cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines.

Survival analysis is a technique for identifying prognostic biomarkers and genetic vulnerabilities in cancer studies. Large-scale consortium-based projects have profiled >11 000 adult and >4000 pediatric tumor cases with clinical outcomes and multiomics approaches. This provides a resource for investigating molecular-level cancer etiologies using clinical correlations. Although cancers often arise from multiple genetic vulnerabilities and have deregulated gene sets (GSs), existing survival analysis protocols can report only on individual genes. Additionally, there is no systematic method to connect clinical outcomes with experimental (cell line) data. To address these gaps, we developed cSurvival (https://tau.cmmt.ubc.ca/cSurvival). cSurvival provides a user-adjustable analytical pipeline with a curated, integrated database and offers three main advances: (i) joint analysis with two genomic predictors to identify interacting biomarkers, including new algorithms to identify optimal cutoffs for two continuous predictors; (ii) survival analysis not only at the gene, but also the GS level; and (iii) integration of clinical and experimental cell line studies to generate synergistic biological insights. To demonstrate these advances, we report three case studies. We confirmed findings of autophagy-dependent survival in colorectal cancers and of synergistic negative effects between high expression of SLC7A11 and SLC2A1 on outcomes in several cancers. We further used cSurvival to identify high expression of the Nrf2-antioxidant response element pathway as a main indicator for lung cancer prognosis and for cellular resistance to oxidative stress-inducing drugs. Altogether, these analyses demonstrate cSurvival's ability to support biomarker prognosis and interaction analysis via gene- and GS-level approaches and to integrate clinical and experimental biomedical studies.

Current-density pathways in figure-eight-shaped octaphyrins.

We have calculated the current density induced by an external magnetic field in a set of figure-eight-shaped expanded porphyrinoids. The studied octaphyrins can be divided into three classes (N2, N4, and N6) based on the number of the inner hydrogen atoms of the pyrrole rings. Using the Runge-Kutta method, the current density is split into diatropic and paratropic contributions that are analyzed separately. The calculations show that one common ring current consists of two rather independent pathways. Each of them follows the outer side of the molecular frame of one half of the molecule and passes to the inner side of the frame on the other half. The ring-current pathways are similar to the ones for [12]infinitene. However, the current density of the octaphyrins is more complex having many branching points and pathways. Vertical through-space current-density pathways pass in the middle of the molecules through a plane that is parallel to the figure-eight-shaped view of the molecules when the magnetic field is perpendicular to the plane. The isolectronic N2 and the N4 dication sustain a weak paratropic ring current inside the molecule, which is also observed in the 1H NMR magnetic shielding constant of the inner hydrogen atoms. The diatropic current-density contribution dominates in the studied molecules. For the N4 and N6 molecules, the global current-density pathways are only diatropic and N6 sustains the strongest global diatropic current-density flux of 13.2 nA T-1.

eVITTA: a web-based visualization and inference toolbox for transcriptome analysis.

Transcriptome profiling is essential for gene regulation studies in development and disease. Current web-based tools enable functional characterization of transcriptome data, but most are restricted to applying gene-list-based methods to single datasets, inefficient in leveraging up-to-date and species-specific information, and limited in their visualization options. Additionally, there is no systematic way to explore data stored in the largest transcriptome repository, NCBI GEO. To fill these gaps, we have developed eVITTA (easy Visualization and Inference Toolbox for Transcriptome Analysis; https://tau.cmmt.ubc.ca/eVITTA/). eVITTA provides modules for analysis and exploration of studies published in NCBI GEO (easyGEO), detailed molecular- and systems-level functional profiling (easyGSEA), and customizable comparisons among experimental groups (easyVizR). We tested eVITTA on transcriptomes of SARS-CoV-2 infected human nasopharyngeal swab samples, and identified a downregulation of olfactory signal transducers, in line with the clinical presentation of anosmia in COVID-19 patients. We also analyzed transcriptomes of Caenorhabditis elegans worms with disrupted S-adenosylmethionine metabolism, confirming activation of innate immune responses and feedback induction of one-carbon cycle genes. Collectively, eVITTA streamlines complex computational workflows into an accessible interface, thus filling the gap of an end-to-end platform capable of capturing both broad and granular changes in human and model organism transcriptomes.

