Mechanism of protein synthesis inhibition by vaccinia viral core and reversal of this inhibition by reticulocyte peptide chain initiation factors

Vaccinia viral core inhibits protein synthesis in heme-supplemented reticulocyte lysate. A reticulocyte cell suPernatant factor, which reversed Protein synthesis inhibition in heme-deficient reticulocyte lysate also reversed vaccinia viral core induced Protein synthesis inhibition in heme-suPPlemented reticulocyte lysate. Significant inhibition reversal activity was also observed with a partially purified eukaryotic initiation factor-2 PreParation and this activity was lost uPon further Purification of eukaryotic initiation factor-2.The ribosomal salt-wash factor Co-eukaryotic initiation factor-2 which like reticulocyte suPernatant factor contains guanine nucleotide exchange factor activity, was comPletely inactive. Vaccinia viral core induced detectable level of eukaryotic initiation factor-2 α-subunit phosphorylation when incubated in the heme-supplemented reticulocyte lysate. This lysate preparation contains guanine nucleotide exchange factor activity. However, when the same reticulocyte lysate was previously incubated with the vaccinia viral core, the guanine nucleotide exchange factor activity during subsequent incubation was almost comPletely inhibited.     

Reduced inhibition of replicon initiation and chain elongation by neocarzinostatin in skin fibroblasts from patients with ataxia telangiectasia

Cells from patients with the genetic disease ataxia telangiectasia are hypersensitive to the DNA-breaking agents X-rays, bleomycin and neocarzinostatin, and show reduced inhibition of DNA synthesis after treatment with these agents, as compared to normal cells. The rate of replicon initiation and chain elongation was measured shortly after brief exposure of two normal and two ataxia telangiectasia fibroblast strains to low doses (0.10–0.30 μg/ml) of neocarzinostatin, by means of alkaline sucrose gradient analysis. Neocarzinostatin was found to inhibit both initiation and elongation, and both components of DNA synthesis were more resistant to this inhibition in the A-T strains.     

Potential defence from herbivory by ‘dazzle effects’ and ‘trickery coloration’ of leaf variegation

The very conspicuous dazzle coloration invented for naval defence during World War I was used in pre‐radar days to mislead attackers of naval units about vessel size, type, speed, and direction. Among several potential types of defences, it is proposed that zebra‐like white leaf variegation may defend leaves and other plant organs from herbivory as a result of dazzle effects. Two different dazzle effects may be involved in defending plants from herbivory, making it hard for herbivores (1) to decide where, in a three‐dimensional space, to bite the leaves (large herbivores) and (2) to land on them (insects). In addition, the related types of leaf coloration described in the present study, comprising parallels of military defensive trickery naval painting, may also deceive herbivores about the actual shape, location, and identity of leaves. Some of these visual defences may operate at the same time as other visual defences, such as aposematism, or serve various physiological functions. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 692–697.     

Lithium inhibits terminal differentiation of erythroleukemia cells : Evidence for a pre-commitment ‘priming’ event

Lithium has been found to be a novel inhibitor of the terminal differentiation of Friend murine erythroleukemia cells. A general method for the quantitative analysis of differentiation inhibitors has been developed and used to compare the site of inhibition by lithium with that by vanadate. Lithium inhibits the commitment to differentiation (K 1/2 approximately 10 mM) induced by DMSO (dimethylsulfoxide) at non-toxic concentrations that have only a small effect on the rate of proliferation. Inhibition is reversible and probably requires entry of Li+ into the cell, since it is blocked by high KCl in the medium. LiCl is most effective when present during the first 10 h of DMSO treatment, before commitment is initiated. Computer-assisted analysis of the kinetics of commitment demonstrate that inhibition by lithium is best described by including a lithium-sensitive 'priming' event, which occurs with high probability prior to commitment.     

