Biophysical studies of the modification of DNA by antitumour platinum coordination complexes

Cisplatin (cis-diamminedichloroplatinum(II] is widely used in the treatment of various human tumours. A large body of experimental evidence indicates that the reaction of cisplatin with DNA is responsible for the cytostatic action of this drug. Several platinum-DNA adducts have been identified and their effect on the conformation of DNA has been investigated. Structural studies of platinum-DNA adducts now permit a reasonably good explanation of the biophysical properties of platinated DNA. Antitumouractive platinum compounds induce in DNA, at low levels of binding, local conformational alterations which have the character of non-denaturing distortions. It is likely that these changes occur in DNA due to the formation of intrastrand cross-links between two adjacent purine residues. On the other hand, the modification of DNA by antitumour-inactive complexes results in the formation of more severe local denaturation changes. Conformational alterations induced in DNA by antitumour-active platinum compounds may be reparable with greater difficulty than those induced by the inactive complexes. Alternatively, non-denaturation change induced in DNA by antitumour platinum drugs could represent more significant steric hindrance against DNA replication as compared with inactive complexes.     

Using essential oils to overcome bacterial biofilm formation and their antimicrobial resistance

The increase of resistant bacteria puts a huge pressure on the antimicrobials in current use. Antimicrobial resistance (AMR) results from antibiotic misuse and abuse over many years and is a global financial burden. New polices must be developed for the use of antimicrobials and to continue research efforts to mitigate AMR. It is essential to target the most harmful bacteria and concentrate on their mechanisms of resistance to develop successful antimicrobials. Essential oils (EOs) are occur naturally in plants and have long been used as antimicrobials, but most have not been researched. This review explores EOs as alternative antimicrobials, investigating their ability to decrease or inhibit biofilm formation, and assess their ability to contribute to AMR control. Low concentrations of EOs can inhibit Gram-positive and Gram-negative pathogenic bacteria. Some EOs have demonstrated strong anti-biofilm activities. If EOs are successful against biofilm formation, particularly in bacteria developing AMR, they could be incorporated into new antimicrobials. Therefore, there is a need to investigate these EOs’ potential, particularly for surface disinfection, and against bacteria from food, clinical and non-clinical environments.     

Granger causality mapping during joint actions reveals evidence for forward models that could overcome sensory-motor delays

Studies investigating joint actions have suggested a central role for the putative mirror neuron system (pMNS) because of the close link between perception and action provided by these brain regions [1], [2], [3]. In contrast, our previous functional magnetic resonance imaging (fMRI) experiment demonstrated that the BOLD response of the pMNS does not suggest that it directly integrates observed and executed actions during joint actions [4]. To test whether the pMNS might contribute indirectly to the integration process by sending information to brain areas responsible for this integration (integration network), here we used Granger causality mapping (GCM) [5]. We explored the directional information flow between the anterior sites of the pMNS and previously identified integrative brain regions. We found that the left BA44 sent more information than it received to both the integration network (left thalamus, right middle occipital gyrus and cerebellum) and more posterior nodes of the pMNS (BA2). Thus, during joint actions, two anatomically separate networks therefore seem effectively connected and the information flow is predominantly from anterior to posterior areas of the brain. These findings suggest that the pMNS is involved indirectly in joint actions by transforming observed and executed actions into a common code and is part of a generative model that could predict the future somatosensory and visual consequences of observed and executed actions in order to overcome otherwise inevitable neural delays.     

The RcsCB His-Asp phosphorelay system is essential to overcome chlorpromazine-induced stress in Escherichia coli

The RcsCB His-Asp phosphorelay system regulates the expression of several genes of Escherichia coli, but the molecular nature of the inducing signal is still unknown. We show here that treatment of an exponentially growing culture of E. coli with the cationic amphipathic compound chlorpromazine (CPZ) stimulates expression of a set of genes positively regulated by the RcsCB system. This induction is abolished in rcsB or rcsC mutant strains. In addition, treatment with CPZ inhibits growth. The wild-type strain is able to recover from this inhibition and resume growth after a period of adaptation. In contrast, strains deficient in the RcsCB His-Asp phosphorelay system are hypersensitive to CPZ. These results suggest that cells must express specific RcsCB-regulated genes in order to cope with the CPZ-induced stress. This is the first report of the essential role of the RcsCB system in a stress situation. These results also strengthen the notion that alterations of the cell envelope induce a signal recognized by the RcsC sensor.     

Characterization of a CV-1 cell cycle. III. Biophysical parameters.

