Examining Sporadic Cancer Mutations Uncovers a Set of Genes Involved in Mitochondrial Maintenance.

Mitochondria are key organelles for cellular health and metabolism and the activation of programmed cell death processes. Although pathways for regulating and re-establishing mitochondrial homeostasis have been identified over the past twenty years, the consequences of disrupting genes that regulate other cellular processes, such as division and proliferation, on affecting mitochondrial function remain unclear. In this study, we leveraged insights about increased sensitivity to mitochondrial damage in certain cancers, or genes that are frequently mutated in multiple cancer types, to compile a list of candidates for study. RNAi was used to disrupt orthologous genes in the model organism Caenorhabditis elegans, and a series of assays were used to evaluate these genes' importance for mitochondrial health. Iterative screening of ~1000 genes yielded a set of 139 genes predicted to play roles in mitochondrial maintenance or function. Bioinformatic analyses indicated that these genes are statistically interrelated. Functional validation of a sample of genes from this set indicated that disruption of each gene caused at least one phenotype consistent with mitochondrial dysfunction, including increased fragmentation of the mitochondrial network, abnormal steady-state levels of NADH or ROS, or altered oxygen consumption. Interestingly, RNAi-mediated knockdown of these genes often also exacerbated α-synuclein aggregation in a C. elegans model of Parkinson's disease. Additionally, human orthologs of the gene set showed enrichment for roles in human disorders. This gene set provides a foundation for identifying new mechanisms that support mitochondrial and cellular homeostasis.

Reduction of Capacity Fading in High-Voltage NMC Batteries with the Addition of Reduced Graphene Oxide.

Lithium-ion batteries for electric vehicles (EV) require high energy capacity, reduced weight, extended lifetime and low cost. EV manufacturers are focused on Ni-rich layered oxides because of their promising attributes, which include the ability to operate at a relatively high voltage. However, these cathodes, usually made with nickel-manganese-cobalt (NMC811), typically experience accelerated capacity fading when operating at a high voltage. In this research, reduced graphene oxide (rGO) is added to a NMC811 cathode material to improve the performance in cyclability studies. Batteries made with rGO/NMC811 cathodes showed a 17% improvement in capacity retention after 100 cycles of testing over a high-voltage operating window of 2.5-4.5 V.

A High-throughput, High-content, Liquid-based C. elegans Pathosystem.

The number of new drugs identified by traditional, in vitro screens has waned, reducing the success of this approach in the search for new weapons to combat multiple drug resistance. This has led to the conclusion that researchers do not only need to find new drugs, but also need to develop new ways of finding them. Amongst the most promising candidate methods are whole-organism, in vivo assays that use high-throughput, phenotypic readouts and hosts that range from Caenorhabditis elegans to Danio rerio. These hosts have several powerful advantages, including dramatic reductions in false positive hits, as compounds that are toxic to the host and/or biounavailable are typically dropped in the initial screen, prior to costly follow up. Here we show how our assay has been used to interrogate host variation in the well-documented C. elegans-Pseudomonas aeruginosa liquid killing pathosystem. We also demonstrate several extensions of this well-worked out technique. For example, we are able to carry out high-throughput genetic screens using RNAi in 24- or 96-well plate formats to query host factors in this host-pathogen interaction. Using this assay, whole genome screens can be completed in only a few months, which can dramatically simplify the task of identifying drug targets, potentially without the need for laborious biochemical purification approaches. We also report here a variation of our method that substitutes the gram-positive bacterium Enterococcus faecalis for the gram-negative pathogen P. aeruginosa. Much as is the case for P. aeruginosa, killing by E. faecalis is time-dependent. Unlike previous C. elegans-E. faecalis assays, our assay for E. faecalis does not require preinfection, improving its safety profile and reducing the chances of contaminating liquid-handling equipment. The assay is highly robust, showing ~95% death rates 96 h post infection.

Regionally compartmentalized resident memory T cells mediate naturally acquired protection against pneumococcal pneumonia.