Mechanism of apoptosis induced by a newly synthesized derivative of macrosphelides with a thiazole side chain

The apoptosis-inducing ability of hybrid compounds composed of macrosphelide and thiazole-containing side chain of epothilones was investigated. Among the tested series of hybrid compounds the one containing thiazole side chain at C15 (MSt-2) showed the maximum potency to induce apoptosis, while another containing thiazole side chain at C3 (MSt-6) was less potent. MSt-2 was found to induce apoptosis in human lymphoma (U937) cells in a dose- and time-dependent manner as confirmed by DNA fragmentation analysis. MSt-2 treated cells showed rapid reactive oxygen species (ROS) formation and c-Jun N-terminal kinase (JNK) activation. Furthermore, significant activation of extrinsic pathway as evident by Fas expression and caspase-8 activation was also observed. MSt-2-mediated decreased expression of Bid is an important event for cross talk between intrinsic and extrinsic signaling. N-acetyl-l-cysteine pre-treatment rescued cells from MSt-2-induced ROS formation, mitochondrial membrane potential (Δψ_m) loss, Fas expression, caspase-8 and -3 activation and DNA fragmentation. Moreover, antioxidant enzymes catalase and/or superoxide dismutase conjugated with polyethylene glycol also inhibit MSt-2-induced ROS formation, apoptosis and Δψ_m loss suggesting thereby pro-oxidant effects of MSt-2. Furthermore, JNK and pan-caspase inhibitors also protect cells from MSt-2-induced apoptosis. In addition to this, MSt-2 was found to be more potent in human colon carcinoma (HCT116) and human gastric cancer (AGS) cells while it has no effect on human normal dermal fibroblast. The important structure-activity relationship observed in the current study which makes MSt-2 more potent than MSt-6 is the position of thiazole side chain and stereochemistry of position 3 in chemical structure. In short the results of our study demonstrate that MSt-2-induced rapid ROS generation and mitochondrial dysfunction in cells trigger events responsible for mitochondria-dependent apoptosis pathway.     

‘Black’ and ‘white’ death: burials in a time of Ebola in Freetown,Sierra Leone

The article examines experiences of the 2014‐15 Ebola crisis in Freetown, Sierra Leone, through an analysis of the performance of burials. While most of the city's residents had no contact with the virus, ‘Ebola’ was inescapable, owing to the onerous state of emergency regulations imposed by national and international authorities. All burials, regardless of the cause of death, were to be performed by newly established official teams operating according to unfamiliar biomedical and bureaucratic protocols. Burials became emblematic of the crisis through presenting a conflict between local practices and novel procedures, which was coded locally in a complex racial language of ‘black’ and ‘white’, recalling a long regional history of violent integration into the Atlantic World. Building on long‐standing anthropological discussion on the relationship between ‘good’ death and social order, the article explores how burials became sites around which opposing ‘orders’ were experienced, negotiated, and reconciled in locally meaningful ways.     

Detection and Identification of ‘Candidatus Phytoplasma prunorum’, ‘Candidatus Phytoplasma mali’ and ‘Candidatus Phytoplasma pyri’ in Stone Fruit Trees in Poland

A survey was made to determine the incidence of phytoplasmas in 39 sweet and sour cherry, peach, nectarine, apricot and plum commercial and experimental orchards in seven growing regions of Poland. Nested polymerase chain reaction (PCR) using the phytoplasma‐universal primer pairs P1/P7 followed by R16F2n/R16R2 showed the presence of phytoplasmas in 29 of 435 tested stone fruit trees. The random fragment length polymorphism (RFLP) patterns obtained after digestion of the nested PCR products separately with RsaI, AluI and SspI endonucleases indicated that selected Prunus spp. trees were infected by phytoplasmas belonging to three different subgroups of the apple proliferation group (16SrX‐A, ‐B, ‐C). Nucleotide sequence analysis of 16S rDNA fragment amplified with primers R16F2n/R16R2 confirmed the PCR/Restriction Fragment Length Polymorphism (RFLP) results and revealed that phytoplasma infecting sweet cherry cv. Regina (Reg), sour cherry cv. Sokowka (Sok), apricots cv. Early Orange (EO) and AI/5, Japanese plum cv. Ozark Premier (OzPr) and peach cv. Redhaven (RedH) was closely related to isolate European stone fruit yellows‐G1 of the ‘Candidatus Phytoplasma prunorum’ (16SrX‐B). Sequence and phylogenetic analyses resulted in the highest similarity of the 16S rDNA fragment of phytoplasma from nectarine cv. Super Queen (SQ) with the parallel sequence of the strain AP15 of the ‘Candidatus Phytoplasma mali’ (16SrX‐A). The phytoplasma infecting sweet cherry cv. Kordia (Kord) was most similar to the PD1 strain of the ‘Candidatus Phytoplasma pyri’ (16SrX‐C). This is the first report of the occurrence of ‘Ca. P. prunorum’, ‘Ca. P. mali’ and ‘Ca. P. pyri’ in naturally infected stone fruit trees in Poland.     

