The Study of Protein–DNA Interactions in CD4+ T-Cells Using ChIPmentation

Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) is an invaluable method to profile of enrichment of histone modifications and transcription factor binding sites across the genome. However, standard ChIP-seq protocols require large numbers of cells (>10^7) as starting material, which are often impossible to obtain for rare immune populations. Here we describe a streamlined ChIP protocol optimised for small cell numbers in conjunction with transposon-tagging mediated sequencing library preparation (ChIPmentation) which allows the analysis of samples of as low as 10^5 cells

Zassenhaus conjecture for central extensions of S5

We confirm a conjecture of Zassenhaus about rational conjugacy of torsion units in integral group rings for a covering group of the symmetric group S5 and for the general linear group GLð2; 5Þ. The first result, together with others from the literature, settles the conjugacy question for units of prime-power order in the integral group ring of a finite Frobenius group

Energy evolution in time-dependent harmonic oscillator

The theory of adiabatic invariants has a long history, and very important implications and applications in many different branches of physics, classically and quantally, but is rarely founded on rigorous results. Here we treat the general time-dependent one-dimensional harmonic oscillator, whose Newton equation $\ddot{q} + \omega^2(t) q=0$ cannot be solved in general. We follow the time-evolution of an initial ensemble of phase points with sharply defined energy $E_0$ at time $t=0$ and calculate rigorously the distribution of energy $E_1$ after time $t=T$, which is fully (all moments, including the variance $\mu^2$) determined by the first moment $\bar{E_1}$. For example, $\mu^2 = E_0^2 [(\bar{E_1}/E_0)^2 - (\omega (T)/\omega (0))^2]/2$, and all higher even moments are powers of $\mu^2$, whilst the odd ones vanish identically. This distribution function does not depend on any further details of the function $\omega (t)$ and is in this sense universal. In ideal adiabaticity $\bar{E_1} = \omega(T) E_0/\omega(0)$, and the variance $\mu^2$ is zero, whilst for finite $T$ we calculate $\bar{E_1}$, and $\mu^2$ for the general case using exact WKB-theory to all orders. We prove that if $\omega (t)$ is of class ${\cal C}^{m}$ (all derivatives up to and including the order $m$ are continuous) $\mu \propto T^{-(m+1)}$, whilst for class ${\cal C}^{\infty}$ it is known to be exponential $\mu \propto \exp (-\alpha T)$.Comment: 26 pages, 5 figure

The Th1 cell regulatory circuitry is largely conserved between human and mouse

Gene expression programs controlled by lineage-determining transcription factors are often conserved between species. However, infectious diseases have exerted profound evolutionary pressure, and therefore the genes regulated by immune-specific transcription factors might be expected to exhibit greater divergence. T-bet (Tbx21) is the immune-specific, lineage-specifying transcription factor for T helper type I (Th1) immunity, which is fundamental for the immune response to intracellular pathogens but also underlies inflammatory diseases. We compared T-bet genomic targets between mouse and human CD4+ T cells and correlated T-bet binding patterns with species-specific gene expression. Remarkably, we found that the majority of T-bet target genes are conserved between mouse and human, either via preservation of binding sites or via alternative binding sites associated with transposon-linked insertion. Species-specific T-bet binding was associated with differences in transcription factor–binding motifs and species-specific expression of associated genes. These results provide a genome-wide cross-species comparison of Th1 gene regulation that will enable more accurate translation of genetic targets and therapeutics from pre-clinical models of inflammatory and infectious diseases and cancer into human clinical trials

Context-Dependent Behavior of the Enterocin Iterative Polyketide Synthase A New Model for Ketoreduction

AbstractHeterologous expression and mutagenesis of the enterocin type II polyketide synthase (PKS) system suggest for the first time that the association of an extended set of proteins and substrates is needed for the effective production of the enterocin-wailupemycin polyketides. In the absence of its endogenous ketoreductase (KR) EncD in either the enterocin producer “Streptomyces maritimus” or the engineered host S. lividans K4-114, the enterocin minimal PKS is unable to produce benzoate-primed polyketides, even when complemented with the homologous actinorhodin KR ActIII or with EncD active site mutants. These data suggest that the enterocin PKS requires EncD to serve a catalytic and not just a structural role in the functional PKS enzyme complex. This strongly implies that EncD reduces the polyketide chain during elongation rather than after its complete assembly, as suggested for most type II PKSs