As children age, they become less susceptible to the diverse microbes causing pneumonia. These microbes are pathobionts that infect the respiratory tract multiple times during childhood, generating immunological memory. To elucidate mechanisms of such naturally acquired immune protection against pneumonia, we modeled a relevant immunological history in mice by infecting their airways with mismatched serotypes of Streptococcus pneumoniae (pneumococcus). Previous pneumococcal infections provided protection against a heterotypic, highly virulent pneumococcus, as evidenced by reduced bacterial burdens and long-term sterilizing immunity. This protection was diminished by depletion of CD4+ cells prior to the final infection. The resolution of previous pneumococcal infections seeded the lungs with CD4+ resident memory T (TRM) cells, which responded to heterotypic pneumococcus stimulation by producing multiple effector cytokines, particularly interleukin (IL)-17A. Following lobar pneumonias, IL-17-producing CD4+ TRM cells were confined to the previously infected lobe, rather than dispersed throughout the lower respiratory tract. Importantly, pneumonia protection also was confined to that immunologically experienced lobe. Thus regionally localized memory cells provide superior local tissue protection to that mediated by systemic or central memory immune defenses. We conclude that respiratory bacterial infections elicit CD4+ TRM cells that fill a local niche to optimize heterotypic protection of the affected tissue, preventing pneumonia.

How Does the Local Electrostatic Field Influence Emitted Wavelengths and Bioluminescent Intensities of Modified Heteroaromatic Luciferins?

The firefly chromophore, oxyluciferin, is in the pocket of the firefly luciferase and is surrounded by the side-chains of some amino acid residues. The charged residues produce the local electrostatic field (LEF) around the oxyluciferin. The emitted wavelengths and intensities of the oxyluciferin and its heterocyclic analogs under the LEF are examined. The common overlapping volumes of the HOMO and LUMO explain why the oscillator strengths vary under the LEF. Three average Ex change rates of the first excited energy are introduced to measure what luciferins are more sensitive to the LEF. The first excited energies and intensities in two enzymatic-like microenvironments are simulated via the LEF. The oscillator strengths and the net electric charges of the O6' and the O4 are applied to explain the experimental bioluminescent intensities.

Theoretical investigation into the structural, thermochemical, and electronic properties of the decathio[10]circulene.

For the first time, a theoretical study has been performed on the prototypical decathio[10]circulene (C(20)S(10)) species, which is an analogue of the novel octathio[8]circulene "Sulflower" molecule (C(16)S(8)). Examinations of the singlet and triplet states of C(20)S(10) were made at the B3LYP/6-311G(d) level. Local minima of C(2) and C(s) symmetry were found for the lowest singlet and triplet states, respectively. The stability of C(20)S(10) was assessed by calculating the ΔH°(f) of C(16)S(8) and C(20)S(10) and the ΔH(o) for their decomposition into C(2)S units. Frontier molecular orbital plots show that structural adjacent steric factors along with the twist and strain orientations of C(20)S(10) do not disturb the aromatic π-delocalizing effects. In fact, C(20)S(10) maintains the same p(z) HOMO character as C(16)S(8). These similarities are further verified by density-of-states characterization. Calculated infrared spectra of C(16)S(8) and C(20)S(10) show broad similarities. Molecular electrostatic potential results reveal that eight of the peripheral sulfur atoms are the most electronegative atoms in the molecule, while the interior ten-membered ring exhibits virtually no electronegativity.

In vitro evaluation of cytotoxicity of engineered carbon nanotubes in selected human cell lines.

In this study, we used a systematic approach to study and compare the in vitro cytotoxicity of selected engineered carbon nanotubes (CNTs) to test cell lines including human skin keratinocytes, lung cells and lymphocytes. Results of fluorescein diacetate (FDA) uptake in T4 lymphocyte A3 cells indicated cytotoxicity caused by single-walled carbon nanotubes (SWCNTs) at concentrations of 2, 5 and 10ppm. At 2ppm, the SWCNT treatment group retained 71.3% viability compared to the PBS control group. At 10ppm, cellular viability further decreased to 56.5% of the PBS control group. In the skin keratinocyte HaCaT cells and lung MSTO-211H cells, the SWCNT did not demonstrate any cytotoxicity at concentrations of 2 and 5ppm but slightly inhibited HaCaT cells and caused significant toxicity to MSTO-211H cells at 10ppm. Multi-walled carbon nanotube (MWCNT) testing showed significant cytotoxicity to A3 cells in a dose-dependent manner. At 10ppm the viability of the cells decreased to 89.1% compared to the PBS control. In MSTO-211H cells, MWCNT caused significant toxicity at concentrations of 2ppm and higher. By comparison, HaCaT cells were inhibited significantly only at 10ppm. Overall, the test CNTs inhibited cellular viabilities in a concentration, cell type, and CNT type-dependent pattern. The viabilities of the MWCNT-impacted cells are higher than the corresponding SWCNT groups. We speculate that on a per volume basis, the greater availability of defects and contaminants for cellular interaction may contribute to the higher cytotoxicity of SWCNT in this study. The interaction between the SWCNTs and A3 lymphocytes was also observed by scanning electron microscopy. The mechanism for causing cell death in this study was attributed to apoptosis and necrosis after physical penetration by CNTs and oxidative stress via formation of reactive oxygen species.