Epigenetic regulator G9a provides glucose as a sweet key to stress resistance.

The ability to adapt to acute and chronic stress is important for organisms to thrive in evolutionary niches and for cells to survive in adverse conditions. The regulatory networks that control stress responses are evolutionarily conserved, and many factors that selectively activate stress responses have been identified. Less well understood are mechanisms that guard against unnecessary induction of cytoprotective factors and that connect stress responses with cellular metabolism to control energy expenditure during stress. The work of Riahi and colleagues represents important progress in this regard because it identifies the histone methyltransferase G9a as a modulator of oxidative stress responses. G9a dampens the expression of antioxidant genes, thus preventing inappropriate energy consumption. Moreover, G9a promotes the well-paced catabolism of storage glycogen and fat during stress. The importance of energy availability during stress is further evidenced by exogenous glucose rescuing the vulnerability of the G9a mutant to oxidative stress. Prior work in multiple model systems has implicated G9a in several other adaptive responses. Therefore, its role in pacing energy consumption and in restraining excessive stress response gene expression under stress may extend to other adaptive responses across species.

MDT-15/MED15 permits longevity at low temperature via enhancing lipidostasis and proteostasis.

Low temperatures delay aging and promote longevity in many organisms. However, the metabolic and homeostatic aspects of low-temperature-induced longevity remain poorly understood. Here, we show that lipid homeostasis regulated by Caenorhabditis elegans Mediator 15 (MDT-15 or MED15), a transcriptional coregulator, is essential for low-temperature-induced longevity and proteostasis. We find that inhibition of mdt-15 prevents animals from living long at low temperatures. We show that MDT-15 up-regulates fat-7, a fatty acid desaturase that converts saturated fatty acids (SFAs) to unsaturated fatty acids (UFAs), at low temperatures. We then demonstrate that maintaining a high UFA/SFA ratio is essential for proteostasis at low temperatures. We show that dietary supplementation with a monounsaturated fatty acid, oleic acid (OA), substantially mitigates the short life span and proteotoxicity in mdt-15(-) animals at low temperatures. Thus, lipidostasis regulated by MDT-15 appears to be a limiting factor for proteostasis and longevity at low temperatures. Our findings highlight the crucial roles of lipid regulation in maintaining normal organismal physiology under different environmental conditions.

Mediator subunit MDT-15/MED15 and Nuclear Receptor HIZR-1/HNF4 cooperate to regulate toxic metal stress responses in Caenorhabditis elegans.

Zinc is essential for cellular functions as it is a catalytic and structural component of many proteins. In contrast, cadmium is not required in biological systems and is toxic. Zinc and cadmium levels are closely monitored and regulated as their excess causes cell stress. To maintain homeostasis, organisms induce metal detoxification gene programs through stress responsive transcriptional regulatory complexes. In Caenorhabditis elegans, the MDT-15 subunit of the evolutionarily conserved Mediator transcriptional coregulator is required to induce genes upon exposure to excess zinc and cadmium. However, the regulatory partners of MDT-15 in this response, its role in cellular and physiological stress adaptation, and the putative role for mammalian MED15 in the metal stress responses remain unknown. Here, we show that MDT-15 interacts physically and functionally with the Nuclear Hormone Receptor HIZR-1 to promote molecular, cellular, and organismal adaptation to cadmium and excess zinc. Using gain- and loss-of-function mutants and qRT-PCR and reporter analysis, we find that mdt-15 and hizr-1 cooperate to induce zinc and cadmium responsive genes. Moreover, the two proteins interact physically in yeast-two-hybrid assays and this interaction is enhanced by the addition of zinc or cadmium, the former a known ligand of HIZR-1. Functionally, mdt-15 and hizr-1 mutants show defective storage of excess zinc in the gut and are hypersensitive to zinc-induced reductions in egg-laying. Furthermore, mdt-15 but not hizr-1 mutants are hypersensitive to cadmium-induced reductions in egg-laying, suggesting potential divergence of regulatory pathways. Lastly, mammalian MDT-15 orthologs bind genomic regulatory regions of metallothionein and zinc transporter genes in a cadmium and zinc-stimulated fashion, and human MED15 is required to induce a metallothionein gene in lung adenocarcinoma cells exposed to cadmium. Collectively, our data show that mdt-15 and hizr-1 cooperate to regulate cadmium detoxification and zinc storage and that this mechanism is at least partially conserved in mammals.

