Pharmacogenetics and anti-arrhythmic drug therapy: a theoretical investigation

Pharmacological management of cardiac arrhythmias has been a long and widely sought goal. One of the difficulties in treating arrhythmia stems, in part, from incomplete understanding of the mechanisms of drug block and how intrinsic properties of channel gating affect drug access, binding affinity, and unblock. In the last decade, a plethora of genetic information has revealed that genetics may play a critical role in determining arrhythmia susceptibility and in efficacy of pharmacological therapy. In this context, we present a theoretical approach for investigating effects of drug-channel interaction. We use as an example open-channel or inactivated-channel block by the local anesthetics mexiletine and lidocaine, respectively, of normal and DeltaKPQ mutant Na(+) channels associated with the long-QT syndrome type 3. Results show how kinetic properties of channel gating, which are affected by mutations, are important determinants of drug efficacy. Investigations of Na(+) channel blockade are conducted at multiple scales (single channel and macroscopic current) and, importantly, during the cardiac action potential (AP). Our findings suggest that channel mean open time is a primary determinant of open state blocker efficacy. Channels that remain in the open state longer, such as the DeltaKPQ mutant channels in the abnormal burst mode, are blocked preferentially by low mexiletine concentrations. AP simulations confirm that a low dose of mexiletine can remove early afterdepolarizations and restore normal repolarization without affecting the AP upstroke. The simulations also suggest that inactivation state block by lidocaine is less effective in restoring normal repolarization and adversely suppresses peak Na(+) current.     

Iron: The Redox-active Center of Oxidative Stress in Alzheimer Disease

Although iron is essential in maintaining the function of the central nervous system, it is a potent source of reactive oxygen species. Excessive iron accumulation occurs in many neurodegenerative diseases including Alzheimer disease (AD), Parkinson’s disease, and Creutzfeldt-Jakob disease, raising the possibility that oxidative stress is intimately involved in the neurodegenerative process. AD in particular is associated with accumulation of numerous markers of oxidative stress; moreover, oxidative stress has been shown to precede hallmark neuropathological lesions early in the disease process, and such lesions, once present, further accumulate iron, among other markers of oxidative stress. In this review, we discuss the role of iron in the progression of AD. Special issue dedicated to Dr. Moussa Youdim.     

The Combined Structural and Kinetic Characterization of a Bacterial Nitronate Monooxygenase from Pseudomonas aeruginosa PAO1 Establishes NMO Class I and II

Nitronate monooxygenase (NMO) oxidizes the mitochondrial toxin propionate 3-nitronate (P3N) to malonate semialdehyde. The enzyme has been previously characterized biochemically in fungi, but no structural information is available. Based on amino acid similarity 4,985 genes are annotated in the GenBank^TM as NMO. Of these, 4,424 (i.e. 89%) are bacterial genes, including several Pseudomonads that have been shown to use P3N as growth substrate. Here, we have cloned and expressed the gene pa4202 of Pseudomonas aeruginosa PAO1, purified the resulting protein, and characterized it. The enzyme is active on P3N and other alkyl nitronates, but cannot oxidize nitroalkanes. P3N is the best substrate at pH 7.5 and atmospheric oxygen with k_cat^app/K_m^app of 12 × 10⁶ m⁻¹ s⁻¹, k_cat^app of 1300 s⁻¹, and K_m^app of 110 μm. Anerobic reduction of the enzyme with P3N yields a flavosemiquinone, which is formed within 7.5 ms, consistent with this species being a catalytic intermediate. Absorption spectroscopy, mass spectrometry, and x-ray crystallography demonstrate a tightly, non-covalently bound FMN in the active site of the enzyme. Thus, PA4202 is the first NMO identified and characterized in bacteria. The x-ray crystal structure of the enzyme was solved at 1.44 Å, showing a TIM barrel-fold. Four motifs in common with the biochemically characterized NMO from Cyberlindnera saturnus are identified in the structure of bacterial NMO, defining Class I NMO, which includes bacterial, fungal, and two animal NMOs. Notably, the only other NMO from Neurospora crassa for which biochemical evidence is available lacks the four motifs, defining Class II NMO.     