Membrane preparations from three independently selected concanavalin A-resistant cell lines incorporated si$\text{g}$nificantly less GDP-[¹⁴C]mannose into lipid, oligosaccharide-lipid and protein fractions than preparations obtained from parental wild populations. The results from experiments with membranes from a revertant concanavalin A-resistant line more closely resembled the wild-type populations. The amount of mannose label incorporated into glycoprotein in the variant cells was higher than expected if it is assumed that the pathway GDP-mannose → mannolipid → oligosaccharide-lipid → mannoprotein is functioning in these cells. Evidence is presented to suggest that conversion of mannose label to fucose occurs in wild-type and variant cell lines and that this pathway may be of greater importance in the variant cells; this result could explain at least in part, the higher than expected levels of ¹⁴C-label in glycoprotein in the variant cell lines. The changes in the glycosyl transferase activities in these lectin-resistant cell lines are probably involved in determining the concanavalin A-resistant property and the accompanying complex phenotype exhibited by these variant cell lines.     

Chemical modification of the essential arginine in malate dehydrogenases

Chemical modification of arginine in malate dehydrogenases from pig heart mitochondria and from Bacillus subtilis was done using 4-hydroxy-3-nitrophenylglyoxal. Incorporation of 2 reagent molecules per subunit was observed concomitantly with complete loss of enzymatic activity. Partial protection was obtained with a substrate analogue and by formation of abortive ternary complexes, whereas coenzyme alone did not inhibit the inactivation. Modified inactive enzymes formed binary complexes with coenzyme as well as the ternary complex with NAD/sulfite. The substrate analogue 8-hydroxy-1,3,6-pyrenetrisulfonate was bound with reduced affinity, however. Because of the known stoichiometry of two reagent molecules per arginine we conclude that one arginine essential for substrate binding was modified in both enzymes.     

The GPSM2/LGN GoLoco motifs are essential for hearing

The planar cell polarity (PCP) pathway is responsible for polarizing and orienting cochlear hair cells during development through movement of a primary cilium, the kinocilium. GPSM2/LGN, a mitotic spindle-orienting protein associated with deafness in humans, is a PCP effector involved in kinocilium migration. Here, we link human and mouse truncating mutations in the GPSM2/LGN gene, both leading to hearing loss. The human variant, p.(Trp326*), was identified by targeted genomic enrichment of genes associated with deafness, followed by massively parallel sequencing. Lgn ^ΔC mice, with a targeted deletion truncating the C-terminal GoLoco motifs, are profoundly deaf and show misorientation of the hair bundle and severe malformations in stereocilia shape that deteriorates over time. Full-length protein levels are greatly reduced in mutant mice, with upregulated mRNA levels. The truncated Lgn ^ΔC allele is translated in vitro, suggesting that mutant mice may have partially functioning Lgn. Gαi and aPKC, known to function in the same pathway as Lgn, are dependent on Lgn for proper localization. The polarization of core PCP proteins is not affected in Lgn mutants; however, Lgn and Gαi are misoriented in a PCP mutant, supporting the role of Lgn as a PCP effector. The kinocilium, previously shown to be dependent on Lgn for robust localization, is essential for proper localization of Lgn, as well as Gαi and aPKC, suggesting that cilium function plays a role in positioning of apical proteins. Taken together, our data provide a mechanism for the loss of hearing found in human patients with GPSM2/LGN variants.     

Biophysical parameters influence actin-based movement, trajectory, and initiation in a cell-free system

Using a biochemically complex cytoplasmic extract to reconstitute actin-based motility of Listeria monocytogenes and polystyrene beads coated with the bacterial protein ActA, we have systematically varied a series of biophysical parameters and examined their effects on initiation of motility, particle speed, speed variability, and path trajectory. Bead size had a profound effect on all aspects of motility, with increasing size causing slower, straighter movement and inhibiting symmetry-breaking. Speed also was reduced by extract dilution, by addition of methylcellulose, and paradoxically by addition of excess skeletal muscle actin, but it was enhanced by addition of nonmuscle (platelet) actin. Large, persistent individual variations in speed were observed for all conditions and their relative magnitude increased with extract dilution, indicating that persistent alterations in particle surface properties may be responsible for intrinsic speed variations. Trajectory curvature was increased for smaller beads and also for particles moving in the presence of methylcellulose or excess skeletal muscle actin. Symmetry breaking and movement initiation occurred by two distinct modes: either stochastic amplification of local variation for small beads in concentrated extracts, or gradual accumulation of strain in the actin gel for large beads in dilute extracts. Neither mode was sufficient to enable spherical particles to break symmetry in the cytoplasm of living cells.     