Divergent Carbocatalytic Routes in Oxidative Coupling of Benzofused Heteroaryl Dimers: A Mechanistic Update.

Mildly thermal air or HNO3 oxidized activated carbons catalyse oxidative dehydrogenative couplings of benzo[b]fused heteroaryl 2,2'-dimers, e.g., 2-(benzofuran-2-yl)-1H-indole, to chiral 3,3'-coupled cyclooctatetraenes or carbazole-type migrative products under O2 atmosphere. DFT calculations show that the radical cation and the Scholl-type arenium cation mechanisms lead to different products with 2-(benzofuran-2-yl)-1H-indole, being in accord with experimental product distributions.

Xenobiotic metabolism and transport in Caenorhabditis elegans.

Caenorhabditis elegans has emerged as a major model in biomedical and environmental toxicology. Numerous papers on toxicology and pharmacology in C. elegans have been published, and this species has now been adopted by investigators in academic toxicology, pharmacology, and drug discovery labs. C. elegans has also attracted the interest of governmental regulatory agencies charged with evaluating the safety of chemicals. However, a major, fundamental aspect of toxicological science remains underdeveloped in C. elegans: xenobiotic metabolism and transport processes that are critical to understanding toxicokinetics and toxicodynamics, and extrapolation to other species. The aim of this review was to initially briefly describe the history and trajectory of the use of C. elegans in toxicological and pharmacological studies. Subsequently, physical barriers to chemical uptake and the role of the worm microbiome in xenobiotic transformation were described. Then a review of what is and is not known regarding the classic Phase I, Phase II, and Phase III processes was performed. In addition, the following were discussed (1) regulation of xenobiotic metabolism; (2) review of published toxicokinetics for specific chemicals; and (3) genetic diversity of these processes in C. elegans. Finally, worm xenobiotic transport and metabolism was placed in an evolutionary context; key areas for future research highlighted; and implications for extrapolating C. elegans toxicity results to other species discussed.

Insights into Molecular Structures and Optical Properties of Stacked [Au3(RN═CR')3]n Complexes.

The molecular structure of stacked cyclic trinuclear gold(I) complexes [Au3(RN═CR')3]n, with n = 1-4, where R = H, methyl (Me), cyclopentyl (cPe), and phenyl (Ph) and R' = OH and methoxy (OMe) were studied computationally at the second-order Møller-Plesset (MP2) and density functional theory (DFT) levels of theory. At the DFT level, the aurophilic and dispersion interactions were accounted for by using the TPSS functional in combination with the semiempirical D3 correction. The structure optimizations yielded the lowest energy for a slided stacked structure of the [Au3(HN═COH)3]2 dimer, where monomers are slightly shifted relative to one another. At the MP2 level, the slided structure is 32 kJ/mol more stable than the staggered dimer structure, which in turn is energetically 11 kJ/mol below the eclipsed structure. The calculations show that aromatic ligands lead to a planar and prismatic structure of [Au3(PhN═COMe)3]4, whereas for [Au3(cPeN═COMe)3]4, a chair conformation is obtained due to steric effects. Excitation energies were calculated for [Au3(RN═CR')3] and [Au3(RN═CR')3]2 with R = H, Me, and cPe and R' = OH and OMe at the time-dependent DFT level using the optimized molecular structures of the singlet ground state. To simulate the luminescence spectra, the lowest triplet excitation energy was also calculated for the molecular structure of the lowest triplet state. The calculated excitation energies of [Au3(HN═COH)3] and [Au3(HN═COH)3]2 are compared with values obtained at the approximate singles and doubles coupled cluster (CC2) and the second-order algebraic diagrammatic construction (ADC(2)) levels of theory. The calculated absorption and emission energies reproduce the experimental trends, with extremely large Stokes shifts. A solvoluminescence mechanism is also proposed.

Genomic and Cytogenetic Characterization of a Balanced Translocation Disrupting NUP98.

