Relevance of lysine snorkeling in the outer transmembrane domain of small viral potassium ion channels

Transmembrane domains (TMDs) are often flanked by Lys or Arg because they keep their aliphatic parts in the bilayer and their charged groups in the polar interface. Here we examine the relevance of this so-called "snorkeling" of a cationic amino acid, which is conserved in the outer TMD of small viral K(+) channels. Experimentally, snorkeling activity is not mandatory for Kcv(PBCV-1) because K29 can be replaced by most of the natural amino acids without any corruption of function. Two similar channels, Kcv(ATCV-1) and Kcv(MT325), lack a cytosolic N-terminus, and neutralization of their equivalent cationic amino acids inhibits their function. To understand the variable importance of the cationic amino acids, we reanalyzed molecular dynamics simulations of Kcv(PBCV-1) and N-terminally truncated mutants; the truncated mutants mimic Kcv(ATCV-1) and Kcv(MT325). Structures were analyzed with respect to membrane positioning in relation to the orientation of K29. The results indicate that the architecture of the protein (including the selectivity filter) is only weakly dependent on TMD length and protonation of K29. The penetration depth of Lys in a given protonation state is independent of the TMD architecture, which leads to a distortion of shorter proteins. The data imply that snorkeling can be important for K(+) channels; however, its significance depends on the architecture of the entire TMD. The observation that the most severe N-terminal truncation causes the outer TMD to move toward the cytosolic side suggests that snorkeling becomes more relevant if TMDs are not stabilized in the membrane by other domains.     

Characteristics of Sprint Fidelis lead failure

Background. The Medtronic Sprint Fidelis ICD lead is prone to failure and the rate of failure seems to be increasing. The aim of this study was to investigate the rate of Sprint Fidelis lead failure, the characteristics, the mode of presentation and possible predictors of lead failure.Methods and Results. The rate, characteristics and presentation of Sprint Fidelis lead failure was assessed in this single-centre survey. 619 Sprint Fidelis ICD leads were implanted at our centre between December 2004 and August 2007. The mean follow-up was 32±10 (range 22–60) months; 35 patients (5.7%) required a lead re-implantation because of failure of the pace-sense conductor. Mean duration of lead survival was 23±12 (2–46) months and the rate of failure did not stabilise during follow-up. The mode of presentation was inappropriate shocks in 16 patients (45.7%), alarm alert in 12 patients (34.3%), and detection at routine follow-up in seven patients (20%). In 31 patients (89%), interrogation data revealed a sudden rise in impedance and/or frequent short VV intervals prior to lead failure and in five patients an isolated decrease of R wave (<2.5 mV). The interrogation data were not different from patients with shocks compared with patients without shocks. The interrogation data at routine follow-up in the first three months after implant were normal and stable.Conclusion. The rate of Sprint Fidelis lead failure reaches 5.7% at a mean follow-up duration of 32 months. The rate of failure does not seem to stabilise. Routine follow-up can not predict lead failure or prevent inappropriate shocks. (Neth Heart J 2010;18:12-7.)     

Exercise rehabilitation on home-dwelling patients with Alzheimer's disease - a randomized, controlled trial. Study protocol

Background

The Turkish population living in the Netherlands has a high prevalence of psychological complaints and has a high threshold for seeking professional help for these problems. Seeking help through the Internet can overcome these barriers. This project aims to evaluate the effectiveness of a guided self-help problem-solving intervention for depressed Turkish migrants that is culturally adapted and web-based.

Methods

This study is a randomized controlled trial with two arms: an experimental condition group and a wait list control group. The experimental condition obtains direct access to the guided web-based self-help intervention, which is based on Problem Solving Treatment (PST) and takes 6 weeks to complete. Turkish adults with mild to moderate depressive symptoms will be recruited from the general population and the participants can choose between a Turkish and a Dutch version. The primary outcome measure is the reduction of depressive symptoms, the secondary outcome measures are somatic symptoms, anxiety, acculturation, quality of life and satisfaction. Participants are assessed at baseline, post-test (6 weeks), and 4 months after baseline. Analysis will be conducted on the intention-to-treat sample.

Discussion

This study evaluates the effectiveness of a guided problem-solving intervention for Turkish adults living in the Netherlands that is culturally adapted and web-based.