Ecophysiological function of leaf ‘windows’ in Lithops species – ‘Living Stones’ that grow underground

Leaf temperatures were lower when light entry at the leaf tip window was prevented through covering the window with reflective tape, relative to leaf temperatures of plants with leaf tip windows covered with transparent tape. This was true when leaf temperatures were measured with an infrared thermometer, but not with a fine‐wire thermocouple. Leaf tip windows of Lithops growing in high‐rainfall regions of southern Africa were larger than the windows of plants (numerous individuals of 17 species) growing in areas with less rainfall and, thus, more annual insolation. The results of this study indicate that leaf tip windows of desert plants with an underground growth habit can allow entry of supra‐optimal levels of radiant energy, thus most likely inhibiting photosynthetic activity. Consequently, the size of the leaf tip windows correlates inversely with habitat solar irradiance, minimising the probability of photoinhibition, while maximising the absorption of irradiance in cloudy, high‐rainfall regions.     

Identification and characterization of the ‘missing’ terminal enzyme for siroheme biosynthesis in α‐proteobacteria

It has recently been shown that the biosynthetic route for both the d₁‐haem cofactor of dissimilatory cd₁ nitrite reductases and haem, via the novel alternative‐haem‐synthesis pathway, involves siroheme as an intermediate, which was previously thought to occur only as a cofactor in assimilatory sulphite/nitrite reductases. In many denitrifiers (which require d₁‐haem), the pathway to make siroheme remained to be identified. Here we identify and characterize a sirohydrochlorin–ferrochelatase from Paracoccus pantotrophus that catalyses the last step of siroheme synthesis. It is encoded by a gene annotated as cbiX that was previously assumed to be encoding a cobaltochelatase, acting on sirohydrochlorin. Expressing this chelatase from a plasmid restored the wild‐type phenotype of an Escherichia coli mutant‐strain lacking sirohydrochlorin–ferrochelatase activity, showing that this chelatase can act in the in vivo siroheme synthesis. A ΔcbiX mutant in P. denitrificans was unable to respire anaerobically on nitrate, proving the role of siroheme as a precursor to another cofactor. We report the 1.9 Å crystal structure of this ferrochelatase. In vivo analysis of single amino acid variants of this chelatase suggests that two histidines, His127 and His187, are essential for siroheme synthesis. This CbiX can generally be identified in α‐proteobacteria as the terminal enzyme of siroheme biosynthesis.     

Peptide synthesis ‘in water’ by a solution‐phase method using water‐dispersible nanoparticle Boc‐amino acid

Regulatory pressure has compelled the chemical manufacturing industry to reduce the use of organic solvents in synthetic chemistry, and there is currently a strong focus on replacing these solvents with water. Here, we describe an efficient in‐water solution‐phase peptide synthesis method using Boc‐amino acids. It is based on a coupling reaction utilizing suspended water‐dispersible nanoparticle reactants. Using this method, peptides were obtained in good yield and with high purity. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

Mechanism of RNA synthesis initiation by the vesicular stomatitis virus polymerase

The minimal RNA synthesis machinery of non-segmented negative-strand RNA viruses comprises a genomic RNA encased within a nucleocapsid protein (N-RNA), and associated with the RNA-dependent RNA polymerase (RdRP). The RdRP is contained within a viral large (L) protein, which associates with N-RNA through a phosphoprotein (P). Here, we define that vesicular stomatitis virus L initiates synthesis via a de-novo mechanism that does not require N or P, but depends on a high concentration of the first two nucleotides and specific template requirements. Purified L copies a template devoid of N, and P stimulates L initiation and processivity. Full processivity of the polymerase requires the template-associated N protein. This work provides new mechanistic insights into the workings of a minimal RNA synthesis machine shared by a broad group of important human, animal and plant pathogens, and defines a mechanism by which specific inhibitors of RNA synthesis function.     

