Translocation of structured polynucleotides through nanopores

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the translocation process. We show that this circumstance may be exploited to determine the full basepairing pattern of polynucleotides, including RNA pseudoknots. The crucial requirement is that the translocation dynamics (i.e., the length of the translocated molecular segment) needs to be recorded as a function of time with a spatial resolution of a few nucleotides. This could be achieved, for instance, by applying a mechanical driving force for translocation and recording force-extension curves (FEC's) with a device such as an atomic force microscope or optical tweezers. Our analysis suggests that with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids.Comment: 9 pages, 5 figure

The occurrence of metacercariae of Petasiger (Digenea: Echinostomatidae) in an unusual site, within the lateral line scales of cyprinid fishes

This is now an open access journal. http://orcid.org/0000-0002-2908-491XThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The file attached is the published version of the article

Health Effects of Naturally Radioactive Water Ingestion: The Need for Enhanced Studies

Background: Radiological pollution is a potentially important aspect of water quality. However, relatively few studies have been conducted to document its possible health effects

Malformations of the gill filaments of the ruffe Gymnocephalus cernuus (L.) (Pisces) caused by echinostomatid metacercariae

In parasite surveys of fishes from Lake Balaton and its tributaries in Hungary, infections with metacercariae of a species of the digenean genus Echinochasmus (Trematoda: Echinostomatidae) were found in seven species of fish. In ruffe, Gymnocephalus cernuus, malformations of the gill filaments apparently caused by these infections were observed. These malformations were in the form of bifurcations of the filaments at about their mid-length. At the point where the filaments bifurcate, an Echinochasmus metacercaria was always embedded in the cartilaginous ray of the gill filament. All specimens of the ruffe were found to be infected by these metacercariae, and each ruffe specimen was infected by 30–300 metacercariae. Such a bifurcation was found in all of the ruffe specimens, but, apart from these gill malformations, the metacercariae produced only local changes in the cartilage. In the other six infected fish species, only local signs were observed in the cartilage. Experimental infections of chicks with metacercariae resulted in the finding of the sexual adult (marita) of an unidentified species of Echinochasmus. ITS sequences of the adult and metacercaria corresponded with each other, and also with a cercaria isolated from a gravel snail (Lithoglyphus naticoides), with a 99.5–100% similarity

An investigation of the host-specificity of metacercariae of species of Apophallus (Digenea: Heterophyidae) in freshwater fishes using morphological, experimental and molecular methods

Metacercariae of species of the genus Apophallus Lühe, 1909, infecting the fins and skin of freshwater fishes, frequently cause black spot disease. Two species, Apophallus muehlingi (Jägerskiöld, 1899) and A. donicus (Skrjabin & Lindtrop, 1919), are known to occur in Hungarian fishes. It has generally been thought that metacercariae of A. muehlingi infect cyprinid fishes, whereas those of A. donicus develop in percids. As part of a morphological, experimental and molecular study, metacercariae were collected from 99 infected specimens of five cyprinid hosts (Abramis brama, Blicca bjoerkna, Chondrostoma nasus, Squalius cephalus, Scardinius erythrophthalmus) and 18 infected specimens of two percid hosts (Gymnocephalus cernua, Perca fluviatilis) in Hungarian natural waters (Lake Balaton, River Danube). Moreover, 1024 common carp (Cyprinus carpio) specimens collected from Hungarian fish ponds were investigated for Apophallus infection, but without positive results. For reliable species identification, experimental infections of chicks were carried in order to produce adult specimens from metacercariae collected from the fins and skin of the cyprinid and percid hosts. Within 8 days, adult specimens of both A. muehlingi and A. donicus developed in chicks infected with metacercariae from the cyprinid common bream (Abramis brama) and the white bream (Blicca bjoerkna) and the ruffe (Gymnocephalus cernua), a percid, respectively. The morphology of the collected metacercariae and adult individuals developed in the feeding experiments was characterised. A molecular analysis was extended to cercarial samples from the snail Lithoglyphus naticoides and to a single adult specimen of Apophallus from a fox. Sequences of 28 specimens were analysed using molecular methods (sequencing the internal transcribed spacer region and the cytochrome oxidase I subunit). Phylogenetic analysis was executed, and the Apophallus samples clustered into three distinct branches using both genes, A. muehlingi from cyprinids, A. donicus from percids and, a third, previously unknown, Apophallus clade, also from cyprinids

Tsunami-Related Data: A Review of Available Repositories Used in Scientific Literature

Various organizations and institutions store large volumes of tsunami-related data, whose availability and quality should benefit society, as it improves decision making before the tsunami occurrence, during the tsunami impact, and when coping with the aftermath. However, the existing digital ecosystem surrounding tsunami research prevents us from extracting the maximum benefit from our research investments. The main objective of this study is to explore the field of data repositories providing secondary data associated with tsunami research and analyze the current situation. We analyze the mutual interconnections of references in scientific studies published in the Web of Science database, governmental bodies, commercial organizations, and research agencies. A set of criteria was used to evaluate content and searchability. We identified 60 data repositories with records used in tsunami research. The heterogeneity of data formats, deactivated or nonfunctional web pages, the generality of data repositories, or poor dataset arrangement represent the most significant weak points. We outline the potential contribution of ontology engineering as an example of computer science methods that enable improvements in tsunami-related data management