Gut content fossilization and evidence for detritus feeding habits in an enrolled trilobite from the Cambrian of China

Enrolment was a major defensive strategy for trilobites that significantly contributed to their evolutionary success. The ability to enrol also helped to constrain the morphological evolution of trilobites, which in part was driven by the need to improve this capability to encapsulate the soft parts of the body within the mineralized dorsal exoskeleton. Here, we describe a unique example of gut content fossilization in an enrolled trilobite from the Cambrian of China, and we propose a taphonomic scenario that considers the possible implication of enrolment in this exceptional preservation. A micro‐facies analysis indicates that the specimen was entombed during an obrution event and remained intact due to limited infaunal activity. The encapsulation of the body did not prevent the decay of soft tissues, but it permitted the delicate gut content to be protected during diagenesis. In isolating the decaying soft tissues from the external environment, enrolment might also have favoured the establishment of microenvironmental conditions conducive to the precipitation of pyrite framboids. Within the gut, the formation of such crystals may have led to the consolidation of the ingested material. These results suggest that fossilized gut contents might be quite common in enrolled trilobites. Textural and compositional analyses reveal that the gut content is similar to the sediment surrounding the fossil except for the presence of pyrite framboids that indicate higher initial organic matter content. The complete enrolment of the body argues against an accidental ingestion of this material or a diagenetic origin for it. Accordingly, detritus feeding habits are inferred for this ptychopariid trilobite.     

Live-cell imaging demonstrates extracellular matrix degradation in association with active cathepsin B in caveolae of endothelial cells during tube formation

Localization of proteases to the surface of endothelial cells and remodeling of the extracellular matrix (ECM) are essential to endothelial cell tube formation and angiogenesis. Here, we partially localized active cathepsin B and its cell surface binding partners, S100A/p11 (p11) of the annexin II heterotetramer (AIIt), to caveolae of human umbilical vein endothelial cells (HUVEC). Via a live-cell proteolysis assay, we observed that degradation products of quenched-fluorescent (DQ)-proteins (i.e. gelatin and collagen IV) colocalized intracellularly with caveolin-1 (cav-1) of HUVEC grown in either monolayer cultures or in vitro tube formation assays. Activity-based probes that bind covalently to active cysteine cathepsins and degradation products of DQ-collagen IV partially localized to intracellular vesicles that contained cav-1 and active cysteine cathepsins. Biochemical analyses revealed that the distribution of active cathepsin B in caveolar fractions increased during in vitro tube formation. Pro-uPA, uPAR, MMP-2 and MMP-14, which have been linked with cathepsin B to ECM degradation pathways, were also found to increase in caveolar fractions during in vitro tube formation. Our findings are the first to demonstrate through live-cell imaging ECM degradation in association with active cathepsin B in caveolae of endothelial cells during tube formation.     

The formation of giant tubular concretions triggered by anaerobic oxidation of methane as revealed by archaeal molecular fossils (Lower Eocene, Varna, Bulgaria)

Impressive, several meters high tubular concretions in shallow marine calcareous sands and sandstones represent part of the well-exposed, subsurface plumbing network of an Early Eocene methane seep system in the Balkanides foreland (Pobiti Kamani area, Varna, NE Bulgaria). An integrated approach, including petrography, inorganic geochemistry and lipid biomarker analyses was used to reconstruct the evolution of pore fluids and cementation conditions during tube formation and particularly, the role of methane-related carbonate diagenesis. Host sediment lithification from marine pore waters was perturbed soon after deposition by oxidation of predominantly microbial methane causing pervasive cementation by a ¹³C-poor, homogeneous calcite cement (δ¹³C values as low as − 44.5‰ V-PDB). The importance of microbially mediated anaerobic oxidation of methane (AOM) is confirmed by extremely ¹³C-depleted archaeal biomarkers (δ¹³C values as low as − 123‰ V-PDB). A suite of macrocyclic dialkyl glycerol diethers (MDGD-0 to -2) and sn-3-hydroxyarchaeol comprises a characteristic trait of the Eocene tubular concretions and might represent molecular fossils of so far unknown methane-oxidizing archaea (ANME). Subsurface calcite cementation surrounding the ascending methane plume, resulted from the changing pore water chemistry in response to AOM and could have, on a local scale, been encouraged by the concurrent alteration of detrital feldspar. Fluctuating δ¹³C (up to − 8‰ V-PDB) and δ¹⁸O (− 0.5 to − 9‰ V-PDB) signatures within a single tubular sandstone concretion are at least partly the consequence of isotopic resetting during late meteoric water circulation.     