Trial Registration

Nederlands Trial Register: NTR2303     

Why Was Thomas A. Sebeok Not a Cognitive Ethologist? From “Animal Mind” to “Semiotic Self”

In the current debates about zoosemiotics its relations with the neighbouring disciplines are a relevant topic. The present article aims to analyse the complex relations between zoosemiotics and cognitive ethology with special attention to their establishers: Thomas A. Sebeok and Donald R. Griffin. It is argued that zoosemiotics and cognitive ethology have common roots in comparative studies of animal communication in the early 1960s. For supporting this claim Sebeok’s works are analysed, the classical and philosophical periods of his zoosemiotic views are distinguished and the changing relations between zoosemiotics and cognitive ethology are described. The animal language controversy can be interpreted as the explicit point of divergence of the two paradigms, which, however, is a mere symptom of a deeper cleavage. The analysis brings out later critical differences between Sebeok’s and Griffin’s views on animal cognition and language. This disagreement has been the main reason for the critical reception and later neglect of Sebeok’s works in cognitive ethology. Sebeok’s position in this debate remains, however, paradigmatic, i.e. it proceeds from understanding of the contextualisation of semiotic processes that do not allow treating the animal mind as a distinct entity. As a peculiar parallel to Griffin’s metaphor of “animal mind”, Sebeok develops his understanding of “semiotic self” as a layered structure, characterised by an ability to make distinctions, foremost between itself and the surrounding environment. It appears that the history of zoosemiotics has two layers: in addition to the chronological history starting in 1963, when Sebeok proposed a name for the field, zoosemiotics is also philosophically rooted in Peircean semiotics and German biological philosophy. It is argued that the confrontation between zoosemiotics and cognitive ethology is related to different epistemological approaches and at least partly induced by underlying philosophical traditions.     

A Defined and Xeno-Free Culture Method Enabling the Establishment of Clinical-Grade Human Embryonic,Induced Pluripotent and Adipose Stem Cells

Background

The growth of stem cells in in vitro conditions requires optimal balance between signals mediating cell survival, proliferation, and self-renewal. For clinical application of stem cells, the use of completely defined conditions and elimination of all animal-derived materials from the establishment, culture, and differentiation processes is desirable.

Methodology/Principal Findings

Here, we report the development of a fully defined xeno-free medium (RegES), capable of supporting the expansion of human embryonic stem cells (hESC), induced pluripotent stem cells (iPSC) and adipose stem cells (ASC). We describe the use of the xeno-free medium in the derivation and long-term (>80 passages) culture of three pluripotent karyotypically normal hESC lines: Regea 06/015, Regea 07/046, and Regea 08/013. Cardiomyocytes and neural cells differentiated from these cells exhibit features characteristic to these cell types. The same formulation of the xeno-free medium is capable of supporting the undifferentiated growth of iPSCs on human feeder cells. The characteristics of the pluripotent hESC and iPSC lines are comparable to lines derived and cultured in standard undefined culture conditions. In the culture of ASCs, the xeno-free medium provided significantly higher proliferation rates than ASCs cultured in medium containing allogeneic human serum (HS), while maintaining the differentiation potential and characteristic surface marker expression profile of ASCs, although significant differences in the surface marker expression of ASCs cultured in HS and RegES media were revealed.

Conclusion/Significance

Our results demonstrate that human ESCs, iPSCs and ASCs can be maintained in the same defined xeno-free medium formulation for a prolonged period of time while maintaining their characteristics, demonstrating the applicability of the simplified xeno-free medium formulation for the production of clinical-grade stem cells. The basic xeno-free formulation described herein has the potential to be further optimized for specific applications relating to establishment, expansion and differentiation of various stem cell types.     

Systematic Analysis of Circadian Genes in a Population-Based Sample Reveals Association of TIMELESS with Depression and Sleep Disturbance