Raman spectroscopy of serum: A study on ‘pre’ and ‘post’ breast adenocarcinoma resection in rat models

Risk of recurrence is a major problem in breast cancer management. Currently available prognostic markers have several disadvantages including low sensitivity and specificity, highlighting the need for new prognostic techniques. One of the candidate techniques is serum‐based Raman spectroscopy (RS). In this study, feasibility of using RS to distinguish ‘pre’ from ‘post’ breast tumor resection serum in rats was explored. Spectral analysis suggests change in proteins and amino acid profiles in ‘post’ compared to ‘pre‐surgical’ group. Principal‐Component‐Linear‐Discriminant‐Analysis shows 87% and 91% classification efficiency for ‘pre’ and ‘post‐surgical’ groups respectively. Thus, the study further supports efficacy of RS for theranostic applications.

     

From mice to elephants: overturning the ‘one size fits all’ paradigm in marine plankton food chains

It is widely believed that consumer control is a weak regulator of marine phytoplankton communities. It remains unclear, however, why this should be the case when marine consumers routinely regulate their prey at higher trophic levels. One possibility is that the weak consumer control of phytoplankton communities results from the inability of field researchers to effectively account for consumer–prey trophic relationships operating at the scale of the plankton. We explored this issue by reviewing studies of trophic control in marine plankton. Experimental studies indicate that size is a critical determinant of feeding relationships among plankton. In sharp contrast, of the 51 field studies reviewed, 78% did not distinguish among the sizes or species of phytoplankton and their consumers, but instead assumed a general bulk phytoplankton–zooplankton trophic connection. Such an approach neglects the possibility that several trophic connections may separate the smallest phytoplankton (0.2 μm) from the larger zooplankton (~ 1000 μm), a remarkable size differential exceeding that between a mouse (~10 cm) and an elephant (~2500 cm). The size‐based approach we propose integrates theory, experiments and field observations and has the potential to greatly enhance our understanding of the causes and consequences of recently documented restructuring of plankton communities.     

Contamination effects by a ‘conventional’ and a ‘biodegradable’ lubricant oil on infaunal recruitment to Antarctic sediments: A field experiment

To investigate the impacts of synthetic lubricants on Antarctic infaunal communities, a field experiment was setup near Australia's Casey Station, East Antarctica. Two types of synthetic lubricants were tested: an ‘Unused’ and ‘Used’ conventional synthetic lubricant, and an alternative marketed as ‘biodegradable’. Clean defaunated sediment was contaminated with the lubricants, decanted into trays, and deployed by divers onto the seabed in a randomised block design. Sediments were sampled 5 and 56 weeks after deployment. After 5 weeks, benthic assemblages that had recruited to the lubricant contaminated sediments were significantly different to those in ‘Control’ sediments, and differences were more pronounced after 56 weeks. Total number of individuals did not significantly differ between treatments after 5 weeks. However, after 56 weeks total individuals in the ‘Control’ sediments were significantly greater than in the contaminated sediments. Nototanais antarcticus (tanaid) and to a lesser extent Monoculodes sp. (gammarid), Tanaid sp. IV and Eudorella sp. (cumacean) had significantly higher abundances in the control sediments after 56 weeks compared to the contaminated sediments. Copepods numerically dominated the benthic assemblages at both sampling times; however, their abundance did not significantly differ across treatments. The community recruiting to the contaminated sediments remained different from that in the ‘Control’ sediments for the duration of the experiment (1 year). The ‘biodegradable’ lubricant was just as environmentally harmful to the Antarctic infauna as the ‘conventional’ lubricant currently used at Australia's Antarctic stations. Our results demonstrate that changes to recruitment are one of the potential environmental consequences of a lubricant spill to Antarctic benthic communities, and reinforce the importance of preventative oil spill management and effective clean-up procedures. Further monitoring of this field experiment will provide much needed information about the long-term impacts by synthetic lubricants in the Antarctic marine environment.     

