Phycodnavirus Potassium Ion Channel Proteins Question the Virus Molecular Piracy Hypothesis

Phycodnaviruses are large dsDNA, algal-infecting viruses that encode many genes with homologs in prokaryotes and eukaryotes. Among the viral gene products are the smallest proteins known to form functional K+ channels. To determine if these viral K+ channels are the product of molecular piracy from their hosts, we compared the sequences of the K+ channel pore modules from seven phycodnaviruses to the K+ channels from Chlorella variabilis and Ectocarpus siliculosus, whose genomes have recently been sequenced. C. variabilis is the host for two of the viruses PBCV-1 and NY-2A and E. siliculosus is the host for the virus EsV-1. Systematic phylogenetic analyses consistently indicate that the viral K+ channels are not related to any lineage of the host channel homologs and that they are more closely related to each other than to their host homologs. A consensus sequence of the viral channels resembles a protein of unknown function from a proteobacterium. However, the bacterial protein lacks the consensus motif of all K+ channels and it does not form a functional channel in yeast, suggesting that the viral channels did not come from a proteobacterium. Collectively, our results indicate that the viruses did not acquire their K+ channel-encoding genes from their current algal hosts by gene transfer; thus alternative explanations are required. One possibility is that the viral genes arose from ancient organisms, which served as their hosts before the viruses developed their current host specificity. Alternatively the viral proteins could be the origin of K+ channels in algae and perhaps even all cellular organisms

A First Attempt at Unreliable News Detection in Swedish

Throughout the COVID-19 pandemic, a parallel infodemic has also been going on such that the information has been spreading faster than the virus itself. During this time, every individual needs to access accurate news in order to take corresponding protective measures, regardless of their country of origin or the language they speak, as misinformation can cause significant loss to not only individuals but also society. In this paper we train several machine learning models (ranging from traditional machine learning to deep learning) to try to determine whether news articles come from either a reliable or an unreliable source, using just the body of the article. Moreover, we use a previously introduced corpus of news in Swedish related to the COVID-19 pandemic for the classification task. Given that our dataset is both unbalanced and small, we use subsampling and easy data augmentation (EDA) to try to solve these issues. In the end, we realize that, due to the small size of our dataset, using traditional machine learning along with data augmentation yields results that rival those of transformer models such as BERT

Analysis of sennoside in drugs contained senna leaves (Cassia sp.) in Iran

Background and objectives: The importance of Cassia angustifulia is due to its laxative properties. A large number of sennosides have been reported in senna but sennoside A and B have been reported as the main causes of its properties. The present study includes the analysis of the effective ingredients of sennosides containing senna products in Iranian pharmaceutical market using UV-Visible and HPLC methods and comparing the obtained amounts with the reported amount of pharmaceutical companies. Methods: The content of sennosides as sennoside B was calculated in drugs purchased from the Iran pharmaceutical market. They were extracted using BP method and the concentration of sennosides was measured at the 500 nm. For HPLC method, sennosides were extracted by 0.1% sodium hydrogen carbonate solution and separation was done by C18 (4.6×250 mm) column as the stationary phase and methanol: water: acetic acid as the mobile phase. The diode-array detector was used to monitor the sennosides. Results: Maximum and the minimum sennosides for both methods were similar. Maximum of sennosides by UV-visible and HPLC methods were 2.75% and 2.55%, respectively. Minimum of sennosides by UV-visible and HPLC methods were 0.8% and 0.64%, respectively. Conclusion: The developed HPLC method was valid for determination of sennosides in senna-containing formulations. Sennosides content by UV-visible method was higher than the HPLC method, because all anthraquinone were calculated by UV but HPLC method separately determines the amount of Sennosides

Molecular dynamics simulation of the cytosolic mouth in Kcv-type potassium channels

The functional effect of mutations near the intracellular mouth of the short viral Kcv potassium channel was studied by molecular dynamics simulations. As a model system we used the analogously mutated and truncated KirBac1.1, a channel with known crystal structure that shares genuine local sequence motifs with Kcv. By a novel simulated annealing methodology for structural averaging, information about the structure and dynamics of the intracellular mouth was extracted and complemented by Poisson-Boltzmann and 3D-RISM (reference interaction site model) integral equation theory for the determination of the K+ free energy surface. Besides the wild-type analogue of Kcv with its experimental reference activity (truncated KirBac1.1), two variants were studied: a deletion mutant where the N-terminus is further truncated by eight amino acids, showing inactivity in the Kcv reference system, and a point mutant where the kink-forming proline at position 13 is substituted by alanine, resulting in hyperactivity. The computations reveal that the change of activity is closely related to a hydrophilic intracellular constriction formed by the C-terminal residues of the monomers. Hyperactivity of the point mutant is correlated with both sterical and electrostatic factors, while inactivity of the deletion mutant is related to a loss of specific salt bridge patterns between the C- and N-terminus at the constriction and to the consequences for ion passage barriers, as revealed by integral equation theory. The cytosolic gate, however, is probably formed by the N-terminal segment up to the proline kink and not by the constriction. The results are compared with design principles found for other channels

