Characterizing the morbid genome of ciliopathies

Background Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; however, our knowledge of their morbid genome, pleiotropy, and variable expressivity remains incomplete. Results We applied genomic approaches on a large patient cohort of 371 affected individuals from 265 families, with phenotypes that span the entire ciliopathy spectrum. Likely causal mutations in previously described ciliopathy genes were identified in 85% (225/265) of the families, adding 32 novel alleles. Consistent with a fully penetrant model for these genes, we found no significant difference in their “mutation load” beyond the causal variants between our ciliopathy cohort and a control non-ciliopathy cohort. Genomic analysis of our cohort further identified mutations in a novel morbid gene TXNDC15, encoding a thiol isomerase, based on independent loss of function mutations in individuals with a consistent ciliopathy phenotype (Meckel-Gruber syndrome) and a functional effect of its deficiency on ciliary signaling. Our study also highlighted seven novel candidate genes (TRAPPC3, EXOC3L2, FAM98C, C17orf61, LRRCC1, NEK4, and CELSR2) some of which have established links to ciliogenesis. Finally, we show that the morbid genome of ciliopathies encompasses many founder mutations, the combined carrier frequency of which accounts for a high disease burden in the study population. Conclusions Our study increases our understanding of the morbid genome of ciliopathies. We also provide the strongest evidence, to date, in support of the classical Mendelian inheritance of Bardet-Biedl syndrome and other ciliopathies

Control of Neural Daughter Cell Proliferation by Multi-level Notch/Su(H)/E(spl)-HLH Signaling

The Notch pathway controls proliferation during development and in adulthood, and is frequently affected in many disorders. However, the genetic sensitivity and multi-layered transcriptional properties of the Notch pathway has made its molecular decoding challenging. Here, we address the complexity of Notch signaling with respect to proliferation, using the developing Drosophila CNS as model. We find that a Notch/Su(H)/E(spl)-HLH cascade specifically controls daughter, but not progenitor proliferation. Additionally, we find that different E(spl)-HLH genes are required in different neuroblast lineages. The Notch/Su(H)/E(spl)-HLH cascade alters daughter proliferation by regulating four key cell cycle factors: Cyclin E, String/Cdc25, E2f and Dacapo (mammalian p21CIP1/p27KIP1/p57Kip2). ChIP and DamID analysis of Su(H) and E(spl)-HLH indicates direct transcriptional regulation of the cell cycle genes, and of the Notch pathway itself. These results point to a multi-level signaling model and may help shed light on the dichotomous proliferative role of Notch signaling in many other systems

The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome

Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that the Drosophila genome is also organized in discrete LADs, which are about five times smaller than human LADs but contain on average a similar number of genes. Systematic comparison to new and published insulator binding maps shows that only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens genome – NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation. Our results provide insights into the evolution of LAD organization and identify SU(HW) as a fine-tuner of genome – NL interactions

Global Chromatin Domain Organization of the Drosophila Genome

In eukaryotes, neighboring genes can be packaged together in specific chromatin structures that ensure their coordinated expression. Examples of such multi-gene chromatin domains are well-documented, but a global view of the chromatin organization of eukaryotic genomes is lacking. To systematically identify multi-gene chromatin domains, we constructed a compendium of genome-scale binding maps for a broad panel of chromatin-associated proteins in Drosophila melanogaster. Next, we computationally analyzed this compendium for evidence of multi-gene chromatin domains using a novel statistical segmentation algorithm. We find that at least 50% of all fly genes are organized into chromatin domains, which often consist of dozens of genes. The domains are characterized by various known and novel combinations of chromatin proteins. The genes in many of the domains are coregulated during development and tend to have similar biological functions. Furthermore, during evolution fewer chromosomal rearrangements occur inside chromatin domains than outside domains. Our results indicate that a substantial portion of the Drosophila genome is packaged into functionally coherent, multi-gene chromatin domains. This has broad mechanistic implications for gene regulation and genome evolution

Lipid (per) oxidation in mitochondria:an emerging target in the ageing process?

Lipids are essential for physiological processes such as maintaining membrane integrity, providing a source of energy and acting as signalling molecules to control processes including cell proliferation, metabolism, inflammation and apoptosis. Disruption of lipid homeostasis can promote pathological changes that contribute towards biological ageing and age-related diseases. Several age-related diseases have been associated with altered lipid metabolism and an elevation in highly damaging lipid peroxidation products; the latter has been ascribed, at least in part, to mitochondrial dysfunction and elevated ROS formation. In addition, senescent cells, which are known to contribute significantly to age-related pathologies, are also associated with impaired mitochondrial function and changes in lipid metabolism. Therapeutic targeting of dysfunctional mitochondrial and pathological lipid metabolism is an emerging strategy for alleviating their negative impact during ageing and the progression to age-related diseases. Such therapies could include the use of drugs that prevent mitochondrial uncoupling, inhibit inflammatory lipid synthesis, modulate lipid transport or storage, reduce mitochondrial oxidative stress and eliminate senescent cells from tissues. In this review, we provide an overview of lipid structure and function, with emphasis on mitochondrial lipids and their potential for therapeutic targeting during ageing and age-related disease

Generalized Principles for the Descriptor-Based Design of Supported Gold Catalysts