A 41-year-old Asian woman with bilateral renal angiomyolipomas (AML) was incidentally identified to have a balanced translocation, 46,XX,t(11;12)(p15.4;q15). She had no other features or family history to suggest a diagnosis of tuberous sclerosis. Her healthy daughter had the same translocation and no renal AML at the age of 3 years. Whole-genome sequencing was performed on genomic maternal DNA isolated from blood. A targeted de novo assembly was then conducted with ABySS for chromosomes 11 and 12. Sanger sequencing was used to validate the translocation breakpoints. As a result, genomic characterization of chromosomes 11 and 12 revealed that the 11p breakpoint disrupted the NUP98 gene in intron 1, causing a separation of the promoter and transcription start site from the rest of the gene. The translocation breakpoint on chromosome 12q was located in a gene desert. NUP98 has not yet been associated with renal AML pathogenesis, but somatic NUP98 alterations are recurrently implicated in hematological malignancies, most often following a gene fusion event. We also found evidence for complex structural events involving chromosome 12, which appear to disrupt the TDG gene. We identified a TDGP1 partially processed pseudogene at 12p12.1, which adds complexity to the de novo assembly. In conclusion, this is the first report of a germline constitutional structural chromosome rearrangement disrupting NUP98 that occurred in a generally healthy woman with bilateral renal AML.

eEF2K inhibition blocks Aß42 neurotoxicity by promoting an NRF2 antioxidant response.

Soluble oligomers of amyloid-ß (Aß) impair synaptic plasticity, perturb neuronal energy homeostasis, and are implicated in Alzheimer's disease (AD) pathogenesis. Therefore, significant efforts in AD drug discovery research aim to prevent the formation of Aß oligomers or block their neurotoxicity. The eukaryotic elongation factor-2 kinase (eEF2K) plays a critical role in synaptic plasticity, and couples neurotransmission to local dendritic mRNA translation. Recent evidence indicates that Aß oligomers activate neuronal eEF2K, suggesting a potential link to Aß induced synaptic dysfunction. However, a detailed understanding of the role of eEF2K in AD pathogenesis, and therapeutic potential of eEF2K inhibition in AD, remain to be determined. Here, we show that eEF2K activity is increased in postmortem AD patient cortex and hippocampus, and in the hippocampus of aged transgenic AD mice. Furthermore, eEF2K inhibition using pharmacological or genetic approaches prevented the toxic effects of Aß42 oligomers on neuronal viability and dendrite formation in vitro. We also report that eEF2K inhibition promotes the nuclear factor erythroid 2-related factor (NRF2) antioxidant response in neuronal cells, which was crucial for the beneficial effects of eEF2K inhibition in neurons exposed to Aß42 oligomers. Accordingly, NRF2 knockdown or overexpression of the NRF2 inhibitor, Kelch-Like ECH-Associated Protein-1 (Keap1), significantly attenuated the neuroprotection associated with eEF2K inhibition. Finally, genetic deletion of the eEF2K ortholog efk-1 reduced oxidative stress, and improved chemotaxis and serotonin sensitivity in C. elegans expressing human Aß42 in neurons. Taken together, these findings highlight the potential utility of eEF2K inhibition to reduce Aß-mediated oxidative stress in AD.

Calculations of current densities for neutral and doubly charged persubstituted benzenes using effective core potentials.

Magnetically induced current density susceptibilities and ring-current strengths have been calculated for neutral and doubly charged persubstituted benzenes C6X6 and C6X62+ with X = F, Cl, Br, I, At, SeH, SeMe, TeH, TeMe, and SbH2. The current densities have been calculated using the gauge-including magnetically induced current (GIMIC) method, which has been interfaced to the Gaussian electronic structure code rendering current density calculations using effective core potentials (ECP) feasible. Relativistic effects on the ring-current strengths have been assessed by employing ECP calculations of the current densities. Comparison of the ring-current strengths obtained in calculations on C6At6 and C6At62+ using relativistic and non-relativistic ECPs show that scalar relativistic effects have only a small influence on the ring-current strengths. Comparisons of the ring-current strengths and ring-current profiles show that the C6I62+, C6At62+, C6(SeH)62+, C6(SeMe)62+, C6(TeH)62+, C6(TeMe)62+, and C6(SbH2)62+ dications are doubly aromatic sustaining spatially separated ring currents in the carbon ring and in the exterior of the molecule. The C6I6+ radical cation is also found to be doubly aromatic with a weaker ring current than obtained for the dication.

