP-3 values (r = 0.447, p = 0.008). In conclusion, proMMP-3 (prostromelysin 1) may play an essential role in degrading and remodeling the ECM in workers with pneumoconiosis. ProMMP-3 may also reflect the stage of pneumoconiosis disease.     

CD36 deficiency increases insulin sensitivity in muscle,but induces insulin resistance in the liver in mice

CD36 (fatty acid translocase) is involved in high-affinity peripheral fatty acid uptake. Mice lacking CD36 exhibit increased plasma free fatty acid and triglyceride (TG) levels and decreased glucose levels. Studies in spontaneous hypertensive rats lacking functional CD36 link CD36 to the insulin-resistance syndrome. To clarify the relationship between CD36 and insulin sensitivity in more detail, we determined insulin-mediated whole-body and tissue-specific glucose uptake in CD36-deficient (CD36-/-) mice. Insulin-mediated whole-body and tissue-specific glucose uptake was measured by d-[3H]glucose and 2-deoxy-d-[1-3H]glucose during hyperinsulinemic clamp in CD36-/- and wild-type control littermates (CD36+/+) mice. Whole-body and muscle-specific insulin-mediated glucose uptake was significantly higher in CD36-/- compared with CD36+/+ mice. In contrast, insulin completely failed to suppress endogenous glucose production in CD36-/- mice compared with a 40% reduction in CD36+/+ mice. This insulin-resistant state of the liver was associated with increased hepatic TG content in CD36-/- mice compared with CD36+/+ mice (110.9 +/- 12.0 and 68.9 +/- 13.6 microg TG/mg protein, respectively). Moreover, hepatic activation of protein kinase B by insulin, measured by Western blot, was reduced by 54%. Our results show a dissociation between increased muscle and decreased liver insulin sensitivity in CD36-/- mice.     

Extrathymic TCR gene rearrangement in human small intestine: identification of new splice forms of recombination activating gene-1 mRNA with selective tissue expression

Two new 5'-untranslated region (5'UTR) exons were identified in the human gene for the lymphocyte-specific endonuclease recombination activating gene-1 (RAG1) required for the somatic recombination yielding functional Ag receptors. These 5'UTR exons were used in three different splice forms by jejunal lymphocytes of the T cell lineage. RAG1 mRNA containing the previously described 5'UTR exon was not expressed in these cells. Conversely, one of the new 5'UTR exons was not expressed in thymus. The new RAG1 mRNA splice forms were all expressed in immature T cells (CD2(+)CD7(+)CD3(-)). This cell population also expressed high levels of mRNA for the pre-T alpha-chain. In situ hybridization demonstrated jejunal cells expressing the new splice forms of RAG1 mRNA, both intraepithelially and in lamina propria. Pre-T alpha-chain mRNA-expressing cells were detected at the same sites. These results strongly suggest ongoing TCR gene rearrangement in human small intestinal mucosa, yielding T cells specially adapted for this environment. This seems to be achieved by two parallel processes, extrathymic T cell development and peripheral Ag-driven TCR editing.     

Bridging the gap between structural and lattice models: a parameterization of energy transfer and trapping in Photosystem I

In the absence of an accurate structural model, the excited state dynamics of energy-transferring systems are often modeled using lattice models. To demonstrate the validity and other potential merits of such an approach we present the results of the modeling of the energy transfer and trapping in Photosystem I based upon the 2.5 A structural model, and show that these results can be reproduced in terms of a lattice model with only a few parameters. It has recently been shown that at room temperature the dynamics of a hypothetical Photosystem I particle, not containing any red chlorophylls (chls), are characterized by a longest (trapping) lifetime of 18 ps. The structure-based modeling of the dynamics of this particle yields an almost linear relationship between the possible values of the intrinsic charge-separation time at P700, 1/gamma, and the average single-site lifetime in the antenna, tauss. Lattice-based modeling, using the approach of a perturbed two-level model, reproduces this linear relation between tauss and 1/gamma. Moreover, this approach results in a value of the (modified) structure-function corresponding to a structure exhibiting a mixture of the characteristics of both a square and a cubic lattice, consistent with the structural model. These findings demonstrate that the lattice model describes the dynamics of the system appropriately. In the lattice model, the total trapping time is the sum of the delivery time to the reaction center and the time needed to quench the excitation after delivery. For the literature value of tauss=150 fs, both these times contribute almost equally to the total trapping time of 18 ps, indicating that the system is neither transfer- nor trap-limited. The value of approximately 9 ps for the delivery time is basically equal to the excitation-transfer time from the bulk chls to the red chls in Synechococcus elongatus, indicating that energy transfer from the bulk to the reaction center and to the red chls are competing processes. These results are consistent with low-temperature time-resolved and steady-state fluorescence measurements. We conclude that lattice models can be used to describe the global energy-transfer properties in complex chromophore networks, with the advantage that such models deal with only a few global, intuitive parameters rather than the many microscopic parameters obtained in structure-based modeling.     

1,2-O-Trichloroethylidene acetal group protected 3,5-dieno-1,4-furanose derivatives

The preparation of 3,5-(E)-dieno-3,5,6,8-tetradeoxy-(S)-1,2-O-trichloroethylidene-alpha-D-glycero-octo-1,4-furano-7-ulose starting from either 1,2-O-(S)-trichloroethylidene-alpha-D-glucofuranose (beta-chloralose) or 1,2-O-(S)-trichloroethylidene-alpha-D-galactofuranose (galactochloralose) and the preparation of methyl 3,5-(E)-dieno-3,5,6-trideoxy-(S)-1,2-O-trichloroethylidene-alpha-D-glycero-hepta-1,4-furano-uronate starting from beta-chloralose are described. Endocyclic double bond formations were realised by the elimination of 3-acetoxy groups using DMF-sodium bicarbonate. This elimination was not successful when the starting compound was 1,2-O-(R)-trichloroethylidene-alpha-D-glucofuranose (alpha-chloralose), where the trichloromethyl group occupies the endo position.