Antibiotic-producing symbionts dynamically transition between plant pathogenicity and insect-defensive mutualism

Pathogenic and mutualistic bacteria associated with eukaryotic hosts often lack distinctive genomic features, suggesting regular transitions between these lifestyles. Here we present evidence supporting a dynamic transition from plant pathogenicity to insect-defensive mutualism in symbiotic Burkholderia gladioli bacteria. In a group of herbivorous beetles, these symbionts protect the vulnerable egg stage against detrimental microbes. The production of a blend of antibiotics by B. gladioli, including toxoflavin, caryoynencin and two new antimicrobial compounds, the macrolide lagriene and the isothiocyanate sinapigladioside, likely mediate this defensive role. In addition to vertical transmission, these insect symbionts can be exchanged via the host plant and retain the ability to initiate systemic plant infection at the expense of the plant’s fitness. Our findings provide a paradigm for the transition between pathogenic and mutualistic lifestyles and shed light on the evolution and chemical ecology of this defensive mutualism

Torsion Units for a Ree group, Tits group and a Steinberg triality group

We investigate the Zassenhaus conjecture for the Steinberg triality group ${}^3D_4(2^3)$, Tits group ${}^2F_4(2)'$ and the Ree group ${}^2F_4(2)$. Consequently, we prove that the Prime Graph question is true for all three groups

microRNAs regulate cell-to-cell variability of endogenous target gene expression in developing mouse thymocytes

The development and homeostasis of multicellular organisms relies on gene regulation within individual constituent cells. Gene regulatory circuits that increase the robustness of gene expression frequently incorporate microRNAs as post-transcriptional regulators. Computational approaches, synthetic gene circuits and observations in model organisms predict that the co-regulation of microRNAs and their target mRNAs can reduce cell-to-cell variability in the expression of target genes. However, whether microRNAs directly regulate variability of endogenous gene expression remains to be tested in mammalian cells. Here we use quantitative flow cytometry to show that microRNAs impact on cell-to-cell variability of protein expression in developing mouse thymocytes. We find two distinct mechanisms that control variation in the activation-induced expression of the microRNA target CD69. First, the expression of miR-17 and miR-20a, two members of the miR-17-92 cluster, is coregulated with the target mRNA Cd69 to form an activation-induced incoherent feed-forward loop. Another microRNA, miR-181a, acts at least in part upstream of the target mRNA Cd69 to modulate cellular responses to activation. The ability of microRNAs to render gene expression more uniform across mammalian cell populations may be important for normal development and for disease

The MAP kinase MpkA controls cell wall integrity, oxidative stress response, gliotoxin production and iron adaptation in Aspergillus fumigatus

The saprophytic fungus Aspergillus fumigatus is the most important air-borne fungal pathogen. The cell wall of A. fumigatus has been studied intensively as a potential target for development of effective antifungal agents. A major role in maintaining cell wall integrity is played by the mitogen-activated protein kinase (MAPK) MpkA. To gain a comprehensive insight into this central signal transduction pathway, we performed a transcriptome analysis of the ΔmpkA mutant under standard and cell wall stress conditions. Besides genes involved in cell wall remodelling, protection against ROS and secondary metabolism such as gliotoxin, pyomelanin and pseurotin A, also genes involved in siderophore biosynthesis were regulated by MpkA. Consistently, northern and western blot analyses indicated that iron starvation triggers phosphorylation and thus activation of MpkA. Furthermore, localization studies indicated that MpkA accumulates in the nucleus under iron depletion. Hence, we report the first connection between a MAPK pathway and siderophore biosynthesis. The measurement of amino acid pools and of the pools of polyamines indicated that arginine was continuously converted into ornithine to fuel the siderophore pool in the ΔmpkA mutant strain. Based on our data, we propose that MpkA fine-tunes the balance between stress response and energy consuming cellular processes