Genetic modification of essential fatty acids biosynthesis in Hansenula polymorpha

The Delta(6)-desaturase gene isoform II involved in the formation of gamma-linolenic acid (GLA) was identified from Mucor rouxii. To study the possibility of alteration of the synthetic pathway of essential fatty acids in the methylotrophic yeast, Hansenula polymorpha, the cloned gene of M. rouxii under the control of the methanol oxidase (MOX) promoter of H. polymorpha, was used for genetic modification of this yeast. Changes in flux through the n-3 and n-6 pathways in the transgenic yeast were observed. The proportion of GLA varied dramatically depending on the growth temperature and media composition. This can be explained by the effects of either substrate availability or enzymatic activity. In addition to the potential application for manipulating the fatty acid profile, this study provides an attractive model system of H. polymorpha for investigating the deviation of fatty acid metabolism in eukaryotes.     

Chemical modification of essential histidine residues in aspartase with diethylpyrocarbonate

Aspartase purified from Escherichia coli W cells was inactivated by diethylpyrocarbonate following pseudo-first order kinetics. Upon treatment of the inactivated enzyme with NH2OH, the enzyme activity was completely restored. The difference absorption spectrum of the modified vs. native enzyme preparations exhibited a prominent peak around 240 nm. The pH-dependence of the inactivation rate suggested that an amino acid residue having a pK value of 6.6 was involved in the inactivation. These results indicate that the inactivation was due to the modification of histidine residues. L-Aspartate and fumarate, substrates for the enzyme, and the Cl- ion, an inhibitor, protected the enzyme against the inactivation. Inspection of the spectral change at 240 nm associated with the inactivation in the presence and absence of the Cl- ion revealed that the number of histidine residues essential for the enzyme activity was less than two. Partial inactivation did not result in an appreciable change in the substrate saturation profiles. These results suggest that one or two histidine residues are located at the active site of aspartase and participate in an essential step in the catalytic reaction.     

Post-translational modification is essential for catalytic activity of nitrile hydratase

Nitrile hydratase from Rhodococcus sp. N-771 is an alphabeta heterodimer with a nonheme ferric iron in the catalytic center. In the catalytic center, alphaCys112 and alphaCys114 are modified to a cysteine sulfinic acid (Cys-SO2H) and a cysteine sulfenic acid (Cys-SOH), respectively. To understand the function and the biogenic mechanism of these modified residues, we reconstituted the nitrile hydratase from recombinant unmodified subunits. The alphabeta complex reconstituted under argon exhibited no activity. However, it gradually gained the enzymatic activity through aerobic incubation. ESI-LC/MS analysis showed that the anaerobically reconstituted alphabeta complex did not have the modification of alphaCys112-SO2H and aerobic incubation induced the modification. The activity of the reconstituted alphabeta complex correlated with the amount of alphaCys112-SO2H. Furthermore, ESI-LC/MS analyses of the tryptic digest of the reconstituted complex, removed of ferric iron at low pH and carboxamidomethylated without reduction, suggested that alphaCys114 is modified to Cys-SOH together with the sulfinic acid modification of alphaCys112. These results suggest that alphaCys112 and alphaCys114 are spontaneously oxidized to Cys-SO2H and Cys-SOH, respectively, and alphaCys112-SO2H is responsible for the catalytic activity solely or in combination with alphaCys114-SOH.     

Epigenetic modification of rhizobial genome is essential for efficient nodulation

CcrM is one of the solitary bacterial DNA methyltransferases which does not have corresponding restriction enzymes. We established a stable ccrM-overexpressing mutant of Mesorhizobium loti, MlccrM-OX, and performed molecular and phenotypic characterization of this strain. In the M. loti MlccrM-OX infected plants, nodulation was apparently delayed at 7 days after inoculation (dai), however, the nodules that eventually formed on the MlccrM-OX roots showed nitrogen fixing ability by at least 21 dai. These results suggest that the initial morphogenic events were affected by ccrM-overexpression and that the correct pattern of DNA methylation of the bacterial genome is not essential for plant-microbe symbiosis, but are required for efficient nodulation.     

Biophysical parameters retrieval of mangrove ecosystem using 3D point cloud descriptions from UAV photographs

The deriving of mangrove biophysical parameters in a cost-effective manner, at a fine spatial scale and over relatively large areas remains a significant challenge. This study aims to provide a comprehensive integrated technical method to map mangrove landscape biophysical characteristic parameters (height, canopy area, canopy perimeter and volume) of two typical mangrove areas in China based on unmanned aerial vehicle (UAV) techniques. In this study, initially, response surface methodology (RSM) was applied to seek the optimal flight parameters for obtaining good-quality synthesized the orthophoto digital composite images. Afterward, a digital surface model (DSM) and a dense photogrammetric point cloud technical method were utilized to derive the mangrove parameters, and artificial visual interpretation was applied to carry out species discrimination and mangrove community canopy coverage. The results showed that the most efficient combination of flight parameters for mangrove extraction is UAV vertical shooting at 30 m altitude and a 75% overlap ratio, which could cover a maximum mangrove investigation area of 0.51 ha during low tide within a day. (2) The integrated technical methods demonstrated good performance in retrieving high-precision mangrove landscape parameters by taking the Dongwei and Daguansha mangrove areas as examples. (3) Transact analysis showed an inverted U-curve of height, canopy area, and volume from the seaward mangrove edge to the landward mangrove edge. Overall, the UAV system with high-resolution (8 cm pixel) images has the potential to enable satisfactory extraction of mangrove landscape parameters by using multisoftware processing. The study will be helpful to the policy-makers, ecologists and environmentalists to formulate and implement various sustainable development programs in mangrove ecosystems.     