The AAT1 locus is critical for the biosynthesis of esters contributing to ‘ripe apple’ flavour in ‘Royal Gala’ and ‘Granny Smith’ apples

The ‘fruity’ attributes of ripe apples (Malus × domestica) arise from our perception of a combination of volatile ester compounds. Phenotypic variability in ester production was investigated using a segregating population from a ‘Royal Gala’ (RG; high ester production) × ‘Granny Smith’ (GS; low ester production) cross, as well as in transgenic RG plants in which expression of the alcohol acyl transferase 1 (AAT1) gene was reduced. In the RG × GS population, 46 quantitative trait loci (QTLs) for the production of esters and alcohols were identified on 15 linkage groups (LGs). The major QTL for 35 individual compounds was positioned on LG2 and co‐located with AAT1. Multiple AAT1 gene variants were identified in RG and GS, but only two (AAT1‐RGa and AAT1‐GSa) were functional. AAT1‐RGa and AAT1‐GSa were both highly expressed in the cortex and skin of ripe fruit, but AAT1 protein was observed mainly in the skin. Transgenic RG specifically reduced in AAT1 expression showed reduced levels of most key esters in ripe fruit. Differences in the ripe fruit aroma could be perceived by sensory analysis. The transgenic lines also showed altered ratios of biosynthetic precursor alcohols and aldehydes, and expression of a number of ester biosynthetic genes increased, presumably in response to the increased substrate pool. These results indicate that the AAT1 locus is critical for the biosynthesis of esters contributing to a ‘ripe apple’ flavour.     

Maximization of dextransucrase activity expressed in <Emphasis Type="Italic">E. coli</Emphasis> by mutation and its functional characterization

A novel dextransucrase gene, DSRN, was obtained by ultrasoft X-ray treatment of the DSRB742 gene. The DSRN gene was further mutated via site-directed mutagenesis producing four mutants: DSRN1 (F196S), DSRN2 (Y346N), DSRN3 (K395T) and DSRN4 (P980T). Dextransucrases derived from DSRB742 and its mutants were expressed in E. coli and affinity-purified using dextran to give 80% purity. They had specific activities of 0.6–17 U/mg with Km values of 18–88 mM. DSRB742 had the lowest (0.02 s⁻¹ · mM⁻¹) and DSRN1 had the highest (0.13 s⁻¹ · mM⁻¹) Kcat/Km values. DSRN3 had the highest enzymatic transglycosylation efficiency with maltose (63% of theoretical), gentiobiose (39%), or salicine (40%).     

Novel approach for optimization of a ‘difficult’ peptide synthesis by utilizing quantitative reaction monitoring assays

Three different synthetic strategies were tested to synthesize EGFRvIII peptide (1), which is a functional variant of the epidermal growth factor receptor, a protein that has been well validated as a target for cancer therapy. The initial synthesis was performed with Applied Biosystem (Carlsbad, CA, USA) 433A peptide synthesizer and it indicated that the last three amino acids coupling and Fmoc removal rates were lower than the rest of the sequence. Purity of the crude peptide was 54.5%. The second synthesis was performed manually utilizing C S Bio (Menlo Park, CA, USA) synthesizer and the Kaiser test for reaction monitoring. Because of non‐optimized reaction conditions and an unexpected by‐product, lower purity crude peptide (40.5%) was obtained. Quantitative assays to monitor reactions were developed and demonstrated in gram scale synthesis with C S Bio synthesizer. The optimized synthetic conditions improved the peptide purity to 68.1%. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

Inhibition of protein synthesis by the β-subunit of spectrin

The 220 kDa β-subunit of erythroid cell spectrin is a potent inhibitor of protein synthesis in lysates from rabbit reticulocytes. On the basis of weight of protein added to a lysate reaction mixture, it has about half the inhibitory activity of highly purified heme-regulated eIF-2 kinase. Inhibition appears to be at the level of peptide initiation but does not involve a kinase that phosphorylates eIF-2 on its -subunit.