Thioglycolic acid on the gold (111) surface and Raman vibrational spectra.

The interaction of thioglycolic acid (HSCH(2)COOH) with the Au(111) surface is investigated, and it is found that at the low coverage the molecule lies down on the substrate. If the mercaptan-hydrogen atom is eliminated, the resulting SCH(2)COOH molecule is randomly oriented on the surface. If the carboxylic acid group in the HSCH(2)COOH molecule is deprotonated instead, the HSCH(2)COO(-) molecule lies down on the surface. However, when the mercaptan-hydrogen atom in the HSCH(2)COO(-) molecule is removed, the resulting SCH(2)COO(-) molecule rises up to a certain level on the substrate. The calculated Raman vibrational spectra decipher which compounds and atomic displacements contribute to the corresponding frequencies. We thus propose a consistent mechanism for the deposition of thioglycolic acid on the Au(111) surface.

Isolation and pharmacological characterization of AdTx1, a natural peptide displaying specific insurmountable antagonism of the alpha1A-adrenoceptor.

BACKGROUND AND PURPOSE: Venoms are a rich source of ligands for ion channels, but very little is known about their capacity to modulate G-protein coupled receptor (GPCR) activity. We developed a strategy to identify novel toxins targeting GPCRs. EXPERIMENTAL APPROACH: We studied the interactions of mamba venom fractions with alpha(1)-adrenoceptors in binding experiments with (3)H-prazosin. The active peptide (AdTx1) was sequenced by Edman degradation and mass spectrometry fragmentation. Its synthetic homologue was pharmacologically characterized by binding experiments using cloned receptors and by functional experiments on rabbit isolated prostatic smooth muscle. KEY RESULTS: AdTx1, a 65 amino-acid peptide stabilized by four disulphide bridges, belongs to the three-finger-fold peptide family. It has subnanomolar affinity (K(i)= 0.35 nM) and high specificity for the human alpha(1A)-adrenoceptor subtype. We showed high selectivity and affinity (K(d)= 0.6 nM) of radio-labelled AdTx1 in direct binding experiments and revealed a slow association constant (k(on)= 6 x 10(6).M(-1).min(-1)) with an unusually stable alpha(1A)-adrenoceptor/AdTx1 complex (t(1/2diss)= 3.6 h). AdTx1 displayed potent insurmountable antagonism of phenylephrine's actions in vitro (rabbit isolated prostatic muscle) at concentrations of 10 to 100 nM. CONCLUSIONS AND IMPLICATIONS: AdTx1 is the most specific and selective peptide inhibitor for the alpha(1A)-adrenoceptor identified to date. It displays insurmountable antagonism, acting as a potent relaxant of smooth muscle. Its peptidic nature can be exploited to develop new tools, as a radio-labelled-AdTx1 or a fluoro-labelled-AdTx1. Identification of AdTx1 thus offers new perspectives for developing new drugs for treating benign prostatic hyperplasia.

A unique phosphatidylinositol 4-phosphate 5-kinase is activated by ADP-ribosylation factor in Plasmodium falciparum.