We postulate generalized principles for determining catalytic descriptors like the adsorption energy of CO*, across interfacial active sites of gold catalysts having varying coordination numbers and differing proximity to the support. These principles are derived using Density Functional Theory (DFT) calculations, linear scaling relationships, and an electronic structure analysis. Considered supports include two-dimensional (2D) and three-dimensional (3D) carbides and nitrides, doped MgO, and MoS2. We show that the stability of gold atoms, across different coordination numbers, is linearly correlated to the adsorption energy of CO* through site-specific scaling relationships. As per definition, the slopes of these site-specific scaling relationships portray the extent of structure-sensitivity of CO* adsorption. This structure-sensitivity indicates the dependence of adsorption energies of CO* on the coordination number of the Au sites. The site-specific scaling relationships inform that interfacial perturbations are localized at the metal layer proximal to the interface. These perturbations are moreover strongest at low-coordinated gold sites. Interestingly, the interaction energies between adsorbates at higher coverages are insensitive to interfacial perturbations, further demonstrating the localized nature of metal–support interactions. Our interpretations of the slopes of site-specific scaling relationships indicate that the structure-sensitivity of interfacial gold sites is determined by the extent of interfacial charge transfer. The CO* adsorption energy is structure-insensitive on supports that induce a negative charge on interfacial gold atoms. This structure-sensitivity proportionally increases with the progressively increasing positive charge on interfacial gold atoms. Such charge transfer-dependent structure-sensitivity is rationalized using Lewis acid–base interactions. We demonstrate that tuning the adsorption energy of CO* by manipulating interfacial charge transfer can endow a Cu-like reactivity to interfacial Au sites for CO2 electro-reduction. By melding the generalized principles derived in this study, we synthesize a scheme for determining site-specific catalytic descriptors at interfacial active sites of supported gold catalysts.Full Tex

Short-Term Intensified Cycle Training Alters Acute and Chronic Responses of PGC1 Alpha and Cytochrome C Oxidase IV to Exercise in Human Skeletal Muscle

Reduced activation of exercise responsive signalling pathways have been reported in response to acute exercise after training; however little is known about the adaptive responses of the mitochondria. Accordingly, we investigated changes in mitochondrial gene expression and protein abundance in response to the same acute exercise before and after 10-d of intensive cycle training. Nine untrained, healthy participants (mean plus or minus SD; VO2peak 44.1 plus or minus 17.6 ml/kg/min) performed a 60 min bout of cycling exercise at 164 plus or minus 18 W (72% of pre-training VO2peak). Muscle biopsies were obtained from the vastus lateralis muscle at rest, immediately and 3 h after exercise. The participants then underwent 10-d of cycle training which included four high-intensity interval training sessions (6x5 min; 90–100% VO2peak) and six prolonged moderate-intensity sessions (45–90 min; 75% VO2peak). Participants repeated the pre-training exercise trial at the same absolute work load (64% of pre-training VO2peak). Muscle PGC1-alpha mRNA expression was attenuated as it increased by 11- and 4- fold (P<0.001) after exercise pre- and post-training, respectively. PGC1-a protein expression increased 1.5 fold (P<0.05) in response to exercise pre-training with no further increases after the post-training exercise bout. RIP140 protein abundance was responsive to acute exercise only (P<0.01). COXIV mRNA (1.6 fold; P<0.01) and COXIV protein expression (1.5 fold; P<0.05) were increased by training but COXIV protein expression was decreased (20%; P<0.01) by acute exercise pre- and post-training. These findings demonstrate that short-term intensified training promotes increased mitochondrial gene expression and protein abundance. Furthermore, acute indicators of exercise-induced mitochondrial adaptation appear to be blunted in response to exercise at the same absolute intensity following short-term training

Implementations of the Parallel-Sampling ADC Architecture

This chapter describes circuit implementations of the parallel-sampling ADC architecture presented in Chap. 3. The parallel-sampling architecture is applied to two ADC architectures (a pipeline and a time-interleaving SAR ADC architecture), which are suitable for designing high-speed and medium-to-high resolution ADCs, to improve the ADC power efficiency for multi-carrier signals. Section 4.1 describes the architecture and operation of a 200 MS/s 12-b switched-capacitor pipeline ADC with a parallel-sampling first stage, which is suitable for broadband multi-carrier receivers for wireless standards such as LTE-advanced and the emerging generation of Wi-Fi (IEEE802.11ac). A circuit implementation of the parallel-sampling first stage of the pipeline ADC is presented and simulation results are given. Section 4.2 presents the architecture and operation of a 4 GS/s 11 b time-interleaved ADC with a parallel-sampling frontend stage, which targets wideband direct sampling receivers for DOCSIS 3.0 cable modems. Circuit implementation and simulation of the 4 GS/s parallel-sampling frontend stage are given. Due to the complexity of implementing the proposed 4 GS/s ADC on chip, a two-step design approach was adopted. In Sect. 4.3, a prototype IC of an 11 b 1 GS/s ADC with a parallel sampling architecture is presented, which serves as a first step to validate the parallel-sampling ADC concept and the performance of the high-speed parallel-sampling frontend and detection circuits. In future work, the frontend stage of the IC can be interleaved by four times to achieve the aggregate sample rate of 4 GHz of the proposed ADC discussed in Sect. 4.2. Conclusions of this chapter are drawn in Sect. 4.4