Seed dispersal in fens

Question: How does seed dispersal reduce fen isolation and contribute to biodiversity? Location: European and North American fens. Methods: This paper reviews the literature on seed dispersal to fens. Results: Landscape fragmentation may reduce dispersal opportunities thereby isolating fens and reducing genetic exchange. Species in fragmented wetlands may have lower reproductive success, which can lead to biodiversity loss. While fens may have always been relatively isolated from each other, they have become increasingly fragmented in modern times within agricultural and urban landscapes in both Europe and North America. Dispersal by water, animals and wind has been hampered by changes related to development in landscapes surrounding fens. Because the seeds of certain species are long‐lived in the seed bank, frequent episodes of dispersal are not always necessary to maintain the biodiversity of fens. However, of particular concern to restoration is that some dominant species, such as the tussock sedge Carex stricta, may not disperse readily between fens. Conclusions: Knowledge of seed dispersal can be used to maintain and restore the biodiversity of fens in fragmented landscapes. Given that development has fragmented landscapes and that this situation is not likely to change, the dispersal of seeds might be enhanced by moving hay or cattle from fens to damaged sites, or by reestablishing lost hydrological connections.     

Fens and floodplains of the temperate zone: Present status,threats, conservation and restoration

Abstract. This Special Feature focuses on lowland fens and flood plains. In this introduction we discuss the most important mire‐related terms, present status, threats and conservation and restoration attempts. Floodplains and especially lowland fens are rare and vulnerable ecosystems. They are highly threatened all over the world because of direct conversion to agricultural land and especially the lack of appropriate management and altered catchment hydrology. Finally we present a framework for the conservation and restoration of these ecosystems. This consists of (1) optimising abiotic conditions; (2) safeguarding propagule availability of the target species; (3) creating and maintaining conditions for (re)establishment of these species, and (4) appropriate management to keep the conditions suitable.     

Genetic analysis of EphA-dependent signaling mechanisms controlling topographic mapping in vivo

Ephrin/Eph ligands and receptors are best known for their prominent role in topographic mapping of neural connectivity. Despite the large amount of work centered on ephrin/Eph-dependent signaling pathways in various cellular contexts, the molecular mechanisms of action of Eph receptors in neural mapping, requiring dynamic interactions between complementary gradients of ephrins and Eph receptors, remain largely unknown. Here, we investigated in vivo the signaling mechanisms of neural mapping mediated by the EphA4 receptor, previously shown to control topographic specificity of thalamocortical axons in the mouse somatosensory system. Using axon tracing analyses of knock-in mouse lines displaying selective mutations for the Epha4 gene, we determined for the first time which intracellular domains of an Eph receptor are required for topographic mapping. We provide direct in vivo evidence that the tyrosine kinase domain of EphA4, as well as a tight regulation of its activity, are required for topographic mapping of thalamocortical axons, whereas non-catalytic functional modules, such as the PDZ-binding motif (PBM) and the Sterile-alpha motif (SAM) domain, are dispensable. These data provide a novel insight into the molecular mechanisms of topographic mapping, and constitute a physiological framework for the dissection of the downstream signaling cascades involved.     

Synthesis and biological evaluation of N-(arylsulfanyl)carbonyl analogues of paclitaxel (taxol)

Four new N-(arylsufanyl)carbonyl paclitaxel analogues (2a-d) were prepared from 7-(triethylsilyl)-protected baccatin III (5). Their cytotoxicities against human ovarian (A2780) and prostate cancer (PC3) cell lines, as well as their tubulin-assembly activities, were determined. In these assays, the new compounds showed rather weak activities, one two orders of magnitude below those of paclitaxel (taxol; 1). The known 3'-N-[(thiophen-2-yl)carbonyl] paclitaxel analogue 3 was also prepared. As previously reported, 3 exhibited strongly improved cytotoxicities and tubulin-assembly activities as compared to paclitaxel (1).