In eukaryotes, calcium signalling has been linked to hydrolysis of the phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P(2)). The final enzyme in the synthesis of this phosphoinositide, a Type I phosphatidylinositol 4-phosphate 5-kinase (PIP5K), is activated by the small G protein ADP-ribosylation factor 1 (ARF1). In mammals, the ARF-PIP5K pathway is a key regulator of cell motility, secretion and cell signalling. We report the characterisation of a unique, putative bifunctional PIP5K in the human malaria parasite Plasmodium falciparum. The protein comprises a C-terminal, functional PIP5K domain with catalytic specificity for phosphatidylinositol 4-phosphate. The recombinant enzyme is activated by ARF1 but not phosphatidic acid. The protein also incorporates an unusual N-terminal domain with potential helix-loop-helix EF-hand-like motifs that is a member of the neuronal calcium sensor family (NCS). Intriguingly, NCS-1 has been shown to stimulate phosphatidylinositol 4-phosphate synthesis by activating mammalian and yeast phosphatidylinositol 4-kinase beta in vitro in a calcium-dependent manner. The unexpected physical attachment of an NCS-like domain to the plasmodial PIP5K might reflect a unique functional link between the calcium and PtdIns(4,5)P(2) pathways allowing modulation of PtdIns(4,5)P(2) production in response to changes in intracellular calcium concentrations within the parasite.

Structure and non-essential function of glycerol kinase in Plasmodium falciparum blood stages.

Malaria pathology is caused by multiplication of asexual parasites within erythrocytes, whereas mosquito transmission of malaria is mediated by sexual precursor cells (gametocytes). Microarray analysis identified glycerol kinase (GK) as the second most highly upregulated gene in Plasmodium falciparum gametocytes with no expression detectable in asexual blood stage parasites. Phosphorylation of glycerol by GK is the rate-limiting step in glycerol utilization. Deletion of this gene from P. falciparum had no effect on asexual parasite growth, but surprisingly also had no effect on gametocyte development or exflagellation, suggesting that these life cycle stages do not utilize host-derived glycerol as a carbon source. Kinetic studies of purified PfGK showed that the enzyme is not regulated by fructose 1,6 bisphosphate. The high-resolution crystal structure of P. falciparum GK, the first of a eukaryotic GK, reveals two domains embracing a capacious ligand-binding groove. In the complexes of PfGK with glycerol and ADP, we observed closed and open forms of the active site respectively. The 27 degree domain opening is larger than in orthologous systems and exposes an extensive surface with potential for exploitation in selective inhibitor design should the enzyme prove to be essential in vivo either in the human or in the mosquito.

How does an external electrical field affect adsorption patterns of thiol and thiolate on the gold substrate?

The responsive behavior of methanethiol and methylthiolate molecules on the Au(111) surface with an applied electrical potential is studied, and it is shown how the sulfur adsorption site, the S-H bond orientation and the interacting energy change with an external electric field strength. The electron charge density corresponding to an electric field minus that obtained in zero field, with zero-field optimal geometry, is calculated to explain the responsive behavior. The interacting energy for the intact methanethiol adsorption is larger than that for the dissociative one, showing that an external electric field cannot make the hydrogen dissociate from the sulfur.

Mutations in the Plasmodium falciparum cytochrome b gene are associated with delayed parasite recrudescence in malaria patients treated with atovaquone-proguanil.

BACKGROUND: Fixed-dose combination antimalarial drugs have played an increasingly important role in the treatment and chemoprophylaxis of falciparum malaria since the worldwide failure of monotherapy with chloroquine. Atovaquone-proguanil is one such combination drug used both for prophylaxis in travellers, and for treatment of acute malaria cases in European hospitals and clinics. METHODS: A series of eight atovaquone-proguanil treatment failures and two prophylaxis breakthroughs from four UK hospitals from 2004-2008 were analysed for evidence of mutations in the pfcyt-b gene, previously found to be associated with failure of the atovaquone component. RESULTS: Parasites carrying pfcyt-b mutations were found in five falciparum malaria patients with recrudescent parasitaemia occurring weeks after apparently successful treatment of a primary infection with atovaquone-proguanil. Four of these cases carried parasites with the Tyr268Cys mutation in pfcyt-b, previously reported in two French patients with malaria. In contrast, mutations in pfcyt-b were not found in three patients treated with atovaquone-proguanil who exhibited delayed clearance of the primary infection, nor in two returning travellers with malaria who had used the combination for prophylaxis. Using current and previously published data, mean time to recrudescence of parasites carrying pfcytb codon 268 mutations was estimated as 28.0 days after treatment (95% C.I. 23.0 - 33.0 days), whereas treatment failures without codon 268 mutations received rescue treatment an average of 4.71 days after initial AP treatment (95% C.I. 1.76 - 7.67 days). CONCLUSION: Genetically-determined parasite resistance to atovaquone is associated with delayed recrudescence of resistant parasites three weeks or more after initial clearance of parasitaemia by atovaquone/proguanil therapy. The 268-Cys allele of pfcyt-b may have been overlooked in previous studies of atovaquone-proguanil treatment failure as it is not detected by current RFLP methods.