Disturbances in the circadian pacemaker system are commonly found in individuals with depression and sleep-related problems. We hypothesized that some of the canonical circadian clock genes would be associated with depression accompanied by signs of disturbed sleep, early morning awakening, or daytime fatigue. We tested this hypothesis in a population-based sample of the Health 2000 dataset from Finland, including 384 depressed individuals and 1270 controls, all with detailed information on sleep and daytime vigilance, and analyzed this set of individuals with regard to 113 single-nucleotide polymorphisms of 18 genes of the circadian system. We found significant association between TIMELESS variants and depression with fatigue (D+FAT+) (rs7486220: pointwise P = 0.000099, OR = 1.66; corrected empirical P for the model of D+FAT+  = 0.0056; haplotype ‘C-A-A-C’ of rs2291739-rs2291738-rs7486220-rs1082214: P = 0.0000075, OR = 1.72) in females, and association to depression with early morning awakening (D+EMA+) (rs1082214: pointwise P = 0.0009, OR = 2.70; corrected empirical P = 0.0374 for the model D+EMA+; haplotype ‘G-T’ of rs7486220 and rs1082214: P = 0.0001, OR = 3.01) in males. There was significant interaction of gender and TIMELESS (for example with rs1082214, P = 0.000023 to D+EMA+ and P = 0.005 to D+FAT+). We obtained supported evidence for involvement of TIMELESS in sleeping problems in an independent set of control individuals with seasonal changes in mood, sleep duration, energy level and social activity in females (P = 0.036, ® = 0.123 for rs1082214) and with early morning awakening or fatigue in males (P = 0.038 and P = 0.0016, respectively, for rs1082214). There was also some evidence of interaction between TIMELESS and PER1 in females to D+FAT+ as well as between TIMELESS and ARNTL, RORA or NR1D1 in males to D+EMA+. These findings support a connection between circadian genes and gender-dependent depression and defective sleep regulation.     

Interaction of αVβ3 and αVβ6 Integrins with Human Parechovirus 1

Human parechovirus (HPEV) infections are very common in early childhood and can be severe in neonates. It has been shown that integrins are important for cellular infectivity of HPEV1 through experiments using peptide blocking assays and function-blocking antibodies to α_V integrins. The interaction of HPEV1 with α_V integrins is presumably mediated by a C-terminal RGD motif in the capsid protein VP1. We characterized the binding of integrins α_Vβ₃ and α_Vβ₆ to HPEV1 by biochemical and structural studies. We showed that although HPEV1 bound efficiently to immobilized integrins, α_Vβ₆ bound more efficiently than α_Vβ₃ to immobilized HPEV1. Moreover, soluble α_Vβ₆, but not α_Vβ₃, blocked HPEV1 cellular infectivity, indicating that it is a high-affinity receptor for HPEV1. We also showed that HPEV1 binding to integrins in vitro could be partially blocked by RGD peptides. Using electron cryo-microscopy and image reconstruction, we showed that HPEV1 has the typical T=1 (pseudo T=3) organization of a picornavirus. Complexes of HPEV1 and integrins indicated that both integrin footprints reside between the 5-fold and 3-fold symmetry axes. This result does not match the RGD position predicted from the coxsackievirus A9 X-ray structure but is consistent with the predicted location of this motif in the shorter C terminus found in HPEV1. This first structural characterization of a parechovirus indicates that the differences in receptor binding are due to the amino acid differences in the integrins rather than to significantly different viral footprints.Picornaviruses consist of a positive-sense, single-stranded infectious RNA genome of approximately 7.3 kb enclosed in a capsid composed of 60 copies of each of the three or four capsid proteins (VP1 to VP4). Human parechovirus 1 (HPEV1) is a member of the Parechovirus genus of the Picornaviridae family (38, 70). There are currently eight completely sequenced human parechovirus types and 14 described types (4, 19, 24, 30, 38, 39, 51, 58, 78). In addition, the Parechovirus genus currently has four Ljungan virus members that infect rodents. HPEV1 exhibits several distinct molecular characteristics compared to other picornaviruses (38, 71). These include the lack of the maturation cleavage of the capsid proteins VP0 to VP4 (N-terminal) and VP2 (C-terminal), existence of an approximately 30-amino-acid-long extension to the N terminus of VP3, a unique nonstructural protein 2A, and a 5′ untranslated region that is more closely related to picornaviruses infecting animals than those infecting humans.HPEV infections are common during the first years of life and are often mild or asymptomatic (20, 28, 42, 73, 80). Recently, a number of new types have been identified, and their prevalence in stool samples, for example, highlights their clinical importance. Normally, they cause gastroenteritis and respiratory infections, but severe illnesses, such as infections of the central nervous system, generalized infections of neonates, and myocarditis, have also been associated with HPEV infections (1, 8, 10, 28, 80). Currently, the role of the unique molecular, structural, and antigenic characteristics of HPEVs in the pathogenesis of infection is unknown.HPEV types 1, 2, 4, 5, and 6 are known to possess an RGD motif near the C terminus of VP1 that is known to facilitate binding of cellular ligands (e.g., fibronectin) to α_v integrins. The motif is in an analogous position to motifs in coxsackievirus A9 (CAV9) and echovirus 9 (EV9; Barty strain) (Fig. ​(Fig.1).1). The role of the RGD sequence in cellular entry and subsequent replication of HPEV1 has been shown through blocking assays with RGD-containing peptides, mutation of the sequence, and function-blocking antibodies to α_v integrins (11, 43, 62, 71). These results strongly suggested that α_v integrins play a central role in the initiation of HPEV1 infection. Direct involvement of α_v integrins in the infectious entry of HPEV1 was further confirmed by overexpression of human α_vβ₁ and α_vβ₃ integrins in Chinese hamster ovary (CHO) cells, allowing successful virus infection (74). There are no reports yet on the identification of receptors for the HPEV types lacking the RGD motif (HPEV3, HPEV7, and HPEV8) (19, 39, 51).Open in a separate windowFIG. 1.Sequence alignments. Amino acid sequence alignment of the viral coat protein VP1 from different picornaviruses with the CAV9 secondary structure derived from the atomic model displayed above the alignment (34). The columns boxed in blue with red letters signify similarity, and the red column signifies identity. There is limited similarity between HPEV and other picornaviruses. C-terminal RGD motifs are boxed in red.Although the crystal structures of several picornaviruses have been determined (3, 26, 34, 35, 44, 57, 59, 65, 68, 72) and the receptor interactions have been studied in detail by X-ray crystallography, electron cryo-microscopy (cryo-EM), and three-dimensional (3D) image reconstruction (6, 9, 23, 31, 32, 47, 83), there is no structural information available for the parechoviruses or parechovirus-receptor complexes. Here, we compare the binding of α_Vβ₃ and α_Vβ₆ to HPEV1 in vitro by biochemical assays and determine the structures of HPEV1 and the corresponding HPEV1-integrin complexes.     