The Mediator complex of Caenorhabditis elegans: insights into the developmental and physiological roles of a conserved transcriptional coregulator.

The Mediator multiprotein complex ('Mediator') is an important transcriptional coregulator that is evolutionarily conserved throughout eukaryotes. Although some Mediator subunits are essential for the transcription of all protein-coding genes, others influence the expression of only subsets of genes and participate selectively in cellular signaling pathways. Here, we review the current knowledge of Mediator subunit function in the nematode Caenorhabditis elegans, a metazoan in which established and emerging genetic technologies facilitate the study of developmental and physiological regulation in vivo. In this nematode, unbiased genetic screens have revealed critical roles for Mediator components in core developmental pathways such as epidermal growth factor (EGF) and Wnt/ß-catenin signaling. More recently, important roles for C. elegans Mediator subunits have emerged in the regulation of lipid metabolism and of systemic stress responses, engaging conserved transcription factors such as nuclear hormone receptors (NHRs). We emphasize instances where similar functions for individual Mediator subunits exist in mammals, highlighting parallels between Mediator subunit action in nematode development and in human cancer biology. We also discuss a parallel between the association of the Mediator subunit MED12 with several human disorders and the role of its C. elegans ortholog mdt-12 as a regulatory hub that interacts with numerous signaling pathways.

Activation of the endoplasmic reticulum unfolded protein response by lipid disequilibrium without disturbed proteostasis in vivo.

The Mediator is a conserved transcriptional coregulator complex required for eukaryotic gene expression. In Caenorhabditis elegans, the Mediator subunit mdt-15 is essential for the expression of genes involved in fatty acid metabolism and ingestion-associated stress responses. mdt-15 loss of function causes defects in reproduction and mobility and shortens lifespan. In the present study, we find that worms with mutated or depleted mdt-15 (mdt-15 worms) exhibit decreased membrane phospholipid desaturation, especially in phosphatidylcholine. Accordingly, mdt-15 worms exhibit disturbed endoplasmic reticulum (ER) homeostasis, as indicated by a constitutively activated ER unfolded protein response (UPR(ER)). Activation of this stress response is only partially the consequence of reduced membrane lipid desaturation, implicating other mdt-15-regulated processes in maintaining ER homeostasis. Interestingly, mdt-15 inactivation or depletion of the lipid metabolism enzymes stearoyl-CoA-desaturases (SCD) and S-adenosyl methionine synthetase (sams-1) activates the UPR(ER) without promoting misfolded protein aggregates. Moreover, these worms exhibit wild-type sensitivity to chemically induced protein misfolding, and they do not display synthetic lethality with mutations in UPR(ER) genes, which cause protein misfolding. Therefore, the constitutively activated UPR(ER) in mdt-15, SCD, and sams-1 worms is not the consequence of proteotoxic stress but likely is the direct result of changes in ER membrane fluidity and composition. Together, our data suggest that the UPR(ER) is induced directly upon membrane disequilibrium and thus monitors altered ER homeostasis.

Synthesis, aromaticity and photophysical behaviour of ferrocene- and ruthenocene-appended semisynthetic chlorin derivatives.

Two novel synthetic strategies to covalently link a metallocene electron-donor unit to a chlorin ring are presented. In one approach, pyropheophorbide a is readily converted into its 13(1) -ferrocenyl dehydro derivative by nucleophilic addition of the ferrocenyl anion to the 13(1) -carbonyl group. In another approach, the corresponding 13(1) -pentamethylruthenocenyl derivative is synthesised from 13(1) -fulvenylchlorin by a facile ligand exchange/deprotonation reaction with the [RuCp*(cod)Cl] (Cp*=pentamethylcyclopentadienyl; cod=1,5-cyclooctadiene) complex. The resulting metallocene-chlorins exhibit reduced aromaticity, which was unequivocally supported by ring-current calculations based on the gauge-including magnetically induced current (GIMIC) method and by calculated nucleus-independent chemical shift (NICS) values. The negative ring current in the isocyclic E ring suggests the antiaromatic character of this moiety and also clarifies the spontaneous reactivity of the complexes with oxygen. The oxidation products were isolated and their electrochemical and photophysical properties were studied. The ruthenocene derivatives turned out to be stable under light irradiation and showed photoinduced charge transfer with charge-separation lifetimes of 152-1029 ps.