Gametogenesis in malaria parasites is mediated by the cGMP-dependent protein kinase.

Malaria parasite transmission requires differentiation of male and female gametocytes into gametes within a mosquito following a blood meal. A mosquito-derived molecule, xanthurenic acid (XA), can trigger gametogenesis, but the signalling events controlling this process in the human malaria parasite Plasmodium falciparum remain unknown. A role for cGMP was revealed by our observation that zaprinast (an inhibitor of phosphodiesterases that hydrolyse cGMP) stimulates gametogenesis in the absence of XA. Using cGMP-dependent protein kinase (PKG) inhibitors in conjunction with transgenic parasites expressing an inhibitor-insensitive mutant PKG enzyme, we demonstrate that PKG is essential for XA- and zaprinast-induced gametogenesis. Furthermore, we show that intracellular calcium (Ca2+) is required for differentiation and acts downstream of or in parallel with PKG activation. This work defines a key role for PKG in gametogenesis, elucidates the hierarchy of signalling events governing this process in P. falciparum, and demonstrates the feasibility of selective inhibition of a crucial regulator of the malaria parasite life cycle.

Venomics: unravelling the complexity of animal venoms with mass spectrometry.

Animal venoms and toxins are now recognized as major sources of bioactive molecules that may be tomorrow's new drug leads. Their complexity and their potential as drug sources have been demonstrated by application of modern analytical technologies, which have revealed venoms to be vast peptide combinatorial libraries. Structural as well as pharmacological diversity is immense, and mass spectrometry is now one of the major investigative tools for the structural investigation of venom components. Recent advances in its use in the study of venom and toxins are reviewed. The application of mass spectrometry techniques to peptide toxin sequence determination by de novo sequencing is discussed in detail, in the light of the search for novel analgesic drugs. We also present the combined application of LC-MALDI separation with mass fingerprinting and ISD fragmentation for the determination of structural and pharmacological classes of peptides in complex spider venoms. This approach now serves as the basis for the full investigation of complex spider venom proteomes, in combination with cDNA analysis.

Sensitivity modeling study for an ozone occurrence during the 1996 Paso Del Norte Ozone Campaign.

Surface ozone pollution has been a persistent environmental problem in the US and Europe as well as the developing countries. A key prerequisite to find effective alternatives to meeting an ozone air quality standard is to understand the importance of local anthropogenic emissions, the significance of biogenic emissions, and the contribution of long-range transport. In this study, an air quality modeling system that includes chemistry and transport, CMAQ, an emission processing model, SMOKE, and a mesoscale numerical meteorological model, WRF, has been applied to investigate an ozone event occurring during the period of the 1996 Paso del Norte Ozone Campaign. The results show that the modeling system exhibits the capability to simulate this high ozone occurrence by providing a comparable temporal variation of surface ozone concentration at one station and to capture the spatial evolution of the event. Several sensitivity tests were also conducted to identify the contributions to high surface ozone concentration from eight VOC subspecies, biogenic VOCs, anthropogenic VOCs and long-range transportation of ozone and its precursors. It is found that the reductions of ETH, ISOP, PAR, OLE and FORM help to mitigate the surface ozone concentration, and like anthropogenic VOCs, biogenic VOC plays a nonnegligible role in ozone formation. But for this case, long-range transport of ozone and its precursors appears to produce an insignificant contribution.

Improved synchronous production of Plasmodium falciparum gametocytes in vitro.