Pyrrolidine Dithiocarbamate Activates p38 MAPK and Protects Brain Endothelial Cells From Apoptosis: A Mechanism for the Protective Effect in Stroke?

The antioxidant and inhibitor of nuclear factor κB pyrrolidine dithiocarbamate (PDTC) potently reduces infarct size in various experimental stroke models. In addition, it has been shown to have a favourable safety profile in humans. In this study, we further investigated the mechanistic actions of PDTC on cerebral microvascular endothelial cells as main components of the blood–brain barrier. We propose activation of p38 MAPK by PDTC as an additional protective mechanism. C57/BL6 mice were subjected to transient MCAO for 2 h and treated with PDTC (100 mg/kg) or vehicle i.p. before reperfusion. Infarct size was determined after 24 h. Apoptosis was induced in a cerebral microvascular endothelial cell line and the effect of pretreatment with PDTC and its dependency on p38 MAPK activity was assayed. PDTC administered 2 h after MCAO reduced infarct size by 61% (P < 0.05) and reduces the apoptotic death rate in vivo. In vitro, PDTC reduces the apoptotic death rate of bEnd.3 cells. p38 MAPK was activated by PDTC and its inhibition abrogated the protective effect of PDTC. PDTC reduces infarct size after stroke with a reasonable time window and decreases apoptotic cell death in vivo and in vitro. The attenuation of apoptotic cell death in brain microvascular endothelial cells is dependent on p38 MAPK activity.     

Impact of structural changes in wood‐using industries on net carbon emissions in Finland

Forests and forest industries can contribute to climate change mitigation by sequestering carbon from the atmosphere, by storing it in biomass, and by fabricating products that substitute more greenhouse gas emission intensive materials and energy. The objectives of the study are to specify alternative scenarios for the diversification of wood product markets and to determine how an increasingly diversified market structure could impact the net carbon emissions (NCEs) of forestry in Finland. The NCEs of the Finnish forest sector were modelled for the period 2016–2056 by using a forest management simulation and optimization model for the standing forests and soil and separate models for product carbon storage and substitution impacts. The annual harvest was fixed at approximately 70 Mm³, which was close to the level of roundwood removals for industry and energy in 2016. The results show that the substitution benefits for a reference scenario with the 2016 market structure account for 9.6 Mt C (35.2 Mt CO₂ equivalent [CO₂ eq]) in 2056, which could be further increased by 7.1 Mt C (26 Mt CO₂ eq) by altering the market structure. As a key outcome, increasing the use of by‐products for textiles and wood–plastic composites in place of kraft pulp and biofuel implies greater overall substitution credits compared to increasing the level of log harvest for construction.