Repression of a potassium channel by nuclear hormone receptor and TGF-ß signaling modulates insulin signaling in Caenorhabditis elegans.

Transforming growth factor ß (TGF-ß) signaling acts through Smad proteins to play fundamental roles in cell proliferation, differentiation, apoptosis, and metabolism. The Receptor associated Smads (R-Smads) interact with DNA and other nuclear proteins to regulate target gene transcription. Here, we demonstrate that the Caenorhabditis elegans R-Smad DAF-8 partners with the nuclear hormone receptor NHR-69, a C. elegans ortholog of mammalian hepatocyte nuclear factor 4α HNF4α), to repress the exp-2 potassium channel gene and increase insulin secretion. We find that NHR-69 associates with DAF-8 both in vivo and in vitro. Functionally, daf-8 nhr-69 double mutants show defects in neuropeptide secretion and phenotypes consistent with reduced insulin signaling such as increased expression of the sod-3 and gst-10 genes and a longer life span. Expression of the exp-2 gene, encoding a voltage-gated potassium channel, is synergistically increased in daf-8 nhr-69 mutants compared to single mutants and wild-type worms. In turn, exp-2 acts selectively in the ASI neurons to repress the secretion of the insulin-like peptide DAF-28. Importantly, exp-2 mutation shortens the long life span of daf-8 nhr-69 double mutants, demonstrating that exp-2 is required downstream of DAF-8 and NHR-69. Finally, animals over-expressing NHR-69 specifically in DAF-28-secreting ASI neurons exhibit a lethargic, hypoglycemic phenotype that is rescued by exogenous glucose. We propose a model whereby DAF-8/R-Smad and NHR-69 negatively regulate the transcription of exp-2 to promote neuronal DAF-28 secretion, thus demonstrating a physiological crosstalk between TGF-ß and HNF4α-like signaling in C. elegans. NHR-69 and DAF-8 dependent regulation of exp-2 and DAF-28 also provides a novel molecular mechanism that contributes to the previously recognized link between insulin and TGF-ß signaling in C. elegans.

Coordinate regulation of lipid metabolism by novel nuclear receptor partnerships.

Mammalian nuclear receptors broadly influence metabolic fitness and serve as popular targets for developing drugs to treat cardiovascular disease, obesity, and diabetes. However, the molecular mechanisms and regulatory pathways that govern lipid metabolism remain poorly understood. We previously found that the Caenorhabditis elegans nuclear hormone receptor NHR-49 regulates multiple genes in the fatty acid beta-oxidation and desaturation pathways. Here, we identify additional NHR-49 targets that include sphingolipid processing and lipid remodeling genes. We show that NHR-49 regulates distinct subsets of its target genes by partnering with at least two other distinct nuclear receptors. Gene expression profiles suggest that NHR-49 partners with NHR-66 to regulate sphingolipid and lipid remodeling genes and with NHR-80 to regulate genes involved in fatty acid desaturation. In addition, although we did not detect a direct physical interaction between NHR-49 and NHR-13, we demonstrate that NHR-13 also regulates genes involved in the desaturase pathway. Consistent with this, gene knockouts of these receptors display a host of phenotypes that reflect their gene expression profile. Our data suggest that NHR-80 and NHR-13's modulation of NHR-49 regulated fatty acid desaturase genes contribute to the shortened lifespan phenotype of nhr-49 deletion mutant animals. In addition, we observed that nhr-49 animals had significantly altered mitochondrial morphology and function, and that distinct aspects of this phenotype can be ascribed to defects in NHR-66- and NHR-80-mediated activities. Identification of NHR-49's binding partners facilitates a fine-scale dissection of its myriad regulatory roles in C. elegans. Our findings also provide further insights into the functions of the mammalian lipid-sensing nuclear receptors HNF4α and PPARα.

The C. elegans CDK8 Mediator module regulates axon guidance decisions in the ventral nerve cord and during dorsal axon navigation.