The sexual stages of the Plasmodium falciparum life cycle are attractive targets for vaccines and transmission blocking drugs. Difficulties in culturing and obtaining large amounts of sexual stage P. falciparum parasites, particularly early stages, have often limited research progress in this area. We present a new protocol which simplifies the process of stimulating gametocytogenesis leading to improved synchronous gametocyte production. This new method can be adapted to enrich for early stage gametocytes (I and II) with a higher degree of purity than has previously been achieved, using MACS magnetic affinity columns. The protocol described lends itself to large scale culturing and harvesting of synchronous parasites suitable for biochemical assays, northern blots, flow cytometry, microarrays and proteomic analysis.

Activity of piperaquine and other 4-aminoquinoline antiplasmodial drugs against chloroquine-sensitive and resistant blood-stages of Plasmodium falciparum. Role of beta-haematin inhibition and drug concentration in vacuolar water- and lipid-phases.

Chloroquine (CQ), a 4-aminoquinoline, accumulates in acidic digestive vacuoles of the malaria parasite, preventing conversion of toxic haematin to beta-haematin. We examine how bis 4-aminoquinoline piperaquine (PQ) and its hydroxy-modification (OH-PQ) retain potency on chloroquine-resistant (CQ-R) Plasmodium falciparum. For CQ, PQ, OH-PQ and 4 and 5, representing halves of PQ, beta-haematin inhibitory activity (BHIA) was assayed, while potency was determined in CQ-sensitive (CQ-S) and CQ-R P. falciparum. From measured pK(a)s and the pH-modulated distribution of base between water and lipid (logD), the vacuolar accumulation ratio (VAR) of charged drug from plasma water (pH 7.4) into vacuolar water (pH 4.8) and lipid accumulation ratio (LAR) were calculated. All agents were active in BHIA. In CQ-S, PQ, OH-PQ and CQ were equally potent while 4 and 5 were 100 times less potent. CQ with two basic centres has a VAR of 143,482, while 4 and 5, with two basic centres of lower pK(a)s have VARs of 1287 and 1966. In contrast PQ and OH-PQ have four basic centres and achieve VARs of 104,378 and 19,874. This confirms the importance of VAR for potency against CQ-S parasites. Contrasting results were seen in CQ-R. 5, PQ and OH-PQ with LARs of 693; 973,492 and 398,118 (compared with 8.25 for CQ) showed similar potency in CQ-S and CQ-R. Importance of LAR for potency against CQ-R parasites probably reflects ability to block efflux by hydrophobic interaction with PfCRT but may relate to beta-haematin inhibition in vacuolar lipid.

Effects of piperaquine, chloroquine, and amodiaquine on drug uptake and of these in combination with dihydroartemisinin against drug-sensitive and -resistant Plasmodium falciparum strains.

Piperaquine is being developed as a long-acting component in artemisinin combination therapies. It was highly active in vitro and drug interaction studies showed that dihydroartemisinin combinations with piperaquine, chloroquine, and amodiaquine were indifferent tending toward antagonism. Competitive uptake of radiolabeled chloroquine and dihydroartemisinin in combination with other antimalarials was observed.

Programmed transcription of the var gene family, but not of stevor, in Plasmodium falciparum gametocytes.

The var genes encode Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) proteins, a set of highly diverse surface-expressed proteins that mediate adhesion of erythrocytes infected with asexual blood-stage parasites to host endothelium. Switching among expressed PfEMP1 variants in the course of a blood-stage infection is a key component of antigenic variation, and thus immune evasion, by the parasite. The majority of var loci are found in the subtelomeric regions of P. falciparum chromosomes associated with members of other multigene families, including stevor. Both PfEMP1 and STEVOR are expressed in gametocytes, the transmissible parasite stage, but the role of these proteins in the biology of sexual-stage parasites remains unknown. PfEMP1 may continue to mediate antigenic variation in gametocytes, which need to persist in the host for many days before reaching maturity. Using quantitative reverse transcription-PCR and Northern hybridization, we demonstrate that transcription of a defined subset of type C var loci occurs during gametocyte development in vitro. This transcriptional program occurs in gametocytes regardless of the var expression phenotype of their asexual progenitors and therefore is subject to regulatory processes distinct from those that manage antigenic variation in the asexual parasite. In contrast, the same stevor variants are transcribed in both gametocytes and their asexual progenitors. We also provide evidence that for both asexual parasites and gametocytes, var and stevor transcription patterns are not linked to each other.