Long-distance interactions within the potassium channel pore are revealed by molecular diversity of viral proteins

Kcv is a 94-amino acid protein encoded by chlorella virus PBCV-1 that corresponds to the pore module of K+ channels. Therefore, Kcv can be a model for studying the protein design of K+ channel pores. We analyzed the molecular diversity generated by similar to1 billion years of evolution on kcv genes isolated from 40 additional chlorella viruses. Because the channel is apparently required for virus replication, the Kcv variants are all functional and contain multiple and dispersed substitutions that represent a repertoire of allowed sets of amino acid substitutions ( from 4 to 12 amino acids). Correlations between amino acid substitutions and the new properties displayed by these channels guided site-directed mutations that revealed synergistic amino acid interactions within the protein as well as previously unknown interactions between distant channel domains. The effects of these multiple changes were not predictable from a priori structural knowledge of the channel pore

Dialysis-associated pseudoporphyria successfully treated with vitamin D. Report of two cases

Pseudoporphyria refers to a rare bullous dermatosis characterized by the clinical and histological features of porfiria cutanea tarda without abnormalities in porphyrin metabolism. The pathogenesis is heterogeneous and several exogenous factors may promote the bullous lesion formation, including medications, end stage renal disease, dialysis and tanning beds. Regarding treatment of this condition, in literature different therapy have been reported, such as glutathione and his precursor N-acetylcysteine, which presents anti-oxidant properties; however even more toxic drugs, such as chloroquine, are used. Moreover, in patients with drug-induced PP discontinuation of the offending agent, if possible, is a crucial aspect of the clinical management. We report two cases of dialysis patients presenting blisters on extremities, which healed with the avoidance of UV exposure and oral Vitamin D supplementation. Interestingly Vitamin D despite the lack of antioxidant properties led to a completely resolution of PP in both our patients within 30 days. A possible explanation of this finding is that Vitamin D, playing a key role in the regulation of serum Ca2+, can modulated cadherin-cadherin interactions and led to healing of pseudoporphyria bullous lesions. Finally we highlight the prominent role of UV-exposure in PP elicitation thus a good photoprotection is essential for all patients with pseudoporphyria

Elongation of outer transmembrane domain alters function of miniature K+ Channel Kcv

The virus-coded channel Kcv has the typical structure of a two-transmembrane domain K+ channel. Exceptional are its cytoplasmic domains: the C terminus basically ends inside the membrane and, hence, precludes the formation of a cytoplasmic gate by the so-called bundle crossing; the cytoplasmic N terminus is composed of only 12 amino acids. According to structural predictions, it is positioned in the membrane/aqueous interface and connected via a proline kink to the outer transmembrane domain (TM1). Here, we show that this proline kink affects channel function by determining the position of TM1 in the membrane bilayer. Extension of the hydrophobic length of TM1 by either eliminating the proline kink or introducing an alanine in TM1 augments a time- and voltage-dependent inward rectification of the channel. This suggests that the positional information of TM1 in the bilayer is transmitted to a channel gate, which is not identical with the cytoplasmic bundle crossing

Salt bridges in the miniature viral channel Kcv are important for function

The viral potassium channel Kcv comprises only 94 amino acids, which represent the pore module of more complex K+ channels. As for Kir-type channels, Kcv also has a short N-terminal helix exposed to the cytoplasm, upstream of the first transmembrane domain. Here we show that this helix is relevant for Kcv function. The presence of charged amino acids, which form dynamic inter- and intra-subunit salt bridges is crucial. Electrophysiological measurements, yeast rescue experiments and molecular dynamics simulations show that mutants in which the critical salt bridge formation is impaired have no or reduced channel activity. We conclude that these salt bridges destabilise the complexation of K+ ions by negative charges on the inner transmembrane domain at the entrance into the cavity. This feature facilitates a continuous and coordinated transfer of ions between the cavity and the cytoplasm for channels without the canonical bundle crossing

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 KCVPBCV-1, because K29 can be replaced by most of the natural amino acids without any corruption of function. Two similar channels, KCVATCV-1 and KCVMT325, 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 KCVPBCV-1 and N-terminally truncated mutants; the truncated mutants mimic KCVATCV-1 and KCVMT325. 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