Receptors expressed on the growth cone of outgrowing axons detect cues required for proper navigation. The pathway choices available to an axon are in part defined by the set of guidance receptors present on the growth cone. Regulated expression of receptors and genes controlling the localization and activity of receptors ensures that axons respond only to guidance cues relevant for reaching their targets. In genetic screens for axon guidance mutants, we isolated an allele of let-19/mdt-13, a component of the Mediator, a large ~30 subunit protein complex essential for gene transcription by RNA polymerase II. LET-19/MDT-13 is part of the CDK8 module of the Mediator. By testing other Mediator components, we found that all subunits of the CDK8 module as well as some other Mediator components are required for specific axon navigation decisions in a subset of neurons. Expression profiling demonstrated that let-19/mdt-13 regulates the expression of a large number of genes in interneurons. A mutation in the sax-3 gene, encoding a receptor for the repulsive guidance cue SLT-1, suppresses the commissure navigation defects found in cdk-8 mutants. This suggests that the CDK8 module specifically represses the SAX-3/ROBO pathway to ensure proper commissure navigation.

The molecular and magnetic structure of carbon-enclosed and partially covered Fe55 particles.

The structure and magnetic moment distribution are studied for an iron nanoparticle with varying degree of carbon adatom coverage. The limiting models of the study are the clean icosahedral Fe55 particle and the iron particle completely enclosed in carbon cages. Between the two extrema, partially covered particles are considered. The iron cluster with partial coverage of carbon adatoms represents a model of active catalysts in the chemical vapor deposition synthesis of carbon nanotubes. The investigated structures are the bare Fe55 cluster, Fe55N4C(x) (x = 27, 37, 47, 54, 65), and Fe55 encapsulated inside C180 and C240. The two latter are extreme examples of an iron particle completely enclosed in a carbon network. Fe55@C180 and Fe55@C240 present novel structures resembling the endohedral metallofullerenes. Two structural isomers of the Fe55@C180 are considered. Enclosing the Fe55 cluster inside C180 and C240 fullerenes gives rise to changes in the Fe-Fe bond lengths. This alters the magnetic structure of the iron cluster considerably. The interaction between the fullerenes and the enclosed iron cluster is reflected in a charge transfer of 8-13 electrons in the considered endohedral complexes. The localization of atomic charges on the C180 and C240 cages suggests site-selective reactivity of the endohedral complexes. The total magnetic moments of the Fe55N4C(x) nanoparticles vary with the degree of adatom coverage. The magnetic moments of individual Fe atoms depend strongly on the element of the nearest-neighbor atoms and on the coordination number and carry therefore information about the local chemistry.

The unfolded protein response of the endoplasmic reticulum protects Caenorhabditis elegans against DNA damage caused by stalled replication forks.

All animals must maintain genome and proteome integrity, especially when experiencing endogenous or exogenous stress. To cope, organisms have evolved sophisticated and conserved response systems: unfolded protein responses (UPRs) ensure proteostasis, while DNA damage responses (DDRs) maintain genome integrity. Emerging evidence suggests that UPRs and DDRs crosstalk, but this remains poorly understood. Here, we demonstrate that depletion of the DNA primases pri-1 or pri-2, which synthesize RNA primers at replication forks and whose inactivation causes DNA damage, activates the UPR of the endoplasmic reticulum (UPR-ER) in Caenorhabditis elegans, with especially strong activation in the germline. We observed activation of both the inositol-requiring-enzyme 1 (ire-1) and the protein kinase RNA-like endoplasmic reticulum kinase (pek-1) branches of the (UPR-ER). Interestingly, activation of the (UPR-ER) output gene heat shock protein 4 (hsp-4) was partially independent of its canonical activators, ire-1 and X-box binding protein (xbp-1), and instead required the third branch of the (UPR-ER), activating transcription factor 6 (atf-6), suggesting functional redundancy. We further found that primase depletion specifically induces the (UPR-ER), but not the distinct cytosolic or mitochondrial UPRs, suggesting that primase inactivation causes compartment-specific rather than global stress. Functionally, loss of ire-1 or pek-1 sensitizes animals to replication stress caused by hydroxyurea. Finally, transcriptome analysis of pri-1 embryos revealed several deregulated processes that could cause (UPR-ER) activation, including protein glycosylation, calcium signaling, and fatty acid desaturation. Together, our data show that the (UPR-ER), but not other UPRs, responds to replication fork stress and that the (UPR-ER) is required to alleviate this stress.