Fragment-based modification of 2,4-diarylaminopyrimidine derivatives as ALK and ROS1 dual inhibitors to overcome secondary mutants

In order to explore novel ALK and ROS1 dual inhibitors capable of overcoming crizotinib-resistant mutants, two series of 2,4-diarylaminopyrimidine derivatives were designed, synthesized and evaluated for their in vitro cytotoxic activity. In this work, we retained the 2,4-diarylaminopyrimidine scaffold and derivatize the DAAP scaffold with sulfonyl and acrylamide moieties to extend the structure–activity relationship (SAR) study. To our delight, some compounds exhibited excellent inhibitory activity with a double-digit nanomolar level in MTT assay. Four compounds were selected for enzymic assays further, the results led to the identification of a potent ALK and ROS1 dual inhibitor X-17, with IC₅₀ values of 3.7 nM, 2.3 nM, 8.9 nM and 1.9 nM against ALK, ALK^L1196M, ALK^G1202R and ROS1, respectively. Ultimately, the molecular docking studies on X-17 clearly disclosed reasonable and optimal binding interactions with ALK.     

Biophysical parameters as informative tools for elucidating the causes of root growth retardation under stressful conditions

The root growth rate in barley (Hordeum vulgare L.) seedlings was measured in parallel with temporal changes in longitudinal (δl) and transverse (δD/D) cell-wall extensibilities and membrane hydraulic conductivity (L _p) in the root extension zone. The root growth rate and biophysical parameters examined were sensitive to UV-B irradiation of shoots or roots and to excessive content of ammonium, glutamate, or nickel in the nutrient medium. The root responses to the above treatments were compared with the effects of abscisic acid, salicylate, hydrogen peroxide, diethylstilbestrol, α-naphthyl acetate, oryzalin, and ionomycin. The progressive reduction of root growth under the action of various stressors was accompanied by typical temporal patterns of the growth zone parameters: the δl extensibility declined monotonically, while δD/D and L _p changed nonmonotonically, exhibiting the reversion from the initial decrease to the eventual increase above the control values. The decline of δl indicated that the root growth suppression was mainly due to changes in cell-wall mechanical properties caused probably by disorganization of cortical microtubules. It was found that the decline in δD/D and L _p was caused primarily by the appearance of oxidative stress, disorders in cytoplasmic H⁺ homeostasis in root cells, and the consequent transient activation of the plasmalemmal H⁺-pump. Conversely, the increase in δD/D and L _p upon the abrupt retardation of root growth was presumably caused by the increase in cytoplasmic Ca²⁺ content, disassembling of cortical microtubules, and by partial inhibition of the plasmalemmal H⁺-pump. The reversion of δD/D and L _p changes upon progressive reduction of root growth can be used as an indicator to distinguish moderate and severe stress conditions in the root growth zone. Furthermore, this reversion indicates the increasing disbalance in the homeostasis of reactive oxygen species, cytosolic Ca²⁺, and cytosolic H⁺ upon severe stress.     

Post-translational modification of protein by tyrosine sulfation: active sulfate PAPS is the essential substrate for this modification.

In vitro tyrosine sulfation of recombinant proteins would be a valuable tool in converting those proteins expressed in prokaryotic vectors to their natural form. For this purpose tyrosylprotein sulfotransferase (TPST), the enzyme responsible for tyrosine sulfation of proteins, was characterized from a bovine liver Golgi preparation. TPST was active in a acidic environment with a pH optimum of 6.25, and displayed a stimulation by the Mn2+, with the optimum activity in the presence of 5mM MnCl2. TPST was able to sulfate recombinant hirudin variant 1 (rHV-1) expressed in Escherichia coli and the C-terminal hirudin fragment 54-65 but not the N-terminal hirudin fragment 1-15 by using 3'-phosphoadenosine 5'-phosphosulfate (PAPS), indicating its specificity for the naturally sulfated tyrosine 63. Comparison of the reaction kinetics on synthetic peptides showed that the bovine liver TPST has a higher affinity and reaction rates for those peptides with a aspartyl residue on the N-terminal side of the tyrosine when compared with a glutamyl residue.