Digenean Holostephanus (Trematoda: Digenea:Cyathocotylidae) metacercariae in commoncarp (Cyprinus carpioLinnaeus, 1758) muscle: zoonotic potential and sensitivity tophysico-chemical treatments

Metacercariae of various species within the genus Holostephanus Szidat, 1936 (Trematoda: Digenea: Cyathocotylidae) occur in muscles of both farmed and wild fish, including common carp (Cyprinus carpio Linnaeus, 1758). The life cycle includes a snail as first intermediate host, fish as second intermediate host and birds or mammals as final hosts. We studied the zoonotic potential and the viability of Holostephanus metacercariae from common carp following exposure to various physical and chemical treatments. Muscle tissue samples of common carp specimens from a fish farm in the north-eastern part of Hungary were examined and metacercariae recovered. The zoonotic potential was evaluated experimentally by using small mammals as models (albino mice, n = 2; and Syrian hamsters, n = 4) infected per os with Holostephanus cysts. Parallelly, Metagonimus metacercariae were used as positive controls. We could not confirm the zoonotic potential of Holostephanus metacercariae as they did not survive in the mammalian intestine whereas Metagonimus metacercariae developed to the adult stage. Weassessed the viability of metacercariae isolated from common carp specimens during exposure to different physical treatments (temperatures of −18°C, +20°C, +40°C and +60°C) and chemical agents (5% and 10% acetic acid and 10% sodium chloride (NaCl)). Metacercariae lost viability by freezing at −18°C (2 h), heating at 60°C (20 min), incubation in 5% and 10% acetic acid (5 min) and 10% NaCl (2 h). These methods served as models to investigate the effectiveness of food preparation techniques (such as cold and hot smoking, freezing, salting and pickling) on the survival of metacercariae

Evidence of the American Myxobolus dechtiari was introduced along with its host Lepomis gibbosus in Europe: Molecular and histological data

The American pumpkinseed Lepomis gibbosus, was introduced to Europe more than one hundred years ago. Currently it is a common fish in European freshwaters but relatively few specific parasites infect this fish in this new habitat. In Europe only a single species, Myxobolus dechtiari seems to represent the American myxosporean fauna of centrarchid fishes. M. dechtiari was found in both Portugal and Hungary. This species forms plasmodia with elongated shape inside the cartilaginous rays of gill filaments. In the advanced stage of infection, after disruption of plasmodia, small groups of myxospores remain enclosed in the cartilaginous gill rays causing distortions in the filaments. Myxospores were ellipsoidal in frontal view and lemon-shape in sutural, length 12.5 ± 0.46 (12–13.4) μm, width 10 ± 0.37 (9.6–10.4) μm, and thickness 7.4 ± 0.37 (7–8) μm; the polar capsules were pyriform, equal in size, length 5.6 ± 0.21 (5.3–6) μm, width 3.2 ± 0.16 (3–3.6) μm; Seven to eight polar tube coils were arranged perpendicularly to the capsule length. There was a small, round, 0.4 ± 0.1 (0.3–05) (N = 50) intercapsular appendix in the spores. The small subunit ribosomal DNA (ssrDNA) of M. dechtiari differed from other myxozoans sequenced to date. Phylogenetic analysis of the ssrDNA gene sequence placed this species in a clade including actinospores and Myxobolus species: Raabeia type1, Triactinomyxon sp., and Myxobolus osburni infecting the same host fish.The focus of our study was to prove that the pumpkinseed, a fish originated from North-America introduced one of its myxosporean parasite to Europe. Emphasis was put on to demonstrate the unique feature of this parasite causing infection in the cartilaginous gill rays

DHODH modulates transcriptional elongation in the neural crest and melanoma

Melanoma is a tumour of transformed melanocytes, which are originally derived from the embryonic neural crest. It is unknown to what extent the programs that regulate neural crest development interact with mutations in the BRAF oncogene, which is the most commonly mutated gene in human melanoma1. We have used zebrafish embryos to identify the initiating transcriptional events that occur on activation of human BRAF(V600E) (which encodes an amino acid substitution mutant of BRAF) in the neural crest lineage. Zebrafish embryos that are transgenic for mitfa:BRAF(V600E) and lack p53 (also known as tp53) have a gene signature that is enriched for markers of multipotent neural crest cells, and neural crest progenitors from these embryos fail to terminally differentiate. To determine whether these early transcriptional events are important for melanoma pathogenesis, we performed a chemical genetic screen to identify small-molecule suppressors of the neural crest lineage, which were then tested for their effects on melanoma. One class of compound, inhibitors of dihydroorotate dehydrogenase (DHODH), for example leflunomide, led to an almost complete abrogation of neural crest development in zebrafish and to a reduction in the self-renewal of mammalian neural crest stem cells. Leflunomide exerts these effects by inhibiting the transcriptional elongation of genes that are required for neural crest development and melanoma growth. When used alone or in combination with a specific inhibitor of the BRAF(V600E) oncogene, DHODH inhibition led to a marked decrease in melanoma growth both in vitro and in mouse xenograft studies. Taken together, these studies highlight developmental pathways in neural crest cells that have a direct bearing on melanoma formation